U.S. patent application number 13/557995 was filed with the patent office on 2013-01-31 for genetic inhibition by double-stranded rna.
The applicant listed for this patent is Samuel E. Driver, Andrew Fire, Stephen Kostas, Craig C. Mello, Mary Montgomery, Hiroaki Tabara, Lisa Timmons, SiQun Xu. Invention is credited to Samuel E. Driver, Andrew Fire, Stephen Kostas, Craig C. Mello, Mary Montgomery, Hiroaki Tabara, Lisa Timmons, SiQun Xu.
Application Number | 20130029425 13/557995 |
Document ID | / |
Family ID | 26749094 |
Filed Date | 2013-01-31 |
United States Patent
Application |
20130029425 |
Kind Code |
A1 |
Fire; Andrew ; et
al. |
January 31, 2013 |
Genetic Inhibition by Double-Stranded RNA
Abstract
A process is provided of introducing an RNA into a living cell
to inhibit gene expression of a target gene in that cell. The
process may be practiced ex vivo or in vivo. The RNA has a region
with double-stranded structure. Inhibition is sequence-specific in
that the nucleotide sequences of the duplex region of the RNA and
of a portion of the target gene are identical. The present
invention is distinguished from prior art interference in gene
expression by antisense or triple-strand methods.
Inventors: |
Fire; Andrew; (Baltimore,
MD) ; Kostas; Stephen; (Chicago, IL) ;
Montgomery; Mary; (St. Paul, MN) ; Timmons; Lisa;
(Lawrence, KS) ; Xu; SiQun; (Ballwin, MO) ;
Tabara; Hiroaki; (Mishima, JP) ; Driver; Samuel
E.; (Providence, RI) ; Mello; Craig C.;
(Shrewsbury, MA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Fire; Andrew
Kostas; Stephen
Montgomery; Mary
Timmons; Lisa
Xu; SiQun
Tabara; Hiroaki
Driver; Samuel E.
Mello; Craig C. |
Baltimore
Chicago
St. Paul
Lawrence
Ballwin
Mishima
Providence
Shrewsbury |
MD
IL
MN
KS
MO
RI
MA |
US
US
US
US
US
JP
US
US |
|
|
Family ID: |
26749094 |
Appl. No.: |
13/557995 |
Filed: |
July 25, 2012 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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11905368 |
Sep 28, 2007 |
8283329 |
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13557995 |
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10282996 |
Oct 30, 2002 |
7538095 |
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11905368 |
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09215257 |
Dec 18, 1998 |
6506559 |
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10282996 |
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60068562 |
Dec 23, 1997 |
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Current U.S.
Class: |
435/468 ;
435/320.1 |
Current CPC
Class: |
A61P 35/02 20180101;
A61P 43/00 20180101; A61K 31/713 20130101; A01K 2227/703 20130101;
C12N 15/8218 20130101; C12N 2310/14 20130101; C12N 2310/321
20130101; C12N 2310/50 20130101; C12N 15/8285 20130101; A61K
31/7105 20130101; A01K 2217/05 20130101; C12N 15/85 20130101; C12N
2310/53 20130101; C12N 2310/11 20130101; C12N 15/113 20130101; A61P
35/00 20180101 |
Class at
Publication: |
435/468 ;
435/320.1 |
International
Class: |
C12N 15/82 20060101
C12N015/82 |
Goverment Interests
GOVERNMENT RIGHTS
[0002] This invention was made with U.S. government support under
grant numbers GM-37706, GM-17164, HD-33769 and GM-07231 awarded by
the National Institutes of Health. The U.S. government has certain
rights in the invention.
Claims
1.-39. (canceled)
40. A method to inhibit expression of a target gene in a plant cell
comprising synthesis of a first ribonucleic acid (RNA) and second
RNA in the plant cell, wherein the first and second RNAs hybridize
to each other to form a double-stranded structure in the cell, the
first RNA consisting essentially of a ribonucleotide sequence which
corresponds to a nucleotide sequence of the target gene and the
second RNA consisting essentially of a ribonucleotide sequence
which is complementary to the nucleotide sequence of the target
gene, wherein said first and said second RNA are synthesized in the
plant cell in an amount sufficient to inhibit the expression of the
target gene.
41. A method to inhibit expression of a target gene in a plant cell
comprising introducing into said cell double-stranded
ribonucleotide (RNA) comprising a first RNA consisting essentially
of a ribonucleotide sequence which corresponds to a nucleotide
sequence of the target gene and a second RNA which consists
essentially of a ribonucleotide sequence which is complementary to
the nucleotide sequence of the target gene and wherein said first
and second RNAs are present in an amount sufficient to inhibit the
expression of the target gene.
42. The method of claim 40 or claim 41 wherein the target gene is
an endogenous gene or a transgene.
43. The method of claim 42 wherein the expression of the target
gene is inhibited in the cell in vitro.
44. The method of claim 40 or claim 41 wherein the target gene
expression is reduced by at least 10%.
45. A kit comprising reagents for inhibiting expression of a target
gene in a plant cell, wherein said kit comprises a means for
introduction of a ribonucleic acid (RNA) into the plant cell in an
amount sufficient to inhibit expression of the target gene, and
wherein the RNA has a double-stranded structure with an identical
nucleotide sequence as compared to a portion of the target
gene.
46. A method of inhibiting expression of a target gene in a plant
cell in a plant comprising providing at least one ribonucleic acid
(RNA) to the plant cell in an amount sufficient to inhibit the
expression of a target gene, wherein said RNA is provided to the
plant cell by synthesizing said RNA in said plant cell, wherein the
RNA comprises or forms a double-stranded structure containing a
first strand consisting essentially of a ribonucleotide sequence
which corresponds to a nucleotide sequence of the target gene and a
second ribonucleotide sequence which is complementary to the target
gene, wherein the first and the second ribonucleotide sequences are
complementary sequences that hybridize to each other to comprise or
form said double-stranded structure, and wherein the RNA comprising
or forming the double-stranded structure inhibits expression of
target gene.
47. The method of claim 46, wherein said RNA is transcribed from an
expression construct.
48. The method of claim 46, wherein said double-stranded structure
is formed by a single self-complementary RNA strand comprising the
first and second ribonucleotide sequences.
49. The method of claim 48, wherein said single self-complementary
RNA strand is transcribed from an expression construct.
50. A method of inhibiting the expression of a target gene in a
plant cell, comprising contacting said plant cell with an
expression construct, wherein said expression construct comprises
an inverted duplication for a segment of the target gene, wherein
said segment of the target gene comprises a nucleotide sequence
substantially identical to at least one portion of the target gene,
wherein a promoter drives expression of said inverted-duplication,
and wherein said inverted-duplication forms a double-stranded RNA
structure which inhibits expression of the target gene.
51. The method of claim 50, wherein the double-stranded RNA
structure is partially double-stranded.
52. An expression construct comprising an inverted-duplication for
a segment of a target gene in a plant cell, wherein said segment of
a target gene comprises a nucleotide sequence substantially
identical to at least a portion of the target gene, wherein a
promoter drives expression of said inverted-duplication, and
wherein said inverted-duplication forms a double-stranded RNA
structure which is capable of inhibiting expression of the target
gene in a plant cell.
53. An expression construct comprising a nucleotide sequence
comprising a regulatory region, wherein said nucleotide sequence is
capable of transcribing a single self-complementary RNA strand
which forms a double-stranded RNA structure, and wherein said
double-stranded RNA structure is capable of inhibiting expression
of a target gene in a plant cell.
Description
RELATED APPLICATION
[0001] This application claims the benefit of U.S. Provisional
Appln. No. 60/068,562, filed Dec. 23, 1997.
BACKGROUND OF THE INVENTION
[0003] 1. Field of the Invention
[0004] The present invention relates to gene-specific inhibition of
gene expression by double-stranded ribonucleic acid (dsRNA).
[0005] 2. Description of the Related Art
[0006] Targeted inhibition of gene expression has been a long-felt
need in biotechnology and genetic engineering. Although a major
investment of effort has been made to achieve this goal, a more
comprehensive solution to this problem was still needed.
[0007] Classical genetic techniques have been used to isolate
mutant organisms with reduced expression of selected genes.
Although valuable, such techniques require laborious mutagenesis
and screening programs, are limited to organisms in which genetic
manipulation is well established (e.g., the existence of selectable
markers, the ability to control genetic segregation and sexual
reproduction), and are limited to applications in which a large
number of cells or organisms can be sacrificed to isolate the
desired mutation. Even under these circumstances, classical genetic
techniques can fail to produce mutations in specific target genes
of interest, particularly when complex genetic pathways are
involved. Many applications of molecular genetics require the
ability to go beyond classical genetic screening techniques and
efficiently produce a directed change in gene expression in a
specified group of cells or organisms. Some such applications are
knowledge-based projects in which it is of importance to understand
what effects the loss of a specific gene product (or products) will
have on the behavior of the cell or organism. Other applications
are engineering based, for example: cases in which is important to
produce a population of cells or organisms in which a specific gene
product (or products) has been reduced or removed. A further class
of applications is therapeutically based in which it would be
valuable for a functioning organism (e.g., a human) to reduce or
remove the amount of a specified gene product (or products).
Another class of applications provides a disease model in which a
physiological function in a living organism is genetically
manipulated to reduce or remove a specific gene product (or
products) without making a permanent change in the organism's
genome.
[0008] In the last few years, advances in nucleic acid chemistry
and gene transfer have inspired new approaches to engineer specific
interference with gene expression. These approaches are described
below.
Use of Antisense Nucleic Acids to Engineer Interference
[0009] Antisense technology has been the most commonly described
approach in protocols to achieve gene-specific interference. For
antisense strategies, stoichiometric amounts of single-stranded
nucleic acid complementary to the messenger RNA for the gene of
interest are introduced into the cell. Some difficulties with
antisense-based approaches relate to delivery, stability, and dose
requirements. In general, cells do not have an uptake mechanism for
single-stranded nucleic acids, hence uptake of unmodified
single-stranded material is extremely inefficient. While waiting
for uptake into cells, the single-stranded material is subject to
degradation. Because antisense interference requires that the
interfering material accumulate at a relatively high concentration
(at or above, the concentration of endogenous mRNA), the amount
required to be delivered is a major constraint on efficacy. As a
consequence, much of the effort in developing antisense technology
has been focused on the production of modified nucleic acids that
are both stable to nuclease digestion and able to diffuse readily
into cells. The use of antisense interference for gene therapy or
other whole-organism applications has been limited by the large
amounts of oligonucleotide that need to be synthesized from
non-natural analogs, the cost of such synthesis, and the difficulty
even with high doses of maintaining a sufficiently concentrated and
uniform pool of interfering material in each cell.
