Synthetic strategies to identify and regulate noncoding RNAs

Long Noncoding RNAs Structures and Functions

Volumn , Issue , 2015, Pages 23-43

  Pandian, Ganesh N ^a   Syed, Junetha ^a   Sugiyama, Hiroshi ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

Chemical Probes; Dna Based Small Molecules; Formation; Gene Expression; Noncoding Rnas; Profiling; Rna Therapeutics; Synthetic Strategies; Triple Helix

Indexed keywords

BINDING SITES; CONSERVATION; GENE EXPRESSION; MACHINE DESIGN; MACHINERY; MAMMALS; RNA;

CHEMICAL PROBES; FORMATION; NON-CODING RNAS; PROFILING; RNA THERAPEUTICS; SMALL MOLECULES; SYNTHETIC STRATEGIES; TRIPLE HELIXES;

NUCLEIC ACIDS;

EID: 84943259091     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-4-431-55576-6_2     Document Type: Chapter

References (103)

1. Agazie YM, Lee JS, Burkholder GD (1994) Characterization of a new monoclonal antibody to triplex DNA and immunofluorescent staining of mammalian chromosomes. J Biol Chem 269:7019–7023
2. Arambula JF, Ramisetty SR, Baranger AM, Zimmerman SC (2009) A simple ligand that selectivel y targets CUG trinucleotide repeats and inhibits MBNL protein binding. Proc Natl Acad Sci U S A 106:16068–16073
3. Barry G, Briggs JA, Vanichkina DP, Poth EM, Beveridge NJ, Ratnu VS, Nayler SP, Nones K, Hu J, Bredy TW, Nakagawa S, Rigof, Taft RJ, Cairns MJ, Blackshaw S, Wolvetang EJ, Mattick JS (2014) The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing. Mol Psychiatry 19:486–494
4. Batista PJ, Chang HY (2013) Long noncoding RNAs: cellular address codes in development and disease. Cell 152:1298–1307
5. Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, Yusupova G, Yusupov M (2011) The structure of the eukaryotic ribosome at 3.0 a resolution. Science 334:1524–1529
6. Bernhart SH, Hofacker IL, Will S, Gruber AR, Stadler PF (2008) RNAalifold: improved consensu s structure prediction for RNA alignments. BMC Bioinforma 9:474
7. Birney E (2012) An integrated encyclopedia of DNA elements in human genome. Nature 489:57–74
8. Bischoff G, Hoffmann S (2002) DNA-binding of drugs used in medicinal therapies. Curr Med Chem 9:312–348
9. Bittencourt D, Auboeuf D (2012) Analysis of co-transcriptional RNA processing by RNA-ChIP assay. Methods Mol Biol 809:563–577
10. Bose D, Jayaraj G, Suryawanshi H, Agarwala P, Pore SK, Banerjee R, Maiti S (2012) The tuberculosis drug Streptomycin as a potential cancer therapeutic: inhibition of miR-21 function by directly targeting its precursor. Angew Chem Int Ed 51:1019–1023
11. Burkholder GD, Latimer LJ, Lee JS (1991) Immunofluorescent localization of triplex DNA in polytene chromosomes of Chironomus and Drosophila. Chromosoma 101:11–18
12. Buske FA, Mattick JS, Bailey TL (2011) Potential in vivo roles of nucleic acid triple-helices. RNA Biol 8:427–439
13. Cabianca DS, Gabellini D (2010) The cell biology of disease: FSHD: copy number variations on the theme of muscular dystrophy. J Cell Biol 191:1049–1060
14. Cabianca DS, Casa V, Bodega B, Xynos A, Ginelli E, Tanaka Y, Gabellini D (2012) A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in fshd muscular dystrophy. Cell 149:819–831
15. Cesana M, Cacchiarelli D, Legnini I, Santini T, Sthandier O, Chinappi M, Tramontano A, Bozzon i I (2011) A long noncoding RNA controls muscle differentiation by functioning as a competin g endogenous RNA. Cell 147:358–369
16. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ (2005) Real-time quantification of microRNA s by stem-loop RT-PCR. Nucleic Acids Res 33:e179
17. Chenoweth DM, Meier JL, Dervan PB (2013) Pyrrole-imidazole polyamides distinguish between double-helical DNA and RNA. Angew Chem Int Ed 52:415–418
18. Childs-Disney JL, Hoskins J, Rzuczek SG, Thornton C, Disney MD (2012) Rationally designed small molecules targeting the RNA that causes myotonic dystrophy type 1 are potently bioactive. ACS Chem Biol 7(5):856–862
