Long intergenic noncoding RNAs: Novel drivers of human lymphocyte differentiation

Frontiers in Immunology

Volumn 6, Issue MAR, 2015, Pages

  Panzeri, Ilaria ^a   Rossetti, Grazisa ^a   Abrignani, Sergio ^a   Pagani, Massimiliano ^a  

^a Istituto Nazionale di Genetica Molecolare   (Italy)

Author keywords

Epigenetic regulation; Long noncoding RNAs; Lymphocyte differentiation

Indexed keywords

BMI1 PROTEIN; LONG UNTRANSLATED RNA; POLYCOMB REPRESSIVE COMPLEX 2; STAT4 PROTEIN; TRANSCRIPTION FACTOR MAF;

ARTICLE; B LYMPHOCYTE; CD4+ T LYMPHOCYTE; CD8+ T LYMPHOCYTE; CELL SPECIFICITY; CYTOKINE PRODUCTION; DNA METHYLATION; DROSOPHILA; EPIGENETICS; GENE EXPRESSION; GENE REPRESSION; GENETIC TRANSCRIPTION; HUMAN; IMMUNE RESPONSE; LYMPHOCYTE DIFFERENTIATION; NONHUMAN; TH1 CELL; TH2 CELL; X CHROMOSOME INACTIVATION;

EID: 84926619103     PISSN: None     EISSN: 16643224     Source Type: Journal    
DOI: 10.3389/fimmu.2015.00175     Document Type: Article

References (230)

1. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome research (2012) 22(9):1775-89. Epub 2012/09/08. doi: 10.1101/gr.132159.111. PubMed PMID: 22955988; PubMed Central PMCID: PMCPmc3431493.
2. Taft RJ, Pheasant M, Mattick JS. The relationship between non-protein-coding DNA and eukaryotic complexity. BioEssays: news and reviews in molecular, cellular and developmental biology (2007) 29(3):288-99. Epub 2007/02/14. doi: 10.1002/bies.20544. PubMed PMID: 17295292.
3. Hoagland MB, Keller EB, Zamecnik PC. Enzymatic carboxyl activation of amino acids. The Journal of biological chemistry (1956) 218(1):345-58. Epub 1956/01/01. PubMed PMID: 13278342.
4. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, et al. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature (2000) 408(6808):86-9. Epub 2000/11/18. doi: 10.1038/35040556. PubMed PMID: 11081512.
5. Baumjohann D, Ansel KM. MicroRNA-mediated regulation of T helper cell differentiation and plasticity. Nature reviews Immunology (2013) 13(9):666-78. Epub 2013/08/03. doi: 10.1038/nri3494. PubMed PMID: 23907446; PubMed Central PMCID: PMCPmc3980848.
6. Bronevetsky Y, Ansel KM. Regulation of miRNA biogenesis and turnover in the immune system. Immunological reviews (2013) 253(1):304-16. Epub 2013/04/05. doi: 10.1111/imr.12059. PubMed PMID: 23550654; PubMed Central PMCID: PMCPmc3621012.
7. Monticelli S. MicroRNAs in T helper cell differentiation and plasticity. Seminars in immunology (2013) 25(4):291-8. Epub 2013/11/13. doi: 10.1016/j.smim.2013.10.015. PubMed PMID: 24216176.
8. Bratkovič T, Rogelj B. The many faces of small nucleolar RNAs. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms (2014) 1839(6):438-43. doi: http://dx.doi.org/10.1016/j.bbagrm.2014.04.009.
9. Dieci G, Preti M, Montanini B. Eukaryotic snoRNAs: a paradigm for gene expression flexibility. Genomics (2009) 94(2):83-8. Epub 2009/05/19. doi: 10.1016/j.ygeno.2009.05.002. PubMed PMID: 19446021.
10. Lui L, Lowe T. Small nucleolar RNAs and RNA-guided post-transcriptional modification. Essays in biochemistry (2013) 54:53-77. Epub 2013/07/09. doi: 10.1042/bse0540053. PubMed PMID: 23829527.
11. Valadkhan S, Gunawardane LS. Role of small nuclear RNAs in eukaryotic gene expression. Essays in biochemistry (2013) 54:79-90. Epub 2013/07/09. doi: 10.1042/bse0540079. PubMed PMID: 23829528.
12. Bamezai S, Rawat VPS, Buske C. Concise Review: The Piwi-piRNA Axis: Pivotal Beyond Transposon Silencing. STEM CELLS (2012) 30(12):2603-11. doi: 10.1002/stem.1237.
13. Ku H-Y, Lin H. PIWI proteins and their interactors in piRNA biogenesis, germline development and gene expression. National Science Review (2014) 1(2):205-18. doi: 10.1093/nsr/nwu014.
14. Luteijn MJ, Ketting RF. PIWI-interacting RNAs: from generation to transgenerational epigenetics. Nat Rev Genet (2013) 14(8):523-34. doi: 10.1038/nrg3495.
15. Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science (New York, NY) (2007) 316(5830):1484-8. Epub 2007/05/19. doi: 10.1126/science.1138341. PubMed PMID: 17510325.
16. Taft RJ, Kaplan CD, Simons C, Mattick JS. Evolution, biogenesis and function of promoter-associated RNAs. Cell cycle (Georgetown, Tex) (2009) 8(15):2332-8. Epub 2009/07/15. PubMed PMID: 19597344.
17. Carthew RW, Sontheimer EJ. Origins and Mechanisms of miRNAs and siRNAs. Cell (2009) 136(4):642-55. doi: http://dx.doi.org/10.1016/j.cell.2009.01.035.
18. Svoboda P. Renaissance of mammalian endogenous RNAi. FEBS Letters (2014) 588(15):2550-6. doi: http://dx.doi.org/10.1016/j.febslet.2014.05.030.
19. Taft RJ, Glazov EA, Cloonan N, Simons C, Stephen S, Faulkner GJ, et al. Tiny RNAs associated with transcription start sites in animals. Nat Genet (2009) 41(5):572-8. doi: http://www.nature.com/ng/journal/v41/n5/suppinfo/ng.312 S1.html.
20. Taft RJ, Simons C, Nahkuri S, Oey H, Korbie DJ, Mercer TR, et al. Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans. Nat Struct Mol Biol (2010) 17(8):1030-4. doi: http://www.nature.com/nsmb/journal/v17/n8/abs/nsmb.1841.html-supplementary-information.
21. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi AM, et al. Landscape of transcription in human cells. Nature (2012) 489(7414):101-8. doi: 10.1038/nature11233. PubMed PMID: PMC3684276.
22. Faghihi MA, Wahlestedt C. Regulatory roles of natural antisense transcripts. Nature reviews Molecular cell biology (2009) 10(9):637-43. Epub 2009/07/30. doi: 10.1038/nrm2738. PubMed PMID: 19638999; PubMed Central PMCID: PMCPmc2850559.
23. Kurokawa R. Promoter-associated long noncoding RNAs repress transcription through a RNA binding protein TLS. Advances in experimental medicine and biology (2011) 722:196-208. Epub 2011/09/15. doi: 10.1007/978-1-4614-0332-6_12. PubMed PMID: 21915790.
24. Zaphiropoulos PG. A promoter-associated RNA downregulates the oncogenic GLI1 transcription factor in rhabdomyosarcoma cells. Rna & disease (2014) 1(1):10-14800/rd. 254.
25. Preker P, Nielsen J, Kammler S, Lykke-Andersen S, Christensen MS, Mapendano CK, et al. RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters. Science (New York, NY) (2008) 322(5909):1851-4. doi: 10.1126/science. 1164096.
26. Imamura T, Yamamoto S, Ohgane J, Hattori N, Tanaka S, Shiota K. Non-coding RNA directed DNA demethylation of Sphk1 CpG island. Biochemical and Biophysical Research Communications (2004) 322(2):593-600. doi: http://dx.doi.org/10.1016/j.bbrc.2004.07.159.
27. Preker P, Almvig K, Christensen MS, Valen E, Mapendano CK, Sandelin A, et al. PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters. Nucleic Acids Research (2011). doi: 10.1093/nar/gkr370.
28. Peng JC, Shen J, Ran ZH. Transcribed ultraconserved region in human cancers. RNA biology (2013) 10(12):1771-7. Epub 2014/01/05. doi: 10.4161/rna.26995. PubMed PMID: 24384562; PubMed Central PMCID: PMCPmc3917980.
