# US 2013/0160160 A1 · Method for sustainable transgene transcription

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- Number: US 2013/0160160 A1
- Document ID: US20130160160A1
- Status: Published application
- Kind: A1
- Application number: 13/775,365
- Filed: 2013-02-25
- Published: 2013-06-20
- Earliest claimed: 2007-05-09
- Assignees: Devgen NV
- Inventors: Bert Wim Oosthuyse
- Web page: https://patentgrep.com/patent/US20130160160A1

## CPC

- C12N 15/8218: {Antisense, co-suppression, viral induced gene silencing [VIGS], post-transcriptional induced gene silencing [PTGS]}
- C12N 15/113: Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; {Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing (when used in plants C12N15/8218)}
- C12N 15/8216: {Methods for controlling, regulating or enhancing expression of transgenes in plant cells}
- C12N 15/8286: {for insect resistance}
- C12N 2310/111: spanning the whole gene, or a large part of it
- C12N 2310/14: interfering nucleic acids [NA]
- Y02A 40/146: Genetically Modified [GMO] plants, e.g. transgenic plants
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)
- Y02A: TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE

## Abstract

The present invention relates to constructs and methods for improving expression of transgenes in plants, animals and humans.

## Claims

### Claim 1

A method for inhibiting expression of a target gene with double stranded RNA, wherein the double stranded RNA consists of:
(a) a first strand comprising:
a sequence substantially identical to 10 to 1000, 10 to 500, 10 to 50, 19 to 999, 19 to 499, 19 to 49, 19 to 39, 19 to 29, 19 to 25, or 19 to 21 consecutive nucleotides of a target gene; or
comprising a sequence having at least 70%, 75%, 80%, 85%, 90%, 95% or 99% sequence identity with a sequence comprising 10 to 1000, 10 to 500, 10 to 50, 19 to 999, 19 to 499, 19 to 49, 19 to 39, 19 to 29, 19 to 25, or 19 to 21 consecutive nucleotides of a target gene, and
(b) a second strand comprising a sequence substantially complementary to the first strand;
wherein the double stranded RNA optionally has a single stranded overhang at either or both ends; and
wherein said double stranded RNA is transcribed in an eukaryotic non-human cell from a DNA construct comprising:
a polynucleotide comprising a sequence consisting of introns and exons, wherein the size of each of the exons is smaller than 60 nucleotides; or
a polynucleotide comprising a sequence consisting of introns and exons wherein the number of nucleotides in each of the exons independently ranges from 1 to 60 nucleotides;
wherein the polynucleotide is operably linked to a transcriptional regulatory region regulating the transcription of said polynucleotide.

### Claim 2

A method for producing a double stranded RNA comprising culturing an eukaryotic non-human cell transformed with:
(i) a DNA construct comprising:
a polynucleotide comprising a sequence consisting of introns and exons wherein the size of each of the exons is smaller than 60 nucleotides, or
a polynucleotide comprising a sequence consisting of introns and exons wherein the number of nucleotides in each of the exons independently ranges from 1 to 60 nucleotides;
wherein said polynucleotide is operably linked to a transcriptional regulatory region regulating the transcription of said polynucleotide, and
wherein said exons upon transcription and splicing encode a double stranded RNA consisting of:
(a) a first strand comprising:
a sequence substantially identical to 10 to 1000, 10 to 500, 10 to 50, 19 to 999, 19 to 499, 19 to 49, 19 to 39, 19 to 29, 19 to 25, or 19 to 21 consecutive nucleotides of a target gene; or
a sequence having at least 70%, 75%, 80%, 85%, 90%, 95% or 99% sequence identity with a sequence comprising 10 to 1000, 10 to 500, 10 to 50, 19 to 999, 19 to 499, 19 to 49, 19 to 39, 19 to 29, 19 to 25, or 19 to 21 consecutive nucleotides of a target gene, and
(b) a second strand comprising a sequence substantially complementary to the first strand;
and wherein the double stranded RNA optionally has a single stranded overhang at either or both ends and wherein the double stranded RNA inhibits expression of the target gene; or
(ii) a vector comprising the DNA construct of (i);
so as to express the double stranded RNA and recovering the product from the host cell culture.

### Claim 3 (depends on 1)

The method according to claim 1, wherein said eukaryotic non-human cell is a plant cell.