19. Childs-Disney JL, Yildrim I, Park H, Lohman JR, Guan L, Tran T, Sarkar P, Schatz GC, Disney MD (2014) Structure of the myotonic dystrophy type 2 RNA and designed small molecules that reduce toxicity. ACS Chem Biol 9(2):538–550
20. Czerwoniec A, Dunin-Horkawicz S, Purta E, Kaminska KH, Kasprzak JM, Bujnicki JM, Grosjean H, Rother K (2009) MODOMICS: a database of RNA modification pathways. 2008 update. Nucleic Acids Res 37:D118–D121
21. Deigan KE, Li TW, Mathews DH, Weeks KM (2009) Accurate SHAPE-directed RNA structure determination. Proc Natl Acad Sci U S A 106:97–102
22. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame R, Harrow J, Guigo R (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22:1775–1789
23. Dervan PB (2001) Molecular recognition of DNA by small molecules. Bioorg Med Chem 9:2215–2235
24. Disney MD, Yildirim I, Childs-Disney JL (2014) Methods to enable the design of bioactive small molecules targeting RNA. Org Biomol Chem 12:1029–1039
25. Du Y, Kong G, You X, Zhang S, Zhang T, Gao Y, Ye L, Zhang X (2012) Elevation of highly upregulated in liver cancer (HULC) by hepatitis B virus X protein promotes hepatoma cell proliferation via down-regulating p18. J Biol Chem 287:26302–26311
26. Duca M, Vekhoff P, Oussedik K, Halby L, Arimondo PB (2008) The triple helix: 50 years later, the outcome. Nucleic Acids Res 36:5123–5138
27. Fedor MJ, Williamson JR (2005) The catalytic diversity of RNAs. Nat Rev Mol Cell Biol 6:399–412
28. Gabellini D, Green MR, Tupler R (2002) Inappropriate gene activation in FSHD: a repressor complex binds a chromosomal repeat deleted in dystrophic muscle. Cell 110:339–348
29. Geisler S, Coller J (2013) RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts. Nat Rev Mol Cell Biol 14:699–712
30. Goñi JR, de la Cruz X, Orozco M (2004) Triplex-formingoligonucleotide target sequences in the human genome. Nucleic Acids Res 32:354–360
31. Grote P, Wittler L, Hendrix D, Koch F, Währisch S, Beisaw A, Macura K, Bläss G, Kellis M, Werber M, Herrmann BG (2013) The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. Dev Cell 24:206–214
32. Guan L, Disney MD (2012) Recent advances in developing small molecules targeting RNA. ACS Chem Biol 7:73–86
33. Guan L, Disney MD (2013) Covalent small molecule-RNA complex formation enables cellular profiling of small molecule-RNA interactions. Angew Chem Int Ed 52:10010–10013
34. Gumireddy K, Young DD, Xiong X, Hogenesch JB, Huang Q, Deiters A (2008) Small-molecule inhibitors of microRNA miR-21 function. Angew Chem Int Ed 47:7482–7484
35. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai M-C, Hung T, Argani P, Rin JL, Wang Y, Brzoska P, Kong B, Li R, West RB, vande Vijver MJ, Sukumar S, Chang HY (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464:1071–1076
36. Han L, Pandian GN, Junetha S, Sato S, Anandhakumar C, Taniguchi J, Saha A, Bando T, Nagase H, Sugiyama H (2013) A synthetic small molecule for targeted transcriptional activation of germ cell genes in a human somatic cell. Angew Chem Int Ed 52:13410–13413
37. Hauptman N, Glavac D (2013) Long non-coding RNA in cancer. Int J Mol Sci 14(3):4655–4669
38. Hermann T, Patel DJ (2000) RNA bulges as architectural and recognition motifs. Structure 8:R47–R54
39. Heward JA, Lindsay MA (2014) Long non-coding RNAs in the regulation of the immune response. Trends Immunol 35:408–419
40. Hoskins JW, Ofori LO, Chen CZ, Kumar A, Sobczak K, Nakamori M, Southall N, Patnaik S, Marugan JJ, Zheng W, Austin CP, Disney MD, Miller BL, Thornton CA (2014) Lomofungin and dilomofungin: inhibitors of MBNL1-CUG RNA binding with distinct cellular effects. Nucleic Acids Res. doi: 10.1093/nar/gku275