Triple-Helix Approaches to Engineer Interference
[0010] A second, proposed method for engineered interference is
based on a triple helical nucleic acid structure. This approach
relies on the rare ability of certain nucleic acid populations to
adopt a triple-stranded structure. Under physiological conditions,
nucleic acids are virtually all single- or double-stranded, and
rarely if ever form triple-stranded structures. It has been known
for some time, however, that certain simple purine- or
pyrimidine-rich sequences could form a triple-stranded molecule in
vitro under extreme conditions of pH (i.e., in a test tube). Such
structures are generally very transient under physiological
conditions, so that simple delivery of unmodified nucleic acids
designed to produce triple-strand structures does not yield
interference. As with antisense, development of triple-strand
technology for use in vivo has focused on the development of
modified nucleic acids that would be more stable and more readily
absorbed by cells in vivo. An additional goal in developing this
technology has been to produce modified nucleic acids for which the
formation of triple-stranded material proceeds effectively at
physiological pH.
Co-Suppression Phenomena and their Use in Genetic Engineering
[0011] A third approach to gene-specific interference is a set of
operational procedures grouped under the name "co-suppression".
This approach was first described in plants and refers to the
ability of transgenes to cause silencing of an unlinked but
homologous gene. More recently, phenomena similar to co-suppression
have been reported in two animals: C. elegans and Drosophila.
Co-suppression was first observed by accident, with reports coming
from groups using transgenes in attempts to achieve over-expression
of a potentially useful locus. In some cases the over-expression
was successful while, in many others, the result was opposite from
that expected. In those cases, the transgenic plants actually
showed less expression of the endogenous gene. Several mechanisms
have so far been proposed for transgene-mediated co-suppression in
plants; all of these mechanistic proposals remain hypothetical, and
no definitive mechanistic description of the process has been
presented. The models that have been proposed to explain
co-suppression can be placed in two different categories. In one
set of proposals, a direct physical interaction at the DNA- or
chromatin-level between two different chromosomal sites has been
hypothesized to occur; an as-yet-unidentified mechanism would then
lead to de novo methylation and subsequent suppression of gene
expression. Alternatively, some have postulated an RNA
intermediate, synthesized at the transgene locus, which might then
act to produce interference with the endogenous gene. The
characteristics of the interfering RNA, as well as the nature of
the interference process, have not been determined. Recently, a set
of experiments with RNA viruses have provided some support for the
possibility of RNA intermediates in the interference process. In
these experiments, a replicating RNA virus is modified to include a
segment from a gene of interest. This modified virus is then tested
for its ability to interfere with expression of the endogenous
gene. Initial results with this technique have been encouraging,
however, the properties of the viral RNA that are responsible for
interference effects have not been determined and, in any case,
would be limited to plants which are hosts of the plant virus.
Distinction Between the Present Invention and Antisense
Approaches
[0012] The present invention differs from antisense-mediated
interference in both approach and effectiveness. Antisense-mediated
genetic interference methods have a major challenge: delivery to
the cell interior of specific single-stranded nucleic acid
molecules at a concentration that is equal to or greater than the
concentration of endogenous mRNA. Double-stranded RNA-mediated
inhibition has advantages both in the stability of the material to
be delivered and the concentration required for effective
inhibition. Below, we disclose that in the model organism C.
elegans, the present invention is at least 100-fold more effective
than an equivalent antisense approach (i.e., dsRNA is at least
100-fold more effective than the injection of purified antisense
RNA in reducing gene expression). These comparisons also
demonstrate that inhibition by double-stranded RNA must occur by a
mechanism distinct from antisense interference.
Distinction Between the Present Invention and Triple-Helix
Approaches
[0013] The limited data on triple strand formation argues against
the involvement of a stable triple-strand intermediate in the
present invention. Triple-strand structures occur rarely, if at
all, under physiological conditions and are limited to very unusual
base sequence with long runs of purines and pyrimidines. By
contrast, dsRNA-mediated inhibition occurs efficiently under
physiological conditions, and occurs with a wide variety of
inhibitory and target nucleotide sequences. The present invention
has been used to inhibit expression of 18 different genes,
providing phenocopies of null mutations in these genes of known
function. The extreme environmental and sequence constraints on
triple-helix formation make it unlikely that dsRNA-mediated
inhibition in C. elegans is mediated by a triple-strand
structure.
Distinction Between Present Invention and Co-Suppression
Approaches
[0014] The transgene-mediated genetic interference phenomenon
called co-suppression may include a wide variety of different
processes. From the viewpoint of application to other types of
organisms, the co-suppression phenomenon in plants is difficult to
extend. A confounding aspect in creating a general technique based
on co-suppression is that some transgenes in plants lead to
suppression of the endogenous locus and some do not. Results in C.
elegans and Drosophila indicate that certain transgenes can cause
interference (i.e., a quantitative decrease in the activity of the
corresponding endogenous locus) but that most transgenes do not
produce such an effect. The lack of a predictable effect in plants,
nematodes, and insects greatly limits the usefulness of simply
adding transgenes to the genome to interfere with gene expression.
Viral-mediated co-suppression in plants appears to be quite
effective, but has a number of drawbacks. First, it is not clear
what aspects of the viral structure are critical for the observed
interference. Extension to another system would require discovery
of a virus in that system which would have these properties, and
such a library of useful viral agents are not available for many
organisms. Second, the use of a replicating virus within an
organism to effect genetic changes (e.g., long- or short-term gene
therapy) requires considerably more monitoring and oversight for
deleterious effects than the use of a defined nucleic acid as in
the present invention.
[0015] The present invention avoids the disadvantages of the
previously-described methods for genetic interference. Several
advantages of the present invention are discussed below, but
numerous others will be apparent to one of ordinary skill in the
biotechnology and genetic engineering arts.
SUMMARY OF THE INVENTION
[0016] A process is provided for inhibiting expression of a target
gene in a cell. The process comprises introduction of RNA with
partial or fully double-stranded character into the cell or into
the extracellular environment. Inhibition is specific in that a
nucleotide sequence from a portion of the target gene is chosen to
produce inhibitory RNA. We disclose that this process is (1)
effective in producing inhibition of gene expression, (2) specific
to the targeted gene, and (3) general in allowing inhibition of
many different types of target gene.
[0017] The target gene may be a gene derived from the cell, an
endogenous gene, a transgene, or a gene of a pathogen which is
present in the cell after infection thereof. Depending on the
particular target gene and the dose of double stranded RNA material
delivered, the procedure may provide partial or complete loss of
function for the target gene. A reduction or loss of gene
expression in at least 99% of targeted cells has been shown. Lower
doses of injected material and longer times after administration of
dsRNA may result in inhibition in a smaller fraction of cells.
Quantitation of gene expression in a cell may show similar amounts
of inhibition at the level of accumulation of target mRNA or
translation of target protein.
[0018] The RNA may comprise one or more strands of polymerized
ribonucleotide; it may include modifications to either the
phosphate-sugar backbone or the nucleoside. The double-stranded
structure may be formed by a single self-complementary RNA strand
or two complementary RNA strands. RNA duplex formation may be
initiated either inside or outside the cell. The RNA may be
introduced in an amount which allows delivery of at least one copy
per cell. Higher doses of double-stranded material may yield more
effective inhibition. Inhibition is sequence-specific in that
nucleotide sequences corresponding to the duplex region of the RNA
are targeted for genetic inhibition. RNA containing a nucleotide
sequences identical to a portion of the target gene is preferred
for inhibition. RNA sequences with insertions, deletions, and
single point mutations relative to the target sequence have also
been found to be effective for inhibition. Thus, sequence identity
may optimized by alignment algorithms known in the art and
calculating the percent difference between the nucleotide
sequences. Alternatively, the duplex region of the RNA may be
defined functionally as a nucleotide sequence that is capable of
hybridizing with a portion of the target gene transcript.
[0019] The cell with the target gene may be derived from or
contained in any organism (e.g., plant, animal, protozoan, virus,
bacterium, or fungus). RNA may be synthesized either in vivo or in
vitro. Endogenous RNA polymerase of the cell may mediate
transcription in vivo, or cloned RNA polymerase can be used for
transcription in vivo or in vitro. For transcription from a
transgene in vivo or an expression construct, a regulatory region
may be used to transcribe the RNA strand (or strands).
[0020] The RNA may be directly introduced into the cell (i.e.,
intracellularly); or introduced extracellularly into a cavity,
interstitial space, into the circulation of an organism, introduced
orally, or may be introduced by bathing an organism in a solution
containing RNA. Methods for oral introduction include direct mixing
of RNA with food of the organism, as well as engineered approaches
in which a species that is used as food is engineered to express an
RNA, then fed to the organism to be affected. Physical methods of
introducing nucleic acids include injection directly into the cell
or extra-cellular injection into the organism of an RNA
solution.
[0021] The advantages of the present invention include: the ease of
introducing double-stranded RNA into cells, the low concentration
of RNA which can be used, the stability of double-stranded RNA, and
the effectiveness of the inhibition. The ability to use a low
concentration of a naturally-occurring nucleic acid avoids several
disadvantages of anti-sense interference. This invention is not
limited to in vitro use or to specific sequence compositions, as
are techniques based on triple-strand formation. And unlike
antisense interference, triple-strand interference, and
co-suppression, this invention does not suffer from being limited
to a particular set of target genes, a particular portion of the
target gene's nucleotide sequence, or a particular transgene or
viral delivery method. These concerns have been a serious obstacle
to designing general strategies according to the prior art for
inhibiting gene expression of a target gene of interest.
[0022] Furthermore, genetic manipulation becomes possible in
organisms that are not classical genetic models. Breeding and
screening programs may be accelerated by the ability to rapidly
assay the consequences of a specific, targeted gene disruption.
Gene disruptions may be used to discover the function of the target
gene, to produce disease models in which the target gene are
involved in causing or preventing a pathological condition, and to
produce organisms with improved economic properties.
BRIEF DESCRIPTION OF THE DRAWINGS
[0023] FIG. 1 shows the genes used to study RNA-mediated genetic
inhibition in C. elegans. Intron-exon structure for genes used to
test RNA-mediated inhibition are shown (exons: filled boxes;
introns: open boxes; 5' and 3' untranslated regions: shaded;
unc-22.sup.9, unc-54.sup.12, fem-1.sup.14, and hlh-1.sup.15).
[0024] FIGS. 2 A-I show analysis of inhibitory RNA effects in
individual cells. These experiments were carried out in a reporter
strain (called PD4251) expressing two different reporter proteins,
nuclear GFP-LacZ and mitochondrial GFP. The micrographs show
progeny of injected animals visualized by a fluorescence
microscope. Panels A (young larva), B (adult), and C (adult body
wall; high magnification) result from injection of a control RNA
(ds-unc22A). Panels D-F show progeny of animals injected with
ds-gfpG. Panels G-I demonstrate specificity. Animals are injected
with ds-lacZL RNA, which should affect the nuclear but not the
mitochondrial reporter construct. Panel H shows a typical adult,
with nuclear GFP-LacZ lacking in almost all body-wall muscles but
retained in vulval muscles. Scale bars are 20 .mu.m.