29. Louro R, Smirnova AS, Verjovski-Almeida S. Long intronic noncoding RNA transcription: Expression noise or expression choice? Genomics (2009) 93(4):291-8. doi: http://dx.doi.org/10.1016/j.ygeno.2008.11.009.
30. Lam MT, Li W, Rosenfeld MG, Glass CK. Enhancer RNAs and regulated transcriptional programs. Trends in biochemical sciences (2014) 39(4):170-82. doi: 10.1016/j.tibs.2014.02.007. PubMed PMID: PMC4266492.
31. Koch F, Fenouil R, Gut M, Cauchy P, Albert TK, Zacarias-Cabeza J, et al. Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters. Nat Struct Mol Biol (2011) 18(8):956-63. Epub 2011/07/19. doi: 10.1038/nsmb.2085. PubMed PMID: 21765417.
32. Natoli G, Andrau JC. Noncoding transcription at enhancers: general principles and functional models. Annual review of genetics (2012) 46:1-19. Epub 2012/08/22. doi: 10.1146/annurev-genet-110711-155459. PubMed PMID: 22905871.
33. Rinn JL, Chang HY. Genome regulation by long noncoding RNAs. Annual review of biochemistry (2012) 81:10.1146/annurev-biochem-051410-92902. doi: 10.1146/annurev-biochem-051410-092902. PubMed PMID: PMC3858397.
34. Merry C, Niland C, Khalil A. Diverse Functions and Mechanisms of Mammalian Long Noncoding RNAs. In: Carmichael GG, editor. Regulatory Non-Coding RNAs. Methods in Molecular Biology. 1206. Springer New York (2015). p. 1-14.
35. Mercer TR, Wilhelm D, Dinger ME, Soldà G, Korbie DJ, Glazov EA, et al. Expression of distinct RNAs from 3' untranslated regions. Nucleic Acids Research (2011) 39(6):2393-403. doi: 10.1093/nar/gkq1158. PubMed PMID: PMC3064787.
36. Lasda E, Parker R. Circular RNAs: diversity of form and function. Rna (2014) 20(12):1829-42. doi: 10.1261/rna.047126.114.
37. Pang KC, Dinger ME, Mercer TR, Malquori L, Grimmond SM, Chen W, et al. Genome-wide identification of long noncoding RNAs in CD8+ T cells. Journal of immunology (Baltimore, Md: 1950) (2009) 182(12):7738-48. Epub 2009/06/06. doi: 10.4049/jimmunol.0900603. PubMed PMID: 19494298.
38. Pagani M, Rossetti G, Panzeri I, de Candia P, Bonnal RJ, Rossi RL, et al. Role of microRNAs and long-non-coding RNAs in CD4(+) T-cell differentiation. Immunological reviews (2013) 253(1):82-96. Epub 2013/04/05. doi: 10.1111/imr.12055. PubMed PMID: 23550640.
39. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature (2009) 458(7235):223-7. Epub 2009/02/03. doi: 10.1038/nature07672. PubMed PMID: 19182780; PubMed Central PMCID: PMCPmc2754849.
40. Dieci G, Conti A, Pagano A, Carnevali D. Identification of RNA polymerase III-transcribed genes in eukaryotic genomes. Biochimica et biophysica acta (2013) 1829(3-4):296-305. Epub 2012/10/09. doi: 10.1016/j.bbagrm.2012.09.010. PubMed PMID: 23041497.
41. Lin R, Maeda S, Liu C, Karin M, Edgington TS. A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas. Oncogene (2007) 26(6):851-8. Epub 2006/08/01. doi: 10.1038/sj.onc.1209846. PubMed PMID: 16878148.
42. Galindo MI, Pueyo JI, Fouix S, Bishop SA, Couso JP. Peptides Encoded by Short ORFs Control Development and Define a New Eukaryotic Gene Family. PLoS Biology (2007) 5(5):e106. doi: 10.1371/journal.pbio.0050106. PubMed PMID: PMC1852585.
43. Lanz RB, McKenna NJ, Onate SA, Albrecht U, Wong J, Tsai SY, et al. A steroid receptor coactivator, SRA, functions as an RNA and is present in an SRC-1 complex. Cell (1999) 97(1):17-27. Epub 1999/04/13. PubMed PMID: 10199399.
44. Ingolia NT, Brar GA, Stern-Ginossar N, Harris MS, Talhouarne GJ, Jackson SE, et al. Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. Cell reports (2014) 8(5):1365-79. Epub 2014/08/28. doi: 10.1016/j.celrep.2014.07.045. PubMed PMID: 25159147; PubMed Central PMCID: PMCPmc4216110.
45. Banfai B, Jia H, Khatun J, Wood E, Risk B, Gundling WE, Jr., et al. Long noncoding RNAs are rarely translated in two human cell lines. Genome research (2012) 22(9):1646-57. Epub 2012/09/08. doi: 10.1101/gr.134767.111. PubMed PMID: 22955977; PubMed Central PMCID: PMCPmc3431482.
46. Lee S, Liu B, Lee S, Huang SX, Shen B, Qian SB. Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. Proceedings of the National Academy of Sciences of the United States of America (2012) 109(37):E2424-32. Epub 2012/08/29. doi: 10.1073/pnas.1207846109. PubMed PMID: 22927429; PubMed Central PMCID: PMCPmc3443142.
47. Slavoff SA, Mitchell AJ, Schwaid AG, Cabili MN, Ma J, Levin JZ, et al. Peptidomic discovery of short open reading frame-encoded peptides in human cells. Nature chemical biology (2013) 9(1):59-64. Epub 2012/11/20. doi: 10.1038/nchembio.1120. PubMed PMID: 23160002; PubMed Central PMCID: PMCPmc3625679.
48. Andrews SJ, Rothnagel JA. Emerging evidence for functional peptides encoded by short open reading frames. Nat Rev Genet (2014) 15(3):193-204. doi: 10.1038/nrg3520.
49. Ulveling D, Francastel C, Hube F. When one is better than two: RNA with dual functions. Biochimie (2011) 93(4):633-44. Epub 2010/11/30. doi: 10.1016/j.biochi.2010.11.004. PubMed PMID: 21111023.
50. Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature (2010) 465(7301):1033-8. doi: http://www.nature.com/nature/journal/v465/n7301/suppinfo/nature09144S1.html.
51. Duret L, Chureau C, Samain S, Weissenbach J, Avner P. The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene. Science (New York, NY) (2006) 312(5780):1653-5. Epub 2006/06/17. doi: 10.1126/science. 1126316. PubMed PMID: 16778056.
52. Elisaphenko EA, Kolesnikov NN, Shevchenko AI, Rogozin IB, Nesterova TB, Brockdorff N, et al. A Dual Origin of the Xist Gene from a Protein-Coding Gene and a Set of Transposable Elements. PLoS ONE (2008) 3(6):e2521. doi: 10.1371/journal.pone.0002521.
53. Horvath JE, Sheedy CB, Merrett SL, Diallo AB, Swofford DL, Program NCS, et al. Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate XIST locus. Genome research (2011) 21(6):850-62. doi: 10.1101/gr.111849.110.
54. Romito A, Rougeulle C. Origin and evolution of the long non-coding genes in the X-inactivation center. Biochimie (2011) 93(11):1935-42. Epub 2011/08/09. doi: 10.1016/j.biochi.2011.07.009. PubMed PMID: 21820484.
55. Bussotti G, Notredame C, Enright A. Detecting and Comparing Non-Coding RNAs in the High-Throughput Era. International Journal of Molecular Sciences (2013) 14(8):15423-58. PubMed PMID: doi:10.3390/ijms140815423.
56. Nigro JM, Cho KR, Fearon ER, Kern SE, Ruppert JM, Oliner JD, et al. Scrambled exons. Cell (1991) 64(3):607-13. doi: http://dx.doi.org/10.1016/0092-8674(91)90244-S.
57. Beltran M, Puig I, Peña C, García JM, Álvarez AB, Peña R, et al. A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes & Development (2008) 22(6):756-69. doi: 10.1101/gad.455708. PubMed PMID: PMC2275429.
58. Martick M, Horan LH, Noller HF, Scott WG. A discontinuous hammerhead ribozyme embedded in a mammalian messenger RNA. Nature (2008) 454(7206):899-902. Epub 2008/07/11. doi: 10.1038/nature07117. PubMed PMID: 18615019; PubMed Central PMCID: PMCPmc2612532.
59. Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, Trapnell C, Jeddeloh JA, et al. Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat Biotech (2012) 30(1):99-104. doi: 10.1038/nbt.2024 http://www.nature.com/nbt/journal/v30/n1/abs/nbt.2024.html-supplementary-information.
60. Group RGER, Genome Science G, the FC, Katayama S, Tomaru Y, Kasukawa T, et al. Antisense Transcription in the Mammalian Transcriptome. Science (New York, NY) (2005) 309(5740):1564-6. doi: 10.1126/science. 1112009.
61. Li Z, Rana TM. Decoding the noncoding: prospective of lncRNA-mediated innate immune regulation. RNA biology (2014) 11(8):979-85. Epub 2014/12/09. doi: 10.4161/rna.29937. PubMed PMID: 25482890.
62. Imamura K, Akimitsu N. Long non-coding RNAs involved in immune responses. Frontiers in immunology (2014) 5. doi: 10.3389/fimmu.2014.00573.
63. Ranzani V RG, Panzeri I, Arrigoni A, Bonnal R, Curti S, Gruarin P, Provasi E, Sugliano E, Marconi M, De Francesco R, Geginat J, Bodega B, Abrignani S, Pagani M LincRNA landscape in human lymphocytes highlights regulation of T cell differentiation by linc-MAF-4. Nature Immunology (2015):In press.
64. Kapusta A, Kronenberg Z, Lynch VJ, Zhuo X, Ramsay L, Bourque G, et al. Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs. PLoS Genet (2013) 9(4):e1003470. doi: 10.1371/journal.pgen. 1003470.
65. Kelley D, Rinn J. Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biology (2012) 13(11):R107. PubMed PMID: doi:10.1186/gb-2012-13-11-r107.
66. Lin N, Chang KY, Li Z, Gates K, Rana ZA, Dang J, et al. An evolutionary conserved long noncoding RNA TUNA controls pluripotency and neural lineage commitment. Molecular cell (2014) 53(6):1005-19. Epub 2014/02/18. doi: 10.1016/j.molcel.2014.01.021. PubMed PMID: 24530304; PubMed Central PMCID: PMCPmc4010157.
67. Klattenhoff CA, Scheuermann JC, Surface LE, Bradley RK, Fields PA, Steinhauser ML, et al. Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell (2013) 152(3):570-83. Epub 2013/01/29. doi: 10.1016/j.cell.2013.01.003. PubMed PMID: 23352431; PubMed Central PMCID: PMCPmc3563769.
68. Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature (2011) 472(7341):120-4. doi: http://www.nature.com/nature/journal/v472/n7341/abs/10.1038-nature09819-unlocked.html-supplementary-information.
69. Keniry A, Oxley D, Monnier P, Kyba M, Dandolo L, Smits G, et al. The H19 lincRNA is a developmental reservoir of miR-675 that suppresses growth and Igf1r. Nat Cell Biol (2012) 14(7):659-65. doi: http://www.nature.com/ncb/journal/v14/n7/abs/ncb2521.html-supplementary-information.
70. Venkatraman A, He XC, Thorvaldsen JL, Sugimura R, Perry JM, Tao F, et al. Maternal imprinting at the H19-Igf2 locus maintains adult haematopoietic stem cell quiescence. Nature (2013) 500(7462):345-9. doi: 10.1038/nature12303 http://www.nature.com/nature/journal/v500/n7462/abs/nature12303.html-supplementary-information.
71. Mourtada-Maarabouni M, Hedge VL, Kirkham L, Farzaneh F, Williams GT. Growth arrest in human T-cells is controlled by the non-coding RNA growth-arrest-specific transcript 5 (GAS5). Journal of Cell Science (2008) 121(7):939-46. doi: 10.1242/jcs.024646.
72. Pickard MR, Mourtada-Maarabouni M, Williams GT. Long non-coding RNA GAS5 regulates apoptosis in prostate cancer cell lines. Biochimica et biophysica acta (2013) 1832(10):1613-23. Epub 2013/05/17. doi: 10.1016/j.bbadis.2013.05.005. PubMed PMID: 23676682.
73. Rossi MN, Antonangeli F. LncRNAs: New Players in Apoptosis Control. International Journal of Cell Biology (2014) 2014:7. doi: 10.1155/2014/473857.
74. Yin D, He X, Zhang E, Kong R, De W, Zhang Z. Long noncoding RNA GAS5 affects cell proliferation and predicts a poor prognosis in patients with colorectal cancer. Medical oncology (Northwood, London, England) (2014) 31(11):253. Epub 2014/10/19. doi: 10.1007/s12032-014-0253-8. PubMed PMID: 25326054.
75. Cesana M, Cacchiarelli D, Legnini I, Santini T, Sthandier O, Chinappi M, et al. A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA. Cell (2011) 147(2):358-69. doi: 10.1016/j.cell.2011.09.028. PubMed PMID: PMC3234495.
76. Fatica A, Bozzoni I. Long non-coding RNAs: new players in cell differentiation and development. Nat Rev Genet (2014) 15(1):7-21. doi: 10.1038/nrg3606.
77. Hu W, Alvarez-Dominguez JR, Lodish HF. Regulation of mammalian cell differentiation by long non-coding RNAs. EMBO reports (2012) 13(11):971-83. doi: 10.1038/embor.2012.145.
78. Lee Jeannie T, Bartolomei Marisa S. X-Inactivation, Imprinting, and Long Noncoding RNAs in Health and Disease. Cell (2013) 152(6):1308-23. doi: http://dx.doi.org/10.1016/j.cell.2013.02.016.
79. Mitsuya K, Meguro M, Lee MP, Katoh M, Schulz TC, Kugoh H, et al. LIT1, an imprinted antisense RNA in the human KvLQT1 locus identified by screening for differentially expressed transcripts using monochromosomal hybrids. Human molecular genetics (1999) 8(7):1209-17. Epub 1999/06/17. PubMed PMID: 10369866.
80. Zhang H, Zeitz MJ, Wang H, Niu B, Ge S, Li W, et al. Long noncoding RNA-mediated intrachromosomal interactions promote imprinting at the Kcnq1 locus. The Journal of Cell Biology (2014) 204(1):61-75. doi: 10.1083/jcb.201304152.
81. Gendrel AV, Heard E. Noncoding RNAs and epigenetic mechanisms during X-chromosome inactivation. Annual review of cell and developmental biology (2014) 30:561-80. Epub 2014/07/09. doi: 10.1146/annurev-cellbio-101512-122415. PubMed PMID: 25000994.
82. Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proceedings of the National Academy of Sciences (2009) 106(28):11667-72. doi: 10.1073/pnas.0904715106.
83. Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi Pier P. A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language? Cell 146(3):353-8. doi: 10.1016/j.cell.2011.07.014.
84. Willingham AT, Orth AP, Batalov S, Peters EC, Wen BG, Aza-Blanc P, et al. A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science (New York, NY) (2005) 309(5740):1570-3. Epub 2005/09/06. doi: 10.1126/science. 1115901. PubMed PMID: 16141075.
85. Carrieri C, Cimatti L, Biagioli M, Beugnet A, Zucchelli S, Fedele S, et al. Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature (2012) 491(7424):454-7. doi: http://www.nature.com/nature/journal/v491/n7424/abs/nature11508.html-supplementary-information.
86. Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, Watt AT, et al. The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation. Molecular cell (2010) 39(6):925-38. doi: http://dx.doi.org/10.1016/j.molcel.2010.08.011.
87. Conrad NK. The emerging role of triple helices in RNA biology. Wiley Interdisciplinary Reviews: RNA (2014) 5(1):15-29. doi: 10.1002/wrna.1194.
88. Cruz JA, Westhof E. The Dynamic Landscapes of RNA Architecture. Cell 136(4):604-9. doi: 10.1016/j.cell.2009.02.003.
89. Lescoute A, Westhof E. Topology of three-way junctions in folded RNAs. Rna (2006) 12(1):83-93. doi: 10.1261/rna.2208106.
90. Jia G, Fu Y, Zhao X, Dai Q, Zheng G, Yang Y, et al. N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO. Nature chemical biology (2011) 7(12):885-7. doi: http://www.nature.com/nchembio/journal/v7/n12/abs/nchembio.687.html-supplementary-information.
