Interplay of chromatin modifications and non-coding RNAs in the heart

References

• Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, Ding H, Wylie JN, Pico AR, Capra JA, et al. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell 2012; 151:206 - 20; http://dx.doi.org/10.1016/j.cell.2012.07.035; PMID: 22981692
   PubMed Web of Science ®Google Scholar
• Strahl BD, Allis CD. The language of covalent histone modifications. Nature 2000; 403:41 - 5; http://dx.doi.org/10.1038/47412; PMID: 10638745
   PubMed Web of Science ®Google Scholar
• Paige SL, Thomas S, Stoick-Cooper CL, Wang H, Maves L, Sandstrom R, Pabon L, Reinecke H, Pratt G, Keller G, et al. A temporal chromatin signature in human embryonic stem cells identifies regulators of cardiac development. Cell 2012; 151:221 - 32; http://dx.doi.org/10.1016/j.cell.2012.08.027; PMID: 22981225
   PubMed Web of Science ®Google Scholar
• Bernardo BC, Weeks KL, Pretorius L, McMullen JR. Molecular distinction between physiological and pathological cardiac hypertrophy: experimental findings and therapeutic strategies. Pharmacol Ther 2010; 128:191 - 227; http://dx.doi.org/10.1016/j.pharmthera.2010.04.005; PMID: 20438756
   PubMed Web of Science ®Google Scholar
• Kehat I, Molkentin JD. Molecular pathways underlying cardiac remodeling during pathophysiological stimulation. Circulation 2010; 122:2727 - 35; http://dx.doi.org/10.1161/CIRCULATIONAHA.110.942268; PMID: 21173361
   PubMed Web of Science ®Google Scholar
• Frey N, Olson EN. Cardiac hypertrophy: the good, the bad, and the ugly. Annu Rev Physiol 2003; 65:45 - 79; http://dx.doi.org/10.1146/annurev.physiol.65.092101.142243; PMID: 12524460
   PubMed Web of Science ®Google Scholar
• Chang L, Kiriazis H, Gao XM, Du XJ, El-Osta A. Cardiac genes show contextual SWI/SNF interactions with distinguishable gene activities. Epigenetics 2011; 6:760 - 8; http://dx.doi.org/10.4161/epi.6.6.16007; PMID: 21586902
   PubMed Web of Science ®Google Scholar
• Backs J, Olson EN. Control of cardiac growth by histone acetylation/deacetylation. Circ Res 2006; 98:15 - 24; http://dx.doi.org/10.1161/01.RES.0000197782.21444.8f; PMID: 16397154
   PubMed Web of Science ®Google Scholar
• Mathiyalagan P, Chang L, Du XJ, El-Osta A. Cardiac ventricular chambers are epigenetically distinguishable. Cell Cycle 2010; 9:612 - 7; http://dx.doi.org/10.4161/cc.9.3.10612; PMID: 20090419
   PubMed Web of Science ®Google Scholar
• Delgado-Olguín P, Huang Y, Li X, Christodoulou D, Seidman CE, Seidman JG, Tarakhovsky A, Bruneau BG. Epigenetic repression of cardiac progenitor gene expression by Ezh2 is required for postnatal cardiac homeostasis. Nat Genet 2012; 44:343 - 7; http://dx.doi.org/10.1038/ng.1068; PMID: 22267199
   PubMed Web of Science ®Google Scholar
• Lai HL, Grachoff M, McGinley AL, Khan FF, Warren CM, Chowdhury SA, Wolska BM, Solaro RJ, Geenen DL, Wang QT. Maintenance of adult cardiac function requires the chromatin factor Asxl2. J Mol Cell Cardiol 2012; 53:734 - 41; http://dx.doi.org/10.1016/j.yjmcc.2012.08.014; PMID: 23046516
   PubMed Web of Science ®Google Scholar
• Han P, Hang CT, Yang J, Chang CP. Chromatin remodeling in cardiovascular development and physiology. Circ Res 2011; 108:378 - 96; http://dx.doi.org/10.1161/CIRCRESAHA.110.224287; PMID: 21293009
   PubMed Web of Science ®Google Scholar
• Takeuchi JK, Lou X, Alexander JM, Sugizaki H, Delgado-Olguín P, Holloway AK, Mori AD, Wylie JN, Munson C, Zhu Y, et al. Chromatin remodelling complex dosage modulates transcription factor function in heart development. Nat Commun 2011; 2:187; http://dx.doi.org/10.1038/ncomms1187; PMID: 21304516
   PubMed Web of Science ®Google Scholar
• Schonrock N, Harvey RP, Mattick JS. Long noncoding RNAs in cardiac development and pathophysiology. Circ Res 2012; 111:1349 - 62; http://dx.doi.org/10.1161/CIRCRESAHA.112.268953; PMID: 23104877
   PubMed Web of Science ®Google Scholar
• Luther HP. Role of endogenous antisense RNA in cardiac gene regulation. J Mol Med (Berl) 2005; 83:26 - 32; http://dx.doi.org/10.1007/s00109-004-0613-5; PMID: 15592803
   PubMed Web of Science ®Google Scholar
• Klattenhoff CA, Scheuermann JC, Surface LE, Bradley RK, Fields PA, Steinhauser ML, Ding H, Butty VL, Torrey L, Haas S, et al. Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell 2013; 152:570 - 83; http://dx.doi.org/10.1016/j.cell.2013.01.003; PMID: 23352431
   PubMed Web of Science ®Google Scholar
• Grote P, Wittler L, Hendrix D, Koch F, Währisch S, Beisaw A, Macura K, Bläss G, Kellis M, Werber M, et al. The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. Dev Cell 2013; 24:206 - 14; http://dx.doi.org/10.1016/j.devcel.2012.12.012; PMID: 23369715
