Title of Invention

A METHOD FOR REDUCING THE EXPRESSION OF A GENE OF INTEREST IN A PLANT CELL

Abstract The present invention provides method for reducing the expression of a gene of interest in a plant cell. The method comprises providing a chimeric gene to the plant cell in which the chimeric gene comprises a DNA dependant RNA polymerase III of type 3 of a plant cell and a DNA fragment which when transcribed yields a short hairpin RNA.
Full Text A METHOD FOR REDUCING THE EXPRESSION OF A GENE OF
INTEREST IN A PLANT CELL
FIELD OF THE INVENTION
The current invention relates generally to the field of genetic modification of plants, more
particularly to the use of short double stranded (dsRNA) sequences to deliberately
silence the expression of one or more genes in plant cells and plants. Methods and means
are provided to increase the efficiency of gene silencing when using dsRNA sequences
which have a stem length shorther than about 200 basepairs.
BACKGROUND
The mechanism of posttranscriptional silencing of gene expression in plants and animals
triggered by target-gene specific dsRNA, provided either exogenously or endogenously
through transcription of dsRNA encoding chimeric genes, has recently become the subject
of numerous studies. Since the initial description of this phenomenon in animals and
plants (Fire et al., 1998; Hamilton et al., 1998; Waterhouse et al., 1998), it has become dear
that the dsRNA is processed by an RNAse with a preference for dsRNA (such as DICER
in Drosophila) into short, approximately 21 nucleotide long RNA molecules that are used
as guide sequences, providing sequence-specificity to a complex capable of degrading
specific mRNA molecules.
The high specificity and efficiency of gene silencing initiated by dsRNA that is
homologous to the gene to be silenced rapidly turned this methodology into the preferred
tool to generate eukaryotic organisms wherein expression of one or more specific
transcribed nucleotide sequences is reduced or inactivated. Such reduction or inactivation
of the expression of a gene of interest may be achieved with a goal to produce eukaryotic
organisms with a preferred phenotype (see e.g. WO 02/029028, wherein Brassica plants
are generated which develop sepals instead petals using dsRNA technology). Reduction
or inactivation of expression of transcribed sequences also plays an important role in
experimental studies trying to allocate a function to the wealth of nucleotide sequences
which have become available through various genome sequencing programs.

Particularly for the latter, it may be advantageous to use short dsRNA sequences, since
such oligonucleotides may conveniently be generated in vitro. In higher animals, the use
of short dsRNA molecules is preferred in view of the fact that larger dsRNA molecules
seem to trigger interferon responses (Elbashir et al. 2001).
Up to now, the production of inhibitory RNA (used herein to describe antisense RNA,
sense RNA and dsRNA) inside the cells of eukaryotic orgiinisms, mostly occurs through
the action of DNA dependent RNA polymerase II (PolII) recognizing the common PolII
type promoters.
Antisense RNA production through the action of RNA polymerase HI in plants has been
documented.
Bourque and Folk (1992) described suppression of the expression of a CAT gene,
transiently delivered to plant cells, by co-electroporation with a DNA comprising inverted
sequences of the chloramphenicol actetyltransferase reporter gene, fused to a soybean
tRNAmet gene lacking a terminator, such that the tRNAmet sequences caused the
transcription of CAT antisense sequences by RNA polymerase III.
US 5,354,854 describes an expression system and method to use the same in plants to
suppress gene expression, the system including a constitutive promoter element from a
tRNA gene and an antisense strand DNA fused to the promoter element for being co-
transcribed with the promoter element by an RNA polymerase HI to suppress expression
of a gene.
Yukawa et al. 2002 described antisense RNA sequences targeted against conserved
structural elements or domains in the RNAs of potato spindle tuber viroid, hop latent
viroid and potato virus S which were embedded in the anticodon region or a Nicotiana
tRNAtyr gene or near the 3' end of an Arabidopsis 7SL RNA gene, and demonstrated in
vitro transcription of such chimeric genes in a homologous plant extract.
EP 0 387 775 describes and claims a DNA molecule, optionally occuring in multiple
copies, containing sections of a gene transcribed by polymerase III and a DNA sequence
encoding for an inhibiting RNA molecule, characterized in that it contains the

transcription units of a tRNA gene necessary for transcription by polymerase III,
including the sequence which determine the secondary structure of the tRNA, and that
the DNA sequence coding for the inhibiting RNA molecule is arranged inside the DNA
molecule in such a way that the inhibiting RNA molecule is a part of the transcript.
Expression of small interfering RNAs in mammalian cells has recently been well
documented. Paddison et al. 2002; Sook Lee et al. 2002; Myagishi et al. 2002, Sui et al.
2002; Brummelkamp et al, 2002 and Paul et al. 2002, all describe the expression of small
interfering RNA in human or mammalian cells using RNA polymerase III specific
promoters derived from either H1-RNA or U6 snRNA.
US 6,146,886 describes and claims a transcribed non-naturally occuring RNA molecule
comprising a desired RNA portion, wherein said non-naturally occuring RNA molecule
comprises an intramolecular stem formed by base-pairing interactions between a 3' region
and 5' complementary nucleotides in said RNA, wherein said intramolecular stem
comprises at least 8 basepairs; wherein said desired RNA portion is selected from the
group consisting of antisense RNA, decoy RNA, enzymatic RNA, agonist RNA and
antagonist RNA, wherin said RNA molecule is transcribed by a type 2 RNA polymerase
HI promoter system.
The prior art remains however deficient in providing methods for highly efficient
expression of small interfering dsRNAs in plant cells. This problem has been solved as
hereinafter described.
SUMMARY OF THE INVENTION
The invention provides methods for reducing the expression of a gene of interest in a
plant cell, comprising the following steps:
(a) providing a chimeric gene to the plant cell, the chimeric gene comprising the
following operably linked DNA fragments:
i) a promoter recognized by a DNA dependent RNA polymerase HI of the plant
cell characterized in that the promoter is a promoter of type HI (type 3)
comprising all cis-acting promoter elements which interact with the DNA
dependent RNA polymerase HI, preferably a type 3 POLIII promoter selected