[0025] FIGS. 3 A-D show effects of double-stranded RNA
corresponding to mex-3 on levels of the endogenous mRNA.
Micrographs show in situ hybridization to embryos (dark stain).
Panel A: Negative control showing lack of staining in the absence
of hybridization probe. Panel B: Embryo from uninjected parent
(normal pattern of endogenous mex-3 RNA.sup.20). Panel C: Embryo
from a parent injected with purified mex-3B antisense RNA. These
embryos and the parent animals retain the mex-3 mRNA, although
levels may have been somewhat less than wild type. Panel D: Embryo
from a parent injected with dsRNA corresponding to mex-3B; no mex-3
RNA was detected. Scale: each embryo is approximately 50 .mu.m in
length.
[0026] FIG. 4 shows inhibitory activity of unc-22A as a function of
structure and concentration. The main graph indicates fractions in
each behavioral class. Embryos in the uterus and already covered
with an eggshell at the time of injection were not affected and,
thus, are not included. Progeny cohort groups are labeled 1 for 0-6
hours, 2 for 6-15 hours, 3 for 15-27 hours, 4 for 27-41 hours, and
5 for 41-56 hours The bottom-left diagram shows genetically derived
relationship between unc-22 gene dosage and behavior based on
analyses of unc-22 heterozygotes and polyploids.sup.8,3.
[0027] FIGS. 5 A-C show examples of genetic inhibition following
ingestion by C. elegans of dsRNAs from expressing bacteria. Panel
A: General strategy for production of dsRNA by cloning a segment of
interest between flanking copies of the bacteriophage T7 promoter
and transcribing both strands of the segment by transfecting a
bacterial strain (BL21/DE3).sup.28 expressing the T7 polymerase
gene from an inducible (Lac) promoter. Panel B: A GFP-expressing C.
elegans strain, PD4251 (see FIG. 2), fed on a native bacterial
host. Panel C: PD4251 animals reared on a diet of bacteria
expressing dsRNA corresponding to the coding region for gfp.
DETAILED DESCRIPTION OF THE INVENTION
[0028] The present invention provides a method of producing
sequence-specific inhibition of gene expression by introducing
double-stranded RNA (dsRNA). A process is provided for inhibiting
expression of a target gene in a cell. The process comprises
introduction of RNA with partial or fully double-stranded character
into the cell. Inhibition is sequence-specific in that a nucleotide
sequence from a portion of the target gene is chosen to produce
inhibitory RNA. We disclose that this process is (1) effective in
producing inhibition of gene expression, (2) specific to the
targeted gene, and (3) general in allowing inhibition of many
different types of target gene.
[0029] The target gene may be a gene derived from the cell (i.e., a
cellular gene), an endogenous gene (i.e., a cellular gene present
in the genome), a transgene (i.e., a gene construct inserted at an
ectopic site in the genome of the cell), or a gene from a pathogen
which is capable of infecting an organism from which the cell is
derived. Depending on the particular target gene and the dose of
double stranded RNA material delivered, this process may provide
partial or complete loss of function for the target gene. A
reduction or loss of gene expression in at least 99% of targeted
cells has been shown.
[0030] Inhibition of gene expression refers to the absence (or
observable decrease) in the level of protein and/or mRNA product
from a target gene. Specificity refers to the ability to inhibit
the target gene without manifest effects on other genes of the
cell. The consequences of inhibition can be confirmed by
examination of the outward properties of the cell or organism (as
presented below in the examples) or by biochemical techniques such
as RNA solution hybridization, nuclease protection, Northern
hybridization, reverse transcription, gene expression monitoring
with a microarray, antibody binding, enzyme linked immunosorbent
assay (ELISA), Western blotting, radioimmunoassay (RIA), other
immunoassays, and fluorescence activated cell analysis (FACS). For
RNA-mediated inhibition in a cell line or whole organism, gene
expression is conveniently assayed by use of a reporter or drug
resistance gene whose protein product is easily assayed. Such
reporter genes include acetohydroxyacid synthase (AHAS), alkaline
phosphatase (AP), beta galactosidase (LacZ), beta glucoronidase
(GUS), chloramphenicol acetyltransferase (CAT), green fluorescent
protein (GFP), horseradish peroxidase (HRP), luciferase (Luc),
nopaline synthase (NOS), octopine synthase (OCS), and derivatives
thereof. Multiple selectable markers are available that confer
resistance to ampicillin, bleomycin, chloramphenicol, gentamycin,
hygromycin, kanamycin, lincomycin, methotrexate, phosphinothricin,
puromycin, and tetracyclin.
[0031] Depending on the assay, quantitation of the amount of gene
expression allows one to determine a degree of inhibition which is
greater than 10%, 33%, 50%, 90%, 95% or 99% as compared to a cell
not treated according to the present invention. Lower doses of
injected material and longer times after administration of dsRNA
may result in inhibition in a smaller fraction of cells (e.g., at
least 10%, 20%, 50%, 75%, 90%, or 95% of targeted cells).
Quantitation of gene expression in a cell may show similar amounts
of inhibition at the level of accumulation of target mRNA or
translation of target protein. As an example, the efficiency of
inhibition may be determined by assessing the amount of gene
product in the cell: mRNA may be detected with a hybridization
probe having a nucleotide sequence outside the region used for the
inhibitory double-stranded RNA, or translated polypeptide may be
detected with an antibody raised against the polypeptide sequence
of that region.
[0032] The RNA may comprise one or more strands of polymerized
ribonucleotide. It may include modifications to either the
phosphate-sugar backbone or the nucleoside. For example, the
phosphodiester linkages of natural RNA may be modified to include
at least one of a nitrogen or sulfur heteroatom. Modifications in
RNA structure may be tailored to allow specific genetic inhibition
while avoiding a general panic response in some organisms which is
generated by dsRNA. Likewise, bases may be modified to block the
activity of adenosine deaminase. RNA may be produced enzymatically
or by partial/total organic synthesis, any modified ribonucleotide
can be introduced by in vitro enzymatic or organic synthesis.
[0033] The double-stranded structure may be formed by a single
self-complementary RNA strand or two complementary RNA strands. RNA
duplex formation may be initiated either inside or outside the
cell. The RNA may be introduced in an amount which allows delivery
of at least one copy per cell. Higher doses (e.g., at least 5, 10,
100, 500 or 1000 copies per cell) of double-stranded material may
yield more effective inhibition; lower doses may also be useful for
specific applications. Inhibition is sequence-specific in that
nucleotide sequences corresponding to the duplex region of the RNA
are targeted for genetic inhibition.
[0034] RNA containing a nucleotide sequences identical to a portion
of the target gene are preferred for inhibition. RNA sequences with
insertions, deletions, and single point mutations relative to the
target sequence have also been found to be effective for
inhibition. Thus, sequence identity may optimized by sequence
comparison and alignment algorithms known in the art (see Gribskov
and Devereux, Sequence Analysis Primer, Stockton Press, 1991, and
references cited therein) and calculating the percent difference
between the nucleotide sequences by, for example, the
Smith-Waterman algorithm as implemented in the BESTFIT software
program using default parameters (e.g., University of Wisconsin
Genetic Computing Group). Greater than 90% sequence identity, or
even 100% sequence identity, between the inhibitory RNA and the
portion of the target gene is preferred. Alternatively, the duplex
region of the RNA may be defined functionally as a nucleotide
sequence that is capable of hybridizing with a portion of the
target gene transcript (e.g., 400 mM NaCl, 40 mM PIPES pH 6.4, 1 mM
EDTA, 50.degree. C. or 70.degree. C. hybridization for 12-16 hours;
followed by washing). The length of the identical nucleotide
sequences may be at least 25, 50, 100, 200, 300 or 400 bases.
[0035] As disclosed herein, 100% sequence identity between the RNA
and the target gene is not required to practice the present
invention. Thus the invention has the advantage of being able to
tolerate sequence variations that might be expected due to genetic
mutation, strain polymorphism, or evolutionary divergence.
[0036] The cell with the target gene may be derived from or
contained in any organism. The organism may a plant, animal,
protozoan, bacterium, virus, or fungus. The plant may be a monocot,
dicot or gymnosperm; the animal may be a vertebrate or
invertebrate. Preferred microbes are those used in agriculture or
by industry, and those that are pathogenic for plants or animals.
Fungi include organisms in both the mold and yeast
morphologies.
[0037] Plants include arabidopsis; field crops (e.g., alfalfa,
barley, bean, corn, cotton, flax, pea, rape, rice, lye, safflower,
sorghum, soybean, sunflower, tobacco, and wheat); vegetable crops
(e.g., asparagus, beet, broccoli, cabbage, carrot, cauliflower,
celery, cucumber, eggplant, lettuce, onion, pepper, potato,
pumpkin, radish, spinach, squash, taro, tomato, and zucchini);
fruit and nut crops (e.g., almond, apple, apricot, banana,
blackberry, blueberry, cacao, cherry, coconut, cranberry, date,
fajoa, filbert, grape, grapefruit, guava, kiwi, lemon, lime, mango,
melon, nectarine, orange, papaya, passion fruit, peach, peanut,
pear, pineapple, pistachio, plum, raspberry, strawberry, tangerine,
walnut, and watermelon); and ornamentals (e.g., alder, ash, aspen,
azalea, birch, boxwood, camellia, carnation, chrysanthemum, elm,
fir, ivy, jasmine, juniper, oak, palm, poplar, pine, redwood,
rhododendron, rose, and rubber).
[0038] Examples of vertebrate animals include fish, mammal, cattle,
goat, pig, sheep, rodent, hamster, mouse, rat, primate, and human;
invertebrate animals include nematodes, other worms, drosophila,
and other insects. Representative generae of nematodes include
those that infect animals (e.g., Ancylostoma, Ascaridia, Ascaris,
Bunostomum, Caenorhabditis, Capillaria, Chabertia, Cooperia,
Dictyocaulus, Haemonchus, Heterakis, Nematodirus, Oesophagostomum,
Ostertagia, Oxyuris, Parascaris, Strongylus, Toxascaris, Trichuris,
Trichostrongylus, Tfhchonema, Toxocara, Uncinaria) and those that
infect plants (e.g., Bursaphalenchus, Criconemella, Diiylenchus,
Ditylenchus, Globodera, Helicotylenchus, Heterodera, Longidorus,
Melodoigyne, Nacobbus, Paratylenchus, Pratylenchus, Radopholus,
Rotelynchus, Tylenchus, and Xiphinema). Representative orders of
insects include Coleoptera, Diptera, Lepidoptera, and
Homoptera.
[0039] The cell having the target gene may be from the germ line or
somatic, totipotent or pluripotent, dividing or non-dividing,
parenchyma or epithelium, immortalized or transformed, or the like.