   PubMed Web of Science ®Google Scholar
• Mattick JS. RNA as the substrate for epigenome-environment interactions: RNA guidance of epigenetic processes and the expansion of RNA editing in animals underpins development, phenotypic plasticity, learning, and cognition. Bioessays 2010; 32:548 - 52; http://dx.doi.org/10.1002/bies.201000028; PMID: 20544741
   PubMed Web of Science ®Google Scholar
• Mercer TR, Dinger ME, Mattick JS. Long non-coding RNAs: insights into functions. Nat Rev Genet 2009; 10:155 - 9; http://dx.doi.org/10.1038/nrg2521; PMID: 19188922
   PubMed Web of Science ®Google Scholar
• Mercer TR, Mattick JS. Structure and function of long noncoding RNAs in epigenetic regulation. Nat Struct Mol Biol 2013; 20:300 - 7; http://dx.doi.org/10.1038/nsmb.2480; PMID: 23463315
   PubMed Web of Science ®Google Scholar
• Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, Ponting CP, Stadler PF, Morris KV, Morillon A, et al. The reality of pervasive transcription. PLoS Biol 2011; 9:e1000625 - , discussion e1001102; http://dx.doi.org/10.1371/journal.pbio.1000625; PMID: 21765801
   PubMed Web of Science ®Google Scholar
• Jacob F, Monod J. Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 1961; 3:318 - 356
   PubMed Web of Science ®Google Scholar
• Belotserkovskii BP, De Silva E, Tornaletti S, Wang G, Vasquez KM, Hanawalt PC. A triplex-forming sequence from the human c-MYC promoter interferes with DNA transcription. J Biol Chem 2007; 282:32433 - 32441
   PubMed Web of Science ®Google Scholar
• Schmitz KM, Mayer C, Postepska A, Grummt I. Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes. Genes Dev 2010; 24:2264 - 2269
   PubMed Web of Science ®Google Scholar
• Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993; 75:843 - 54; http://dx.doi.org/10.1016/0092-8674(93)90529-Y; PMID: 8252621
   PubMed Web of Science ®Google Scholar
• Wightman B, Ha I, Ruvkun G. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 1993; 75:855 - 62; http://dx.doi.org/10.1016/0092-8674(93)90530-4; PMID: 8252622
   PubMed Web of Science ®Google Scholar
• Chen JF, Murchison EP, Tang R, Callis TE, Tatsuguchi M, Deng Z, Rojas M, Hammond SM, Schneider MD, Selzman CH, et al. Targeted deletion of Dicer in the heart leads to dilated cardiomyopathy and heart failure. Proc Natl Acad Sci U S A 2008; 105:2111 - 6; http://dx.doi.org/10.1073/pnas.0710228105; PMID: 18256189
   PubMed Web of Science ®Google Scholar
• Schlesinger J, Schueler M, Grunert M, Fischer JJ, Zhang Q, Krueger T, Lange M, Tönjes M, Dunkel I, Sperling SR. The cardiac transcription network modulated by Gata4, Mef2a, Nkx2.5, Srf, histone modifications, and microRNAs. PLoS Genet 2011; 7:e1001313; http://dx.doi.org/10.1371/journal.pgen.1001313; PMID: 21379568
   PubMedGoogle Scholar
• Zhao Y, Ransom JF, Li A, Vedantham V, von Drehle M, Muth AN, Tsuchihashi T, McManus MT, Schwartz RJ, Srivastava D. Dysregulation of cardiogenesis, cardiac conduction, and cell cycle in mice lacking miRNA-1-2. Cell 2007; 129:303 - 17; http://dx.doi.org/10.1016/j.cell.2007.03.030; PMID: 17397913
   PubMed Web of Science ®Google Scholar
• van Rooij E, Sutherland LB, Qi X, Richardson JA, Hill J, Olson EN. Control of stress-dependent cardiac growth and gene expression by a microRNA. Science 2007; 316:575 - 9; http://dx.doi.org/10.1126/science.1139089; PMID: 17379774
   PubMed Web of Science ®Google Scholar
• Dinger ME, Amaral PP, Mercer TR, Pang KC, Bruce SJ, Gardiner BB, Askarian-Amiri ME, Ru K, Soldà G, Simons C, et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 2008; 18:1433 - 45; http://dx.doi.org/10.1101/gr.078378.108; PMID: 18562676
   PubMed Web of Science ®Google Scholar
• Tani H, Mizutani R, Salam KA, Tano K, Ijiri K, Wakamatsu A, Isogai T, Suzuki Y, Akimitsu N. Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals. Genome Res 2012; 22:947 - 56; http://dx.doi.org/10.1101/gr.130559.111; PMID: 22369889
   PubMed Web of Science ®Google Scholar
• Kaneko S, Li G, Son J, Xu CF, Margueron R, Neubert TA, Reinberg D. Phosphorylation of the PRC2 component Ezh2 is cell cycle-regulated and up-regulates its binding to ncRNA. Genes Dev 2010; 24:2615 - 20; http://dx.doi.org/10.1101/gad.1983810; PMID: 21123648
   PubMed Web of Science ®Google Scholar
• Han Y, Liu Y, Gui Y, Cai Z. Long intergenic non-coding RNA TUG1 is overexpressed in urothelial carcinoma of the bladder. J Surg Oncol 2013; 107:555 - 9; http://dx.doi.org/10.1002/jso.23264; PMID: 22961206
   PubMed Web of Science ®Google Scholar
• Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A 2009; 106:11667 - 72; http://dx.doi.org/10.1073/pnas.0904715106; PMID: 19571010
   PubMed Web of Science ®Google Scholar
• Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, Young G, Lucas AB, Ach R, Bruhn L, et al. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature 2011; 477:295 - 300; http://dx.doi.org/10.1038/nature10398; PMID: 21874018
   PubMed Web of Science ®Google Scholar
• Schmidt LH, Spieker T, Koschmieder S, Schäffers S, Humberg J, Jungen D, Bulk E, Hascher A, Wittmer D, Marra A, et al. The long noncoding MALAT-1 RNA indicates a poor prognosis in non-small cell lung cancer and induces migration and tumor growth. [RNA indicates a poor prognosis in non-small cell lung cancer and induces migration and tumor growth.] J Thorac Oncol 2011; 6:1984 - 92; http://dx.doi.org/10.1097/JTO.0b013e3182307eac; PMID: 22088988
   PubMed Web of Science ®Google Scholar
• Hu W, Yuan B, Flygare J, Lodish HF. Long noncoding RNA-mediated anti-apoptotic activity in murine erythroid terminal differentiation. Genes Dev 2011; 25:2573 - 8; http://dx.doi.org/10.1101/gad.178780.111; PMID: 22155924
   PubMed Web of Science ®Google Scholar
• Faghihi MA, Modarresi F, Khalil AM, Wood DE, Sahagan BG, Morgan TE, Finch CE, St Laurent G 3rd, Kenny PJ, Wahlestedt C. Expression of a noncoding RNA is elevated in Alzheimer’s disease and drives rapid feed-forward regulation of beta-secretase. Nat Med 2008; 14:723 - 30; http://dx.doi.org/10.1038/nm1784; PMID: 18587408
   PubMed Web of Science ®Google Scholar
• Chung DW, Rudnicki DD, Yu L, Margolis RL. A natural antisense transcript at the Huntington’s disease repeat locus regulates HTT expression. Hum Mol Genet 2011; 20:3467 - 77; http://dx.doi.org/10.1093/hmg/ddr263; PMID: 21672921
   PubMed Web of Science ®Google Scholar
• Rinn JL, Chang HY. Genome regulation by long noncoding RNAs. Annu Rev Biochem 2012; 81:145 - 66; http://dx.doi.org/10.1146/annurev-biochem-051410-092902; PMID: 22663078
   PubMed Web of Science ®Google Scholar
• Margueron R, Reinberg D. The Polycomb complex PRC2 and its mark in life. Nature 2011; 469:343 - 9; http://dx.doi.org/10.1038/nature09784; PMID: 21248841
   PubMed Web of Science ®Google Scholar
• Kanhere A, Jenner RG. Noncoding RNA localisation mechanisms in chromatin regulation. Silence 2012; 3:2; http://dx.doi.org/10.1186/1758-907X-3-2; PMID: 22292981
   PubMedGoogle Scholar
• Benetatos L, Voulgaris E, Vartholomatos G, Hatzimichael E. Non-coding RNAs and EZH2 interactions in cancer: long and short tales from the transcriptome. Int J Cancer 2013; 133:267 - 74; http://dx.doi.org/10.1002/ijc.27859; PMID: 23001607
   PubMed Web of Science ®Google Scholar
• Nagano T, Mitchell JA, Sanz LA, Pauler FM, Ferguson-Smith AC, Feil R, Fraser P. The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 2008; 322:1717 - 20; http://dx.doi.org/10.1126/science.1163802; PMID: 18988810
   PubMed Web of Science ®Google Scholar
• Pagans S, Kauder SE, Kaehlcke K, Sakane N, Schroeder S, Dormeyer W, Trievel RC, Verdin E, Schnolzer M, Ott M. The Cellular lysine methyltransferase Set7/9-KMT7 binds HIV-1 TAR RNA, monomethylates the viral transactivator Tat, and enhances HIV transcription. Cell Host Microbe 2010; 7:234 - 44; http://dx.doi.org/10.1016/j.chom.2010.02.005; PMID: 20227666
   PubMed Web of Science ®Google Scholar
• Krajewski WA, Nakamura T, Mazo A, Canaani E. A motif within SET-domain proteins binds single-stranded nucleic acids and transcribed and supercoiled DNAs and can interfere with assembly of nucleosomes. Mol Cell Biol 2005; 25:1891 - 9; http://dx.doi.org/10.1128/MCB.25.5.1891-1899.2005; PMID: 15713643
   PubMed Web of Science ®Google Scholar
• Xu S, Wu J, Sun B, Zhong C, Ding J. Structural and biochemical studies of human lysine methyltransferase Smyd3 reveal the important functional roles of its post-SET and TPR domains and the regulation of its activity by DNA binding. Nucleic Acids Res 2011; 39:4438 - 49; http://dx.doi.org/10.1093/nar/gkr019; PMID: 21266482
   PubMed Web of Science ®Google Scholar
• Ruthenburg AJ, Allis CD, Wysocka J. Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Mol Cell 2007; 25:15 - 30; http://dx.doi.org/10.1016/j.molcel.2006.12.014; PMID: 17218268
   PubMed Web of Science ®Google Scholar
• Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA, et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 2011; 472:120 - 4; http://dx.doi.org/10.1038/nature09819; PMID: 21423168
   PubMed Web of Science ®Google Scholar
• Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY. Long noncoding RNA as modular scaffold of histone modification complexes. Science 2010; 329:689 - 93; http://dx.doi.org/10.1126/science.1192002; PMID: 20616235
   PubMed Web of Science ®Google Scholar
• He A, Ma Q, Cao J, von Gise A, Zhou P, Xie H, Zhang B, Hsing M, Christodoulou DC, Cahan P, et al. Polycomb repressive complex 2 regulates normal development of the mouse heart. Circ Res 2012; 110:406 - 15; http://dx.doi.org/10.1161/CIRCRESAHA.111.252205; PMID: 22158708
   PubMed Web of Science ®Google Scholar
• Kotake Y, Nakagawa T, Kitagawa K, Suzuki S, Liu N, Kitagawa M, Xiong Y. Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15(INK4B) tumor suppressor gene. Oncogene 2011; 30:1956 - 62; http://dx.doi.org/10.1038/onc.2010.568; PMID: 21151178
   PubMed Web of Science ®Google Scholar
• Broadbent HM, Peden JF, Lorkowski S, Goel A, Ongen H, Green F, Clarke R, Collins R, Franzosi MG, Tognoni G, et al, PROCARDIS consortium. Susceptibility to coronary artery disease and diabetes is encoded by distinct, tightly linked SNPs in the ANRIL locus on chromosome 9p. Hum Mol Genet 2008; 17:806 - 14; http://dx.doi.org/10.1093/hmg/ddm352; PMID: 18048406
   PubMed Web of Science ®Google Scholar
• McPherson R, Pertsemlidis A, Kavaslar N, Stewart A, Roberts R, Cox DR, Hinds DA, Pennacchio LA, Tybjaerg-Hansen A, Folsom AR, et al. A common allele on chromosome 9 associated with coronary heart disease. Science 2007; 316:1488 - 91; http://dx.doi.org/10.1126/science.1142447; PMID: 17478681
   PubMed Web of Science ®Google Scholar
• Visel A, Zhu Y, May D, Afzal V, Gong E, Attanasio C, Blow MJ, Cohen JC, Rubin EM, Pennacchio LA. Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice. Nature 2010; 464:409 - 12; http://dx.doi.org/10.1038/nature08801; PMID: 20173736
   PubMed Web of Science ®Google Scholar
• Yap KL, Li S, Muñoz-Cabello AM, Raguz S, Zeng L, Mujtaba S, Gil J, Walsh MJ, Zhou MM. Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol Cell 2010; 38:662 - 74; http://dx.doi.org/10.1016/j.molcel.2010.03.021; PMID: 20541999
   PubMed Web of Science ®Google Scholar
• Sato K, Nakagawa H, Tajima A, Yoshida K, Inoue I. ANRIL is implicated in the regulation of nucleus and potential transcriptional target of E2F1. Oncol Rep 2010; 24:701 - 7; PMID: 20664976
   PubMed Web of Science ®Google Scholar
• Krenz M, Robbins J. Impact of beta-myosin heavy chain expression on cardiac function during stress. J Am Coll Cardiol 2004; 44:2390 - 7; http://dx.doi.org/10.1016/j.jacc.2004.09.044; PMID: 15607403
   PubMed Web of Science ®Google Scholar
• Mahdavi V, Chambers AP, Nadal-Ginard B. Cardiac alpha- and beta-myosin heavy chain genes are organized in tandem. Proc Natl Acad Sci U S A 1984; 81:2626 - 30; http://dx.doi.org/10.1073/pnas.81.9.2626; PMID: 6585819
   PubMed Web of Science ®Google Scholar
• Haddad F, Qin AX, Bodell PW, Zhang LY, Guo H, Giger JM, Baldwin KM. Regulation of antisense RNA expression during cardiac MHC gene switching in response to pressure overload. Am J Physiol Heart Circ Physiol 2006; 290:H2351 - 61; http://dx.doi.org/10.1152/ajpheart.01111.2005; PMID: 16415074
   PubMedGoogle Scholar
• Haddad F, Jiang W, Bodell PW, Qin AX, Baldwin KM. Cardiac myosin heavy chain gene regulation by thyroid hormone involves altered histone modifications. Am J Physiol Heart Circ Physiol 2010; 299:H1968 - 80; http://dx.doi.org/10.1152/ajpheart.00644.2010; PMID: 20833952
   PubMedGoogle Scholar
• Hang CT, Yang J, Han P, Cheng HL, Shang C, Ashley E, Zhou B, Chang CP. Chromatin regulation by Brg1 underlies heart muscle development and disease. Nature 2010; 466:62 - 7; http://dx.doi.org/10.1038/nature09130; PMID: 20596014
   PubMed Web of Science ®Google Scholar
• Huang WY, Liew CC. A conserved GATA motif in a tissue-specific DNase I hypersensitive site of the cardiac alpha-myosin heavy chain gene. Biochem J 1997; 325:47 - 51; PMID: 9224628
   PubMed Web of Science ®Google Scholar
• Lee JH, Gao C, Peng G, Greer C, Ren S, Wang Y, Xiao X. Analysis of transcriptome complexity through RNA sequencing in normal and failing murine hearts. Circ Res 2011; 109:1332 - 41; http://dx.doi.org/10.1161/CIRCRESAHA.111.249433; PMID: 22034492
   PubMed Web of Science ®Google Scholar
• Movassagh M, Choy MK, Knowles DA, Cordeddu L, Haider S, Down T, Siggens L, Vujic A, Simeoni I, Penkett C, et al. Distinct epigenomic features in end-stage failing human hearts. Circulation 2011; 124:2411 - 22; http://dx.doi.org/10.1161/CIRCULATIONAHA.111.040071; PMID: 22025602
   PubMed Web of Science ®Google Scholar