### Claim 4

A method for producing transgenic plants comprising
(a) transforming a plant cell with:
(i) a DNA construct comprising:
a polynucleotide comprising a sequence consisting of introns and exons wherein the size of each of the exons is smaller than 60 nucleotides, or
a polynucleotide comprising a sequence consisting of introns and exons wherein the number of nucleotides in each of the exons independently ranges from 1 to 60 nucleotides;
wherein said polynucleotide is operably linked to a transcriptional regulatory region regulating the transcription of said polynucleotide, and wherein said exons upon transcription and splicing encode a double stranded RNA:
(1a) consisting of a first strand comprising a sequence substantially identical to 10 to 1000, 10 to 500, 10 to 50, 19 to 999, 19 to 499, 19 to 49, 19 to 39, 19 to 29, 19 to 25, or 19 to 21 consecutive nucleotides of a target gene; or
(1b) comprising a sequence having at least 70%, 75%, 80%, 85%, 90%, 95% or 99% sequence identity with a sequence comprising 10 to 1000, 10 to 500, 10 to 50, 19 to 999, 19 to 499, 19 to 49, 19 to 39, 19 to 29, 19 to 25, or 19 to 21 consecutive nucleotides of a target gene;
and
(2) a second strand comprising a sequence substantially complementary to the first strand;
wherein the double stranded RNA optionally has a single stranded overhang at either or both ends, and wherein the double stranded RNA inhibits expression of the target gene; or
(ii) a vector comprising the DNA construct of (i),
(b) regenerating a transgenic plant from said plant cell, and
(c) growing the transformed plant under conditions suitable for the transcription of said polynucleotide.

### Claim 5

A method for making a product of interest in a plant comprising:
(a) transforming a plant cell with:
(i) a polynucleotide comprising a sequence consisting of introns and exons wherein the size of each of the exons is smaller than 60 nucleotides;
(ii) a polynucleotide comprising a sequence consisting of introns and exons wherein the number of nucleotides in each of the exons independently ranges from 1 to 60 nucleotides,
wherein said polynucleotide is operably linked to an RNA polymerase promoter or wherein said polynucleotide is inserted downstream and in frame of a transcriptional regulatory region regulating the transcription of the polynucleotide;
(iii) a DNA construct comprising the polynucleotide of (i) or (ii) operably linked to a transcriptional regulatory region regulating the transcription of said polynucleotide;
(iv) the DNA construct of (iii), wherein the exons upon transcription and splicing encode a product of interest;
(v) the DNA construct of (iii), wherein said exons upon transcription and splicing encode a double stranded RNA consisting of:
(1) a first strand comprising:
a sequence substantially identical to 10 to 1000, 10 to 500, 10 to 50, 19 to 999, 19 to 499, 19 to 49, 19 to 39, 19 to 29, 19 to 25, or 19 to 21 consecutive nucleotides of a target gene; or
a sequence having at least 70%, 75%, 80%, 85%, 90%, 95% or 99% sequence identity with a sequence comprising 10 to 1000, 10 to 500, 10 to 50, 19 to 999, 19 to 499, 19 to 49, 19 to 39, 19 to 29, 19 to 25, or 19 to 21 consecutive nucleotides of a target gene, and
(2) a second strand comprising a sequence substantially complementary to the first strand,
wherein the double stranded RNA optionally has a single stranded overhang at either or both ends, and wherein the double stranded RNA inhibits expression of the target gene; or
(vi) a vector comprising the polynucleotide of (i) or (ii) or the DNA construct of any of (iii) to (v),
(b) regenerating a transgenic plant from said plant cell, and
(c) isolating plant cells or plant parts comprising the product of interest from said plant.

### Claim 6

A method for improving transcription of a transgene in a plant comprising:
(a) transforming a plant cell with:
(i) a polynucleotide comprising a sequence consisting of introns and exons wherein the size of each of the exons is smaller than 60 nucleotides;
(ii) a polynucleotide comprising a sequence consisting of introns and exons wherein the number of nucleotides in each of the exons independently ranges from 1 to 60 nucleotides,
wherein said polynucleotide is operably linked to an RNA polymerase promoter, or wherein said polynucleotide is inserted downstream and in frame of a transcriptional regulatory region regulating the transcription of the polynucleotide;
(iii) a DNA construct comprising the polynucleotide of (i) or (ii) operably linked to a transcriptional regulatory region regulating the transcription of said polynucleotide;
(iv) the DNA construct of (iii), wherein the exons upon transcription and splicing encode a product of interest; or
(v) the DNA construct of (iii), wherein said exons upon transcription and splicing encode a double stranded RNA consisting of:
(1) a first strand comprising:
a sequence substantially identical to 10 to 1000, 10 to 500, 10 to 50, 19 to 999, 19 to 499, 19 to 49, 19 to 39, 19 to 29, 19 to 25, or 19 to 21 consecutive nucleotides of a target gene; or
a sequence having at least 70%, 75%, 80%, 85%, 90%, 95% or 99% sequence identity with a sequence comprising 10 to 1000, 10 to 500, 10 to 50, 19 to 999, 19 to 499, 19 to 49, 19 to 39, 19 to 29, 19 to 25, or 19 to 21 consecutive nucleotides of a target gene, and
(2) a second strand comprising a sequence substantially complementary to the first strand,
wherein the double stranded RNA optionally has a single stranded overhang at either or both ends, and wherein the double stranded RNA inhibits expression of the target gene; or
(vi) a vector comprising the polynucleotide of (i) or (ii) or the DNA construct of any of (iii) to (v); and
(b) regenerating a transgenic plant from said plant cell.

