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.
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1. A method of inducing expression of a non-imprinted target gene in a cell, wherein expression of the target gene is inhibited by a PRC2-binding RNA, the method comprising delivering to the cell a composition comprising an isolated single stranded oligonucleotide of 8 to 40 nucleotides in length ha
1. A method of inducing expression of a non-imprinted target gene in a cell, wherein expression of the target gene is inhibited by a PRC2-binding RNA, the method comprising delivering to the cell a composition comprising an isolated single stranded oligonucleotide of 8 to 40 nucleotides in length having a region of complementarity that is complementary with at least 5 contiguous nucleotides of the PRC2-binding RNA that inhibits expression of the target gene, wherein the PRC2-binding RNA is transcribed from a sequence of the chromosomal locus of the target gene, wherein the target gene is A1BG, ABCB4, ABCC2, ACADM, ACOT12, ACY1, AGXT, AHSG, AIRE, AK4, ALDH1L1, ANG, ANGPTL6, ARF6, ASCL1, ASGR2, ASNS, ASPDH, ASS1, ATF5, AURKA, BDH1, C19ORF80, CBG, CAD, CARD10, CCDC39, CCDC40, CDHR5, CEBPA, CEBPG, CFLAR, CITED2, CLEC4M, COBL, CSNK2A1, CSNK2A2, CSNK2B, CUX2, CX3CR1, CYP1A1, CYP26A1, CYP2A13, CYP2A4, CYP2A5, CYP2A6, CYP3A7, CYP4F13, CYP4F18, CYP4F3, DBP, DDHD2, DNAAF1, DNAJC25, DNMT3L, EGFR, ENTPDS, EPHX1, F2, F5, FABP1, FCN2, FOXA3, FPGS, FUOM, GLDC, GLS2, GLTPD2, GM6484, GNPNAT1, GPBAR1, GPLD1, H2-M3, H2-OA, HES1, HFE2, HLA-C, HLA-DOA, HLA-F, HLA-G, HLX, HMOX1, HNF1B, HNRNPD, IGF2R, IL1B, IL23A, IL6R, IL6RA, ITGA2, ITPA, JARID2, KHK, KNG2, LEAP2, LIPE, LOXL2, LPL, LSR, MAN2A1, MED1, MESP1, MST1, MTTP, MYC, NF1, NFKBIA, NPW, OSGIN1, PAQR9, PCNA, PCSK9, PFKL, PHKA2, PHKG2, PKD1, PKD2, PKM, PLK1, PNPLA1, PNPLA2, PNPLA3, PON3, PPARA, PPP1R3F, PRAP1, PRG4, PRKCE, PRKCSH, PROS1, PRPF31, PTPN1, PTPN3, RAP1A, RB1CC1, RBP4, REEP6, RELA, RIPPLY1, RNASE4, RND1, RPGRIP1L, RPL32, RTP3, RXRA, SAA2-SAA4, SAA4, SDS, SEC14L2, SEC63, SERAC1, SERPINA7, SERPINE1, SLC10A1, SLC13A5, SLC22A1, SLC22A7, SLC25A18, SLC28A1, SLC51A, SOD2, SP3, SRSFS, TAF10, TGFB1, THBS2, THPO, THRSP, TMEM82, TMPRSS6, TRIM55, UGT1A1, UGT1A10, UGT1A2, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A6A, UGT1A6B, UGT1A7, UGT1A8, UGT1A9, UPF2, VDR, WNT1, or ZIC3. 2. The method of claim 1, 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 single stranded oligonucleotide is suitable for increasing expression of the target gene in the cell. 3. The method of claim 1, further comprising detecting a change in expression of the target gene following delivery of the single stranded oligonucleotide to the cell, wherein an increase in expression of the target gene compared with an appropriate control cell indicates effectiveness of the single stranded oligonucleotide. 4. The method of claim 1, wherein a decrease in recruitment of PRC2 to the target gene in the cell following delivery of the single stranded oligonucleotide to the cell, compared with an appropriate control cell to which the single stranded oligonucleotide has not been delivered, indicates effectiveness of the single stranded oligonucleotide. 5. The method of claim 1, wherein the cell is in vitro. 6. The method of claim 1, wherein the cell is in vivo. 7. The method of claim 1, wherein the RNA is a lncRNA. 8. The method of claim 1, wherein at least one nucleotide of the oligonucleotide is a modified nucleotide. 9. A method of inducing expression of a non-imprinted target gene in a cell, wherein expression of the target gene is inhibited by a PRC2-binding RNA, the method comprising delivering to the cell a composition comprising an isolated single stranded oligonucleotide of 8 to 40 nucleotides in length having a region of complementarity that is complementary with at least 5 contiguous nucleotides of the PRC2-binding RNA that inhibits expression of the target gene, wherein the PRC2-binding RNA is transcribed from a sequence of the chromosomal locus of the 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, and wherein the target gene is