Polycomb-associated non-coding RNAs

• US 9,920,317 B2
• Filed: 06/19/2013
• Issued: 03/20/2018
• Est. Priority Date: 11/12/2010
• Status: Active Grant

• Current Assignee: The General Hospital Corporation (Mass General Brigham, Inc.)
• Original Assignee: The General Hospital Corporation (Mass General Brigham, Inc.)
• Inventors: Lee, Jeannie T., Zhao, Jing, Sarma, Kavitha, Borowsky, Mark, Ohsumi, Toshiro Kendrick
• Primary Examiner(s): Bowman, Amy
• Application Number:
  US13/921,738
• Publication Number:
  US 20170037396A1
• Time in Patent Office: 1,735 Days
• CPC Class Codes: 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
• CPC Class Codes: C12N 2310/11 Antisense
• CPC Class Codes: C12N 2310/113 targeting other non-coding nucleic acids, e.g. antagomirs
• CPC Class Codes: C12N 2310/20 involving clustered regularly interspaced short palindromic repeats [CRISPRs]
• CPC Class Codes: C12N 2310/3231 having an additional ring, e.g. LNA, ENA

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.

Claims

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.