from the promoter of a gene encoding U6snRNA , the promoter of a gene
encoding U3snRNA, the promoter of a gene encoding 7SL RNA, more
preferably a promoter comprising the nucleotide sequence of promoter is
selected from the nucleotide sequences of SEQ ID Nr 1, SEQ ID Nr 2, SEQ ID
Nr 3, SEQ ID Nr 4, SEQ ID Nr 5, SEQ ID Nr 6, SEQ ID Nr 7 or SEQ ID Nr 8;
ii) a DNA fragment which, when transcribed, yields an RNA molecule, the RNA
molecule comprising a sense and antisense nucleotide sequence,
(1) the sense nucleotide sequence comprising about 19 contiguous nucleotides
having about 90 to about 100% sequence identity to a nucleotide sequence
of about 19 contiguous nucleotide sequences from the RNA transcribed
from the gene of interest;
(2) the antisense nucleotide sequence comprising about 19 contiguous
nudeotides having about 90 to 100% sequence identity to the complement
of a nudeotide sequence of about 19 contiguous nucleotide sequence of the
sense sequence;
wherein the sense and antisense nudeotide sequence are capable of
forming a double stranded RNA of about 19 to about 200 nudeotides in
length; and
iii) an oligo dT stretch comprising at least 4 consecutive T-residues; and
(b) identifying plant cells wherein the expression of the gene of interest is reduced
when compared to the expression of the gene of interest in plant cells which do
not comprise the chimeric gene.
The invention further provides a chimeric gene comprising the following operably
linked DNA fragments:
i) a promoter recognized by a DNA dependent RNA polymerase III of the plant
cell characterized in that the promoter is a promoter of type III comprising all
ds-acting promoter elements which interact with the DNA dependent RNA
polymerase El, preferably a type 3 POLIII promoters selected from the
promoter of a gene encoding U6snRNA , the promoter of a gene encoding
U3snRNA, the promoter of a gene encoding 7SL RNA, more preferably a
promoter comprising the nudeotide sequence of promoter is selected from the
nudeotide sequences of SEQ ID Nr 1, SEQ ID Nr 2, SEQ ID Nr 3, SEQ ID Nr 4,
SEQ ID Nr 5, SEQ ID Nr 6, SEQ ID Nr 7 or SEQ ID Nr 8;

ii) a DNA fragment which, when transcribed, yields an RNA molecule, the RNA
molecule comprising a sense and antisense nucleoti.de sequence,
(1) the sense nucleotide sequence comprising about 19 contiguous nucleotides
having about 90 to about 100% sequence identity to a nucleotide sequence
of about 19 contiguous nucleotide sequences from the RNA transcribed
from a gene of interest in a plant cell;
(2) the antisense nucleotide sequence comprising about 19 contiguous
nucleotides having about 90 to 100% sequence identity to the complement
of a nucleotide sequence of about 19 contiguous nucleotide sequence of the
sense sequence;
wherein the sense and antisense nucleotide sequence are capable of
forming a double stranded RNA of about 19 to about 200 nucleotides in
length; and
iii) an oligo dT stretch comprising at least 4 consecutive T-residues
The invention further provides plant cell and plants comprising the above mentioned
chimeric genes
BRIEF DESCRIPTION OF THE FIGURE
Figure 1 outlines schematically a convenient cloning strategy for creating and handling a
coding region encoding short dsRNA sequences.
DETAILED DESCRIPTION
The current invention is based on the observation that chimeric genes encoding short
dsRNA molecules, preferably ranging between about 20 basepairs (bp) and about 100 bp
under control of type 3 promoters recognized by RNA polymerase III, resulted in more
efficient gene silencing than similar constructs driven by the strong constitutive RNA
Polymerase II promoter CaMV 35S.
These type 3 promoters have the additional advantage that all required cis-acting
elements of the promoter are located in the region upstream of the transcribed region, in

contrast to type 2 promoters recognized by RNA polymerase III, which had been used in
the prior art to direct expression of antisense RNA.
Thus, in a first embodiment, the current invention relates to a method for reducing the
expression of a gene of interest in a plant cell, comprising the following steps:
(a) providing a chimeric gene to the plant cell, the chimeric gene comprising the
following operably linked DNA fragments :
i) a promoter recognized by a DNA dependent RNA polymerase III of the plant
cell whereby the promoter is a promoter of type 3 comprising all as-acting
promoter elements which interact with DNA dependent RNA polymerase III;
ii) a DNA fragment which, when transcribed, yields an RNA molecule, the RNA
molecule comprising a sense and antisense nucleotide sequence, and wherein
(1) the sense nucleotide sequence comprises about 19 contiguous nudeotides
having about 90 to about 100% sequence identity to a nucleotide sequence
of about 19 contiguous nucleotide sequences from the RNA transcribed
from the gene of interest;
(2) the antisense nucleotide sequence comprising about 19 contiguous
nucleotides having about 90 to 100% sequence identity to the complement
of a nucleotide sequence of about 19 contiguous nucleotide sequence of the
sense sequence;
wherein the sense and antisense nucleotide sequence are capable of
forming a double stranded RNA of about 19 to about 200 nucleotides in
length; and
iii) an oligo dT stretch comprising at least 4 consecutive T-residues; and
(b) identifying plant cells wherein the expression of the gene of interest is reduced
when compared to the expression of the gene of interest in plant cells which do
not comprise the chimeric gene.
As used herein « a promoter recognized by the DNA dependent RNA polymerase III» is
a promoter which directs transcription of the associated DNA region through the
polymerase action of RNA polymerase III. These include genes encoding 5S RNA, tRNA,
7SL RNA, U6 snRNA and a few other small stable RNAs, many involved in RNA
processing. Most of the promoters used by Pol III require sequence elements downstream
of +1, within the transcribed region. A minority of pol III templates however, lack any