• Gibb EA, Vucic EA, Enfield KS, Stewart GL, Lonergan KM, Kennett JY, Becker-Santos DD, MacAulay CE, Lam S, Brown CJ, et al. Human cancer long non-coding RNA transcriptomes. PLoS One 2011; 6:e25915; http://dx.doi.org/10.1371/journal.pone.0025915; PMID: 21991387
   PubMed Web of Science ®Google Scholar
• Annilo T, Kepp K, Laan M. Natural antisense transcript of natriuretic peptide precursor A (NPPA): structural organization and modulation of NPPA expression. BMC Mol Biol 2009; 10:81; http://dx.doi.org/10.1186/1471-2199-10-81; PMID: 19671135
   PubMed Web of Science ®Google Scholar
• Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, et al, RIKEN Genome Exploration Research Group, Genome Science Group (Genome Network Project Core Group), FANTOM Consortium. Antisense transcription in the mammalian transcriptome. Science 2005; 309:1564 - 6; http://dx.doi.org/10.1126/science.1112009; PMID: 16141073
   PubMed Web of Science ®Google Scholar
• Core LJ, Waterfall JJ, Lis JT. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science 2008; 322:1845 - 8; http://dx.doi.org/10.1126/science.1162228; PMID: 19056941
   PubMed Web of Science ®Google Scholar
• Haddad F, Qin AX, Giger JM, Guo H, Baldwin KM. Potential pitfalls in the accuracy of analysis of natural sense-antisense RNA pairs by reverse transcription-PCR. BMC Biotechnol 2007; 7:21; http://dx.doi.org/10.1186/1472-6750-7-21; PMID: 17480233
   PubMed Web of Science ®Google Scholar
• Voigtsberger S, Bartsch H, Baumann G, Luther HP. Cell type-specific expression of endogenous cardiac Troponin I antisense RNA in the neonatal rat heart. Mol Cell Biochem 2009; 324:1 - 11; http://dx.doi.org/10.1007/s11010-008-9974-3; PMID: 19184367
   PubMed Web of Science ®Google Scholar
• He Y, Vogelstein B, Velculescu VE, Papadopoulos N, Kinzler KW. The antisense transcriptomes of human cells. Science 2008; 322:1855 - 7; http://dx.doi.org/10.1126/science.1163853; PMID: 19056939
   PubMed Web of Science ®Google Scholar
• Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A. Comprehensive comparative analysis of strand-specific RNA sequencing methods. Nat Methods 2010; 7:709 - 15; http://dx.doi.org/10.1038/nmeth.1491; PMID: 20711195
   PubMed Web of Science ®Google Scholar
• Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, Kingsmore SF, Schroth GP, Burge CB. Alternative isoform regulation in human tissue transcriptomes. Nature 2008; 456:470 - 6; http://dx.doi.org/10.1038/nature07509; PMID: 18978772
   PubMed Web of Science ®Google Scholar
• Mironov AA, Fickett JW, Gelfand MS. Frequent alternative splicing of human genes. Genome Res 1999; 9:1288 - 93; http://dx.doi.org/10.1101/gr.9.12.1288; PMID: 10613851
   PubMed Web of Science ®Google Scholar
• Chooniedass-Kothari S, Emberley E, Hamedani MK, Troup S, Wang X, Czosnek A, Hube F, Mutawe M, Watson PH, Leygue E. The steroid receptor RNA activator is the first functional RNA encoding a protein. FEBS Lett 2004; 566:43 - 7; http://dx.doi.org/10.1016/j.febslet.2004.03.104; PMID: 15147866
   PubMed Web of Science ®Google Scholar
• Burd CE, Jeck WR, Liu Y, Sanoff HK, Wang Z, Sharpless NE. Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk. PLoS Genet 2010; 6:e1001233; http://dx.doi.org/10.1371/journal.pgen.1001233; PMID: 21151960
   PubMed Web of Science ®Google Scholar
• Bartsch H, Voigtsberger S, Baumann G, Morano I, Luther HP. Detection of a novel sense-antisense RNA-hybrid structure by RACE experiments on endogenous troponin I antisense RNA. RNA 2004; 10:1215 - 24; http://dx.doi.org/10.1261/rna.5261204; PMID: 15272119
   PubMed Web of Science ®Google Scholar
• Pandey RR, Mondal T, Mohammad F, Enroth S, Redrup L, Komorowski J, Nagano T, Mancini-Dinardo D, Kanduri C. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell 2008; 32:232 - 46; http://dx.doi.org/10.1016/j.molcel.2008.08.022; PMID: 18951091
   PubMed Web of Science ®Google Scholar
• van der Brug M, Nalls MA, Cookson MR. Deep sequencing of coding and non-coding RNA in the CNS. Brain Res 2010; 1338:146 - 54; http://dx.doi.org/10.1016/j.brainres.2010.03.039; PMID: 20307502
   PubMed Web of Science ®Google Scholar
• Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, Mattick JS, Rinn JL. Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat Biotechnol 2012; 30:99 - 104; http://dx.doi.org/10.1038/nbt.2024; PMID: 22081020
   PubMed Web of Science ®Google Scholar
• Kampa D, Cheng J, Kapranov P, Yamanaka M, Brubaker S, Cawley S, Drenkow J, Piccolboni A, Bekiranov S, Helt G, et al. Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res 2004; 14:331 - 42; http://dx.doi.org/10.1101/gr.2094104; PMID: 14993201