The cell may be a stem cell or a differentiated cell. Cell types
that are differentiated include adipocytes, fibroblasts, myocytes,
cardiomyocytes, endothelium, neurons, glia, blood cells,
megakaryocytes, lymphocytes, macrophages, neutrophils, eosinophils,
basophils, mast cells, leukocytes, granulocytes, keratinocytes,
chondrocytes, osteoblasts, osteoclasts, hepatocytes, and cells of
the endocrine or exocrine glands.
[0040] RNA may be synthesized either in vivo or in vitro.
Endogenous RNA polymerase of the cell may mediate transcription in
vivo, or cloned RNA polymerase can be used for transcription in
vivo or in vitro. For transcription from a transgene in vivo or an
expression construct, a regulatory region (e.g., promoter,
enhancer, silencer, splice donor and acceptor, polyadenylation) may
be used to transcribe the RNA strand (or strands). Inhibition may
be targeted by specific transcription in an organ, tissue, or cell
type; stimulation of an environmental condition (e.g., infection,
stress, temperature, chemical inducers); and/or engineering
transcription at a developmental stage or age. The RNA strands may
or may not be polyadenylated; the RNA strands may or may not be
capable of being translated into a polypeptide by, a cell's
translational apparatus. RNA may be chemically or enzymatically
synthesized by manual or automated reactions. The RNA may be
synthesized by a cellular RNA polymerase or a bacteriophage. RNA
polymerase (e.g., T3, T7, SP6). The use and production of an
expression construct are known in the art.sup.32,33,34 (see also WO
97/32016; U.S. Pat. Nos. 5,593,874, 5,698,425, 5,712,135,
5,789,214, and 5,804,693; and the references cited therein). If
synthesized chemically or by in vitro enzymatic synthesis, the RNA
may be purified prior to introduction into the cell. For example,
RNA can be purified from a mixture by extraction with a solvent or
resin, precipitation, electrophoresis, chromatography, or a
combination thereof. Alternatively, the RNA may be used with no or
a minimum of purification to avoid losses due to sample processing.
The RNA may be dried for storage or dissolved in an aqueous
solution. The solution may contain buffers or salts to promote
annealing, and/or stabilization of the duplex strands.
[0041] RNA may be directly introduced into the cell (i.e.,
intracellularly); or introduced extracellularly into a cavity,
interstitial space, into the circulation of an organism, introduced
orally, or may be introduced by bathing an organism in a solution
containing the RNA. Methods for oral introduction include direct
mixing of the RNA with food of the organism, as well as engineered
approaches in which a species that is used as food is engineered to
express the RNA, then fed to the organism to be affected. For
example, the RNA may be sprayed onto a plant or a plant may be
genetically engineered to express the RNA in an amount sufficient
to kill some or all of a pathogen known to infect the plant.
Physical methods of introducing nucleic acids, for example,
injection directly into the cell or extracellular injection into
the organism, may also be used. We disclose herein that in C.
elegans, double-stranded RNA introduced outside the cell inhibits
gene expression. Vascular or extravascular circulation, the blood
or lymph system, the phloem, the roots, and the cerebrospinal fluid
are sites where the RNA may be introduced. A transgenic organism
that expresses RNA from a recombinant construct may be produced by
introducing the construct into a zygote, an embryonic stem cell, or
another multipotent cell derived from the appropriate organism.
[0042] Physical methods of introducing nucleic acids include
injection of a solution containing the RNA, bombardment by
particles covered by the RNA, soaking the cell or organism in a
solution of the RNA, or electroporation of cell membranes in the
presence of the RNA. A viral construct packaged into a viral
particle would accomplish both efficient introduction of an
expression construct into the cell and transcription of RNA encoded
by the expression construct. Other methods known in the art for
introducing nucleic acids to cells may be used, such as
lipid-mediated carrier transport, chemical-mediated transport, such
as calcium phosphate, and the like. Thus the RNA may be introduced
along with components that perform one or more of the following
activities: enhance RNA uptake by the cell, promote annealing of
the duplex strands, stabilize the annealed strands, or other-wise
increase inhibition of the target gene.
[0043] The present invention may be used to introduce RNA into a
cell for the treatment or prevention of disease. For example, dsRNA
may be introduced into a cancerous cell or tumor and thereby
inhibit gene expression of a gene required for maintenance of the
carcinogenic/tumorigenic phenotype. To prevent a disease or other
pathology, a target gene may be selected which is required for
initiation or maintenance of the disease/pathology. Treatment would
include amelioration of any symptom associated with the disease or
clinical indication associated with the pathology.
[0044] A gene derived from any pathogen may be targeted for
inhibition. For example, the gene could cause immunosuppression of
the host directly or be essential for replication of the pathogen,
transmission of the pathogen, or maintenance of the infection. The
inhibitory RNA could be introduced in cells in vitro or ex vivo and
then subsequently placed into an animal to affect therapy, or
directly treated by in vivo administration. A method of gene
therapy can be envisioned. For example, cells at risk for infection
by a pathogen or already infected cells, particularly human
immunodeficiency virus (HIV) infections, may be targeted for
treatment by introduction of RNA according to the invention. The
target gene might be a pathogen or host gene responsible for entry
of a pathogen into its host, drug metabolism by the pathogen or
host, replication or integration of the pathogen's genome,
establishment or spread of an infection in the host, or assembly;
of the next generation of pathogen. Methods of prophylaxis (i.e.,
prevention or decreased risk of infection), as well as reduction in
the frequency or severity of symptoms associated with infection,
can be envisioned.
[0045] The present invention could be used for treatment or
development of treatments for cancers of any type, including solid
tumors and leukemias, including: apudoma, choristoma, branchioma,
malignant carcinoid syndrome, carcinoid heart disease, carcinoma
(e.g., Walker, basal cell, basosquamous, Brown-Pearce, ductal,
Ehrlich tumor, in situ, Krebs 2, Merkel cell, mucinous, non-small
cell lung, oat cell, papillary, scirrhous, bronchiolar,
bronchogenic, squamous cell, and transitional cell), histiocytic
disorders, leukemia (e.g., B cell, mixed cell, null cell, T cell,
T-cell chronic, HTLV-II-associated, lymphocytic acute, lymphocytic
chronic, mast cell, and myeloid), histiocytosis malignant, Hodgkin
disease, immunoproliferative small, non-Hodgkin lymphoma,
plasmacytoma, reticuloendotheliosis, melanoma, chondroblastoma,
chondroma, chondrosarcoma, fibroma, fibrosarcoma, giant cell
tumors, histiocytoma, lipoma, liposarcoma, mesothelioma, myxoma,
myxosarcoma, osteoma, osteosarcoma, Ewing sarcoma, synovioma,
adenofibroma, adenolymphoma, carcinosarcoma, chordoma,
cranio-pharyngioma, dysgerminoma, hamartoma, mesenchymoma,
mesonephroma, myosarcoma, ameloblastoma, cementoma, odontoma,
teratoma, thymoma, trophoblastic tumor, adenocarcinoma, adenoma,
cholangioma, cholesteatoma, cylindroma, cystadenocarcinoma,
cystadenoma, granulosa cell tumor, gynandroblastoma, hepatoma,
hidradenoma, islet cell tumor, Leydig cell tumor, papilloma,
Sertoli cell tumor, theca cell tumor, leiomyoma, leiomyosarcoma,
myoblastoma, myoma, myosarcoma, rhabdomyoma, rhabdomyosarcoma,
ependymoma, ganglioneuroma, glioma, medulloblastoma, meningioma,
neurilemmoma, neuroblastoma, neuroepithelioma, neurofibroma,
neuroma, paraganglioma, paraganglioma nonchromaffin, angiokeratoma,
angiolymphoid hyperplasia with eosinophilia, angioma sclerosing,
angiomatosis, glomangioma, hemangioendothelioma, hemangioma,
hemangiopericytoma, hemangiosarcoma, lymphangioma, lymphangiomyoma,
lymphangiosarcoma, pinealoma, carcinosarcoma, chondrosarcoma,
cystosarcoma phyllodes, fibrosarcoma, hemangiosarcoma,
leiomyosarcoma, leukosarcoma, liposarcoma, lymphangiosarcoma,
myosarcoma, myxosarcoma, ovarian carcinoma, rhabdomyosarcoma,
sarcoma (e.g., Ewing, experimental, Kaposi, and mast cell),
neoplasms (e.g., breast, digestive system, colorectal, liver,
pancreatic, pituitary, testicular, orbital, head and neck, central
nervous system, acoustic, pelvic, respiratory tract, and
urogenital), neurofibromatosis, and cervical dysplasia, and for
treatment of other conditions in which cells have become
immortalized or transformed. The invention could be used in
combination with other treatment modalities, such as chemotherapy,
cryotherapy, hyperthermia, radiation therapy, and the like.
[0046] As disclosed herein, the present invention may is not
limited to any type of target gene or nucleotide sequence. But the
following classes of possible target genes are listed for
illustrative purposes: developmental genes (e.g., adhesion
molecules, cyclin kinase inhibitors, Wnt family members, Pax family
members, Winged helix family members, Hox family members,
cytokines/lymphokines and their receptors, growth/differentiation
factors and their receptors, neurotransmitters and their
receptors); oncogenes (e.g., ABL1, BCL1, BCL2, BCL6, CBFA2, CBL,
CSF1R, ERBA, ERBB, EBRB2, ETS1, ETS1, ETV6, FGR, FOS, FYN, HCR,
HRAS, JUN, KRAS, LCK, LYN, MDM2, MLL, MYB, MYC, MYCL1, MYCN, NRAS,
PIM1, PML, RET, SRC, TAL1, TCL3, and YES); tumor suppressor genes
(e.g., APC, BRCA1, BRCA2, MADH4, MCC, NF1, NF2, RB1, TP53, and
WT1); and enzymes (e.g., ACC synthases and oxidases, ACP
desaturases and hydroxylases, ADP-glucose pyrophorylases, ATPases,
alcohol dehydrogenases, amylases, amyloglucosidases, catalases,
cellulases, chalcone synthases, chitinases, cyclooxygenases,
decarboxylases, dextrinases, DNA and RNA polymerases,
galactosidases, glucanases, glucose oxidases, granule-bound starch
synthases, GTPases, helicases, hemicellulases, integrases,
inulinases, invertases, isomerases, kinases, lactases, lipases,
lipoxygenases, lysozymes, nopaline synthases, octopine synthases,
pectinesterases, peroxidases, phosphatases, phospholipases,
phosphorylases, phytases, plant growth regulator synthases,
polygalacturonases, proteinases and peptidases, pullanases,
recombinases, reverse transcriptases, RUBISCOs, topoisomerases, and
xylanases).