requirement for intragenic promoter elements. These are referred to as type 3 promoters.
In other words, «type 3 Pol III promoters », are those promoters which are recognized by
RNA polymerase III and contain all as-acting elements, interacting with the RNA
polymerase III upstream of the region normally transcribed by RNA polymerase III. Such
type 3 Pol III promoters can thus easily be combined in a chimeric gene with a
heterologous region, the transcription of which is desired, such as the dsRNA coding
regions of the current invention.
Typically, type 3 Pol III promoters contain a TATA box (located between -25 and -30 in
Human U6 snRNA gene) and a Proximal Sequence element (PSE; located between —47
and -66 in Human U6 snRNA). They may also contain a Distal Sequence Element (DSE;
located between -214 and -244 in Human U6 snRNA).
Type 3 Pol III promoters can be found e.g. associated with the genes encoding 7SL RNA,
U3 snRNA and U6 snRNA. Such sequences have been isolated from Arabidopsis, rice and
tomato and representative sequences of such promoters are represented in the sequence
listing under the entries SEQ ID No 1-8.
Other nucleotide sequences for type 3 Pol HI promoters can be found in nucleotide
sequence databases under the entries for the A. thaliana gene AT7SL-1 for 7SL RNA
(X72228), A. thaliana gene AT7SL-2 for 7SL RNA (X72229), A. thaliana gene AT7SL-3 for
7SL RNA (AJ290403), Humulus luptdus H17SL-1 gene (AJ236706), Humulus lupulus
H17SL-2 gene (AJ236704), Humulus lupulus H17SL-3 gene (AJ236705), Humulus lupulus
H17SL-4 gene (AJ236703), A. thaliana U6-1 snRNA gene (X52527), A. thaliana U6-26
snRNA gene (X52528), A. thaliana U6-29 snRNA gene (X52529), A. thaliana U6-1 snRNA
gene (X52527), Zea mays U3 snRNA gene (Z29641), Solanum tuberosum U6 snRNA gene
(Z17301; X 60506; S83742), Tomato U6 smal nuclear RNA gene (X51447), A. thaliana U3C
snRNA gene (X52630), A. thaliana U3B snRNA gene (X52629), Oxyza sativa U3 snRNA
promoter (X79685), Tomato U3 smal nuclear RNA gene (X14411), Triticum aestivum U3
snRNA gene (X63065), Triticum aestivum U6 snRNA gene (X63066).
It goes without saying that variant type 3 Pol III promoters may be isolated from other
varieties of tomato, rice or Arabidopsis, or from other plant species without little
experimentation. E.g. libraries of genomic clones from such plants may be isolated using

U6 snRNA, U3 snRNA or 7SL RNA coding sequences (such as the coding sequences of
any of the above mentioned sequences identified by their accession number and
additionally the Vicia alba U6snRNA coding sequence (X04788), the maize DMA for U6
snRNA (X52315) or the maize DNA for 7SL RNA (X14661)) as a probe, and the upstream
sequences, preferably the about 300 to 400 bp upstream of the transcribed regions may be
isolated and used as type 3 Pol III promoters. Alternatively, PCR based techniques such as
inverse-PCR or TAIL®-PCR may be used to isolate the genomic sequences including the
promoter sequences adjacent to known transcribed regions;. Moreover, any of the type 3
Po1III promoter sequences attached or of the above mentioned promoter sequences,
identified by their accession numbers, may be used as probes under stringent
hybridization conditions or as source of information to generate PCR primers to isolate
the corresponding promoter sequences from other varieties or plant species.
"Stringent hybridization conditions" as used herein mean that hybridization will
generally occur if there is at least 95% and preferably at least 97% sequence identity
between the probe and the target sequence. Examples of stringent hybridization
conditions are overnight incubation in a solution comprising 50% formamide, 5 x SSC (150
mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5x Denhardfs
solution, 10% dextran sulfate, and 20 µg/ml denatured, sheared carrier DNA such as
salmon sperm DNA, followed by washing the hybridization support in 0.1 x SSC at
approximately 65 °C. Other hybridization and wash conditions are well known and are
exemplified in Sambrook et al. Molecular Cloning: A Laboratory Manual, Second Edition,
Cold Spring Harbor, NY (1989), particularly chapter 11.
Although the type 3 Pol HI promoters have no requirement for cis-acting elements located
with the transcribed region, it is clear that sequences normally located downstream of the
transcription initiation site may nevertheless be included in the chimeric constructs of the
invention.
It has also been observed that type 3 Pol III promoters originally isolated from
monocotyeldonous plants can be used to good effect in both dicotyledonous and
monocotyleodous plant cells and plants, whereas type 3 Pol III promoters originally
isolated from dicotyledonous plants can only be efficiently used in dicotyledonous plant

cells and plants. Moreover, the most efficient gene silencing has been obtained when
chimeric genes were used comprising a type 3 Pol III promoter derived from the same or
closely related species.
As used herein, a «gene of interest» may be any nucleic acid of interest, which is
transcribed (or replicated) into an RNA molecule, and which is prone to post
transcriptional RNA degradation. These include but are not limited to transgenes,
endogenous genes and transcribed viral sequences. It will also be immediately apparent
that for the methods of the invention, it is not required to have knowledge of the
nucleotide sequence: of the gene of interest. Indeed, it may be possible to directly derive
small fragments and operably link them in inverted repeat orientation, under control of a
type 3 Pol III promoter
As indicated above, the transcribed DNA region should be capable of encoding an RNA
molecule comprising a sense and antisense nucleotide region, whereby the sense
nucleotide sequence comprises about 19 contiguous nucleotides having about 90 to about
100% sequence identity to a nucleotide sequence of about 19 contiguous nucleotide
sequences from the RNA transcribed from the gene of interest and whereby the antisense
nucleotide sequence comprising about 19 contiguous nucleotides having about 90 to 100%
sequence identity to the complement of a nucleotide sequence of about 19 contiguous
nucleotide sequence of the sense sequence. The sense and antisense nucleotide sequence
should be capable of forming a double stranded RNA of about 19 to about 200
nucleotides, particularly about 21 to about 90 or 100 nucleotides, more particularly about
40 to about 50 nucleotides in length. However, the length of the dsRNA stem may also be
about 30, about 60, about 70 or about 80 nucleotides in length. It will be clear that where
the dsRNA region is larger than 19 nucleotides, there is only a requirement that there is at
least one double stranded region of about 19 nucleotides (whereby there can be about one
mismatch between the sense and antisense region) the sense strand of which is
«identical» (allowing for one mismatch) with 19 consecutive nucleotides of the target
nucleic acid or gene of interest.
For the purpose of this invention, the "sequence identity" of two related nucleotide
sequences, expressed as a percentage, refers to the number of positions in the two
optimally aligned sequences which have identical residues (x100) divided by the number