   PubMed Web of Science ®Google Scholar
• Hurwitz J, Furth JJ, Anders M, Evans A. The role of deoxyribonucleic acid in ribonucleic acid synthesis. II. The influence of deoxyribonucleic acid on the reaction. J Biol Chem 1962; 237:3752 - 9; PMID: 13955883
   PubMed Web of Science ®Google Scholar
• Clark MB, Johnston RL, Inostroza-Ponta M, Fox AH, Fortini E, Moscato P, Dinger ME, Mattick JS. Genome-wide analysis of long noncoding RNA stability. Genome Res 2012; 22:885 - 98; http://dx.doi.org/10.1101/gr.131037.111; PMID: 22406755
   PubMed Web of Science ®Google Scholar
• Hah N, Danko CG, Core L, Waterfall JJ, Siepel A, Lis JT, Kraus WL. A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell 2011; 145:622 - 34; http://dx.doi.org/10.1016/j.cell.2011.03.042; PMID: 21549415
   PubMed Web of Science ®Google Scholar
• Churchman LS, Weissman JS. Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature 2011; 469:368 - 73; http://dx.doi.org/10.1038/nature09652; PMID: 21248844
   PubMed Web of Science ®Google Scholar
• Levsky JM, Singer RH. Fluorescence in situ hybridization: past, present and future. J Cell Sci 2003; 116:2833 - 8; http://dx.doi.org/10.1242/jcs.00633; PMID: 12808017
   PubMed Web of Science ®Google Scholar
• Chureau C, Chantalat S, Romito A, Galvani A, Duret L, Avner P, Rougeulle C. Ftx is a non-coding RNA which affects Xist expression and chromatin structure within the X-inactivation center region. Hum Mol Genet 2011; 20:705 - 18; http://dx.doi.org/10.1093/hmg/ddq516; PMID: 21118898
   PubMed Web of Science ®Google Scholar
• Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, Watt AT, Freier SM, Bennett CF, Sharma A, Bubulya PA, et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 2010; 39:925 - 38; http://dx.doi.org/10.1016/j.molcel.2010.08.011; PMID: 20797886
   PubMed Web of Science ®Google Scholar
• Korostowski L, Sedlak N, Engel N. The Kcnq1ot1 long non-coding RNA affects chromatin conformation and expression of Kcnq1, but does not regulate its imprinting in the developing heart. PLoS Genet 2012; 8:e1002956; http://dx.doi.org/10.1371/journal.pgen.1002956; PMID: 23028363
   PubMedGoogle Scholar
• Mondal T, Rasmussen M, Pandey GK, Isaksson A, Kanduri C. Characterization of the RNA content of chromatin. Genome Res 2010; 20:899 - 907; http://dx.doi.org/10.1101/gr.103473.109; PMID: 20404130
   PubMed Web of Science ®Google Scholar
• Gregory RI, Randall TE, Johnson CA, Khosla S, Hatada I, O’Neill LP, Turner BM, Feil R. DNA methylation is linked to deacetylation of histone H3, but not H4, on the imprinted genes Snrpn and U2af1-rs1. Mol Cell Biol 2001; 21:5426 - 36; http://dx.doi.org/10.1128/MCB.21.16.5426-5436.2001; PMID: 11463825
   PubMed Web of Science ®Google Scholar
• Zappulla DC, Cech TR. RNA as a flexible scaffold for proteins: yeast telomerase and beyond. Cold Spring Harb Symp Quant Biol 2006; 71:217 - 24; http://dx.doi.org/10.1101/sqb.2006.71.011; PMID: 17381300
   PubMedGoogle Scholar
• Chu C, Qu K, Zhong FL, Artandi SE, Chang HY. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell 2011; 44:667 - 78; http://dx.doi.org/10.1016/j.molcel.2011.08.027; PMID: 21963238
   PubMed Web of Science ®Google Scholar
• Simon MD, Wang CI, Kharchenko PV, West JA, Chapman BA, Alekseyenko AA, Borowsky ML, Kuroda MI, Kingston RE. The genomic binding sites of a noncoding RNA. Proc Natl Acad Sci U S A 2011; 108:20497 - 502; http://dx.doi.org/10.1073/pnas.1113536108; PMID: 22143764
   PubMed Web of Science ®Google Scholar
• Ule J, Jensen KB, Ruggiu M, Mele A, Ule A, Darnell RB. CLIP identifies Nova-regulated RNA networks in the brain. Science 2003; 302:1212 - 5; http://dx.doi.org/10.1126/science.1090095; PMID: 14615540
   PubMed Web of Science ®Google Scholar
• Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M Jr., Jungkamp AC, Munschauer M, et al. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 2010; 141:129 - 41; http://dx.doi.org/10.1016/j.cell.2010.03.009; PMID: 20371350
   PubMed Web of Science ®Google Scholar
• Guil S, Soler M, Portela A, Carrère J, Fonalleras E, Gómez A, Villanueva A, Esteller M. Intronic RNAs mediate EZH2 regulation of epigenetic targets. Nat Struct Mol Biol 2012; 19:664 - 70; http://dx.doi.org/10.1038/nsmb.2315; PMID: 22659877
   PubMed Web of Science ®Google Scholar
• Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K, Lee CS, Flockhart RJ, Groff AF, Chow J, et al. Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature 2013; 493:231 - 5; http://dx.doi.org/10.1038/nature11661; PMID: 23201690
   PubMed Web of Science ®Google Scholar