91. Yang Y, Zhou X, Jin Y. ADAR-mediated RNA editing in non-coding RNA sequences. Science China Life sciences (2013) 56(10):944-52. Epub 2013/09/07. doi: 10.1007/s11427-013-4546-5. PubMed PMID: 24008387.
92. Squires JE, Patel HR, Nousch M, Sibbritt T, Humphreys DT, Parker BJ, et al. Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA. Nucleic Acids Res (2012) 40(11):5023-33. Epub 2012/02/22. doi: 10.1093/nar/gks144. PubMed PMID: 22344696; PubMed Central PMCID: PMCPmc3367185.
93. Chi SW, Hannon GJ, Darnell RB. An alternative mode of microRNA target recognition. Nat Struct Mol Biol (2012) 19(3):321-7. Epub 2012/02/22. doi: 10.1038/nsmb.2230. PubMed PMID: 22343717; PubMed Central PMCID: PMCPmc3541676.
94. Mariner PD, Walters RD, Espinoza CA, Drullinger LF, Wagner SD, Kugel JF, et al. Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Molecular cell (2008) 29(4):499-509. Epub 2008/03/04. doi: 10.1016/j.molcel.2007.12.013. PubMed PMID: 18313387.
95. Kutter C, Watt S, Stefflova K, Wilson MD, Goncalves A, Ponting CP, et al. Rapid Turnover of Long Noncoding RNAs and the Evolution of Gene Expression. PLoS Genet (2012) 8(7):e1002841. doi:.
96. Ponjavic J, Ponting CP, Lunter G. Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome research (2007) 17(5):556-65. doi: 10.1101/gr.6036807. PubMed PMID: PMC1855172.
97. Marques AC, Ponting CP. Intergenic lncRNAs and the evolution of gene expression. Current Opinion in Genetics & Development (2014) 27(0):48-53. doi: http://dx.doi.org/10.1016/j.gde.2014.03.009.
98. Engreitz Jesse M, Sirokman K, McDonel P, Shishkin AA, Surka C, Russell P, et al. RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites. Cell 159(1):188-99. doi: 10.1016/j.cell.2014.08.018.
99. Chu C, Qu K, Zhong FL, Artandi SE, Chang HY. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Molecular cell (2011) 44(4):667-78. Epub 2011/10/04. doi: 10.1016/j.molcel.2011.08.027. PubMed PMID: 21963238; PubMed Central PMCID: PMCPmc3249421.
100. 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(20):2264-9. Epub 2010/10/19. doi: 10.1101/gad.590910. PubMed PMID: 20952535; PubMed Central PMCID: PMCPmc2956204.
101. Clemson CM, Hutchinson JN, Sara SA, Ensminger AW, Fox AH, Chess A, et al. An Architectural Role for a Nuclear Noncoding RNA: NEAT1 RNA Is Essential for the Structure of Paraspeckles. Molecular cell 33(6):717-26. doi: 10.1016/j.molcel.2009.01.026.
102. Imamura K, Imamachi N, Akizuki G, Kumakura M, Kawaguchi A, Nagata K, et al. Long noncoding RNA NEAT1-dependent SFPQ relocation from promoter region to paraspeckle mediates IL8 expression upon immune stimuli. Molecular cell (2014) 53(3):393-406. Epub 2014/02/11. doi: 10.1016/j.molcel.2014.01.009. PubMed PMID: 24507715.
103. Abarrategui I, Krangel MS. Noncoding transcription controls downstream promoters to regulate T-cell receptor alpha recombination. The EMBO journal (2007) 26(20):4380-90. Epub 2007/09/21. doi:10.1038/sj.emboj.7601866. PubMed PMID: 17882258; PubMed Central PMCID: PMCPmc2034674.
104. Bolland DJ, Wood AL, Johnston CM, Bunting SF, Morgan G, Chakalova L, et al. Antisense intergenic transcription in V(D)J recombination. Nat Immunol (2004) 5(6):630-7. doi: http://www.nature.com/ni/journal/v5/n6/suppinfo/ni1068S1.html.
105. Verma-Gaur J, Torkamani A, Schaffer L, Head SR, Schork NJ, Feeney AJ. Noncoding transcription within the Igh distal VH region at PAIR elements affects the 3D structure of the Igh locus in pro-B cells. Proceedings of the National Academy of Sciences (2012) 109(42):17004-9. doi: 10.1073/pnas.1208398109.
106. Kino T, Hurt DE, Ichijo T, Nader N, Chrousos GP. Noncoding RNA gas5 is a growth arrest-and starvation-associated repressor of the glucocorticoid receptor. Science signaling (2010) 3(107):ra8. Epub 2010/02/04. doi: 10.1126/scisignal.2000568. PubMed PMID: 20124551; PubMed Central PMCID: PMCPmc2819218.
107. Williams GT, Mourtada-Maarabouni M, Farzaneh F. A critical role for non-coding RNA GAS5 in growth arrest and rapamycin inhibition in human T-lymphocytes. Biochemical Society transactions (2011) 39(2):482-6. Epub 2011/03/25. doi: 10.1042/bst0390482. PubMed PMID: 21428924.
108. Bird A. Perceptions of epigenetics. Nature (2007) 447(7143):396-8.
109. Goldberg AD, Allis CD, Bernstein E. Epigenetics: A Landscape Takes Shape. Cell (2007) 128(4):635-8. doi: http://dx.doi.org/10.1016/j.cell.2007.02.006.
110. Costa FF. Non-coding RNAs, epigenetics and complexity. Gene (2008) 410(1):9-17. doi: http://dx.doi.org/10.1016/j.gene.2007.12.008.
111. Ansel KM, Lee DU, Rao A. An epigenetic view of helper T cell differentiation. Nat Immunol (2003) 4(7):616-23. Epub 2003/06/28. doi: 10.1038/ni0703-616. PubMed PMID: 12830136.
112. Tripathi SK, Lahesmaa R. Transcriptional and epigenetic regulation of T-helper lineage specification. Immunological reviews (2014) 261(1):62-83. doi: 10.1111/imr.12204.
113. Ansel KM, Djuretic I, Tanasa B, Rao A. Regulation of Th2 differentiation and Il4 locus accessibility. Annual review of immunology (2006) 24:607-56. Epub 2006/03/23. doi: 10.1146/annurev.immunol.23.021704.115821. PubMed PMID: 16551261.
114. Balasubramani A, Mukasa R, Hatton RD, Weaver CT. Regulation of the Ifng locus in the context of T-lineage specification and plasticity. Immunological reviews (2010) 238(1):216-32. Epub 2010/10/26. doi: 10.1111/j.1600-065X.2010.00961.x. PubMed PMID: 20969595; PubMed Central PMCID: PMCPmc3096439.
115. Chang S, Aune TM. Dynamic changes in histone-methylation 'marks' across the locus encoding interferon-gamma during the differentiation of T helper type 2 cells. Nat Immunol (2007) 8(7):723-31. Epub 2007/06/05. doi: 10.1038/ni1473. PubMed PMID: 17546034.
116. Ballas ZK. The use of 5-azacytidine to establish constitutive interleukin 2-producing clones of the EL4 thymoma. The Journal of Immunology (1984) 133(1):7-9.
117. Young HA, Ghosh P, Ye J, Lederer J, Lichtman A, Gerard JR, et al. Differentiation of the T helper phenotypes by analysis of the methylation state of the IFN-gamma gene. Journal of immunology (Baltimore, Md: 1950) (1994) 153(8):3603-10. Epub 1994/10/15. PubMed PMID: 7523497.
118. Bird JJ, Brown DR, Mullen AC, Moskowitz NH, Mahowald MA, Sider JR, et al. Helper T cell differentiation is controlled by the cell cycle. Immunity (1998) 9(2):229-37. Epub 1998/09/05. PubMed PMID: 9729043.
119. Morinobu A, Kanno Y, O'Shea JJ. Discrete roles for histone acetylation in human T helper 1 cell-specific gene expression. The Journal of biological chemistry (2004) 279(39):40640-6. Epub 2004/07/29. doi: 10.1074/jbc. M407576200. PubMed PMID: 15280353.
120. Valapour M, Guo J, Schroeder JT, Keen J, Cianferoni A, Casolaro V, et al. Histone deacetylation inhibits IL4gene expression in T cells. The Journal of allergy and clinical immunology (2002) 109(2):238-45. Epub 2002/02/14. PubMed PMID: 11842291.