41. Iguchi A, Fukuda N, Takahashi T, Watanabe T, Matsuda H, Nagase H, Bando T, Sugiyama H, Shimizu K (2013) RNA binding properties of novel gene silencing pyrrole-imidazole polyamides. Biol Pharm Bull 36:1152–1158
42. Kanak M, Alseiari M, Balasubramanian P, Addanki K, Aggarwal M, Noorali S, Kalsum A, Mahalingam K, Pace G, Panasik N, Bagasra O (2010) Triplex-forming MicroRNAs form stable complexes with HIV-1 provirus and inhibit its replication. Appl Immunohistochem Mol Morphol 18:532–545
43. Khalil AM, Faghihi MA, Modarresi F, Brothers SP, Wahlestedt C (2008) A novel RNA transcript with antiapoptotic function is silenced in fragile X syndrome. PLoS One 3:e1486
44. Kilburn D, Roh JH, Guo L, Briber RM, Woodson SA (2010) Molecular crowding stabilizes folded RNA structure by the excluded volume effect. J Am Chem Soc 132:8690–8696
45. Kladwang W, Mann TH, Becka A, Tian S, Kim H, Yoon S, Das R (2014) Standardization of RNA chemical mapping experiments. Biochemistry 53:3063–3065
46. Klattenhoff CA, Scheuermann JC, Surface LE, Bradley RK, Fields PA, Steinhauser ML, Ding H, Butty VL, Torrey L, Haas S, Abo R, Tabebordbar M, Lee RT, Burge CB, Boyer LA (2013) Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell 152:570–583
47. Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K, Lee CS, Flockhart RJ, Groff AF, Chow J, Johnston D, Kim GE, Spitale RC, Flynn RA, Zheng GXY, Aiyer S, Raj R, Rinn JL, Howard Y, Chang HY, Paul A, Khavari PA (2013) Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature 493:231–235
48. Lee MM, Pushechnikov A, Disney MD (2009) Rational and modular design of potent ligand s targeting the RNA that causes myotonic muscular dystrophy 2. ACS Chem Biol 4:345–355
49. Lubitz I, Zikich D, Kotlyar A (2010) Specific high-affinity binding of thiazole orange to triplex and g-quadruplex DNA. Biochemistry 49:3567–3574
50. Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP (2011) Multiplexed RNA structure characterization with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-seq). Proc Natl Acad Sci U S A 108:11063–11068
51. Maass PG, Rump A, Schulz H, Stricker S, Schulze L, Platzer K, Aydin A, Tinschert S, Goldring MB, Luft FC, Bahring S (2012) A misplaced lncRNA causes brachydactyly in humans. J Clin Invest 122:3990–4002
52. Maass PG, Luft FC, Bahring S (2014) Long non-coding RNA in health and disease. J Mol Med 92:337–346
53. Martianov I, Ramadass A, Serra Barros A, Chow N, Akoulitchev A (2007) Repression of the humandihydrofolate reductase gene by a non-coding interfering transcript. Nature 445:666–670
54. McGinnis JL, Dunkle JA, Cate JH, Weeks KM (2012) The mechanisms of RNA SHAPE chemistry. J Am Chem Soc 134:6617–6624
55. Meyer ST, Hergenrother PJ (2009) Small molecule ligands for bulged RNA secondary structures. Org Lett 11:4052–4055
56. Modarresi F, Faghihi MA, Lopez-Toledano MA, Fatemi RP, Magistri M, Brothers SP, Brug MP, Wahlestedt C (2012) Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation. Nat Biotechnol 30:453–459
57. Morgan AR, Wells RD (1968) Specificity of the three-stranded complex formation between double- stranded DNA and single-stranded RNA containing repeating nucleotide sequences. J Mol Biol 37:63–80
58. Mustoe AM, Brooks CL, Al-Hashimi HM (2014) Hierarchy of RNA functional dynamics. Annu Rev Biochem 83:441–466
59. Ng S-Y, Lin L, Soh BS, Stanton LW (2013) Long noncoding RNAs in development and disease of the central nervous system. Trends Genet 29:461–468
60. Novikova IV, Hennelly SP, Sanbonmatsu KY (2012) Structural architecture of the human long non-coding RNA, steroid receptor RNA activator. Nucleic Acids Res 40:5034–5051
61. Novikova IV, Hennelly SP, Sanbonmatsu KY (2013) Tackling structures of long noncoding RNAs. Int J Mol Sci 14:23672–23684