[0047] The present invention could comprise a method for producing
plants with reduced susceptibility to climatic injury,
susceptibility to insect damage, susceptibility to infection by a
pathogen, or altered fruit ripening characteristics. The targeted
gene may be an enzyme, a plant structural protein, a gene involved
in pathogenesis, or an enzyme that is involved in the production of
a non-proteinaceous part of the plant (i.e., a carbohydrate or
lipid). If an expression construct is used to transcribe the RNA in
a plant, transcription by a wound- or stress-inducible;
tissue-specific (e.g., fruit, seed, anther, flower, leaf, root); or
otherwise regulatable (e.g., infection, light, temperature,
chemical) promoter may be used. By inhibiting enzymes at one or
more points in a metabolic pathway or genes involved in
pathogenesis, the effect may be enhanced: each activity will be
affected and the effects may be magnified by targeting multiple
different components. Metabolism may also be manipulated by
inhibiting feedback control in the pathway or production of
unwanted metabolic byproducts.
[0048] The present invention may be used to reduce crop destruction
by other plant pathogens such as arachnids, insects, nematodes,
protozoans, bacteria, or fungi. Some such plants and their
pathogens are listed in Index of Plant Diseases in the United
States (U.S. Dept. of Agriculture Handbook No. 165, 1960);
Distribution of Plant-Parasitic Nematode Species in North America
(Society of Nematologists, 1985); and Fungi on Plants and Plant
Products in the United States (American Phytopathological Society,
1989). Insects with reduced ability to damage crops or improved
ability to prevent other destructive insects from damaging crops
may be produced. Furthermore, some nematodes are vectors of plant
pathogens, and may be attacked by other beneficial nematodes which
have no effect on plants. Inhibition of target gene activity could
be used to delay or prevent entry into a particular developmental
step (e.g., metamorphosis), if plant disease was associated with a
particular stage of the pathogen's life cycle. Interactions between
pathogens may also be modified by the invention to limit crop
damage. For example, the ability of beneficial nematodes to attack
their harmful prey may be enhanced by inhibition of
behavior-controlling nematode genes according to the invention.
[0049] Although pathogens cause disease, some of the microbes
interact with their plant host in a beneficial manner. For example,
some bacteria are involved in symbiotic relationships that fix
nitrogen and some fungi produce phytohormones. Such beneficial
interactions may be promoted by using the present invention to
inhibit target gene activity in the plant and/or the microbe.
[0050] Another utility of the present invention could be a method
of identifying gene function in an organism comprising the use of
double-stranded RNA to inhibit the activity of a target gene of
previously unknown function. Instead of the time consuming and
laborious isolation of mutants by traditional genetic screening,
functional genomics would envision determining the function of
uncharacterized genes by employing the invention to reduce the
amount and/or alter the timing of target gene activity. The
invention could be used in determining potential targets for
pharmaceutics, understanding normal and pathological events
associated with development, determining signaling pathways
responsible for postnatal development/aging, and the like. The
increasing speed of acquiring nucleotide sequence information from
genomic and expressed gene sources, including total sequences for
the yeast, D. melanogaster, and C. elegans genomes, can be coupled
with the invention to determine gene function in an organism (e.g.,
nematode). The preference of different organisms to use particular
codons, searching sequence databases for related gene products,
correlating the linkage map of genetic traits with the physical map
from which the nucleotide sequences are derived, and artificial
intelligence methods may be used to define putative open reading
frames from the nucleotide sequences acquired in such sequencing
projects.
[0051] A simple assay would be to inhibit gene expression according
to the partial sequence available from an expressed sequence tag
(EST). Functional alterations in growth, development, metabolism,
disease resistance, or other biological processes would be
indicative of the normal role of the EST's gene product.
[0052] The ease with which RNA can be introduced into an intact
cell/organism containing the target gene allows the present
invention to be used in high throughput screening (HTS). For
example, duplex RNA can be produced by an amplification reaction
using primers flanking the inserts of any gene library derived from
the target cell/organism. Inserts may be derived from genomic DNA
or mRNA (e.g., cDNA and cRNA). Individual clones from the library
can be replicated and then isolated in separate reactions, but
preferably the library is maintained in individual reaction vessels
(e.g., a 96-well microtiter plate) to minimize the number of steps
required to practice the invention and to allow automation of the
process. Solutions containing duplex RNAs that are capable of
inhibiting the different expressed genes can be placed into
individual wells positioned on a microtiter plate as an ordered
array, and intact cells/organisms in each well can be assayed for
any changes or modifications in behavior or development due to
inhibition of target gene activity. The amplified RNA can be fed
directly to, injected into, the cell/organism containing the target
gene. Alternatively, the duplex RNA can be produced by in vivo or
in vitro transcription from an expression construct used to produce
the library. The construct can be replicated as individual clones
of the library and transcribed to produce the RNA; each clone can
then be fed to, or injected into, the cell/organism containing the
target gene. The function of the target gene can be assayed from
the effects it has on the cell/organism when gene activity is
inhibited. This screening could be amenable to small subjects that
can be processed in large number, for example: arabidopsis,
bacteria, drosophila, fungi, nematodes, viruses, zebrafish, and
tissue culture cells derived from mammals.
[0053] A nematode or other organism that produces a colorimetric,
fluorogenic, or luminescent signal in response to a regulated
promoter (e.g., transfected with a reporter gene construct) can be
assayed in an HTS format to identify DNA-binding proteins that
regulate the promoter. In the assay's simplest form, inhibition of
a negative regulator results in an increase of the signal and
inhibition of a positive regulator results in a decrease of the
signal.
[0054] If a characteristic of an organism is determined to be
genetically linked to a polymorphism through RFLP or QTL analysis,
the present invention can be used to gain insight regarding whether
that genetic polymorphism might be directly responsible for the
characteristic. For example, a fragment defining the genetic
polymorphism or sequences in the vicinity of such a genetic
polymorphism can be amplified to produce an RNA, the duplex RNA can
be introduced to the organism, and whether an alteration in the
characteristic is correlated with inhibition can be determined. Of
course, there may be trivial explanations for negative results with
this type of assay, for example: inhibition of the target gene
causes lethality, inhibition of the target gene may not result in
any observable alteration, the fragment contains nucleotide
sequences that are not capable of inhibiting the target gene, or
the target gene's activity is redundant.
[0055] The present invention may be useful in allowing the
inhibition of essential genes. Such genes may be required for cell
or organism viability at only particular stages of development or
cellular compartments. The functional equivalent of conditional
mutations may be produced by inhibiting activity of the target gene
when or where it is not required for viability. The invention
allows addition of RNA at specific times of development and
locations in the organism without introducing permanent mutations
into the target genome.
[0056] If alternative splicing produced a family of transcripts
that were distinguished by usage of characteristic exons, the
present invention can target inhibition through the appropriate
exons to specifically inhibit or to distinguish among the functions
of family members. For example, a hormone that contained an
alternatively spliced transmembrane domain may be expressed in both
membrane bound and secreted forms. Instead of isolating a nonsense
mutation that terminates translation before the transmembrane
domain, the functional consequences of having only secreted hormone
can be determined according to the invention by targeting the exon
containing the transmembrane domain and thereby inhibiting
expression of membrane-bound hormone.
[0057] The present invention may be used alone or as a component of
a kit having at least one of the reagents necessary to carry out
the in vitro or in vivo introduction of RNA to test samples or
subjects. Preferred components are the dsRNA and a vehicle that
promotes introduction of the dsRNA. Such a kit may also include
instructions to allow a user of the kit to practice the
invention.
[0058] Pesticides may include the RNA molecule itself, an
expression construct capable of expressing the RNA, or organisms
transfected with the expression construct. The pesticide of the
present invention may serve as an arachnicide, insecticide,
nematicide, viricide, bactericide, and/or fungicide. For example,
plant parts that are accessible above ground (e.g., flowers,
fruits, buds, leaves, seeds, shoots, bark, stems) may be sprayed
with pesticide, the soil may be soaked with pesticide to access
plant parts growing beneath ground level, or the pest may be
contacted with pesticide directly. If pests interact with each
other, the RNA may be transmitted between them. Alternatively, if
inhibition of the target gene results in a beneficial effect on
plant growth or development, the aforementioned RNA, expression
construct, or transfected organism may be considered a nutritional
agent. In either case, genetic engineering of the plant is not
required to achieve the objectives of the invention.
[0059] Alternatively, an organism may be engineered to produce
dsRNA which produces commercially or medically beneficial results,
for example, resistance to a pathogen or its pathogenic effects,
improved growth, or novel developmental patterns.
[0060] Used as either an pesticide or nutrient, a formulation of
the present invention may be delivered to the end user in dry or
liquid form: for example, as a dust, granulate, emulsion, paste,
solution, concentrate, suspension, or encapsulation. Instructions
for safe and effective use may also be provided with the
formulation. The formulation might be used directly, but
concentrates would require dilution by mixing with an extender
provided by the formulator or the end user. Similarly, an emulsion,
paste, or suspension may require the end user to perform certain
preparation steps before application. The formulation may include a
combination of chemical additives known in the art such as solid
carriers, minerals, solvents, dispersants, surfactants,
emulsifiers, tackifiers, binders, and other adjuvants.
Preservatives and stabilizers may also be added to the formulation
to facilitate storage. The crop area or plant may also be treated
simultaneously or separately with other pesticides or fertilizers.
Methods of application include dusting, scattering or pouring,
soaking, spraying, atomizing, and coating. The precise physical
form and chemical composition of the formulation, and its method of
application, would be chosen to promote the objectives of the
invention and in accordance with prevailing circumstances.
Expression constructs and transfected hosts capable of replication
may also promote the persistence and/or spread of the
formulation.
Description of the dsRNA Inhibition Phenomenon in C. elegans
[0061] The operation of the present invention was shown in the
model genetic organism Caenorhabditis elegans.
[0062] Introduction of RNA into cells had been seen in certain
biological systems to interfere with function of an endogenous
gene.sup.1,2. Many such effects were believed to result from a
simple antisense mechanism dependent on hybridization between
injected single-stranded RNA and endogenous transcripts. In other
cases, a more complex mechanism had been suggested. One instance of
an RNA-mediated mechanism was RNA interference (RNAi) phenomenon in
the nematode C. elegans. RNAi had been used in a variety of studies
to manipulate gene expression.sup.3,4.
[0063] Despite the usefulness of RNAi in C. elegans, many features
had been difficult to explain. Also, the lack of a clear
understanding of the critical requirements for interfering RNA led
to a sporadic record of failure and partial success in attempts to
extend RNAi beyond the earliest stages following injection. A
statement frequently made in the literature was that sense and
antisense RNA preparations are each sufficient to cause
interference.sup.3,4. The only precedent for such a situation was
in plants where the process of co-suppression had a similar history
of usefulness in certain cases, failure in others, and no ability
to design interference protocols with a high chance of success.
Working with C. elegans, we discovered an RNA structure that would
give effective and uniform genetic inhibition. The prior art
did-not teach or suggest that RNA structure was a critical feature
for inhibition of gene expression. Indeed the ability of crude
sense and antisense preparations to produce interference.sup.3,4
had been taken as an indication that RNA structure was not a
critical factor. Instead, the extensive plant literature and much
of the ongoing research in C. elegans was focused on the
possibility that detailed features of the target gene sequence or
its chromosomal locale was the critical feature for interfering
with gene expression.