• Hsu MT, Coca-Prados M. Electron microscopic evidence for the circular form of RNA in the cytoplasm of eukaryotic cells. Nature 1979; 280:339 - 40; http://dx.doi.org/10.1038/280339a0; PMID: 460409
   PubMed Web of Science ®Google Scholar
• Surono A, Takeshima Y, Wibawa T, Ikezawa M, Nonaka I, Matsuo M. Circular dystrophin RNAs consisting of exons that were skipped by alternative splicing. Hum Mol Genet 1999; 8:493 - 500; http://dx.doi.org/10.1093/hmg/8.3.493; PMID: 9949208
   PubMed Web of Science ®Google Scholar
• Zaphiropoulos PG. Exon skipping and circular RNA formation in transcripts of the human cytochrome P-450 2C18 gene in epidermis and of the rat androgen binding protein gene in testis. Mol Cell Biol 1997; 17:2985 - 93; PMID: 9154796
   PubMed Web of Science ®Google Scholar
• Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS One 2012; 7:e30733; http://dx.doi.org/10.1371/journal.pone.0030733; PMID: 22319583
   PubMed Web of Science ®Google Scholar
• Li XF, Lytton J. A circularized sodium-calcium exchanger exon 2 transcript. J Biol Chem 1999; 274:8153 - 60; http://dx.doi.org/10.1074/jbc.274.12.8153; PMID: 10075718
   PubMed Web of Science ®Google Scholar
• Hansen TB, Jensen TI, Clausen BH, Bramsen JB, Finsen B, Damgaard CK, Kjems J. Natural RNA circles function as efficient microRNA sponges. Nature 2013; 495:384 - 8; http://dx.doi.org/10.1038/nature11993; PMID: 23446346
   PubMed Web of Science ®Google Scholar
• Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak SD, Gregersen LH, Munschauer M, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 2013; 495:333 - 8; http://dx.doi.org/10.1038/nature11928; PMID: 23446348
   PubMed Web of Science ®Google Scholar
• Hansen TB, Wiklund ED, Bramsen JB, Villadsen SB, Statham AL, Clark SJ, Kjems J. miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA. EMBO J 2011; 30:4414 - 22; http://dx.doi.org/10.1038/emboj.2011.359; PMID: 21964070
   PubMed Web of Science ®Google Scholar
• Al-Balool HH, Weber D, Liu Y, Wade M, Guleria K, Nam PL, Clayton J, Rowe W, Coxhead J, Irving J, et al. Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant. Genome Res 2011; 21:1788 - 99; http://dx.doi.org/10.1101/gr.116442.110; PMID: 21948523
   PubMed Web of Science ®Google Scholar
• Squires JE, Patel HR, Nousch M, Sibbritt T, Humphreys DT, Parker BJ, Suter CM, Preiss T. Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Res 2012; 40:5023 - 33; http://dx.doi.org/10.1093/nar/gks144; PMID: 22344696
   PubMed Web of Science ®Google Scholar
• Motorin Y, Helm M. RNA nucleotide methylation. Wiley Interdiscip Rev RNA 2011; 2:611 - 31; http://dx.doi.org/10.1002/wrna.79; PMID: 21823225
   PubMed Web of Science ®Google Scholar
• Underwood JG, Uzilov AV, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR, Haussler D. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat Methods 2010; 7:995 - 1001; http://dx.doi.org/10.1038/nmeth.1529; PMID: 21057495
   PubMed Web of Science ®Google Scholar
• Westhof E, Romby P. The RNA structurome: high-throughput probing. Nat Methods 2010; 7:965 - 7; http://dx.doi.org/10.1038/nmeth1210-965; PMID: 21116245
   PubMed Web of Science ®Google Scholar
• Benhamed M, Herbig U, Ye T, Dejean A, Bischof O. Senescence is an endogenous trigger for microRNA-directed transcriptional gene silencing in human cells. Nat Cell Biol 2012; 14:266 - 75; http://dx.doi.org/10.1038/ncb2443; PMID: 22366686
   PubMed Web of Science ®Google Scholar
• Morris KV, Chan SW, Jacobsen SE, Looney DJ. Small interfering RNA-induced transcriptional gene silencing in human cells. Science 2004; 305:1289 - 92; http://dx.doi.org/10.1126/science.1101372; PMID: 15297624
   PubMed Web of Science ®Google Scholar
• Huang XA, Yin H, Sweeney S, Raha D, Snyder M, Lin H. A major epigenetic programming mechanism guided by piRNAs. Dev Cell 2013; 24:502 - 16; http://dx.doi.org/10.1016/j.devcel.2013.01.023; PMID: 23434410
   PubMed Web of Science ®Google Scholar
• Schubert T, Pusch MC, Diermeier S, Benes V, Kremmer E, Imhof A, Längst G. Df31 protein and snoRNAs maintain accessible higher-order structures of chromatin. Mol Cell 2012; 48:434 - 44; http://dx.doi.org/10.1016/j.molcel.2012.08.021; PMID: 23022379
   PubMed Web of Science ®Google Scholar
• Han J, Kim D, Morris KV. Promoter-associated RNA is required for RNA-directed transcriptional gene silencing in human cells. Proc Natl Acad Sci U S A 2007; 104:12422 - 7; http://dx.doi.org/10.1073/pnas.0701635104; PMID: 17640892
   PubMed Web of Science ®Google Scholar