of positions compared. A gap, i.e. a position in an alignment: where a residue is present in
one sequence but not in the other is regarded as a position with non-identical residues.
The alignment of the two sequences is performed by tine Needleman and Wunsch
algorithm (Needleman and Wunsch 1970) Computer-assisted sequence alignment, can be
conveniently performed using standard software program such as GAP which is part of
the Wisconsin Package Version 10.1 (Genetics Computer Group, Madison, Wisconsin,
USA) using the default scoring matrix with a gap creation penalty of 50 and a gap
extension penalty of 3.
The transcribed DNA region may comprise a stretch of nudeotides ranging from 3 to
about 100 nudeotides or more spedfically from about 6 to about 40 nudeotides, which are
located between the sense and antisense encoding nudeotide region, and which are not
related to the nudeotide sequence of the target gene (a so-called spacer region).
The diimeric genes of the current invention, comprising a transcribed DNA region with
short antisense and sense fragments may conveniently be: constructed using a stuffer
DNA sequence between the short antisense and sense fragments during the cloning
procedures, which may thereafter be removed. To that end, the stuffer segment may be
equipped with restriction enzymes recognitions sites, sudi as rare-cutting restriction
enzymes for the easy removal of the stuffer sequence and re-ligation (self-ligation) of the
doning vector, whereby the short sense and antisense region are now brought in vicinity
of each other. As outlined in Figure 1, a DNA fragment comprising a short sense
sequence, a short, antisense sequence complementary to the sense sequence, and a stuffer
DNA sequence may be conveniently construct by PCR amplification using
oligonudeotide primers comprising the sense or antisense sequence and a sequence
corresponding to part of the stuffer DNA sequence.
The above mentioned « oligo dT stretch » is a stretch of consecutive T-residues which
serve as a terminator for the RNA polymerase III activity. It should comprise at least 4 T-
residues, but obviously may contain more T-residues.
Chimeric genes according to the invention may be provided to plant cells by introduction
into plant cells using any means of DNA transformation available in the art, induding but
not limited to Agrobacterium mediated transformation, microprojectile bombardment,

direct DNA uptake into protoplasts or plant tissues (by eleetroporation, PEG-mediated
uptake, etc.) and may result in transiently or stably transformed plant cells. The chimeric
genes may also be provided to the plant cells using viral vectors, capable of replicating in
plant cells. Chimeric genes may also be provided to plant cells by crossing parental plants,
at least one of which comprises a chimeric gene according to the invention.
As used herein, « reducing the expression of a gene of interest » refers to the comparison
of the expression of the gene of interest in the plant cell in the presence of the dsRNA or
chimeric genes of the invention, to the expression of the gene of interest in the absence of
the dsRNA or chimeric genes of the invention. The expression in the presence of the
chimeric RNA of the invention should thus be lower than the expression in absence
thereof, e.g. be only about 75% or 50% or 10% or about 5% of the expression in absence of
the chimeric RNA. The expression may be completely inhibited for all practical purposes
by the presence of the chimeric RNA or the chimeric gene encoding such an RNA.
A reduction of expression of a gene of interest may be measured as a reduction in
transcription of (part of) that gene, a reduction in translation of (part of) that gene or a
reduction in the effect the presence of the transcribed RNA(s) or translated polypeptide(s)
have on the plant cell or the plant, and will ultimately lead to altered phenotypic traits. It
is clear that the reduction in expression of a gene of interest, may be accompanied by or
correlated to an increase in expression of another gene. Although the main effect of
dsRNA is the post-transcriptional degradation of specific RNAs, effects of dsRNA on the
transcription process have been documented. Such additional effects will also contribute
to the reduction of expression of a gene of interest mediated by dsRNA.
Other embodiments of the invention relate to the chimeric genes as herein described, as
well as to plants, plant cells, plant tissues or seeds comprising the chimeric genes of the
invention.
It is also an object of the invention to provide plant cells and plants containing the
chimeric genes according to the invention. Gametes, seeds, embryos, either zygotic or
somatic, progeny or hybrids of plants comprising the chimeric genes of the present
invention, which are produced by traditional breeding methods are also included within
the scope of the present invention.

The methods and means described herein are believed to be suitable for all plant cells and
plants, both dicotyledonous and monocotyledonous pliant cells and plants including but
not limited to cotton, Brassica vegetables, oilseed rape, wheat, corn or maize, barley,
sunflowers, rice, oats, sugarcane, soybean, vegetables (including chicory, lettuce, tomato),
tobacco, potato, sugarbeet, papaya, pineapple, mango, Arabidopsis thaliana, but also
plants used in horticulture, floriculture or forestry.
The following non-limiting Examples describe the construction of chimeric genes for the
reduction of the expression of a gene of interest in a plant cell by small dsRNA and the
use of such genes.
Unless stated otherwise in the Examples, all recombinamt DNA techniques are carried out
according to standard protocols as described in Sambrook et al. (1989) Molecular Cloning:
A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, NY and in
Volumes 1 and 2 of Ausubel et al. (1994) Current Protocols in Molecular Biology, Current
Protocols, USA. Standard materials and methods for plant molecular work are described
in Plant Molecular Biology Labfax (1993) by R.D.D. Croy, jointly published by BIOS
Scientific Publications Ltd (UK) and Blackwell Scientific Publications, UK. Other
references for standard molecular biology techniques include Sambrook and Russell
(2001) Molecular Cloning: A Laboratory Manual, Third Edition, Cold Spring Harbor
Laboratory Press, NY, Volumes I and E of Brown (1998) Molecular Biology LabFax,
Second Edition, Academic Press (UK). Standard materials and methods for polymerase
chain reactions can be found in Dieffenbach and Dveksler (1995) PCR Primer: A
Laboratory Manual, Cold Spring Harbor Laboratory Press, and in McPherson at al. (2000)
PCR - Basics: From Background to Bench, First Edition, Springer Verlag, Germany.
Throughout the description and Examples, reference is made to the following sequences:
SEQ ID No. 1: sequence of the promoter of the 7SL-2 gene of Arabidopsis thaliana var.
Landsberg erecta, followed by a unique restriction site in front of an oligo
dT stretch.
SEQ ID No. 2: sequence of the promoter of the 7SL-2 gene of Arabidopsis thaliana var.
Landsberg erecta including 86 bases downstream of the transcription

