Polycomb-Associated Non-Coding RNAS

Patent metadata

Field	Value
Publication number	US-2016376598-A1
Application number	US-201615171883-A
Country	US
Kind code	A1
Filing date	Jun 2, 2016
Priority date	Nov 12, 2010
Publication date	Dec 29, 2016
Grant date	—

Abstract

This invention relates to long non-coding RNAs (lncRNAs), libraries of those ncRNAs that bind chromatin modifiers, such as Polycomb Repressive Complex 2, inhibitory nucleic acids and methods and compositions for targeting lncRNAs.

First claim

1 . (canceled)

2 . A method of producing an oligonucleotide for inducing expression of a target gene, the method comprising:
i) performing an immunoprecipitation assay using an antibody directed against PRC2 to immunoprecipitate a PRC2-binding RNA, wherein the PRC2-binding RNA is transcribed from a sequence of the chromosomal locus of the target gene and inhibits expression of the target gene; and ii) producing an oligonucleotide of 5 to 40 nucleotides in length having a region of complementarity that is complementary with at least 5 contiguous nucleotides of the PRC2-binding RNA.

3 . The method of claim 2 , further comprising detecting a PRC2-binding region of the PRC2-binding RNA, wherein the PRC2 binding region has a RNA nucleotide sequence that is protected from nucleases during the immunoprecipitation assay, wherein the oligonucleotide produced in step ii) is complementary to and binds specifically within the PRC2-binding region of the PRC2-binding RNA.

4 . The method of claim 3 , wherein the oligonucleotide interferes with binding of PRC2 to the PRC2-binding region without inducing degradation of the PRC2-binding RNA.

5 . The method of claim 3 , further comprising sequencing the immunoprecipitated RNA from the cell to detect the RNA nucleotide sequence that is protected from nucleases during the procedure.

6 . The method of claim 2 , further comprising delivering the oligonucleotide to a cell.

7 . The method of claim 6 , further comprising detecting a decrease in recruitment of PRC2 to the target gene in the cell following delivery of the oligonucleotide to the cell, wherein the decrease in recruitment of PRC2 to the target gene in the cell, compared with an appropriate control cell to which the oligonucleotide has not been delivered, indicates effectiveness of the oligonucleotide for inducing expression of the target gene.

8 . The method of claim 2 , wherein the RNA is a lncRNA.

9 . The method of claim 6 , further comprising detecting expression of the PRC2-binding RNA in the cell, wherein expression of the PRC2-binding RNA in the cell indicates that the oligonucleotide is suitable for inducing expression of the target gene in the cell.

10 . The method of claim 6 , further comprising detecting a change in expression of the target gene following delivery of the oligonucleotide to the cell, wherein an increase in expression of the target gene compared with an appropriate control cell indicates effectiveness of the oligonucleotide.

11 . The method of claim 6 , wherein the cell is in vitro.

12 . The method of claim 6 , wherein the cell is in vivo.

13 . The method of claim 2 , wherein the PRC2-binding RNA is transcribed from the same strand as the target gene in a genomic region containing the target gene.

14 . The method of claim 2 , 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.

15 . The method of claim 2 , wherein the oligonucleotide has complementarity to a region of the PRC2-binding RNA transcribed from the same strand as the target gene within a chromosomal region within −2.0 kb to +0.001 kb of the transcription start site of the target gene.

16 . The method of claim 2 , wherein the oligonucleotide has complementarity to a region of the PRC2-binding RNA transcribed from the opposite strand of the target gene within a chromosomal region within −0.5 to +0.1 kb of the transcription start site of the target gene.

17 . The method of claim 2 , wherein the oligonucleotide has complementarity to the PRC2-binding RNA in a region of the PRC2-binding RNA that forms a stem-loop structure.

18 . The method of claim 2 , wherein at least one nucleotide of the oligonucleotide is an RNA or DNA nucleotide.

19 . The method of claim 2 , wherein the target gene is a protein-coding gene.

20 . The method of claim 2 , wherein the target gene is a gene of an autosomal chromosome.

21 . The method of claim 2 , wherein the cell is a cell of a male subject.

22 . The method of claim 2 , wherein the oligonucleotide has complementarity to a region of the PRC2-binding RNA transcribed from a portion of the target gene corresponding to an intron-exon junction or an intron.

23 . The method of claim 2 , wherein the oligonucleotide has complementarity to a region of the PRC2-binding RNA transcribed from a portion of the target gene corresponding to a translation initiation region or a translation termination region.

24 . The method of claim 2 , wherein the oligonucleotide has complementarity to a region of the PRC2-binding RNA transcribed from a portion of the target gene corresponding to a promoter.

25 . The method of claim 2 , wherein the oligonucleotide has complementarity to a region of the PRC2-binding RNA transcribed from a portion of the target gene corresponding to a 5′-UTR or a 3′-UTR.

26 . The method of claim 2 , wherein the oligonucleotide comprises having at least one nucleotide having a 2′-O-methoxyethyl modified sugar moiety and locked nucleic acid (LNA) nucleotides.

27 . The method of claim 2 , 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.

28 . The method of claim 27 , wherein the ribonucleic acid analogue comprises a methylene bridge between the 2′-oxygen and the 4′-carbon.

29 . The method of claim 2 , wherein at least one nucleotide has a 2′-O-methoxyethyl modified sugar moiety.

30 . The method of claim 2 , wherein the oligonucleotide comprises at least one modified internucleoside linkage.

31 . A method of producing an oligonucleotide for inducing expression of a target gene in a cell, the method comprising:
producing an 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 is transcribed from a sequence of the chromosomal locus of the target gene and that inhibits expression of the target gene, wherein the oligonucleotide is complementary to and bind specifically within a PRC2-binding region of the PRC2-binding RNA, wherein the PRC2-binding region is determined to have a nucleotide sequence that is protected from nucleases during an RNA immunoprecipitation procedure using an antibody directed against PRC2, and wherein the oligonucleotide interferes with binding of PRC2 to the PRC2-binding region without inducing degradation of the PRC2-binding RNA.

Assignees

• Massachusetts Gen Hospital

Inventors

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

Classifications

• A61P9/00

  Drugs for disorders of the cardiovascular system · CPC title

• A61P35/00

  Antineoplastic agents · CPC title

• A61P3/00

  Drugs for disorders of the metabolism (of the blood or the extracellular fluid A61P7/00) · CPC title

• A61P29/00

  Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID] · CPC title

• A61P13/00

  Drugs for disorders of the urinary system · CPC title