### Claim 7

A method for producing an RNA transcript in a plant comprising:
(a) transforming a plant cell with:
(i) a polynucleotide comprising a sequence consisting of introns and exons wherein the size of each of the exons is smaller than 60 nucleotides;
(ii) a polynucleotide comprising a sequence consisting of introns and exons wherein the number of nucleotides in each of the exons independently ranges from 1 to 60 nucleotides, wherein said polynucleotide is operably linked to an RNA polymerase promoter or wherein said polynucleotide is inserted downstream and in frame of a transcriptional regulatory region regulating the transcription of the polynucleotide;
(iii) a DNA construct comprising the polynucleotide of (i) or (ii) operably linked to a transcriptional regulatory region regulating the transcription of said polynucleotide;
(iv) the DNA construct of (iii), wherein the exons upon transcription and splicing encode a product of interest; or
(v) the DNA construct of (iii), wherein said exons upon transcription and splicing encode a double stranded RNA consisting of:
(1) a first strand comprising:
a sequence substantially identical to 10 to 1000, 10 to 500, 10 to 50, 19 to 999, 19 to 499, 19 to 49, 19 to 39, 19 to 29, 19 to 25, or 19 to 21 consecutive nucleotides of a target gene; or
a sequence having at least 70%, 75%, 80%, 85%, 90%, 95% or 99% sequence identity with a sequence comprising 10 to 1000, 10 to 500, 10 to 50, 19 to 999, 19 to 499, 19 to 49, 19 to 39, 19 to 29, 19 to 25, or 19 to 21 consecutive nucleotides of a target gene, and
(2) a second strand comprising a sequence substantially complementary to the first strand,
wherein the double stranded RNA optionally has a single stranded overhang at either or both ends, and wherein the double stranded RNA inhibits expression of the target gene; or
(vi) a vector comprising the polynucleotide of (i) or (ii) or the DNA construct of any of (iii) to (v); and
(b) regenerating a transgenic plant from said plant cell,
wherein said RNA transcript is chosen from a double stranded RNA, shRNA, miRNA, siRNA, stRNA or ribozyme.

### Claim 8

A method of inhibiting infection of a first non-human organism by a target organism comprising:
(a) transforming a cell of said first organism with:
(i) a polynucleotide comprising a sequence consisting of introns and exons wherein the size of each of the exons is smaller than 60 nucleotides;
(ii) a polynucleotide comprising a sequence consisting of introns and exons wherein the number of nucleotides in each of the exons independently ranges from 1 to 60 nucleotides, wherein said polynucleotide is operably linked to an RNA polymerase promoter or wherein said polynucleotide is inserted downstream and in frame of a transcriptional regulatory region regulating the transcription of the polynucleotide;
(iii) a DNA construct comprising the polynucleotide of (i) or (ii) operably linked to a transcriptional regulatory region regulating the transcription of said polynucleotide;
(iv) the DNA construct of (iii), wherein the exons upon transcription and splicing encode a product of interest; or
(v) the DNA construct of (iii), wherein said exons upon transcription and splicing encode a double stranded RNA consisting of:
(1) a first strand comprising:
a sequence substantially identical to 10 to 1000, 10 to 500, 10 to 50, 19 to 999, 19 to 499, 19 to 49, 19 to 39, 19 to 29, 19 to 25, or 19 to 21 consecutive nucleotides of a target gene; or
a sequence having at least 70%, 75%, 80%, 85%, 90%, 95% or 99% sequence identity with a sequence comprising 10 to 1000, 10 to 500, 10 to 50, 19 to 999, 19 to 499, 19 to 49, 19 to 39, 19 to 29, 19 to 25, or 19 to 21 consecutive nucleotides of a target gene, and
(2) a second strand comprising a sequence substantially complementary to the first strand,
wherein the double stranded RNA optionally has a single stranded overhang at either or both ends, and wherein the double stranded RNA inhibits expression of the target gene; or
(vi) a vector comprising the polynucleotide of (i) or (ii) or the DNA construct of any of (iii) to (v); and
(b) regenerating an organism from said cell,
wherein said polynucleotide after transcription and splicing, or wherein said product of interest after transcription and splicing, down regulates expression of a target gene in said target organism.