initiation site, followed by a unique restriction site in front of an oligo dT
stretch.
SEQ ID No. 3: sequence of the promoter of the USB snRNA of Arabidopsis thaliana var.
Landsberg erecta, followed by a unique restriction site in front of an oligo
dT stretch.
SEQ ID No. 4: sequence of the promoter of the U3B snRNA gene of Arabidopsis thaliana
var. Landsberg erecta including 136 bases downstream of the
transcription initiation site, followed by a unique restriction site in front
of an oligo dT stretch.
SEQ ID No. 5: sequence of the promoter of the U6-26 snRNA gene of Arabidopsis thaliana
var. Landsberg erecta including 3 bases downstream of the transcription
initiation site, followed by a unique restriction site in front of an oligo dT
stretch.
SEQ ID No. 6: sequence of the promoter of the U6-26 snRNA gene of Arabidopsis thaliana
var. Landsberg erecta including 20 bases downstream of the transcription
initiation site, followed by a unique restriction site in front of an oligo dT
stretch.
SEQ ID No. 7: sequence of the promoter of the U3 snRNA of rice (Oryza sativa Indica
ER36), followed by a unique restriction site in front of an oligo dT stretch.
SEQ ID No. 8: sequence of the promoter of the U3 snRMA of tomato (a garden variety
with small gourd-shaped yellow fruit), followed by a unique restriction
site in front of an oligo dT stretch,
SEQ ID No. 9: sequence of the dsRNA encoding region of 94bp for silencing expression of
the GUS gene (GUShp94).
SEQ ID No. 10: sequence of the dsRNA encoding region of 41 bp for silencing expression
of the GUS gene (GUShp41).
SEQ ID No. 11: sequence of the dsRNA encoding region of 21 bp for silencing expression
of the GUS gene (GUShp21).
SEQ ID No. 12: sequence of the dsRNA encoding region of 42 bp for silencing expression
of the PHYB gene, derived from the 5' end of PHYB (PHYB5hp42)-upper
strand.
SEQ ID No. 13: sequence of the dsRNA encoding region of 42 bp for silencing expression
of the PHYB gene, derived from the 5' end of PHYB (PHYB5hp42)-Iower
strand.

SEQ ID No. 14: sequence of the dsRNA encoding region of 21 bp for silencing expression
of the PHYB gene, derived from the 5' end of PHYB (PHYB5hp21)-upper
strand.
SEQ ID No. 15: sequence of the dsRNA encoding region, of 21 bp for silencing expression
of the PHYB gene, derived from the 5' end of PHYB (PHYB5hp21)-lower
strand.
SEQ ID No. 16: sequence of the dsRNA encoding region of 42 bp for silencing expression
of the PHYB gene, derived from the center of PHYB (PHYBChp42)-upper
strand.
SEQ ID No. 17: sequence of the dsRNA encoding region of 42 bp for silencing expression
of the PHYB gene, derived from the carter of PHYB (PHYBChp42)-lower
strand.
SEQ ID No. 18: sequence of the dsRNA encoding region of 21 bp for silencing expression
of the PHYB gene, derived from the center of PHYB (PHYBChp21)-upper
strand.
SEQ ID No. 19: sequence of the dsRNA encoding region of 21 bp for silencing expression
of the PHYB gene, derived from the center of PHYB (PHYBChp21)-lower
strand.
SEQ ID No. 20: sequence of the dsRNA encoding region of 42 bp for silencing expression
of the PHYB gene, derived from the 3' end of PHYB (PHYB3hp42)-upper
strand.
SEQ ID No. 21: sequence of the dsRNA encoding region of 42 bp for silencing expression
of the PHYB gene, derived from the 3' end of PHYB (PHYB3hp42)-lower
strand.
SEQ ID No. 22: sequence of the dsRNA encoding region of 21 bp for silencing expression
of the PHYB gene, derived from the 3' end of PHYB (PHYB3hp21)-upper
strand.
SEQ ID No. 23: sequence of the dsRNA encoding region of 21 bp for silencing expression
of the PHYB gene, derived from the 3' end of PHYB (PHYB3hp21)-lower
strand.
SEQ ID No. 24: sequence of the dsRNA encoding region of 42 bp for silencing expression
of the PDS gene (PDS42)-upper strand .
SEQ ID No. 25: sequence of the dsRNA encoding region of 42 bp for silencing expression
of the PDS gene (PDS42)-lower strand.

SEQ ID No. 26: sequence of the dsRNA encoding region of 21 bp for silencing expression
of the PDS gene (PDS21)-upper strand.
SEQ ID No. 27: sequence of the dsRNA encoding region of 21 bp for silencing expression
of the PDS gene (PDS21)-lower strand.
SEQ ID No. 28: sequence of a dsRNA encoding region of 42 bp for silencing expression of
a GUS gene(GUS-A)
SEQ ID No. 29: sequence of a dsRNA encoding region of 42 bp for silencing expression of
a GUS gene(GUS-B).
SEQ ID No. 30: sequence of a dsRNA encoding region of 42 .bp for silencing expression of
a GUS gene(GUS-C).
SEQ ID No. 31: sequence of a dsENA encoding region of 42 bp for silencing expression of
EIN (EIN-A).
SEQ ID No. 32: sequence of a dsRNA encoding region of 42 bp for silencing expression of
EIN (EIN-B).
SEQ ID No. 33: sequence of a dsRNA encoding region of 42 bp for silencing expression of
EIN(EIN-C).

EXAMPLES
Example 1. Construction of type 3 Pol III promoter-oligodT stretch cassettes.
Type 3 Pol III promoters were isolated from Arabidopsis, rice or tomato 7SL,
U3snRNA or U6snRNA genes using PCR amplification, designed in such a way
that
a) the resulting fragments were flanked by restriction enzyme recognition sites
not present within the amplified fragment;
b) the promoter fragments were followed by a unique restriction site (Sall, Xhol
or Pvul), followed by
c) a poly(T) sequence (with 7-9 T residues) as Pol. III terminator.
In some of the cloned promoter fragments, additional sequences of the coding region
downstream of the transcription initiation site were included to investigate the possible
effect of conserved motifs in the coding region of the small RNAs on transcription and/or
gene silencing. The resulting fragments (represented in SEQ IDs No 1 to 8) were cloned in
intermediate cloning vectors (see Table 1). Sense, antisense or inverted repeat sequences
can readily be inserted in the unique restriction site between the type 3 Pol HI promoters
and the polyT stretch.