[0064] The inventors carefully purified sense or antisense RNA for
unc-22 and tested each for gene-specific inhibition. While the
crude sense and antisense preparations had strong interfering
activity, it was found that the purified sense and antisense RNAs
had only marginal inhibitory activity. This was unexpected because
many techniques in molecular biology are based on the assumption
that RNA produced with specific in vitro promoters (e.g., T3 or T7
RNA polymerase), or with characterized promoters in vivo, is
produced predominantly from a single strand. The inventors had
carried out purification of these crude preparations to investigate
whether a small fraction of the RNA had an unusual structure which
might be responsible for the observed genetic inhibition. To
rigorously test whether double-stranded character might contribute
to genetic inhibition, the inventors carried out additional
purification of single-stranded RNAs and compared inhibitory
activities of individual strands with that of the double-stranded
hybrid.
[0065] The following examples are meant to be illustrative of the
present invention; however, the practice of the invention is not
limited or restricted in any way by them.
Analysis of RNA-Mediated Inhibition of C. elegans Genes
[0066] The unc-22 gene was chosen for initial comparisons of
activity as a result of previous genetic analysis that yields a
semi-quantitative comparison between unc-22 gene activity and the
movement phenotypes of animals.sup.3,8: decreases in activity
produce an increasingly severe twitching phenotype, while complete
loss of function results in the additional appearance of muscle
structural defects and impaired motility. unc-22 encodes an
abundant but non-essential myofilament protein.sup.7-9. unc-22 mRNA
is present at several thousand copies per striated muscle
cell.sup.3.
[0067] Purified antisense and sense RNAs covering a 742 nt segment
of unc-22 had only marginal inhibitory activity, requiring a very
high dose of injected RNA for any observable effect (FIG. 4). By
contrast, a sense+antisense mixture produced a highly effective
inhibition of endogenous gene activity (FIG. 4). The mixture was at
least two orders of magnitude more effective than either single
strand in inhibiting gene expression. The lowest dose of the
sense+antisense mixture tested, approximately 60,000 molecules of
each strand per adult, led to twitching phenotypes in an average of
100 progeny. unc-22 expression begins in embryos with approximately
500 cells. At this point, the original injected material would be
diluted to at most a few molecules per cell.
[0068] The potent inhibitory activity of the sense+antisense
mixture could reflect formation of double-stranded RNA (dsRNA), or
conceivably some alternate synergy between the strands.
Electrophoretic analysis indicated that the injected material was
predominantly double stranded. The dsRNA was gel purified from the
annealed mixture and found to retain potent inhibitory activity.
Although annealing prior to injection was compatible with
inhibition, it was not necessary. Mixing of sense and antisense
RNAs in low salt (under conditions of minimal dsRNA formation), or
rapid sequential injection of sense and antisense strands, were
sufficient to allow complete inhibition. A long interval (>1
hour) between sequential injections of sense and antisense RNA
resulted in a dramatic decrease in inhibitory activity. This
suggests that injected single strands may be degraded or otherwise
rendered inaccessible in the absence of the complementary
strand.
[0069] An issue of specificity arises when considering known
cellular responses to dsRNA. Some organisms have a dsRNA-dependent
protein kinase that activates a panic response mechanism.sup.10.
Conceivably, the inventive sense+antisense synergy could reflect a
non-specific potentiation of antisense effects by such a panic
mechanism. This was not found to be the case: co-injection of dsRNA
segments unrelated to unc-22 did not potentiate the ability of
unc-22 single strands to mediate inhibition. Also investigated was
whether double-stranded structure could potentiate inhibitory
activity when placed in cis to a single-stranded segment. No such
potentiation was seen; unrelated double-stranded sequences located
5' or 3' of a single-stranded unc-22 segment did not stimulate
inhibition. Thus potentiation of gene-specific inhibition was
observed only when dsRNA sequences exist within the region of
homology with the target gene.
[0070] The phenotype produced by unc-22 dsRNA was specific. Progeny
of injected animals exhibited behavior indistinguishable from
characteristic unc-22 loss of function mutants. Target-specificity
of dsRNA effects using three additional genes with well
characterized phenotypes (FIG. 1 and Table 1). unc-54 encodes a
body wall muscle myosin heavy chain isoform required for full
muscle contraction.sup.7,11,12, fem-1 encodes an ankyrin-repeat
containing protein required in hermaphrodites for sperm
production.sup.13,14, and hlh-1 encodes a C. elegans homolog of the
myoD family required for proper body shape and motility.sup.15,16.
For each of these genes, injection of dsRNA produced progeny broods
exhibiting the known null mutant phenotype, while the purified
single strands produced no significant reduction in gene
expression. With one exception, all of the phenotypic consequences
of dsRNA injection were those expected from inhibition of the
corresponding gene. The exception (segment unc54C, which led to an
embryonic and larval arrest phenotype not seen with unc-54 null
mutants) was illustrative. This segment covers the highly conserved
myosin motor domain, and might have been expected to inhibit the
activity of other highly related myosin heavy chain genes.sup.17.
This interpretation would support uses of the present invention in
which nucleotide sequence comparison of dsRNA and target gene show
less than 100% identity. The unc54C segment has been unique in our
overall experience to date: effects of 18 other dsRNA segments have
all been limited to those expected from characterized null
mutants.
[0071] The strong phenotypes seen following dsRNA injection are
indicative of inhibitory effects occurring in a high fraction of
cells. The unc-54 and hlh-1 muscle phenotypes, in particular, are
known to result from a large number of defective muscle
cells.sup.11,16. To examine inhibitory effects of dsRNA on a
cellular level, a transgenic line expressing two different
GFP-derived fluorescent reporter proteins in body muscle was used.
Injection of dsRNA directed to gfp produced dramatic decreases in
the fraction of fluorescent cells (FIG. 2). Both reporter proteins
were absent from the negative cells, while the few positive cells
generally expressed both GFP forms.
[0072] The pattern of mosaicism observed with gfp inhibition was
not random. At low doses of dsRNA, the inventors saw frequent
inhibition in the embryonically-derived muscle cells present when
the animal hatched. The inhibitory effect in these differentiated
cells persisted through larval growth: these cells produced little
or no additional GFP as the affected animals grew. The 14
postembryonically-derived striated muscles are born during early
larval stages and were more resistant to inhibition. These cells
have come through additional divisions (13-14 versus 8-9 for
embryonic muscles.sup.18,19). At high concentrations of gfp dsRNA,
inhibition was noted in virtually all striated bodywall muscles,
with occasional single escaping cells including cells born in
embryonic or postembryonic stages. The nonstriated vulval muscles,
born during late larval development, appeared resistant to genetic
inhibition at all tested concentrations of injected RNA. The latter
result is important for evaluating the use of the present invention
in other systems. First, it indicates that failure in one set of
cells from an organism does not necessarily indicate complete
non-applicability of the invention to that organism. Second, it is
important to realize that not all tissues in the organism need to
be affected for the invention to be used in an organism. This may
serve as an advantage in some situations.
[0073] A few observations serve to clarify the nature of possible
targets and mechanisms for RNA-mediated genetic inhibition in C.
elegans:
[0074] First, dsRNA segments corresponding to a variety of intron
and promoter sequences did not produce detectable inhibition (Table
1). Although consistent with possible inhibition at a
post-transcriptional level, these experiments do not rule out
inhibition at the level of the gene.
[0075] Second, dsRNA injection produced a dramatic decrease in the
level of the endogenous mRNA transcript (FIG. 3). Here, a mex-3
transcript that is abundant in the gonad and early embryos.sup.20
was targeted, where straightforward in situ hybridization can be
performed.sup.5. No endogenous mex-3 mRNA was observed in animals
injected with a dsRNA segment derived from mex-3 (FIG. 3D), but
injection of purified mex-3 antisense RNA resulted in animals that
retained substantial endogenous mRNA levels (FIG. 3C).
[0076] Third, dsRNA-mediated inhibition showed a surprising ability
to cross cellular boundaries. Injection of dsRNA for unc-22, gfp,
or lacZ into the body cavity of the head or tail produced a
specific and robust inhibition of gene expression in the progeny
brood (Table 2). Inhibition was seen in the progeny of both gonad
arms; ruling out a transient "nicking" of the gonad in these
injections. dsRNA injected into body cavity or gonad of young
adults also produced gene-specific inhibition in somatic tissues of
the injected animal (Table 2).
[0077] Table 3 shows that C. elegans can respond in a gene-specific
manner to dsRNA encountered in the environment. Bacteria are a
natural food source for C. elegans. The bacteria are ingested,
ground in the animal's pharynx, and the bacterial contents taken up
in the gut. The results show that E. coli bacteria expressing
dsRNAs can confer specific inhibitory effects on C. elegans
nematode larvae that feed on them.
[0078] Three C. elegans genes were analyzed. For each gene,
corresponding dsRNA was expressed in E. coli by inserting a segment
of the coding region into a plasmid construct designed for
bidirectional transcription by bacteriophage T7 RNA polymerase. The
dsRNA segments used for these experiments were the same as those
used in previous microinjection experiments (see FIG. 1). The
effects resulting from feeding these bacteria to C. elegans were
compared to the effects achieved by microinjecting animals with
dsRNA.
[0079] The C. elegans gene unc-22 encodes an abundant muscle
filament protein. unc-22 null mutations produce a characteristic
and uniform twitching phenotype in which the animals can sustain
only transient muscle contraction. When wild-type animals were fed
bacteria expressing a dsRNA segment from unc-22, a high fraction
(85%) exhibited a weak but still distinct twitching phenotype
characteristic of partial loss of function for the unc-22 gene. The
C. elegans fem-1 gene encodes a late component of the sex
determination pathway. Null mutations prevent the production of
sperm and lead euploid (XX) animals to develop as females, while
wild type XX animals develop as hermaphrodites. When wild-type
animals were fed bacteria expressing dsRNA corresponding to fem-1,
a fraction (43%) exhibit a sperm-less (female) phenotype and were
sterile. Finally, the ability to inhibit gene expression of a
transgene target was assessed. When animals carrying a gfp
transgene were fed bacteria expressing dsRNA corresponding to the
gfp reporter, an obvious decrease in the overall level of GFP
fluorescence was observed, again in approximately 12% of the
population (see FIG. 5, panels B and C).
[0080] The effects of these ingested RNAs were specific. Bacteria
carrying different dsRNAs from fem-1 and gfp produced no twitching,
dsRNAs from unc-22 and fem-1 did not reduce gfp expression, and
dsRNAs from gfp and unc-22 did not produce females. These
inhibitory effects were apparently mediated by dsRNA: bacteria
expressing only the sense or antisense strand for either gfp or
unc-22 caused no evident phenotypic effects on their C. elegans
predators.