62. Ofori LO, Hoskins J, Nakamori M, Thornton CA, Miller BL (2012) From dynamic combinatorial ‘hit’ to lead: in vitro and in vivo activity of compounds targeting the pathogenic RNAs that cause myotonic dystrophy. Nucleic Acids Res 40:6380–6390
63. Orkin SH, Hochedlinger K (2011) Chromatin connections to pluripotency and cellular reprogramming. Cell 145:835–850
64. Ouyang Z, Snyder MP, Chang HY (2013) Seqfold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data. Genome Res 23:377–387
65. Pan T, Sosnick T (2006) RNA folding during transcription. Annu Rev Biophys Biomol Struct 35:161–175
66. Pandian GN, Sugiyama H (2012) Programmable genetic switches to control transcriptional machinery of pluripotency. Biotechnol J 7(6):798–809
67. Pandian GN, Sugiyama H (2013) Strategies to modulate heritable epigenetic defects in cellular machinery: lessons from nature. Pharmaceuticals 6(1):1–24
68. Pandian GN, Nakano Y, Sato S, Morinaga H, Bando T, Nagase H, Sugiyama H (2012) A synthetic small molecule for rapid induction of multiple pluripotency genes in mouse embryonic fibroblasts. Sci Rep 2:544
69. Pandian GN, Taniguchi J, Junetha S, Sato S, Han L, Anandhakumar C, Bando T, Nagase H, Vaijayanthi T, Taylor RD, Sugiyama H (2014a) Distinct DNA-based epigenetic switches trigger transcriptional activation of silent genes in humandermal fibroblasts. Sci Rep 4:3843
70. Pandian GN, Taylor RD, Junetha S, Saha A, Anandhakumar C, Vaijayanthi T, Sugiyama H (2014b) Alteration of epigenetic program to recover memory and alleviate neurodegeneration: prospects of multi-target molecules. Biomater Sci 2:1043–1056
71. Pandian GN, Sato S, Anandhakumar C, Taniguchi J, Takashima K, Syed J, Han L, Saha A, Band o T, Nagase H, Sugiyama H (2014c) Identification of a small molecule that turns ‘ON’ the pluripotency gene circuitry in human fibroblasts. ACS Chem Biol 9:2729–2736
72. Pang KC, Frith MC, Mattick JS (2006) Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends Genet 22:1–5
73. Prensner JR, Iyer MK, Balbin OA, Dhanasekaran SM, Cao Q, Brenner JC, Laxman B, Asangani IA, Grasso CS, Kominsky HD, Cao X, Jing X, Wang X, Siddiqui J, Wei JT, Robinson D, Iyer HK, Palanisamy N, Maher CA, Chinnaiyan AM (2011) Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol 29:742–749
74. Prensner JR, Iyer MK, Sahu A, Asangani IA, Cao Q, Patel L, Vergara IA, Davicioni E, Erho N, Ghadessi M, Jenkins RB, Triche TJ, Malik R, Bedenis R, McGregor N, Ma T, Chen W, Han S, Jing X, Cao X, Wang X, Chandler B, Yan J, Siddiqui J, Kunju LP, Dhanasekaran SM, Pienta KJ, Feng FY, Chinnaiyan AM (2013) The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex. Nat Genet 45:1392–1398
75. Quagliata L, Matter MS, Piscuoglio S, Arabi L, Ruiz C, Procino A, Kovac M, Moretti F, Makowsk a Z, Boldanova T, Anderson JB, Hammerie M, Tornillo L, Heim MH, Diedericha S, Cillo C, Terracciano L (2013) Long noncoding RNA HOTTIP/HOXA13 expression is associated with disease progression and predicts outcome in hepatocellular carcinoma patients. Hepatology. doi: 10.1002/hep.26740
76. Rask-Andersen M, Almen MS, Schioth HB (2011) Trends in the exploitation of novel drug targets. Nat Rev Drug Discov 10:579–590
77. Reuter JS, Mathews DH (2010) RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinforma 11:129
78. Saha A, Pandian GN, Sato S, Taniguchi J, Hashiya K, Bando T, Sugiyama H (2013) Synthesis and biological evaluation of a targeted DNA-binding transcriptional activator with HDAC8 inhibitory activity. Bioorg Med Chem 21(14):4201–4209
79. Schmidt LH, Spieker T, Koschmieder S, Humberg J, Jungen D, Bulk E, Hascher A, Wittmer D, Marra A, Hillejan L, Wiebe K, Berdel WE, Wiewrodt R, Müller-Tidow C (2011) The long noncoding MALAT-1 RNA indicates a poor prognosis in non-small cell lung cancer and induces migration and tumor growth. J Thorac Oncol 6:1984–1992