**This number represents the sequence from the coding region of the small RNA gene.
***The sizes given include the restriction sites and the oligo (dT)s added to the PCR
primers.
Example 2. Testing of the PolIII promoters in gene silencing constructs against a GUS
reporter gene (Nicotians tabacum).
To test these Point promoters for silencing, a GUS inve:rted-repeat sequence (SEQ ID No
9) was synthesized, which consists of 186 bp sense sequence of GUS (nt. 690-875 of GUS
coding sequence) fused at the 3' end with an antisense version of the first 94 bp in the 186
bp fragment (nt. 690-783 of GUS coding sequence). This i/r sequence is flanked by two
Sail sites and two Pvul sites, and can therefore be cloned into the PolIII promoter vectors
as a Sail or Pvul fragment. Constructs were prepared with all the PolIII promoters
described in Table 1 using the i/rGUS sequence (GUShp94) (see Table 2). In addition to
the GUShp94 sequence, constructs were also prepared with the AtU3B+136 promoter

(SEQ ID No 4.) and the CaMV35S promoter using smaller i/r GUS sequences such
GUShp41a (41 bp in the stem spaced by a 9 bp non-GUS sequence; SEQ ID No 10) and
GUShp21 (21 bp in the stem spaced by a 6 bp non-GUS sequence, SEQ ID No 11) (Table
2),

These constructs were introduced to binary vectors pART27 or pWBVec4a for plant
transformation. Two different transgenic tobacco lines expressing GUS, were transformed
by all these constructs. A control construct in which the GUShp94 sequence was driven by
a 35S promoter (in pART7) was also included.
Leaf tissue from transformed tobacco plantlets on rooting medium was assayed for GUS
activity (fluorometric MUG assay) and the results are summarized in Table 3.
The results show that the GUShp94 constructs with AtU3 (pMBW468), At7SL (pMBW470),
At7SL+86 (pMBW472), AtU3+3 (pMBW476), AtU3+20 (pMBW477) and TomU3
(pLMW64) promoters all activated silencing of the GUS gene in tobacco. The AtU3,
AtU6+20, and TomU3 constructs appeared to perform better than the others. The

AtU3+136 construct (pMBW466) did not seem to give significant GUS silencing in
tobacco. Also, the OsU3 construct (pMBW473) appeared to confer only a low level of GUS
silencing. The PoM promoter construct pLMW58 (AtU3+136-GUShp41a) gave significant
levels of GUS silencing in tobacco whereas the 35S consteuct pLMW53 (35S-GUShp41a)
did not, suggesting that the PolDI promoters are more effective than the PolII promoters
in driving the expression of small hairpin RNA.




Table 4. Summary of constructs tested in Arabidopsis

Leaf tissues from T1 plants that showed high-levels of resistance to the selective agent
PPT were assayed for GUS activity. The MUG assay data are summarized in Table 5.
For the GUShp94 sequence all the U3 and U6 promoter-driven constructs conferred GUS
silencing, although the TomU3 and AtU6+20 gave more consistent and better silencing..
The two At7SL promoter constructs did not appear to confer significant GUS silencing
although a few lines showed moderate silencing, which may be due to T-DNA insertion
next to endogenous promoters.
With the GUShp41 sequence, the AtU3+136 construct: performed better than the 35S
construct in terms of the degree of GUS silencing, again suggesting that PolIII promoters
are more effective than PolII promoters for driving expression of small hairpin RNA
expression in plants.


Example 4. Testing of the PolIII promoters in gene silencing constructs against a GUS
reporter gene (Ozyza sativa).
The constructs pMBW479, pMBW481, pMBW485, pMBVV486 and pLMW62 (see Table 4)
were super-transformed into rice that expresses a Ubil-GUS-nos gene. GUS staining
showed that only pMBW485 (OsU3-GUShp94) and pMBW479 (35S-GUShp94) conferred
significant silencing to the resident GUS gene. These results indicate that dicotyldonous
type 3 PolIII promoters will not function in monocots.

Example 5. Testing of the PolIII promoters in gene silencing constructs against
Arabidopsis endogenous genes.
The Arabidopsis U6-26 construct contains the promoter from -446 to +3 bp (SEQ ID 5)
and additional sequences added by PCR creating Xhol sites at each end of the fragment.
These were used to clone the PCR product into the Sail site of a pGEM derived plasmid.
The insert was excised with NotI and inserted into the pART27 binary vector for plant
transformation. The PCR also incorporated a Sail site between the promoter and
termination sequences (T8) for insertion of oligonucleotide sequences.
Two genes were targeted, phytoene desaturase (PDS - silencing gives a photobleached
phenotype) and phytochrome B (PHYB - silencing gives hypocotyl elongation in white
light). For PDS a single target region was chosen, for PHYB, three target regions were
used, respectively from the 5'UTR, a region of the coding region conserved between
phytochromes and the 3' UTR. For each target region two oligonucleotides were made,
one to make a double stranded section of 21 bp long, the other to make a 42bp double
stranded section. The double stranded oligos were made as two single strands (upper and
lower) and annealed to form a double stranded DNA fragment. Overhang sequences were
included at the 5' and 3' ends to create Sail compatible ends. The oligo sequences are
represented in the sequence listing as SEQ ID 12 to 23 for the PHYB constructs and SEQ
ID 24 to 27 for PDS constructs.
The PDShp42 constructs gave phenotypes in most of the examined plants. The results are
summarized in table 6.


Insertion of the construct with the dsRNA coding region PDS42 under control of the 35S
promoter resulted in more plants with no silencing phenotype than the construct with the
dsRNA coding region PDS42 under control of the U6 promoter, and plants with a
phenotype only showed the weak bleached cotyledon phenotype and no bleaching of the
leaves.
For the PHYB silencing experiments, most satisfactory silencing results are obtained with
the PHYBC42 dsJRNA coding region, where most of the plants show more elongation than
the controls. Most of the other constructs do not show a phenotype or else only have one
or two plants showing a phenotype suggesting that the choice of target sequence may be
important.
Hypocotyl lengths of white light grown plants were measured and grouped in 5 mm
categories From the summary of the data in Table 7, it appears that the U6 promoter
driven construct is more effective that the CaMV35S promoter driven construct, buth the
results are not as pronounced as for the above mentioned PDS gene silencing
experiments.
Table 7. Silencing of PHYB.

