Polycomb-associated non-coding RNAs

Patent metadata

Field	Value
Publication number	US-9920317-B2
Application number	US-201313921738-A
Country	US
Kind code	B2
Filing date	Jun 19, 2013
Priority date	Nov 12, 2010
Publication date	Mar 20, 2018
Grant date	Mar 20, 2018

Abstract

This invention relates to polycomb-associated long non-coding RNAs (lncRNAs), libraries and fragments of those ncRNAs, inhibitory nucleic acids and methods and compositions for targeting lncRNAs.

First claim

What is claimed is:

1. A single stranded oligonucleotide of 5 to 40 nucleotides in length having a region of complementarity that is complementary with at least 5 contiguous nucleotides of a PRC2-binding RNA that regulates expression of a target gene, wherein the oligonucleotide is complementary to and binds specifically within a PRC2-binding region of the PRC2-binding RNA and interferes with binding of PRC2 to the PRC2-binding region without inducing degradation of the PRC2-binding RNA, wherein the PRC2-binding region has a nucleotide sequence protected from nucleases during an RNA immunoprecipitation procedure using an antibody directed against PRC2, wherein the PRC2-binding RNA is transcribed from a sequence of the chromosomal locus of the target gene, wherein at least one nucleotide of the oligonucleotide is a modified nucleotide, wherein the target gene is G6PC or OTC.

2. The single stranded oligonucleotide of claim 1 , wherein the RNA is a long non-coding RNA (lncRNA).

3. The single stranded oligonucleotide of claim 1 , wherein the PRC2-binding RNA regulates expression of the target gene in a cis manner.

4. The single stranded oligonucleotide of claim 1 , wherein the PRC2-binding RNA is transcribed from the same strand as the target gene.

5. The single stranded oligonucleotide of claim 1 , wherein the oligonucleotide has complementarity to a region of the PRC2-binding RNA transcribed from a portion of the target gene corresponding to an exon, intron-exon junction, a translation initiation region, a translation termination region, a promoter, an intron, a 5′-UTR, or a 3′-UTR.

6. The single stranded oligonucleotide of claim 1 , wherein the oligonucleotide has complementarity to the PRC2-binding RNA in a region of the PRC2-binding RNA that forms a stem-loop structure.

7. The single stranded oligonucleotide of claim 1 , wherein at least one nucleotide of the oligonucleotide is an RNA or DNA nucleotide.

8. The single stranded oligonucleotide of claim 1 , wherein at least one nucleotide of the oligonucleotide is a ribonucleic acid analogue comprising a ribose ring having a bridge between its 2′-oxygen and 4′-carbon.

9. The single stranded oligonucleotide of claim 8 , wherein the ribonucleic acid analogue comprises a methylene bridge between the 2′-oxygen and the 4′-carbon.

10. The single stranded oligonucleotide of claim 1 , wherein at least one nucleotide of the oligonucleotide comprises a modified sugar moiety.

11. The single stranded oligonucleotide of claim 10 , wherein the modified sugar moiety comprises a 2′-O-methoxyethyl modified sugar moiety, a 2′-methoxy modified sugar moiety, a 2′-O-alkyl modified sugar moiety, or a bicyclic sugar moiety.

12. The single stranded oligonucleotide of claim 1 comprising at least one modified internucleoside linkage.

13. The single stranded oligonucleotide of claim 12 , wherein the at least one modified internucleoside linkage is selected from phosphorothioate, phosphorodithioate, alkylphosphonothioate, phosphoramidate, carbamate, carbonate, phosphate triester, acetamidate, carboxymethyl ester, and combinations thereof.

14. The single stranded oligonucleotide of claim 1 configured such that hybridization of the single stranded oligonucleotide to the PRC2-binding RNA does not activate an RNAse H pathway in a cell.

15. A compound comprising the single stranded oligonucleotide of claim 1 conjugated to a second single stranded oligonucleotide of 5 to 40 nucleotides in length having a region of complementarity that is complementary with at least 5 contiguous nucleotides of a PRC2-binding RNA.

16. A single stranded oligonucleotide of 5 to 40 nucleotides in length having a region of complementarity that is complementary with at least 5 contiguous nucleotides of a PRC2-binding RNA that inhibits expression of a target gene in cis, wherein the oligonucleotide has complementarity to the PRC2-binding RNA in a PRC2-binding region of the PRC2-binding RNA that is transcribed from the sense strand of the target gene, wherein the oligonucleotide interferes with binding of PRC2 to the PRC2-binding region without inducing degradation of the PRC2-binding RNA, wherein the PRC2-binding region has a nucleotide sequence protected from nucleases during an RNA immunoprecipitation procedure using an antibody directed against PRC2, wherein the PRC2-binding RNA is transcribed from a sequence of the chromosomal locus of the target gene, wherein the target gene is G6PC or OTC.

17. The single stranded oligonucleotide of claim 16 , wherein the RNA is a IncRNA.

Assignees

• Massachusetts Gen Hospital

Inventors

• Lee Jeannie T
• Zhao Jing
• Sarma Kavitha
• Borowsky Mark
• Ohsumi Toshiro Kendrick

Classifications

• C12N2310/20

  involving clustered regularly interspaced short palindromic repeats [CRISPR] · CPC title

• C12N2310/3231

  having an additional ring, e.g. LNA, ENA · CPC title

• C12N2310/11

  Antisense · CPC title

• C12N15/113 Primary

  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)} · CPC title

• C12N2310/113

  targeting other non-coding nucleic acids, e.g. antagomirs · CPC title