121. Hutchins AS, Mullen AC, Lee HW, Sykes KJ, High FA, Hendrich BD, et al. Gene silencing quantitatively controls the function of a developmental trans-activator. Molecular cell (2002) 10(1):81-91. Epub 2002/08/02. PubMed PMID: 12150909.
122. Lee PP, Fitzpatrick DR, Beard C, Jessup HK, Lehar S, Makar KW, et al. A critical role for Dnmt1 and DNA methylation in T cell development, function, and survival. Immunity (2001) 15(5):763-74. Epub 2001/12/01. PubMed PMID: 11728338.
123. Makar KW, Perez-Melgosa M, Shnyreva M, Weaver WM, Fitzpatrick DR, Wilson CB. Active recruitment of DNA methyltransferases regulates interleukin 4 in thymocytes and T cells. Nat Immunol (2003) 4(12):1183-90. Epub 2003/11/05. doi: 10.1038/ni1004. PubMed PMID: 14595437.
124. Yamashita M, Hirahara K, Shinnakasu R, Hosokawa H, Norikane S, Kimura MY, et al. Crucial role of MLL for the maintenance of memory T helper type 2 cell responses. Immunity (2006) 24(5):611-22. Epub 2006/05/23. doi: 10.1016/j.immuni.2006.03.017. PubMed PMID: 16713978.
125. Onodera A, Yamashita M, Endo Y, Kuwahara M, Tofukuji S, Hosokawa H, et al. STAT6-mediated displacement of polycomb by trithorax complex establishes long-term maintenance of GATA3 expression in T helper type 2 cells. The Journal of experimental medicine (2010) 207(11):2493-506. Epub 2010/10/20. doi: 10.1084/jem.20100760. PubMed PMID: 20956546; PubMed Central PMCID: PMCPmc2964576.
126. Kimura M, Koseki Y, Yamashita M, Watanabe N, Shimizu C, KatsumotoT, et al. Regulation of Th2 cell differentiation by mel-18, a mammalian polycomb group gene. Immunity (2001) 15(2):275-87. Epub 2001/08/25. PubMed PMID: 11520462.
127. Yamashita M, Kuwahara M, Suzuki A, Hirahara K, Shinnaksu R, Hosokawa H, et al. Bmi1 regulates memory CD4Tcell survival via repression of the Noxa gene. The Journal of experimental medicine (2008) 205(5):1109-20. Epub 2008/04/16. doi: 10.1084/jem.20072000. PubMed PMID: 18411339; PubMed Central PMCID: PMCPmc2373843.
128. Koyanagi M, Baguet A, Martens J, Margueron R, Jenuwein T, Bix M. EZH2 and histone 3 trimethyl lysine 27 associated with Il4 and Il13 gene silencing in Th1 cells. The Journal of biological chemistry (2005) 280(36):31470-7. Epub 2005/07/13. doi: 10.1074/jbc. M504766200. PubMed PMID: 16009709.
129. Su IH, Dobenecker MW, Dickinson E, Oser M, Basavaraj A, Marqueron R, et al. Polycomb group protein ezh2 controls actin polymerization and cell signaling. Cell (2005) 121(3):425-36. Epub 2005/05/11. doi: 10.1016/j.cell.2005.02.029. PubMed PMID: 15882624.
130. Wei G, Wei L, Zhu J, Zang C, Hu-Li J, Yao Z, et al. Global Mapping of H3K4me3 and H3K27me3 Reveals Specificity and Plasticity in Lineage Fate Determination of Differentiating CD4+ T Cells. Immunity 30(1):155-67. doi: 10.1016/j.immuni.2008.12.009.
131. Hirahara K, Vahedi G, Ghoreschi K, Yang XP, Nakayamada S, Kanno Y, et al. Helper T-cell differentiation and plasticity: insights from epigenetics. Immunology (2011) 134(3):235-45. Epub 2011/10/08. doi: 10.1111/j.1365-2567.2011.03483.x. PubMed PMID: 21977994; PubMed Central PMCID: PMCPmc3209564.
132. Bernstein BE, Meissner A, Lander ES. The mammalian epigenome. Cell (2007) 128(4):669-81. Epub 2007/02/27. doi: 10.1016/j.cell.2007.01.033. PubMed PMID: 17320505.
133. Grogan JL, Mohrs M, Harmon B, Lacy DA, Sedat JW, Locksley RM. Early Transcription and Silencing of Cytokine Genes Underlie Polarization of T Helper Cell Subsets. Immunity (2001) 14(3):205-15. doi: http://dx.doi.org/10.1016/S1074-7613(01)00103-0.
134. Mullen AC, High FA, Hutchins AS, Lee HW, Villarino AV, Livingston DM, et al. Role of T-bet in Commitment of TH1 Cells Before IL-12-Dependent Selection. Science (New York, NY) (2001) 292(5523):1907-10. doi: 10.1126/science. 1059835.
135. Panzer M, Sitte S, Wirth S, Drexler I, Sparwasser T, Voehringer D. Rapid in vivo conversion of effector T cells into Th2 cells during helminth infection. Journal of immunology (Baltimore, Md: 1950) (2012) 188(2):615-23. Epub 2011/12/14. doi: 10.4049/jimmunol. 1101164. PubMed PMID: 22156341.
136. +Th1/Th2 Hybrid Cells Arise In Vivo, Can Develop Directly from Naive Precursors, and Limit Immunopathologic Inflammation. PLoS Biol (2013) 11(8):e1001633. doi: 10.1371/journal.pbio. 1001633.
137. Zhao J, Ohsumi TK, Kung JT, Ogawa Y, Grau DJ, Sarma K, et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular cell (2010) 40(6):939-53. Epub 2010/12/22. doi: 10.1016/j.molcel.2010.12.011. PubMed PMID: 21172659; PubMed Central PMCID: PMCPmc3021903.
138. Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science (New York, NY) (2010) 329(5992):689-93. Epub 2010/07/10. doi: 10.1126/science. 1192002. PubMed PMID: 20616235; PubMed Central PMCID: PMCPmc2967777.
139. Guttman M, Donaghey J, Carey BW, Garber M, Grenier JK, Munson G, et al. lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature (2011) 477(7364):295-300. doi: http://www.nature.com/nature/journal/v477/n7364/abs/nature10398.html-supplementary-information.
140. Schuettengruber B, Ganapathi M, Leblanc B, Portoso M, Jaschek R, Tolhuis B, et al. Functional Anatomy of Polycomb and Trithorax Chromatin Landscapes in Drosophila Embryos. PLoS Biol (2009) 7(1):e1000013. doi: 10.1371/journal.pbio. 1000013.
141. Kassis JA, Brown JL. Polycomb group response elements in Drosophila and vertebrates. Advances in genetics (2013) 81:83-118. Epub 2013/02/20. doi: 10.1016/b978-0-12-407677-8.00003-8. PubMed PMID: 23419717; PubMed Central PMCID: PMCPmc4157523.
142. Bernstein E, Allis CD. RNA meets chromatin. Genes Dev (2005) 19(14):1635-55. Epub 2005/07/19. doi: 10.1101/gad.1324305. PubMed PMID: 16024654.
143. Jeffery L, Nakielny S. Components of the DNA methylation system of chromatin control are RNA-binding proteins. The Journal of biological chemistry (2004) 279(47):49479-87. Epub 2004/09/03. doi: 10.1074/jbc. M409070200. PubMed PMID: 15342650.
144. Hiragami-Hamada K, Fischle W. RNAs-physical and functional modulators of chromatin reader proteins. Biochimica et biophysica acta (2014) 1839(8):737-42. Epub 2014/04/08. doi:10.1016/j.bbagrm.2014.03.015. PubMed PMID: 24704208.
145. Zhao J, Sun BK, Erwin JA, Song J-J, Lee JT. Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome. Science (New York, NY) (2008) 322(5902):750-6. doi: 10.1126/science. 1163045.
146. Pandey RR, Mondal T, Mohammad F, Enroth S, Redrup L, Komorowski J, et al. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Molecular cell (2008) 32(2):232-46. Epub 2008/10/28. doi: 10.1016/j.molcel.2008.08.022. PubMed PMID: 18951091.
147. Yang L, Lin C, Liu W, Zhang J, Ohgi KA, Grinstein JD, et al. ncRNA-and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs. Cell (2011) 147(4):773-88. Epub 2011/11/15. doi: 10.1016/j.cell.2011.08.054. PubMed PMID: 22078878; PubMed Central PMCID: PMCPmc3297197.