• Melo CA, Drost J, Wijchers PJ, van de Werken H, de Wit E, Oude Vrielink JA, Elkon R, Melo SA, Léveillé N, Kalluri R, et al. eRNAs are required for p53-dependent enhancer activity and gene transcription. Mol Cell 2013; 49:524 - 35; http://dx.doi.org/10.1016/j.molcel.2012.11.021; PMID: 23273978
   PubMed Web of Science ®Google Scholar
• Johnsson P, Ackley A, Vidarsdottir L, Lui WO, Corcoran M, Grandér D, Morris KV. A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells. Nat Struct Mol Biol 2013; 20:440 - 6; http://dx.doi.org/10.1038/nsmb.2516; PMID: 23435381
   PubMed Web of Science ®Google Scholar
• Hawkins PG, Morris KV. Transcriptional regulation of Oct4 by a long non-coding RNA antisense to Oct4-pseudogene 5. Transcription 2010; 1:165 - 75; http://dx.doi.org/10.4161/trns.1.3.13332; PMID: 21151833
   PubMedGoogle Scholar
• Bond AM, Vangompel MJ, Sametsky EA, Clark MF, Savage JC, Disterhoft JF, Kohtz JD. Balanced gene regulation by an embryonic brain ncRNA is critical for adult hippocampal GABA circuitry. Nat Neurosci 2009; 12:1020 - 7; http://dx.doi.org/10.1038/nn.2371; PMID: 19620975
   PubMed Web of Science ®Google Scholar
• Horard B, Gilson E. Telomeric RNA enters the game. Nat Cell Biol 2008; 10:113 - 5; http://dx.doi.org/10.1038/ncb0208-113; PMID: 18246034
   PubMed Web of Science ®Google Scholar
• Haeger P, Cuevas R, Forray MI, Rojas R, Daza C, Rivadeneira J, Gysling K. Natural expression of immature Ucn antisense RNA in the rat brain. Evidence favoring bidirectional transcription of the Ucn gene locus. Brain Res Mol Brain Res 2005; 139:115 - 28; http://dx.doi.org/10.1016/j.molbrainres.2005.05.024; PMID: 15979199
   PubMedGoogle Scholar
• Ishii N, Ozaki K, Sato H, Mizuno H, Saito S, Takahashi A, Miyamoto Y, Ikegawa S, Kamatani N, Hori M, et al. Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction. J Hum Genet 2006; 51:1087 - 99; http://dx.doi.org/10.1007/s10038-006-0070-9; PMID: 17066261
   PubMed Web of Science ®Google Scholar
• Roeszler KN, Itman C, Sinclair AH, Smith CA. The long non-coding RNA, MHM, plays a role in chicken embryonic development, including gonadogenesis. Dev Biol 2012; 366:317 - 26; http://dx.doi.org/10.1016/j.ydbio.2012.03.025; PMID: 22546690
   PubMed Web of Science ®Google Scholar
• Tran VG, Court F, Duputié A, Antoine E, Aptel N, Milligan L, Carbonell F, Lelay-Taha MN, Piette J, Weber M, et al. H19 antisense RNA can up-regulate Igf2 transcription by activation of a novel promoter in mouse myoblasts. PLoS One 2012; 7:e37923; http://dx.doi.org/10.1371/journal.pone.0037923; PMID: 22662250
   PubMedGoogle Scholar
• Khalil AM, Faghihi MA, Modarresi F, Brothers SP, Wahlestedt C. A novel RNA transcript with antiapoptotic function is silenced in fragile X syndrome. PLoS One 2008; 3:e1486; http://dx.doi.org/10.1371/journal.pone.0001486; PMID: 18213394
   PubMed Web of Science ®Google Scholar
• Sleutels F, Zwart R, Barlow DP. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 2002; 415:810 - 3; http://dx.doi.org/10.1038/415810a; PMID: 11845212
   PubMed Web of Science ®Google Scholar
• Ritter O, Luther HP, Haase H, Baltas LG, Baumann G, Schulte HD, Morano I. Expression of atrial myosin light chains but not alpha-myosin heavy chains is correlated in vivo with increased ventricular function in patients with hypertrophic obstructive cardiomyopathy. J Mol Med (Berl) 1999; 77:677 - 85; http://dx.doi.org/10.1007/s001099900030; PMID: 10569205
   PubMed Web of Science ®Google Scholar
• Potts JD, Vincent EB, Runyan RB, Weeks DL. Sense and antisense TGF beta 3 mRNA levels correlate with cardiac valve induction. Dev Dyn 1992; 193:340 - 5; http://dx.doi.org/10.1002/aja.1001930407; PMID: 1511174
   PubMed Web of Science ®Google Scholar
• Robb GB, Carson AR, Tai SC, Fish JE, Singh S, Yamada T, Scherer SW, Nakabayashi K, Marsden PA. Post-transcriptional regulation of endothelial nitric-oxide synthase by an overlapping antisense mRNA transcript. J Biol Chem 2004; 279:37982 - 96; http://dx.doi.org/10.1074/jbc.M400271200; PMID: 15234981
   PubMed Web of Science ®Google Scholar
• Friedrichs F, Zugck C, Rauch GJ, Ivandic B, Weichenhan D, Müller-Bardorff M, Meder B, El Mokhtari NE, Regitz-Zagrosek V, Hetzer R, et al. HBEGF, SRA1, and IK: Three cosegregating genes as determinants of cardiomyopathy. Genome Res 2009; 19:395 - 403; http://dx.doi.org/10.1101/gr.076653.108; PMID: 19064678
   PubMed Web of Science ®Google Scholar
• Rodríguez-Campos A, Azorín F. RNA is an integral component of chromatin that contributes to its structural organization. PLoS One 2007; 2:e1182; http://dx.doi.org/10.1371/journal.pone.0001182; PMID: 18000552
   PubMed Web of Science ®Google Scholar