[0081] Table 4 shows the effects of bathing C. elegans in a
solution containing dsRNA. Larvae were bathed for 24 hours in
solutions of the indicated dsRNAs (1 mg/ml), then allowed to
recover in normal media and allowed to grow under standard
conditions for two days. The unc-22 dsRNA was segment ds-unc22A
from FIG. 1. pos-1 and sqt-3 dsRNAs were from the full length cDNA
clones. pos-1 encodes an essential maternally provided component
required early in embyogenesis. Mutations removing pos-1 activity
have an early embryonic arrest characteristic of skin-like
mutations.sup.29,30. Cloning and activity patterns for sqt-3 have
been described.sup.31. C. elegans sqt-3 mutants have mutations in
the col-I collagen gene.sup.31. Phenotypes of affected animals are
noted. Incidences of clear phenotypic effects in these experiments
were 5-10% for unc-22, 50% for pos-1, and 5% for sqt-3. These are
frequencies of unambiguous phenocopies; other treated animals may
have had marginal defects corresponding to the target gene that
were not observable. Each treatment was fully gene-specific in that
unc-22 dsRNA produced only Unc-22 phenotypes, pos-1 dsRNA produced
only Pos-1 phenotypes, and sqt-3 dsRNA produced only Sqt-3
phenotypes.
[0082] Some of the results described herein were published after
the filing of our provisional application. Those publications and a
review can be cited as Fire, A., et al. Nature, 391, 806-811, 1998;
Timmons, L. & Fire, A. Nature, 395, 854, 1998; and Montgomery,
M. K. & Fire, A. Trends in Genetics, 14,255-258, 1998.
[0083] The effects described herein significantly augment available
tools for studying gene function in C. elegans and other organisms.
In particular, functional analysis should now be possible for a
large number of interesting coding regions.sup.21 for which no
specific function have been defined. Several of these observations
show the properties of dsRNA that may affect the design of
processes for inhibition of gene expression. For example, one case
was observed in which a nucleotide sequence shared between several
myosin genes may inhibit gene expression of several members of a
related gene family.
Methods of RNA Synthesis and Microinjection
[0084] RNA was synthesized from phagemid clones with T3 and T7 RNA
polymerase.sup.6, followed by template removal with two sequential
DNase treatments. In cases where sense, antisense, and mixed RNA
populations were to be compared, RNAs were further purified by
electrophoresis on low-gelling-temperature agarose. Gel-purified
products appeared to lack many of the minor bands seen in the
original "sense" and "antisense" preparations. Nonetheless, RNA
species accounting for less than 10% of purified RNA preparations
would not have been observed. Without gel purification, the "sense"
and "antisense" preparations produced significant inhibition. This
inhibitory activity was reduced or eliminated upon gel
purification. By contrast, sense+antisense mixtures of gel purified
and non-gel-purified RNA preparations produced identical
effects.
[0085] Following a short (5 minute) treatment at 68.degree. C. to
remove secondary structure, sense+antisense annealing was carried
out in injection buffer.sup.27 at 37.degree. C. for 10-30 minutes.
Formation of predominantly double stranded material was confirmed
by testing migration on a standard (non-denaturing) agarose gel:
for each RNA pair, gel mobility was shifted to that expected for
double-stranded RNA of the appropriate length. Co-incubation of the
two strands in a low-salt buffer (5 mM Tris-HCl pH 7.5, 0.5 mM
EDTA) was insufficient for visible formation of double-stranded RNA
in vitro. Non-annealed sense+antisense RNAs for unc22B and gfpG
were tested for inhibitory effect and found to be much more active
than the individual single strands, but 2-4 fold less active than
equivalent pre-annealed preparations.
[0086] After pre-annealing of the single strands for unc22A, the
single electrophoretic species corresponding in size to that
expected for dsRNA was purified using two rounds of gel
electrophoresis: This material retained a high degree of inhibitory
activity.
[0087] Except where noted, injection mixes were constructed so
animals would receive an average of 0.5.times.10.sup.6 to
1.0.times.10.sup.6 molecules of RNA. For comparisons of sense,
antisense, and dsRNA activities, injections were compared with
equal masses of RNA (i.e., dsRNA at half the molar concentration of
the single strands). Numbers of molecules injected per adult are
given as rough approximations based on concentration of RNA in the
injected material (estimated from ethidium bromide staining) and
injection volume (estimated from visible displacement at the site
of injection). A variability of several-fold in injection volume
between individual animals is possible; however, such variability
would not affect any of the conclusions drawn herein.
Methods for Analysis of Phenotypes
[0088] Inhibition of endogenous genes was generally assayed in a
wild type genetic background (N2). Features analyzed included
movement, feeding, hatching, body shape, sexual identity, and
fertility. Inhibition with gfp.sup.27 and lacZ activity was
assessed using strain PD4251. This strain is a stable transgenic
strain containing an integrated array (ccIs4251) made up of three
plasmids: pSAK4 (myo-3 promoter driving mitochondrially targeted
GFP), pSAK2 (myo-3 promoter driving a nuclear targeted GFP-LacZ
fusion), and a dpy-20 subclone.sup.26, as a selectable marker. This
strain produces GFP in all body muscles, with a combination of
mitochondrial and nuclear localization. The two distinct
compartments are easily distinguished in these cells, allowing a
facile distinction between cells expressing both, either, or
neither of the original GFP constructs.
[0089] Gonadal injection was performed by inserting the
microinjection needle into the gonadal syncitium of adults and
expelling 20-100 pl of solution (see Reference 25). Body cavity
injections followed a similar procedure, with needle insertion into
regions of the head and tail beyond the positions of the two gonad
arms. Injection into the cytoplasm of intestinal cells was another
effective means of RNA delivery, and may be the least disruptive to
the animal. After recovery and transfer to standard solid media,
injected animals were transferred to fresh culture plates at 16
hour intervals. This yields a series of semi-synchronous cohorts in
which it was straightforward to identify phenotypic differences. A
characteristic temporal pattern of phenotypic severity is observed
among progeny. First, there is a short "clearance" interval in
which unaffected progeny are produced. These include impermeable
fertilized eggs present at the time of injection. After the
clearance period, individuals are produced which show the
inhibitory phenotype. After injected animals have produced eggs for
several days, gonads can in some cases "revert" to produce
incompletely affected or phenotypically normal progeny.
Additional Description of the Results
[0090] FIG. 1 shows genes used to study RNA-mediated genetic
inhibition in C. elegans. Intron-exon structure for genes used to
test RNA-mediated inhibition are shown (exons: filled boxes;
introns: open boxes; 5' and 3' untranslated regions: shaded;
sequence references are as follows: unc-22.sup.9, unc-54.sup.12,
fem-1.sup.14, and hlh-1.sup.15). These genes were chosen based on:
(1) a defined molecular structure, (2) classical genetic data
showing the nature of the null phenotype. Each segment tested for
inhibitory effects is designated with the name of the gene followed
by a single letter (e.g., unc22C). Segments derived from genomic
DNA are shown above the gene, segments derived from cDNA are shown
below the gene. The consequences of injecting double-stranded RNA
segments for each of these genes is described in Table 1. dsRNA
sequences from the coding region of each gene produced a phenotype
resembling the null phenotype for that gene.
[0091] The effects of inhibitory RNA were analyzed in individual
cells (FIG. 2, panels A-H). These experiments were carried out in a
reporter strain (called PD4251) expressing two different reporter
proteins: nuclear GFP-LacZ and mitochondrial GFP, both expressed in
body muscle. The fluorescent nature of these reporter proteins
allowed us to examine individual cells under the fluorescence
microscope to determine the extent and generality of the observed
inhibition of gene. ds-unc22A RNA was injected as a negative
control. GFP expression in progeny of these injected animals was
not affected. The GFP patterns of these progeny appeared identical
to the parent strain, with prominent fluorescence in nuclei (the
nuclear localized GFP-LacZ) and mitochondria (the mitochondrially
targeted GFP): young larva (FIG. 2A), adult (FIG. 2B), and adult
body wall at high magnification (FIG. 2C).
[0092] In contrast, the progeny of animals injected with ds-e/G RNA
are affected (FIGS. 2D-F). Observable GFP fluorescence is
completely absent in over 95% of the cells. Few active cells were
seen in larvae (FIG. 2D shows a larva with one active cell;
uninjected controls show GFP activity in all 81 body wall muscle
cells). Inhibition was not effective in all tissues: the entire
vulval musculature expressed active GFP in an adult animal (FIG.
2E). Rare GFP positive body wall muscle cells were also seen adult
animals (two active cells are shown in FIG. 2F). Inhibition was
target specific (FIGS. 2G-I). Animals were injected with ds-lacZL
RNA, which should affect the nuclear but not the mitochondrial
reporter construct. In the animals derived from this injection,
mitochondrial-targeted GFP appeared unaffected while the
nuclear-targeted GFP-LacZ was absent from almost all cells (larva
in FIG. 2G). A typical adult lacked nuclear GFP-LacZ in almost all
body-wall muscles but retained activity in vulval muscles (FIG.
2H). Scale bars in FIG. 2 are 20 .mu.m.
[0093] The effects of double-stranded RNA corresponding to mex-3 on
levels of the endogenous mRNA was shown by in situ hybridization to
embryos (FIG. 3, panels AD). The 1262 nt mex-3 cDNA clone.sup.20
was divided into two segments, mex-3A and mex-3B with a short (325
nt) overlap. Similar results were obtained in experiments with no
overlap between inhibiting and probe segments. mex-3B antisense or
dsRNA was injected into the gonads of adult animals, which were
maintained under standard culture conditions for 24 hours before
fixation and in situ hybridization (see Reference 5). The mex-3B
dsRNA produced 100% embryonic arrest, while >90% of embryos from
the antisense injections hatched. Antisense probes corresponding to
mex-3A were used to assay distribution of the endogenous mex-3 mRNA
(dark stain). Four-cell stage embryos were assayed; similar results
were observed from the 1 to 8 cell stage and in the germline of
injected adults. The negative control (the absence of hybridization
probe) showed a lack of staining (FIG. 3A). Embryos from uninjected
parents showed a normal pattern of endogenous mex-3 RNA (FIG. 3B).
The observed pattern of mex-3 RNA was as previously described in
Reference 20. Injection of purified mex-3B antisense RNA produced
at most a modest effect: the resulting embryos retained mex-3 mRNA,
although levels may have been somewhat less than wild type (FIG.
3C). In contrast, no mex-3 RNA was detected in embryos from parents
injected with dsRNA corresponding to mex-3B (FIG. 3D). The scale of
FIG. 3 is such that each embryo is approximately 50 .mu.m in
length.
[0094] Gene-specific inhibitory activity by unc-22A RNA was
measured as a function of RNA structure and concentration (FIG. 4).