### Claim 9

A method for making a plant resistant to pest infestation comprising:
(a) transforming a plant cell with a DNA construct comprising:
a polynucleotide comprising a sequence consisting of introns and exons wherein the size of each of the exons is smaller than 60 nucleotides; or
a polynucleotide comprising a sequence consisting of introns and exons wherein the number of nucleotides in each of the exons independently ranges from 1 to 60 nucleotides;
wherein said polynucleotide is operably linked to a transcriptional regulatory region regulating the transcription of said polynucleotide, and wherein said exons upon transcription and splicing encode a double stranded RNA consisting of:
(i) a first strand comprising
a sequence substantially identical to 10 to 1000, 10 to 500, 10 to 50, 19 to 999, 19 to 499, 19 to 49, 19 to 39, 19 to 29, 19 to 25, or 19 to 21 consecutive nucleotides of a target gene; or
a sequence having at least 70%, 75%, 80%, 85%, 90%, 95% or 99% sequence identity with a sequence comprising 10 to 1000, 10 to 500, 10 to 50, 19 to 999, 19 to 499, 19 to 49, 19 to 39, 19 to 29, 19 to 25, or 19 to 21 consecutive nucleotides of a target gene; and
(ii) a second strand comprising a sequence substantially complementary to the first strand;
wherein the double stranded RNA optionally has a single stranded overhang at either or both ends, and wherein the double stranded RNA inhibits expression of the target gene; and
(b) regenerating a transgenic plant from said plant cell.

### Claim 10 (depends on 4)

A pesticide comprising a transgenic plant obtained by the method of claim 4, or any harvestable plant part thereof.

### Claim 11 (depends on 9)

A pesticide comprising a transgenic plant obtained by the method of claim 9, or any harvestable plant part thereof.

### Claim 12

A method for preventing transcriptional gene silencing (TGS) of a transgene in a plant comprising:
(a) providing a polynucleotide consisting of a coding sequence to be transcribed optionally under the control of a transcriptional regulatory region,
(b) introducing into the coding sequence splice intron sequences to limit the exon sizes to less than 60 by so that stretches of double stranded RNA formed from expression of the transcript are of a size not capable of base-pairing with the nuclear transgene expression cassette sequence necessary to conduct the DNA methylation process,
(c) transforming a plant cell with the polynucleotide obtained in step (b) wherein said polynucleotide is operably linked to said transcriptional regulatory region or wherein said polynucleotide is inserted downstream and in frame of an (endogenous) transcriptional regulatory region regulating the transcription of the polynucleotide, and
(d) regenerating a transgenic plant from said plant cell.

### Claim 13

The method according to any one of the preceding claims, wherein the number of nucleotides in each of the exons is independently chosen from the group comprising 60, 59, 58, 57, 56, 55, 54, 53, 52, 51, 50, 49, 48, 47, 46, 45, 44, 43, 42, 41, 40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 nucleotide(s), or wherein the number of nucleotides in each of the exons independently ranges from 1 to 60, 1 to 50, 1 to 40, 1 to 30, 1 to 26, 1 to 21, 1 to 17, 1 to 15, 1 to 10, 2 to 60, 2 to 50, 2 to 40, 2 to 30, 2 to 26, 2 to 21, 2 to 17, 2 to 15, 2 to 10, 4 to 60, 4 to 50, 4 to 40, 4 to 30, 4 to 26, 4 to 21, 4 to 17, 4 to 15, 4 to 10, 5 to 20, 9 to 16 or from 10 to 15 nucleotides.

### Claim 14 (depends on 2)

A method for inhibiting expression of a target gene comprising
obtaining a dsRNA product produced by the method according to claim 2, and
contacting an organism that expresses the target gene with the dsRNA product.

### Claim 15 (depends on 2)

A method for inhibiting infection of a first non-human organism by a target organism comprising
obtaining a dsRNA product produced by the method according to claim 2, and
contacting said target organism with the dsRNA product, wherein said dsRNA down regulates expression of a target gene in said target organism.

### Claim 16 (depends on 4)

A method for producing a product of interest comprising growing or culturing a plant produced by the method according to claim 4.

### Claim 17 (depends on 4)

A method for producing dsRNA comprising growing or culturing a plant produced by the method according to claim 4.