148. Chalei V, Sansom SN, Kong L, Lee S, Montiel JF, Vance KW, et al. The long non-coding RNA Dali is an epigenetic regulator of neural differentiation. eLife (2014) 3. Epub 2014/11/22. doi: 10.7554/eLife.04530. PubMed PMID: 25415054.
149. Steffen PA, Ringrose L. What are memories made of? How Polycomb and Trithorax proteins mediate epigenetic memory. Nature reviews Molecular cell biology (2014) 15(5):340-56. Epub 2014/04/24. doi: 10.1038/nrm3789. PubMed PMID: 24755934.
150. Arab K, Park YJ, Lindroth AM, Schafer A, Oakes C, Weichenhan D, et al. Long noncoding RNA TARID directs demethylation and activation of the tumor suppressor TCF21 via GADD45A. Molecular cell (2014) 55(4):604-14. Epub 2014/08/05. doi: 10.1016/j.molcel.2014.06.031. PubMed PMID: 25087872.
151. Iyer LM, Abhiman S, Aravind L. Natural history of eukaryotic DNA methylation systems. Progress in molecular biology and translational science (2011) 101:25-104. Epub 2011/04/22. doi: 10.1016/b978-0-12-387685-0.00002-0. PubMed PMID: 21507349.
152. Ponnaluri VK, Maciejewski JP, Mukherji M. A mechanistic overview of TET-mediated 5-methylcytosine oxidation. Biochem Biophys Res Commun (2013) 436(2):115-20. Epub 2013/06/04. doi: 10.1016/j.bbrc.2013.05.077. PubMed PMID: 23727577.
153. Lee JT. Epigenetic Regulation by Long Noncoding RNAs. Science (New York, NY) (2012) 338(6113):1435-9. doi: 10.1126/science. 1231776.
154. Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell (2007) 129(7):1311-23. Epub 2007/07/03. doi: 10.1016/j.cell.2007.05.022. PubMed PMID: 17604720; PubMed Central PMCID: PMCPmc2084369.
155. Cremer T, Cremer C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet (2001) 2(4):292-301. doi: http://www.nature.com/nrg/journal/v2/n4/suppinfo/nrg0401292aS1.html.
156. Sleeman JE, Trinkle-Mulcahy L. Nuclear bodies: new insights into assembly/dynamics and disease relevance. Current Opinion in Cell Biology (2014) 28(0):76-83. doi: http://dx.doi.org/10.1016/j.ceb.2014.03.004.
157. Reddy KL, Zullo JM, Bertolino E, Singh H. Transcriptional repression mediated by repositioning of genes to the nuclear lamina. Nature (2008) 452(7184):243-7. Epub 2008/02/15. doi: 10.1038/nature06727. PubMed PMID: 18272965.
158. Kumaran RI, Thakar R, Spector DL Chromatin Dynamics and Gene Positioning. Cell 132(6):929-34. doi: 10.1016/j.cell.2008.03.004.
159. Kosak ST, Skok JA, Medina KL, Riblet R, Le Beau MM, Fisher AG, et al. Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science (New York, NY) (2002) 296(5565):158-62. Epub 2002/04/06. doi: 10.1126/science.1068768. PubMed PMID: 11935030.
160. Yao H, Brick K, Evrard Y, Xiao T, Camerini-Otero RD, Felsenfeld G. Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA. Genes Dev (2010) 24(22):2543-55. Epub 2010/10/23. doi: 10.1101/gad.1967810. PubMed PMID: 20966046; PubMed Central PMCID: PMCPmc2975930.
161. Xiang J-F, Yin Q-F, Chen T, Zhang Y, Zhang X-O, Wu Z, et al. Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus. Cell Res (2014) 24(5):513-31. doi: 10.1038/cr.2014.35.
162. Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L, et al. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol (2014) 21(2):198-206. doi: 10.1038/nsmb.2764 http://www.nature.com/nsmb/journal/v21/n2/abs/nsmb.2764.html-supplementary-information.
163. Lai F, Orom UA, Cesaroni M, Beringer M, Taatjes DJ, Blobel GA, et al. Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature (2013) 494(7438):497-501. Epub 2013/02/19. doi: 10.1038/nature11884. PubMed PMID: 23417068; PubMed Central PMCID: PMCPmc4109059.
164. Orom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, et al. Long noncoding RNAs with enhancer-like function in human cells. Cell (2010) 143(1):46-58. Epub 2010/10/05. doi: 10.1016/j.cell.2010.09.001. PubMed PMID: 20887892; PubMed Central PMCID: PMCPmc4108080.
165. Krivega I, Dean A. Enhancer and promoter interactions-long distance calls. Curr Opin Genet Dev (2012) 22(2):79-85. Epub 2011/12/16. doi: 10.1016/j.gde.2011.11.001. PubMed PMID: 22169023; PubMed Central PMCID: PMCPmc3342482.
166. Kagey MH, Newman JJ, Bilodeau S, Zhan Y, Orlando DA, van Berkum NL, et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature (2010) 467(7314):430-5. doi: http://www.nature.com/nature/journal/v467/n7314/abs/nature09380.html-supplementary-information.
167. O'Shea JJ, Paul WE. Mechanisms underlying lineage commitment and plasticity of helper CD4+ T cells. Science (New York, NY) (2010) 327(5969):1098-102. Epub 2010/02/27. doi: 10.1126/science.1178334. PubMed PMID: 20185720; PubMed Central PMCID: PMCPmc2997673.
168. Geginat J, Paroni M, Maglie S, Alfen JS, Kastirr I, Gruarin P, et al. Plasticity of human CD4 T cell subsets. Frontiers in immunology (2014) 5:630. Epub 2015/01/08. doi: 10.3389/fimmu.2014.00630. PubMed PMID: 25566245; PubMed Central PMCID: PMCPmc4267263.
169. Hedrich CM, Bream JH. Cell type-specific regulation of IL-10 expression in inflammation and disease. Immunologic research (2010) 47(1-3):185-206. doi: 10.1007/s12026-009-8150-5. PubMed PMID: PMC2892196.
170. Chen Z, Tato CM, Muul L, Laurence A, O'Shea JJ. Distinct regulation of interleukin-17 in human T helper lymphocytes. Arthritis and rheumatism (2007) 56(9):2936-46. Epub 2007/09/01. doi: 10.1002/art.22866. PubMed PMID: 17763419; PubMed Central PMCID: PMCPmc2323677.
171. Wilson NJ, Boniface K, Chan JR, McKenzie BS, Blumenschein WM, Mattson JD, et al. Development, cytokine profile and function of human interleukin 17-producing helper T cells. Nat Immunol (2007) 8(9):950-7. Epub 2007/08/07. doi: 10.1038/ni1497. PubMed PMID: 17676044.
172. Zhang F, Meng G, Strober W. Interactions among the transcription factors Runx1, RORgammat and Foxp3 regulate the differentiation of interleukin 17-producing T cells. Nat Immunol (2008) 9(11):1297-306. Epub 2008/10/14. doi: 10.1038/ni.1663. PubMed PMID: 18849990.
173. Klunker S, Chong MM, Mantel PY, Palomares O, Bassin C, Ziegler M, et al. Transcription factors RUNX1 and RUNX3 in the induction and suppressive function of Foxp3+ inducible regulatory T cells. The Journal of experimental medicine (2009) 206(12):2701-15. Epub 2009/11/18. doi: 10.1084/jem. 20090596. PubMed PMID: 19917773; PubMed Central PMCID: PMCPmc2806624.
174. Li L, Patsoukis N, Petkova V, Boussiotis VA. Runx1 and Runx3 Are Involved in the Generation and Function of Highly Suppressive IL-17-Producing T Regulatory Cells. PLoS ONE (2012) 7(9):e45115. doi: 10.1371/journal.pone.0045115.
175. Chung Y, Tanaka S, Chu F, Nurieva RI, Martinez GJ, Rawal S, et al. Follicular regulatory T cells expressing Foxp3 and Bcl-6 suppress germinal center reactions. Nat Med (2011) 17(8):983-8. doi: http://www.nature.com/nm/journal/v17/n8/abs/nm.2426.html-supplementary-information.