Purified antisense and sense RNA from unc22A were injected
individually or as an annealed mixture. "Control" was an unrelated
dsRNA (gfpG). Injected animals were transferred to fresh culture
plates 6 hours (columns labeled 1), 15 hours (columns labeled 2),
27 hours (columns labeled 3), 41 hours (columns labeled 4), and 56
hours (columns labeled 5) after injection. Progeny grown to
adulthood were scored for movement in their growth environment,
then examined in 0.5 mM levamisole. The main graph indicates
fractions in each behavioral class. Embryos in the uterus and
already covered with an eggshell at the time of injection were not
affected and, thus, are not included in the graph. The bottom-left
diagram shows the genetically derived relationship between unc-22
gene dosage and behavior based on analyses of unc-22 heterozygotes
and polyploids.sup.8,3.
[0095] FIGS. 5 A-C show a process and examples of genetic
inhibition following ingestion by C. elegans of dsRNAs from
expressing bacteria. A general strategy for production of dsRNA is
to clone segments of interest between flanking copies of the
bacteriophage T7 promoter into a bacterial plasmid construct (FIG.
5A). A bacterial strain (BL21/DE3).sup.28 expressing the T7
polymerase gene from an inducible (Lac) promoter was used as a
host. A nuclease-resistant dsRNA was detected in lysates of
transfected bacteria. Comparable inhibition results were obtained
with the two bacterial expression systems. A GFP-expressing C.
elegans strain, PD4251 (see FIG. 2), was fed on a native bacterial
host. These animals show a uniformly high level of GFP fluorescence
in body muscles (FIG. 5B). PD4251 animals were also reared on a
diet of bacteria expressing dsRNA corresponding to the coding
region for gfp. Under the conditions of this experiment, 12% of
these animals showed dramatic decreases in GFP (FIG. 5C). As an
alternative strategy, single copies of the T7 promoter were used to
drive expression of an inverted-duplication for a segment of the
target gene, either unc-22 or gfp. This was comparably
effective.
[0096] All references (e.g., books, articles, applications, and
patents) cited in this specification are indicative of the level of
skill in the art and their disclosures are incorporated herein in
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TABLE-US-00001 [0130] TABLE 1 Effects of sense, antisense, and
mixed RNAs on progeny of injected animals. Gene and Segment Size
Injected RNA F1 Phenotype unc-22 unc-22 null mutants: strong
twitchers.sup.7,8 unc22A.sup.a exon 21-22 742 sense wild type
antisense wild type sense + antisense strong twitchers (100%)
unc22B exon 27 1033 sense wild type antisense wild type sense +
antisense strong twitchers (100%) unc22C exon 21-22.sup.b 785 sense
+ antisense strong twitchers (100%) fem-1 fem-1 null mutants:
female (no sperm).sup.13 fem1A exon 10.sup.c 531 sense
hermaphrodite (98%) antisense hermaphrodite (>98%) sense +
antisense female (72%) fem1B intron 8 556 sense + antisense
hermaphrodite (>98%) unc-54 unc-54 null mutants:
paralyzed.sup.7,11 unc54A exon 6 576 sense wild type (100%)
antisense wild type (100%) sense + antisense paralyzed (100%).sup.d
unc54B exon 6 651 sense wild type (100%) antisense wild type (100%)
sense + antisense paralyzed (100%).sup.d unc54C exon 1-5 1015 sense
+ antisense arrested embryos and larvae (100%) unc54D promoter 567
sense + antisense wild type (100%) unc54E intron 1 369 sense +
antisense wild type (100%) unc54F intron 3 386 sense + antisense
wild type (100%) hlh-1 hlh-1 null mutants: lumpy-dumpy
larvae.sup.16 hlh1A exons 1-6 1033 sense wild type (<2% lpy-dpy)
antisense wild type (<2% lpy-dpy) sense + antisense lpy-dpy
larvae (>90%).sup.e hlh1B exons 1-2 438 sense + antisense
lpy-dpy larvae (>80%).sup.e hlh1C exons 4-6 299 sense +
antisense lpy-dpy larvae (>80%).sup.e hlh1D intron 1 697 sense +
antisense wild type (<2% lpy-dpy) myo-3 driven GFP
transgenes.sup.f myo-3::NLS::gfp::lacZ makes nuclear GFP in body
muscle gfpG exons 2-5 730 sense nuclear GFP-LacZ pattern of parent
strain antisense nuclear GFP-LacZ pattern of parent strain sense +
antisense nuclear GFP-LacZ absent in 98% of cells lacZL exon 12-14
830 sense + antisense nuclear GFP-LacZ absent in >95% of cells
myo-3::MtLS::gfp makes mitochondrial GFP in body muscle gfpG exons
2-5 730 sense mitochondrial GFP pattern of parent strain antisense
mitochondrial GFP pattern of parent strain sense + antisense
mitochondrial GFP absent in 98% of cells lacZL exon 12-14 830 sense
+ antisense mitochondrial GFP pattern of parent strain Legend of
Table 1 Each RNA was injected into 6-10 adult hermaphrodites (0.5-1
.times. 10.sup.6 molecules into each gonad arm). After 4-6 hours
(to clear pre-fertilized eggs from the uterus) injected animals wre
transferred and eggs collected for 20-22 hours. Progeny phenotypes
were scored upon hatching and subsequently at 12-24 hour intervals.
.sup.aTo obtain a semi-quantitative assessment of the relationship
between RNA dose and phenotypic response, we injected each unc22A
RNA preparation at a series of different concentrations. At the
highest dose tested (3.6 .times. 10.sup.6 molecules per gonad), the
individual sense and antisense unc22A preparations produced some
visible twitching (1% and 11% of progeny respectively). Comparable
doses of ds-unc22A RNA produced visible twitching in all progeny,
while a 120-fold lower dose of ds-unc22A RNA produced visible
twitching in 30% of progeny. .sup.bunc22C also carries the
intervening intron (43 nt). .sup.cfem1A also carries a portion (131
nt) of intron 10. .sup.dAnimals in the first affected broods (laid
at 4-24 hours after injection) showed movement defects
indistinguishable from those of null mutants in unc-54. A variable
fraction of these animals (25-75%) failed to lay eggs (another
phenotype of unc-54 null mutants), while the remainder of the
paralyzed animals were egg-laying positive. This may indicate
partial inhibition of unc-54 activity in vulval muscles. Animals
from later broods frequently exhibit a distinct partial
loss-of-function phenotype, with contractility in a subset of body
wall muscles. .sup.ePhenotypes of hlh-1 inhibitory RNA include
arrested embryos and partially elongated L1 larvae (the hlh-1 null
phenotype) seen in virtually all progeny from injection of ds-hlh1A
and about half of the affected animals from ds-hlh1B and ds-hlh1C)
and a set of less severe defects (seen with the remainder of the
animals from ds-hlh1B and ds-hlh1C). The less severe phenotypes are
characteristic of partial loss of function for hlh-1. .sup.fThe
host for these injections, PD4251, expresses both mitochondrial GFP
and nuclear GFP-LacZ. This allows simultaneous assay for inhibition
of gfp (loss of all fluorescence) and lacZ (loss of nuclear
fluorescence). The table describes scoring of animals as L1 larvae.
ds-gfpG caused a loss of GFP in all but 0-3 of the 85 body muscles
in these larvae. As these animals mature to adults, GFP activity
was seen in 0-5 additional bodywall muscles and in the eight vulval
muscles.
TABLE-US-00002 TABLE 2 Effect of injection point on genetic
inhibition in injected animals and their progeny. Injected dsRNA
Site of injection animal phenotype Progeny Phenotype None gonad or
body no twitching no twitching cavity None gonad or body strong
nuclear & strong nuclear & cavity mitochondrial GFP
mitochondrial GFP unc22B Gonad weak twitchers strong twitchers
unc22B Body Cavity Head weak twitchers strong twitchers unc22B Body
Cavity Tail weak twitchers strong twitchers gfpG Gonad lower
nuclear & rare or absent mitochondrial GFP nuclear &
mitochondrial GFP gfpG Body Cavity Tail lower nuclear & rare or
absent mitochondrial GFP nuclear & mitochondrial GFP lacZL
Gonad lower nuclear GFP rare or absent nuclear GFP lacZL Body
Cavity Tail lower nuclear GFP rare or absent nuclear GFP
TABLE-US-00003 TABLE 3 C. elegans can respond in a gene-specific
manner to environmental dsRNA. Germline Bacterial Food Movement
Phenotype GFP-Transgene Expression BL21(DE3) 0% twitch <1%
female <1% faint GFP BL21(DE3) 0% twitch 43% female <1% faint
GFP [fem-1 dsRNA] BL21(DE3) 85% twitch <1% female <1% faint
GFP [unc22 dsRNA] BL21(DE3) 0% twitch <1% female 12% faint GFP
[gfp dsRNA]
TABLE-US-00004 TABLE 4 Effects of bathing C. elegans in a solution
containing dsRNA. dsRNA Biological Effect unc-22 Twitching (similar
to partial loss of unc-22 function) pos-1 Embryonic arrest (similar
to loss of pos-1 function) sqt-3 Shortened body (Dpy) (similar to
partial loss of sqt-3 function)
[0131] In Table 2, gonad injections were carried out into the GFP
reporter strain PD4251, which expresses both mitochondrial GFP and
nuclear GFP-LacZ. This allowed simultaneous assay of inhibition
with gfp (fainter overall fluorescence), lacZ (loss of nuclear
fluorescence), and unc-22 (twitching). Body cavity injections were
carried out into the tail region, to minimize accidental injection
of the gonad; equivalent results have been observed with injections
into the anterior region of the body cavity. An equivalent set of
injections was also performed into a single gonad arm. For all
sites of injection, the entire progeny brood showed phenotypes
identical to those described in Table 1. This included progeny
produced from both injected and uninjected gonad arms. Injected
animals were scored three days after recovery and showed somewhat
less dramatic phenotypes than their progeny. This could in part be
due to the persistence of products already present in the injected
adult. After ds-unc22B injection, a fraction of the injected
animals twitch weakly under standard growth conditions (10 out of
21 animals). Levamisole treatment led to twitching of 100% (21/21)
of these animals. Similar effects were seen with ds-unc22A.
Injections of ds-gfpG or ds-lacZL produced a dramatic decrease (but
not elimination) of the corresponding GFP reporters. In some cases,
isolated cells or parts of animals retained strong GFP activity.
These were most frequently seen in the anterior region and around
the vulva. Injections of ds-gfpG and ds-lacZL produced no
twitching, while injections of ds-unc22A produced no change in GFP
fluorescence pattern.
[0132] While the present invention has been described in connection
with what is presently considered to be practical and preferred
embodiments, it is understood that the invention is not to be
limited or restricted to the disclosed embodiments but, on the
contrary, is intended to cover various modifications and equivalent
arrangements included within the spirit and scope of the appended
claims.
[0133] Thus it is to be understood that variations in the described
invention will be obvious to those skilled in the art without
departing from the novel aspects of the present invention and such
variations are intended to come within the scope of the present
invention.
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