Categories
Hypocotyl length
(cm) WT 35S-PHYbC42 U6-PHYbC42
0.1-0.5
0.6-1.0 13 1 2
1.1-1.5 10 2 5
1.6-2.0 3 5 10
2.1-2.5 6 6
2.6-3.0 5 9
3.1-3.5 3 3 2
3.6-4.0 1 11
4.1-4.5 2
4.6-5.0 1 1

Thus, the following conclusion scan be drawn from the experiments :
1. Type 3 Pol III promoters can be used to effectively drive the expression of
dsRNA molecules in plant cells.
2. The At U6 promoter seems to be the most effective promoter tested.
3. The monocot PolIIII promoter is functional both in monocotyledonous and
dicotyledonous plants, but the dicotyledonous promoters seem not to be
functional in monocotyledonous plants.
4. The type III Pol III promoters appear to be more effective than CaMV35S
promoter for gene silencing with relatively short hairpin sequences.
Example 6. Additional experiments with small hairpin RNA encoding constructs
By using a the cloning strategy as outlined Figure 1, 20 new small hairpin constructs, as
summarized in Table 7, were prepared . The predicted small hpRNAs from all of these
constructs comprise a 42 bp dsRNA stem (corresponding to the target gene sequences)
and a 9-nt loop (non-target sequence). Three target sequences corresponding to different
regions of EIN2 (represented in SEQ ID 31 to 33) or GUS (represented in SEQ ID 28 to 30)
were selected. These constructs have been used to transform tobacco to assess their
efficacy for inducing the silencing of corresponding endogenous (EIN2) or reporter (GUS)
genes.
Tobacco shoots were assayed for GUS expression, and the result is shown in Table 8.
The result shows that
1) most of the small GUS hairpin constructs conferred good GUS silencing; and
2) the Poim promoter driven constructs pLMW164 and pLMW165 result in more
consistent GUS silencing than the 35S promoter driven, construct pLMW155.

Table 7. Summary of additional small hairpinRNA encoding constructs



The tobacco tissue assayed was mostly leaf pieces from small regenerating shoots
growing on medium with hygromycin, which usually gives tight selection.
References
Bourque and Folk (1992) Plant Mol Biol. 19:641-647
Brummelkamp et al. (2002) Science296 : 550-553
Elbashir et al. (2001) Nature411:494-498
Fire etal. (1998) Nature391:806-811
Hamilton et al. (1998) Plant J. 15:737-746
Miyagishi et al. (2002) Nature Biotechnology20: 497-499
Needleman and Wunsch (1970) J. Mol. Biol. 48:443-453
Paddison et al. (2002) Genes & Development 16: 948-958
Paul et al. (2002) Nature Biotechnology20. 505-508

Sook Lee et al. (2002) Nature Biotechnology 20: 500-505
Sui et al. (2002) Proa Natl. Acad. Sd. USA 99:5515-5520
Waterhouse et al(1998) Proc. Natl. Acad. Sci. USA 95:13959-13964
Yukawa et al. (2002) Plant Mol. Biol 50:713-723

WE CLAIM:
1. A method for reducing the expression of a gene of interest in a plant cell, comprising
the following steps :
(a) providing a chimeric gene to said plant cell, said chimeric gene comprising the
following operably linked DNA fragments :
i) a promoter recognized by a DNA dependent RNA polymerase III of said plant
cell characterized in that said promoter is a promoter of type 3 comprising all
cis-acting promoter elements which interact with said DNA dependent RNA
polymerase III;
ii) a DNA fragment which, when transcribed, yields an RNA molecule, said RNA
molecule comprising a sense nucleotide sequence and an antisense nucleotide
sequence,
(1) said sense nucleotide sequence comprising 19 contiguous nucleotides
having 90 to 100% sequence identity to a nucleotide sequence of 19
contiguous nucleotides from the RNA transcribed from said gene of
interest;
(2) said antisense nucleotide sequence comprising 19 contiguous nucleotides
having 90 to 100% sequence identity to the complement of a nucleotide
sequence of 19 contiguous nucleotides of said sense sequence;
wherein said sense and antisense nucleotide sequences are capable of
forming a double stranded RNA of 19 to 200 nucleotides in length ; and
iii) an oligo dT stretch comprising at least 4 consecutive T-residues; and
(b) identifying plant cells wherein said expression of said gene of interest is reduced
when compared to the expression of said gene of interest in plant cells which do
not comprise said chimeric gene.
2. The method as claimed in claim 1, wherein said promoter is a type 3 POLIII promoter
selected from a promoter of a plant gene encoding U6snRNA, a promoter of a plant
gene encoding U3snRNA and a promoter of a plant gene encoding 7SL RNA.
3. The method as claimed in claim 1 or claim 2, wherein said chimeric gene comprises a
promoter consisting of a nucleotide sequence selected from the nucleotide sequence of
SEQ ID NO:1 from the nucleotide at position 7 to the nucleotide at position 322, SEQ

ID NO:2 from the nucleotide at position 7 to the nucleotide at position 408, SEQ ID
NO:3 from the nucleotide at position 7 to the nucleotide at position 313, SEQ ID
NO:4 from the nucleotide at position 7 to the nucleotide at position 446, SEQ ID
NO:5 from the nucleotide at position 7 to the nucleotide at position 436, SEQ ID
NO:6 from the nucleotide at position 7 to the nucleotide at position 468, SEQ ID
NO:7 from the nucleotide at position 7 to the nucleotide at position 384 or SEQ ID
NO:8 from the nucleotide at position 7 to the nucleotide at position 421.
4. The method as claimed in claim 1 or claim 2, wherein said plant cell is a
dicotyledonous plant cell and said promoter is derived from a dicotyledonous or
monocotyledonous plant or plant cell.
5. The method as claimed in claim 1 or claim 2, wherein said plant cell is a
monocotyledonous plant cell, and said promoter is derived from a monocotyledonous
plant or plant cell.
6. The method as claimed in claim 1 or claim 2 wherein said promoter is endogenous to
said plant cell.
7. The method as claimed in claim 1 or claim 2, wherein said gene of interest is a
transgene.
8. The method as claimed in claim 1 or claim 2, wherein said gene of interest is an
endogenous gene.
9. The method as claimed in claim 1 or claim 2, wherein said plant cell is comprised
within a plant.
10. The method as claimed in claim 1 or claim 2, wherein said DNA fragment ii)
comprises a spacer region of 3 to 100 nucleotides which is located between the DNA
encoding the sense nucleotide sequence and the DNA encoding the antisense
nucleotide sequence.
11. The method as claimed in claim 1 or claim 2, wherein the length of said double
stranded RNA is between 20 and 100 basepairs.