176. Tsuji M, Komatsu N, Kawamoto S, Suzuki K, Kanagawa O, Honjo T, et al. Preferential generation of follicular B helper T cells from Foxp3+ T cells in gut Peyer's patches. Science (New York, NY) (2009) 323(5920):1488-92. Epub 2009/03/17. doi: 10.1126/science. 1169152. PubMed PMID: 19286559.
177. Rossi RL, Rossetti G, Wenandy L, Curti S, Ripamonti A, Bonnal RJP, et al. Distinct microRNA signatures in human lymphocyte subsets and enforcement of the naive state in CD4+ T cells by the microRNA miR-125b. Nat Immunol (2011) 12(8):796-803. doi: http://www.nature.com/ni/journal/v12/n8/abs/ni.2057.html-supplementary-information.
178. Turner M, Galloway A, Vigorito E. Noncoding RNA and its associated proteins as regulatory elements of the immune system. Nat Immunol (2014) 15(6):484-91. doi: 10.1038/ni.2887.
179. Barabasi A-L, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet (2004) 5(2):101-13.
180. Zhang B, Arun G, Mao Yuntao S, Lazar Z, Hung G, Bhattacharjee G, et al. The lncRNA Malat1 Is Dispensable for Mouse Development but Its Transcription Plays a cis-Regulatory Role in the Adult. Cell reports 2(1):111-23. doi: 10.1016/j.celrep.2012.06.003.
181. Necsulea A, Kaessmann H. Evolutionary dynamics of coding and non-coding transcriptomes. Nat Rev Genet (2014) 15(11):734-48. doi: 10.1038/nrg3802.
182. Pollard KS, Salama SR, King B, Kern AD, Dreszer T, Katzman S, et al. Forces Shaping the Fastest Evolving Regions in the Human Genome. PLoS Genet (2006) 2(10):e168. doi: 10.1371/journal.pgen.0020168.
183. Schorderet P, Duboule D. Structural and Functional Differences in the Long Non-Coding RNA Hotair in Mouse and Human. PLoS Genet (2011) 7(5):e1002071. doi:10.1371/journal.pgen.1002071.
184. Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, et al. Comparative analysis of the transcriptome across distant species. Nature (2014) 512(7515):445-8. Epub 2014/08/29. doi: 10.1038/nature13424. PubMed PMID: 25164755; PubMed Central PMCID: PMCPmc4155737.
185. On T, Xiong X, Pu S, Turinsky A, Gong Y, Emili A, et al. The evolutionary landscape of the chromatin modification machinery reveals lineage specific gains, expansions, and losses. Proteins (2010) 78(9):2075-89. Epub 2010/05/11. doi: 10.1002/prot.22723. PubMed PMID: 20455264.
186. Hrdlickova B, Kumar V, Kanduri K, Zhernakova D, Tripathi S, Karjalainen J, et al. Expression profiles of long non-coding RNAs located in autoimmune disease-associated regions reveal immune cell-type specificity. Genome Medicine (2014) 6(10):88. PubMed PMID: doi:10.1186/s13073-014-0088-0.
187. Xia F, Dong F, Yang Y, Huang A, Chen S, Sun D, et al. Dynamic Transcription of Long Non-Coding RNA Genes during CD4+ T Cell Development and Activation. PLoS ONE (2014) 9(7):e101588. doi:10.1371/journal.pone.0101588.
188. Aoki K, Harashima A, Sano M, Yokoi T, Nakamura S, Kibata M, et al. A thymus-specific noncoding RNA, Thy-ncR1, is a cytoplasmic riboregulator of MFAP4 mRNA in immature T-cell lines. BMC Molecular Biology (2010) 11(1):99. PubMed PMID: doi:10.1186/1471-2199-11-99.
189. Hu G, Tang Q, Sharma S, Yu F, Escobar TM, Muljo SA, et al. Expression and regulation of intergenic long noncoding RNAs during T cell development and differentiation. Nat Immunol (2013) 14(11):1190-8. doi: 10.1038/ni.2712 http://www.nature.com/ni/journal/v14/n11/abs/ni.2712.html-supplementary-information.
190. Kimura T, Jiang S, Nishizawa M, Yoshigai E, Hashimoto I, Nishikawa M, et al. Stabilization of human interferon-alpha1 mRNA by its antisense RNA. Cellular and molecular life sciences: CMLS (2013) 70(8):1451-67. Epub 2012/12/12. doi: 10.1007/s00018-012-1216-x. PubMed PMID: 23224365; PubMed Central PMCID: PMCPmc3607724.
191. Yan M-D, Hong C-C, Lai G-M, Cheng A-L, Lin Y-W, Chuang S-E. Identification and characterization of a novel gene Saf transcribed from the opposite strand of Fas. Human molecular genetics (2005) 14(11):1465-74. doi: 10.1093/hmg/ddi156.
192. Sehgal L, Mathur R, Braun FK, Wise JF, Berkova Z, Neelapu S, et al. FAS-antisense 1 lncRNA and production of soluble versus membrane Fas in B-cell lymphoma. Leukemia (2014) 28(12):2376-87. doi: 10.1038/leu.2014.126.
193. Haasch D, Chen YW, Reilly RM, Chiou XG, Koterski S, Smith ML, et al. T cell activation induces a noncoding RNA transcript sensitive to inhibition by immunosuppressant drugs and encoded by the proto-oncogene, BIC. Cellular immunology (2002) 217(1-2):78-86. Epub 2002/11/12. PubMed PMID: 12426003.
194. Liu AY, Torchia BS, Migeon BR, Siliciano RF. The human NTT gene: identification of a novel 17-kb noncoding nuclear RNA expressed in activated CD4+ T cells. Genomics (1997) 39(2):171-84. Epub 1997/01/15. doi: 10.1006/geno.1996.4463. PubMed PMID: 9027504.
195. Abarrategui I, Krangel MS. Regulation of T cell receptor-alpha gene recombination by transcription. Nat Immunol (2006) 7(10):1109-15. Epub 2006/08/29. doi: 10.1038/ni1379. PubMed PMID: 16936730.
196. Collier SP, Collins PL, Williams CL, Boothby MR, Aune TM. Cutting edge: influence of Tmevpg1, a long intergenic noncoding RNA, on the expression of Ifng by Th1 cells. Journal of immunology (Baltimore, Md: 1950) (2012) 189(5):2084-8. Epub 2012/08/02. doi: 10.4049/jimmunol.1200774. PubMed PMID: 22851706; PubMed Central PMCID: PMCPmc3424368.
197. Gomez JA, Wapinski OL, Yang YW, Bureau JF, Gopinath S, Monack DM, et al. The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-gamma locus. Cell (2013) 152(4):743-54. Epub 2013/02/19. doi: 10.1016/j.cell.2013.01.015. PubMed PMID: 23415224; PubMed Central PMCID: PMCPmc3577098.
198. Zhang H, Nestor CE, Zhao S, Lentini A, Bohle B, Benson M, et al. Profiling of human CD4+ T-cell subsets identifies the TH2-specific noncoding RNA GATA3-AS1. The Journal of allergy and clinical immunology (2013) 132(4):1005-8. Epub 2013/07/23. doi: 10.1016/j.jaci.2013.05.033. PubMed PMID: 23870669.
199. Seok J, Warren HS, Cuenca AG, Mindrinos MN, Baker HV, Xu W, et al. Genomic responses in mouse models poorly mimic human inflammatory diseases. Proceedings of the National Academy of Sciences (2013) 110(9):3507-12. doi: 10.1073/pnas.1222878110.
200. Takao K, Miyakawa T. Genomic responses in mouse models greatly mimic human inflammatory diseases. Proceedings of the National Academy of Sciences (2014). doi: 10.1073/pnas.1401965111.
201. Tuomela S, Lahesmaa R. Early T helper cell programming of gene expression in human. Seminars in immunology (2013) 25(4):282-90. Epub 2013/11/20. doi: 10.1016/j.smim.2013.10.013. PubMed PMID: 24246225.
202. Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, et al. The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature (2014) 505(7485):635-40. doi: 10.1038/nature12943 http://www.nature.com/nature/journal/v505/n7485/abs/nature12943.html-supplementary-information.
203. Nesterova TB, Slobodyanyuk SY, Elisaphenko EA, Shevchenko AI, Johnston C, Pavlova ME, et al. Characterization of the genomic Xist locus in rodents reveals conservation of overall gene structure and tandem repeats but rapid evolution of unique sequence. Genome research (2001) 11(5):833-49. Epub 2001/05/05. doi: 10.1101/gr.174901. PubMed PMID: 11337478; PubMed Central PMCID: PMCPmc311126.
204. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev (2011) 25(18):1915-27. Epub 2011/09/06. doi: 10.1101/gad.17446611. PubMed PMID: 21890647; PubMed Central PMCID: PMCPmc3185964.
205. Church DM, Goodstadt L, Hillier LW, Zody MC, Goldstein S, She X, et al. Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse. PLoS Biol (2009) 7(5):e1000112. doi: 10.1371/journal.pbio. 1000112.
206. Pang KC, Frith MC, Mattick JS. Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends in Genetics (2006) 22(1):1-5. doi: http://dx.doi.org/10.1016/j.tig.2005.10.003.
207. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, et al. The transcriptional landscape of the mammalian genome. Science (New York, NY) (2005) 309(5740):1559-63. Epub 2005/09/06. doi:10.1126/science.1112014. PubMed PMID: 16141072.
208. Ulitsky I, Shkumatava A, Jan Calvin H, Sive H, Bartel David P. Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution. Cell 147(7):1537-50. doi: 10.1016/j.cell.2011.11.055.
209. He S, Liu S, Zhu H. The sequence, structure and evolutionary features of HOTAIR in mammals. BMC evolutionary biology (2011) 11:102. Epub 2011/04/19. doi: 10.1186/1471-2148-11-102. PubMed PMID: 21496275; PubMed Central PMCID: PMCPmc3103462.
210. Schorderet P, Duboule D. Structural and functional differences in the long non-coding RNA hotair in mouse and human. PLoS genetics (2011) 7(5):e1002071. Epub 2011/06/04. doi:10.1371/journal.pgen. 1002071. PubMed PMID: 21637793; PubMed Central PMCID: PMCPmc3102750.
211. Zhang X, Lian Z, Padden C, Gerstein MB, Rozowsky J, Snyder M, et al. A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster. Blood (2009) 113(11):2526-34. Epub 2009/01/16. doi: 10.1182/blood-2008-06-162164. PubMed PMID: 19144990; PubMed Central PMCID: PMCPmc2656274.
212. Wright PW, Huehn A, Cichocki F, Li H, Sharma N, Dang H, et al. Identification of a KIR antisense lncRNA expressed by progenitor cells. Genes and immunity (2013) 14(7):427-33. Epub 2013/07/19. doi: 10.1038/gene.2013.36. PubMed PMID: 23863987; PubMed Central PMCID: PMCPmc3808466.
213. Wang P, Xue Y, Han Y, Lin L, Wu C, Xu S, et al. The STAT3-binding long noncoding RNA lnc-DC controls human dendritic cell differentiation. Science (New York, NY) (2014) 344(6181):310-3. Epub 2014/04/20. doi: 10.1126/science.1251456. PubMed PMID: 24744378.
214. Sehgal L, Mathur R, Braun FK, Wise JF, Berkova Z, Neelapu S, et al. FAS-antisense 1 lncRNA and production of soluble versus membrane Fas in B-cell lymphoma. Leukemia (2014). Epub 2014/05/09. doi: 10.1038/leu.2014.126. PubMed PMID: 24811343.
215. Xing Z, Lin A, Li C, Liang K, Wang S, Liu Y, et al. lncRNA Directs Cooperative Epigenetic Regulation Downstream of Chemokine Signals. Cell (2014) 159(5):1110-25. doi: http://dx.doi.org/10.1016/j.cell.2014.10.013.
216. Carpenter S, Aiello D, Atianand MK, Ricci EP, Gandhi P, Hall LL, et al. A Long Noncoding RNA Mediates Both Activation and Repression of Immune Response Genes. Science (New York, NY) (2013) 341(6147):789-92. doi: 10.1126/science. 1240925.
217. Rapicavoli NA, Qu K, Zhang J, Mikhail M, Laberge R-M, Chang HY. A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics. Gingeras T, editor(2013).
218. Li Z, Chao T-C, Chang K-Y, Lin N, Patil VS, Shimizu C, et al. The long noncoding RNA THRIL regulates TNFa expression through its interaction with hnRNPL. Proceedings of the National Academy of Sciences (2014) 111(3):1002-7. doi: 10.1073/pnas.1313768111.
219. Imamura K, Imamachi N, Akizuki G, Kumakura M, Kawaguchi A, Nagata K, et al. Long Noncoding RNA NEAT1-Dependent SFPQ Relocation from Promoter Region to Paraspeckle Mediates IL8 Expression upon Immune Stimuli. Molecular cell (2014) 53(3):393-406. doi: http://dx.doi.org/10.1016/j.molcel.2014.01.009.
220. Kino T, Hurt DE, Ichijo T, Nader N, Chrousos GP. Noncoding RNA Gas5 Is a Growth Arrest and Starvation-Associated Repressor of the Glucocorticoid Receptor. Science signaling (2010) 3(107):ra8. doi: 10.1126/scisignal.2000568. PubMed PMID: PMC2819218.
221. Pang KC, Dinger ME, Mercer TR, Malquori L, Grimmond SM, Chen W, et al. Genome-Wide Identification of Long Noncoding RNAs in CD8+ T Cells. The Journal of Immunology (2009) 182(12):7738-48. doi: 10.4049/jimmunol. 0900603.
222. Hu G, Tang Q, Sharma S, Yu F, Escobar TM, Muljo SA, et al. Expression and regulation of lincRNAs during T cell development and differentiation. Nature immunology (2013) 14(11):1190-8. doi: 10.1038/ni.2712. PubMed PMID: PMC3805781.
223. Verma-Gaur J, Torkamani A, Schaffer L, Head SR, Schork NJ, Feeney AJ. Noncoding transcription within the Igh distal V(H) region at PAIR elements affects the 3D structure of the Igh locus in pro-B cells. Proceedings of the National Academy of Sciences of the United States of America (2012) 109(42):17004-9. doi: 10.1073/pnas.1208398109. PubMed PMID: PMC3479473.
224. Mosmann TR, Cherwinski H, Bond MW, Giedlin MA, Coffman RL. Two types of murine helper T cell clone. I. Definition according to profiles of lymphokine activities and secreted proteins. Journal of immunology (Baltimore, Md: 1950) (1986) 136(7):2348-57. Epub 1986/04/01. PubMed PMID: 2419430.
225. Chang S, Aune TM. Histone hyperacetylated domains across the Ifng gene region in natural killer cells and T cells. Proceedings of the National Academy of Sciences of the United States of America (2005) 102(47):17095-100. Epub 2005/11/16. doi: 10.1073/pnas.0502129102. PubMed PMID: 16286661; PubMed Central PMCID: PMCPmc1283154.
226. Zhou W, Chang S, Aune TM. Long-range histone acetylation of the Ifng gene is an essential feature of T cell differentiation. Proceedings of the National Academy of Sciences of the United States of America (2004) 101(8):2440-5. Epub 2004/02/26. PubMed PMID: 14983028; PubMed Central PMCID: PMCPmc356969.
227. Ho IC, Lo D, Glimcher LH. c-maf promotes T helper cell type 2 (Th2) and attenuates Th1 differentiation by both interleukin 4-dependent and-independent mechanisms. The Journal of experimental medicine (1998) 188(10):1859-66. Epub 1998/11/17. PubMed PMID: 9815263; PubMed Central PMCID: PMCPmc2212398.
228. Liu X, Nurieva RI, Dong C. Transcriptional regulation of follicular T-helper (Tfh) cells. Immunological reviews (2013) 252(1):139-45. Epub 2013/02/15. doi: 10.1111/imr.12040. PubMed PMID: 23405901; PubMed Central PMCID: PMCPmc3579502.
229. Sato K, Miyoshi F, Yokota K, Araki Y, Asanuma Y, Akiyama Y, et al. Marked induction of c-Maf protein during Th17 cell differentiation and its implication in memory Th cell development. The Journal of biological chemistry (2011) 286(17):14963-71. Epub 2011/03/16. doi: 10.1074/jbc. M111.218867. PubMed PMID: 21402704; PubMed Central PMCID: PMCPmc3083235.
230. Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature (2010) 464(7291):1071-6. Epub 2010/04/16. doi: 10.1038/nature08975. PubMed PMID: 20393566; PubMed Central PMCID: PMCPmc3049919.