A1BG, ABCB4, ABCC2, ACADM, ACOT12, ACY1, AGXT, AHSG, AIRE, AK4, ALDH1L1, ANG, ANGPTL6, ARF6, ASCL1, ASGR2, ASNS, ASPDH, ASS1, ATF5, AURKA, BDH1, C19ORF80, CBG, CAD, CARD10, CCDC39, CCDC40, CDHR5, CEBPA, CEBPG, CFLAR, CITED2, CLEC4M, COBL, CSNK2A1, CSNK2A2, CSNK2B, CUX2, CX3CR1, CYP1A1, CYP26A1, CYP2A13, CYP2A4, CYP2A5, CYP2A6, CYP3A7, CYP4F13, CYP4F18, CYP4F3, DBP, DDHD2, DNAAF1, DNAJC25, DNMT3L, EGFR, ENTPD5, EPHX1, F2, F5, FABP1, FCN2, FOXA3, FPGS, FUOM, GLDC, GLS2, GLTPD2, GM6484, GNPNAT1, GPBAR1, GPLD1, H2-M3, H2-OA, HES1, HFE2, HLA-C, HLA-DOA, HLA-F, HLA-G, HLX, HMOX1, HNF1B, HNRNPD, IGF2R, IL1B, IL23A, IL6R, IL6RA, ITGA2, ITPA, JARID2, KHK, KNG2, LEAP2, LIPE, LOXL2, LPL, LSR, MAN2A1, MED1, MESP1, MST1, MTTP, MYC, NF1, NFKBIA, NPW, OSGIN1, PAQR9, PCNA, PCSK9, PFKL, PHKA2, PHKG2, PKD1, PKD2, PKM, PLK1, PNPLA1, PNPLA2, PNPLA3, PON3, PPARA, PPP1R3F, PRAP1, PRG4, PRKCE, PRKCSH, PROS1, PRPF31, PTPN1, PTPN3, RAP1A, RB1CC1, RBP4, REEP6, RELA, RIPPLY1, RNASE4, RND1, RPGRIP1L, RPL32, RTP3, RXRA, SAA2-SAA4, SAA4, SDS, SEC14L2, SEC63, SERAC1, SERPINA7, SERPINE1, SLC10A1, SLC13A5, SLC22A1, SLC22A7, SLC25A18, SLC28A1, SLC51A, SOD2, SP3, SRSF5, TAF10, TGFB1, THBS2, THPO, THRSP, TMEM82, TMPRSS6, TRIM55, UGT1A1, UGT1A10, UGT1A2, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A6A, UGT1A6B, UGT1A7, UGT1A8, UGT1A9, UPF2, VDR, WNT1, or ZIC3. 10. The method of claim 1, wherein the PRC2-binding RNA is transcribed from the same strand as the target gene in a genomic region containing the target gene. 11. The method 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. 12. The method 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 intron-exon junction or an intron. 13. The method 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 a translation initiation region or a translation termination region. 14. The method 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 a promoter. 15. The method 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 a 5′-UTR. 16. The method 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 a 3′-UTR. 17. The method of claim 1, 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. 18. The method of claim 1, 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. 19. The method 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. 20. The method of claim 1, wherein at least one nucleotide of the oligonucleotide is an RNA or DNA nucleotide. 21. The method 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. 22. The method of claim 21, wherein the ribonucleic acid analogue comprises a methylene bridge between the 2′-oxygen and the 4′-carbon. 23. The method of claim 1, wherein at least one nucleotide of the oligonucleotide comprises a modified sugar moiety. 24. The method of claim 23, 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. 25. The method of claim 1, wherein the oligonucleotide comprises at least one modified internucleoside linkage. 26. The method of claim 25, 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. 27. The method of claim 1, wherein the target gene is a gene of an autosomal chromosome. 28. The method of claim 1, wherein the cell is a cell of a male subject. 29. The method of claim 9, wherein the PRC2-binding RNA is transcribed from the same strand as the target gene in a genomic region containing the target gene. 30. The method of claim 9, 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. 31. The method of claim 9, 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. 32. The method of claim 9, 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. 33. The method of claim 9, 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. 34. The method of claim 9, 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. 35. The method of claim 9, wherein the oligonucleotide has complementarity to a region of the PRC2-binding RNA transcribed from a portion of the target gene corresponding to a 3′-UTR. 36. The method of claim 9, 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. 37. The method of claim 9, 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. 38. The method of claim 9, wherein the oligonucleotide has complementarity to the PRC2-binding RNA in a region of the PRC2-binding RNA that forms a stem-loop structure. 39. The method of claim 9, wherein at least one nucleotide of the oligonucleotide is an RNA or DNA nucleotide. 40. The method of claim 9, 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. 41. The method of claim 40, wherein the ribonucleic acid analogue comprises a methylene bridge between the 2′-oxygen and the 4′-carbon. 42. The method of claim 9, wherein at least one nucleotide of the oligonucleotide comprises a modified sugar moiety. 43. The method of claim 42, 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. 44. The method of claim 9, wherein the oligonucleotide comprises at least one modified internucleoside linkage. 45. The method of claim 44, 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.
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