12. A chimeric gene for use in a plant cell, comprising the following operably linked
DNA fragments :
i) a promoter recognized by a DNA dependent RNA polymerase III of said plant
cell characterized in that said promoter is a promoter of type 3 comprising all
cis-acting promoter elements which interact with said DNA dependent RNA
polymerase III;
ii) a DNA fragment which, when transcribed, yields an RNA molecule, said RNA
molecule comprising a sense nucleotide sequence and an antisense nucleotide
sequence,
(1) said sense nucleotide sequence comprising 19 contiguous nucleotides
having 90 to 100% sequence identity to a nucleotide sequence of 19
contiguous nucleotides from the RNA transcribed from a plant gene of
interest;
(2) said antisense nucleotide sequence comprising 19 contiguous nucleotides
having 90 to 100% sequence identity to the complement of a nucleotide
sequence of 19 contiguous nucleotides of said sense nucleotide sequence;
wherein said sense and antisense nucleotide sequences are capable of
forming a double stranded RNA of 19 to 200 nucleotides in length ; and
iii) an oligo dT stretch comprising at least 4 consecutive T-residues,
wherein said chimeric gene when provided to said plant cell reduces the expression of
the plant gene of interest.
13. The chimeric gene as claimed in claim 12, wherein said promoter is a type 3 POLIII
promoter selected from a promoter of a plant gene encoding U6snRNA, a promoter of
a plant gene encoding U3snRNA and a promoter of a plant gene encoding 7SL RNA.
14. The chimeric gene as claimed in claim 12 or claim 13, wherein said chimeric gene
comprises a promoter consisting of a nucleotide sequence selected from the nucleotide
sequence of SEQ ID NO:1 from the nucleotide at position 7 to the nucleotide at
position 322, SEQ ID NO:2 from the nucleotide at position 7 to the nucleotide at
position 408, SEQ ID NO:3 from the nucleotide at position 7 to the nucleotide at
position 313, SEQ ID NO:4 from the nucleotide at position 7 to the nucleotide at
position 446, SEQ ID NO:5 from the nucleotide at position 7 to the nucleotide at
position 436, SEQ ID NO:6 from the nucleotide at position 7 to the nucleotide at

position 468, SEQ ID NO:7 from the nucleotide at position 7 to the nucleotide at
position 384 or SEQ ID NO:8 from the nucleotide at position 7 to the nucleotide at
position 421.
15. The chimeric gene as claimed in claim 12 or claim 13, wherein said plant cell is a
dicotyledonous plant cell and said promoter is derived from a dicotyledonous or
monocotyledonous plant or plant cell.
16. The chimeric gene as claimed in claim 12 or claim 13, wherein said plant cell is a
monocotyledonous plant cell, and said promoter is derived from a monocotyledonous
plant or plant cell.
17. The chimeric gene as claimed in claim 12 or claim 13 wherein said promoter is
endogenous to said plant cell.
18. The chimeric gene as claimed in claim 12 or claim 13, wherein said gene of interest is
a transgene.
19. The chimeric gene as claimed in claim 12 or claim 13, wherein said gene of interest is
an endogenous gene.
20. The chimeric gene as claimed in claim 12 or claim 13, wherein said plant cell is
comprised within a plant.
21. The chimeric gene as claimed in claim 12 or claim 13, wherein said DNA fragment ii)
comprises a spacer region of 3 to 100 nucleotides which is located between the DNA
encoding the sense nucleotide sequence and the DNA encoding the antisense
nucleotide sequence.
22. The chimeric gene as claimed in claim 12 or claim 13, wherein the length of said
double stranded RNA is between 20 and 100 basepairs.

The present invention provides method for reducing the expression of a gene of interest in a
plant cell. The method comprises providing a chimeric gene to the plant cell in which the
chimeric gene comprises a DNA dependant RNA polymerase III of type 3 of a plant cell and
a DNA fragment which when transcribed yields a short hairpin RNA.

Documents:

1563-KOLNP-2005-FORM-27.pdf

1563-kolnp-2005-granted-abstract.pdf

1563-kolnp-2005-granted-assignment.pdf

1563-kolnp-2005-granted-claims.pdf

1563-kolnp-2005-granted-correspondence.pdf

1563-kolnp-2005-granted-description (complete).pdf

1563-kolnp-2005-granted-drawings.pdf

1563-kolnp-2005-granted-examination report.pdf

1563-kolnp-2005-granted-form 1.pdf

1563-kolnp-2005-granted-form 13.pdf

1563-kolnp-2005-granted-form 18.pdf

1563-kolnp-2005-granted-form 3.pdf

1563-kolnp-2005-granted-form 5.pdf

1563-kolnp-2005-granted-gpa.pdf

1563-kolnp-2005-granted-reply to examination report.pdf

1563-kolnp-2005-granted-sequence listing.pdf

1563-kolnp-2005-granted-specification.pdf


Patent Number 226736
Indian Patent Application Number 1563/KOLNP/2005
PG Journal Number 52/2008
Publication Date 26-Dec-2008
Grant Date 24-Dec-2008
Date of Filing 08-Aug-2005
Name of Patentee COMMONWEALTH SCIENTIFIC AND INDUSTRIAL RESEARCH ORGANISATION
Applicant Address LIMESTONE AVENUE, CAMPBELL, AUSTRALIAN CAPITAL TERRITORY 2601
Inventors:
# Inventor's Name Inventor's Address
1 WANG MING BO 3 KIEWA STREET, KALEEN, AUSTRALIAN CAPITAL TERRITORY 2617
2 HELLIWELL CHRISTOPHER ANDREW 167 WATTLE STREET, O'CONNOR, AUSTRALIAN CAPITAL TERRITORY 2602
3 WATERHOUSE PETER MICHAEL 5 BANJINE STREET, O'CONNOR, AUSTRALIAN CAPITAL TERRITORY 2602
PCT International Classification Number A01H 1/00
PCT International Application Number PCT/AU2004/000199
PCT International Filing date 2004-02-19
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 60/447,711 2003-02-19 U.S.A.