# US 2014/0193821 A1 · Exonic splicing enhancers and exonic splicing silencers

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- Number: US 2014/0193821 A1
- Document ID: US20140193821A1
- Status: Published application
- Kind: A1
- Application number: 14/235,476
- Filed: 2012-07-27
- Published: 2014-07-10
- Earliest claimed: 2011-07-28
- Assignees: The Regents of the University of California
- Applicants: The Regents of the University of California
- Inventors: Jeremy Sanford; Timothy Steme-Weiler
- Web page: https://patentgrep.com/patent/US20140193821A1

## CPC

- C12Q 1/6883: for diseases caused by alterations of genetic material
- 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 2310/11: Antisense
- C12N 2320/33: Alteration of splicing
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00)

## Abstract

Compounds and methods for regulation of exonic splicing enhancers and exonic splicing silencers. Compounds include polynucleotides targeted to aberrant exonic splicing enhancers and exonic splicing silencers. Compounds and methods for the diagnosis of diseases and conditions associated with aberrant exonic splicing enhancers and exonic splicing silencers. Methods for identifying splicing-sensitive disease mutations, and functional RNA elements as targets for amelioration of aberrant pre-mRNA splicing.

## Claims

### Claim 1

A compound comprising a polynucleotide, wherein the polynucleotide comprises a sequence selected from the group consisting of SEQ ID NO:1-25.

### Claim 2 (depends on 1)

The compound of claim 1, wherein the polynucleotide consists of a sequence selected from the group consisting of SEQ ID NO:1-25.

### Claim 3 (depends on 1)

The compound of claim 1, wherein the polynucleotide is an antisense oligomer.

### Claim 4 (depends on 1)

The compound of claim 1, wherein the polynucleotide is a polynucleotide-targeting analog or an antisense polynucleotide-targeting analog.

### Claim 5

(canceled)

### Claim 6 (depends on 1)

The compound of claim 1, wherein the polynucleotide is a short interfering RNA.

### Claim 7

(canceled)

### Claim 8 (depends on 1)

The compound of claim 1, wherein the polynucleotide comprises one or more polynucleotide monomers selected from one or more RNA monomers and one or more DNA monomers.

### Claim 9 (depends on 8)

The compound of claim 8, wherein the one or more polynucleotide monomers are selected from the group consisting of one or more 2′-O-methyl ribonucleic acid monomers, one or more locked nucleoside analog monomers, one or more phosphorodiamidate morpholino monomers and one or more peptide nucleic acid monomers.

### Claim 10

(canceled)

### Claim 11

(canceled)

### Claim 12

(canceled)

### Claim 13

(canceled)

### Claim 14

A method for diagnosing a disease or condition related to aberrant splicing of a disease-related gene, the method comprising:
a) providing a cell comprising the disease-related gene,
b) providing a compound that binds specifically to the disease-related gene having an aberrant ESS hexamer, and
c) detecting specific binding of the compound to the gene.

### Claim 15 (depends on 14)

The method of claim 14, wherein the disease-related gene is selected from the group consisting of OPA1, PYGM, TFR2, RPS6KA3, APC, SLC5A1, and COL4A3.

### Claim 16 (depends on 15)

The method of claim 15, wherein the aberrant ESS hexamer has a sequence selected from the group consisting of ACUAGG, CUUAGG, AUUAGG, UAGGUA, and GUAGUU.

### Claim 17 (depends on 16)

The method of claim 16, wherein the disease-related gene is OPA1 and the aberrant ESS hexamer has the sequence ACUAGG.

### Claim 18

A method for reducing aberrant exon splice suppression, the method comprising:
a) providing a cell comprising an ESS hexamer having a sequence selected from the group consisting of ACUAGG, CUUAGG, AUUAGG, UAGGUA, and GUAGUU;
b) providing a compound that interacts with the ESS hexamer; and
c) contacting the ESS hexamer with the compound.

### Claim 19 (depends on 18)

The method of claim 18, wherein the compound binds specifically to the ESS hexamer wherein the compound is selected from a group consisting of a small molecule, a polynucleotide, an antisense oligomer, a polypeptide or a polynucleotide.

### Claim 20

(canceled)

### Claim 21

(canceled)

### Claim 22

(canceled)

### Claim 23

(canceled)

### Claim 24 (depends on 18)

The method of claim 18, wherein the cell comprises a disease-related gene selected from the group consisting of OPA1, PYGM, TFR2, RPS6KA3, APC, SLC5A1, and COL4A3.

### Claim 25

A method for reducing aberrant pre-mRNA splicing, the method comprising:
a) providing a cell comprising a cis-acting element comprising a sequence selected from the group consisting of ACUAGG, CUUAGG, AUUAGG, UAGGUA, and GUAGUU;
b) providing a compound that interacts with the cis-acting element; and
c) contacting, or directly competing for contact with, the cis-acting element with the compound.

### Claim 26 (depends on 25)

The method of claim 25, wherein the compound binds specifically to part or the whole of the cis-acting element.

### Claim 26 (depends on 25)

The method of claim 25, wherein the compound is s selected from a group consisting of a polynucleotide, an antisense oligomer, a polypeptide or a polynucleotide a small molecule.

### Claim 27

(canceled)

### Claim 28

(canceled)

### Claim 29

(canceled)

### Claim 30 (depends on 25)

The method of claim 25, wherein the cell comprises a disease-related gene selected from the group consisting of OPA1, PYGM, TFR2, RPS6KA3, APC, SLC5A1, and COL4A3.

### Claim 31 (depends on 30)

The method of claim 30, wherein the cis-acting element comprises the sequence ACUAGG and the cell comprises the disease-related gene OPA1.

### Claim 32

(canceled)

### Claim 33 (depends on 31)

The method of claim 31, wherein the cis-acting element is located within 50 nucleotides from an exon-intron junction.

### Claim 34 (depends on 31)

The method of claim 31, wherein the cis-acting element is located within an exon of the disease-related gene OPA1.

### Claim 35 (depends on 31)

The method of claim 31, wherein the cis-acting element is located within an intron of the disease-related gene OPA1.

### Claim 36 (depends on 31)

The method of claim 31, wherein the cis-acting element if located within 50 nucleotides from an exon-intron junction of the disease-related gene OPA1.

### Claim 37 (depends on 31)

The method of claim 31, wherein the compound binds specifically to the RNA corresponding to human chromosome 3, coordinate location 193361220 (Homo sapiens, build GRCh37/hg19).

### Claim 38

(canceled)