80. Schmitz KM, Mayer C, Postepska A, Grummt I (2010) Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes. Genes Dev 24:2264–2269
81. Shappell SB (2008) Clinical utility of prostate carcinoma molecular diagnostic tests. Rev Urol 10:44–69
82. Spitale RC, Crisalli P, Flynn RA, Torre EA, Kool ET, Chang HY (2013) RNA shape analysis in living cells. Nat Chem Biol 9:18–20
83. Stelzer AC, Frank AT, Kratz JD, Swanson MD, Gonzalez-Hernandez MJ, Lee J, Andricioaei I, Markovitz DM, Al-Hashimi HM (2011) Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble. Nat Chem Biol 7(8):553–559
84. Syed J, Pandian GN, Sato S, Taniguchi J, Chandran A, Hashiya K, Bando T, Sugiyama H (2014) Targeted suppression of EVI1 oncogene expression by sequence-specific pyrrole-imidazole polyamide. Chem Biol. doi: 10.1016/j.chembiol.2014.07.019
85. Takahashi K, Yan I, Haga H, Patel T (2014) Long noncoding RNA in Liver diseases. Hepatology 60:744–753
86. Takayama K, Horie-Inoue K, Katayama S, Suzuki T, Tsutsumi S, Ikeda K, Urano T, Fujimura T, Takagi K, Takahashi S, Homma Y, Ouchi Y, Aburatani H, Hayashizaki Y, Inoue S (2013) Androgen-responsive long noncoding RNA CTBP1-AS promotes prostate cancer. EMBO J 32:1665–1680
87. Ulitsky I, Shkumatava A, Jan CH, Sive H, Bartel DP (2011) Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell 147:1537–1550
88. Underwood JG, Uzilov AV, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR, Haussler D (2010) FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods 7(12):995–1001
89. Vaijayanthi T, Bando T, Hashiya K, Pandian GN, Sugiyama H (2013) Design of a new fluorescent probe: pyrrole/imidazole hairpin polyamides with pyrene conjugation at their γ-turn. Bioorg Med Chem 21:852–855
90. Vandijk M, Thulluru HK, Oudejans CBM (2012) HELLP babies link a novel lincRNA to the trophoblast cell cycle. J Clin Invest 122:4003–4011
91. Velagapudi SP, Gallo SM, Disney MD (2014) Sequence-based design of bioactive small molecule s that target precursor microRNAs. Nat Chem Biol 10:291–297
92. Wang KC, Chang HY (2011) Molecular mechanisms of long noncoding RNAs. Mol Cell 43(6):904–914
93. Washietl S, Kellis M, Garber M (2014) Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals. Genome Res 24:616–628
94. Weeks KM (2010) Advances in RNA structure analysis by chemical probing. Curr Opin Struct Biol 20:295–304
95. Wells SE, Hughes JM, Igel AH, Ares M Jr (2000) Use of dimethyl sulfate to probe RNA structure in vivo. Methods Enzymol 318:479–493
96. Wheeler TM, Leger AJ, Pandey SK, Macleod AR, Nakamori M, Cheng SH, Wentworth BM, Bennett CF, Thornton CA (2012) Targeting nuclear RNA for in vivo correction of myotonic dystrophy. Nature 488:111–115
97. Wilkinson KA, Merino EJ, Weeks KM (2006) Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat Protoc 1:1610–1616
98. Wilusz JE, JnBaptiste CK, Lu LY, Kuhn CD, Joshua-Tor L, Sharp PA (2012) A triple helix stabilizes the 3′ ends of long noncoding RNAs that lack poly(A) tails. Genes Dev 26:2392–2407
99. Wong TN, Sosnick TR, Pan T (2007) Folding of noncoding RNAs during transcription facilitated by pausing-induced nonnative structures. Proc Natl Acad Sci U S A 104:17995–18000
100. Yang L, Duff MO, Graveley BR, Carmichael GG, Chen LL (2011) Genome wide characterization of non-polyadenylated RNAs. Genome Biol 12:R16
101. Yildirim E, Kirby JE, Brown DE, Mercier FE, Sadreyev RI, Scadden DT, Lee JT (2013) Xist RNA is a potent suppressor of hematologic cancer in mice. Cell 152:727–742
102. Zengeya T, Li M, Rozners E (2011) PNA containing isocytidine nucleobase: synthesis and recognition of double helical RNA. Bioorg Med Chem Lett 21:2121–2124
103. Zhao J, Ohsumi TK, Kung JT, Ogawa Y, Grau DJ, Sarma K, Song JJ, Kingston RE, Borowsky M, Lee JT (2010) Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol Cell 40:939–953