Long noncoding RNA and epigenomics

Advances in Experimental Medicine and Biology

Volumn 722, Issue , 2011, Pages 174-195

  Kanduri, Chandrasekhar ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

UNTRANSLATED RNA;

ARTICLE; CHROMATIN; CHROMATIN STRUCTURE; DEVELOPMENT; EMBRYOLOGY; EPIGENETICS; EUKARYOTE; GENETIC CODE; GENETIC TRANSCRIPTION; GENOME; GENOME IMPRINTING; HETEROCHROMATIN; HOMEOBOX; HUMAN; NONHUMAN; PHYSIOLOGY; PRIORITY JOURNAL; TRANSCRIPTION REGULATION; X CHROMOSOME;

ANIMALS; CENTROMERE; CHROMATIN; DROSOPHILA MELANOGASTER; EPIGENESIS, GENETIC; EPIGENOMICS; HUMANS; MICE; MICRORNAS; MODELS, GENETIC; RNA, SMALL INTERFERING; RNA, SMALL NUCLEOLAR; RNA, UNTRANSLATED; SCHIZOSACCHAROMYCES;

EUKARYOTA;

EID: 80053585923     PISSN: 00652598     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4614-0332-6_11     Document Type: Article

References (98)

1. Mattick JS. RNA regulation: a new genetics?. Nat Rev Genet 2004; 5(4):316-323. (Pubitemid 38435628)
2. Kapranov P, Cheng J, Dike S et al. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 2007; 316(5830):1484-1488. (Pubitemid 46906616)
3. Cheng J, Kapranov P, Drenkow J et al. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 2005; 308(5725):1149-1154. (Pubitemid 40696429)
4. PrasanthKV, SpectorDL. Eukaryotic regulatory RNAs: ananswertothe 'genome complexity' conundrum. Genes Dev 2007; 21(1):11-42.
5. Mercer TR, Dinger ME, Mattick JS. Long noncoding RNAs: insights into functions. Nat Rev Genet 2009; 10(3):155-159.
6. Whitehead J, Pandey GK, Kanduri C. Regulation of the mammalian epigenome by long noncoding RNAs. Biochim Biophys Acta 2008.
7. Faghihi MA, Wahlestedt C. Regulatory roles of natural antisense transcripts. Nat Rev Mol Cell Biol 2009; 10(9):637-643.
8. Collins LJ, Penny D. The RNA infrastructure: dark matter of the eukaryotic cell?. Trends Genet 2009; 25(3):120-128.
9. Collins LJ, Chen XS. Ancestral RNA: the RNA biology of the eukaryotic ancestor. RNA Biol 2009; 6(5):495-502.
10. Guttman M, Amit I, Garber M et al. Chromatin signature reveals over a thousand highly conserved large noncoding RNAs in mammals. Nature 2009; 458(7235):223-227.
11. Brosnan CA, Voinnet O. The long and the short of noncoding RNAs. Curr Opin Cell Biol 2009; 21(3):416-425.
12. Seto AG, Kingston RE, Lau NC. The coming ofage for Piwi proteins. Mol Cell 2007; 26(5):603-609.
13. Aravin AA, Hannon GJ, Brennecke J. The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science 2007; 318(5851):761-764. (Pubitemid 351411762)
14. Kanduri C, Whitehead J, Mohammad F. The long and the short of it: RNA-directed chromatin asymmetry in mammalian X-chromosome inactivation. FEBS Lett 2009; 583(5):857-864.
15. Lee JT. Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome. Genes Dev 2009; 23(16):1831-1842.
16. Mohammad F, Mondal T, Kanduri C. Epigenetics of imprinted long noncoding RNAs. Epigenetics 2009; 4(5):277-286.
17. ClemsonCM, Hutchinson JN, SaraSAet al. An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure ofparaspeckles. Mol Cell 2009; 33(6):717-726.
18. Sasaki YT, Ideue T, Sano M et al. MENepsilon/beta noncoding RNAs are essential for structural integrity ofnuclear paraspeckles. Proc Natl Acad Sci USA 2009; 106(8):2525-2530.
19. Schoeftner S, Blasco MA. A'higher order' of telomere regulation: telomere heterochromatin and telomeric RNAs. EMBO J 2009; 28(16):2323-2336.
20. Wong LH, Brettingham-Moore KH, Chan L et al. Centromere RNA is a key component for the assembly of nucleoproteins atthe nucleolus and centromere. Genome Res 2007; 17(8):1146-1160. (Pubitemid 47204858)
21. Ferri F, Bouzinba-Segard H, Velasco G et al. Non-coding murine centromeric transcripts associate with and potentiate Aurora B kinase. Nucleic Acids Res 2009; 37(15):5071-5080.
22. Willingham AT, Orth AP, Batalov S et al. A strategy for probing the function of noncoding RNAs finds arepressor ofNFAT. Science 2005; 309(5740):1570-1573. (Pubitemid 41266484)
23. Mondal T, Rasmussen M, Pandey GK et al. Characterization of the RNA content of chromatin. Genome Res 2010; 20:899-907.
24. Kanduri C. Functional insights into long antisense noncoding RNA Kcnq1ot1 mediated bidirectional silencing. RNA Biol 2008; 5(4):208-211.
25. Wilusz JE, Sunwoo H, Spector DL. Long noncoding RNAs: functional surprises from the RNA world. Genes Dev 2009; 23(13):1494-1504.
26. Rinn JL, Kertesz M, Wang JK et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 2007; 129(7):1311-1323. (Pubitemid 46962090)
27. Katayama S, Tomaru Y, Kasukawa T et al. Antisense transcription in the mammalian transcriptome. Science 2005; 309(5740):1564-1566.
28. Yu W, Gius D, Onyango P et al. Epigenetic silencing of tumour suppressor gene pl5 by its antisense RNA. Nature 2008; 451(7175):202-206.
29. Houseley J, Rubbi L, Grunstein M et al. A ncRNA modulates histone modification and mRNA induction in the yeast GAL gene cluster. Mol Cell 2008; 32(5):685-695.
30. Ligtenberg MJ, Kuiper RP, Chan TL et al. Heritable somatic methylation and inactivation of MSH2 in families withLynch syndrome due to deletion ofthe3'exonsofTACSTDl. NatGenet2009;41(l):112-117.
31. Tufarelli C, Stanley JA, Garrick D et al. Transcription of antisense RNA leading to gene silencing and methylation as anovel cause ofhuman genetic disease. Nat Genet 2003; 34(2):157-165. (Pubitemid 36666926)
32. Hekimoglu B, Ringrose L. Non-coding RNAs in polycomb/trithorax regulation. RNA Biol 2009; 6(2):129-137.
33. Hirota K, Miyoshi T, Kugou K et al. Stepwise chromatin remodelling by a cascade of transcription initiation ofnoncoding RNAs. Nature 2008; 456(7218):130-134.
34. Morris KV, Santoso S, Turner AM et al. Bidirectional transcription directs both transcriptional gene activation and suppression in human cells. PLoS Genet 2008; 4(11):e1000258.
35. Ringrose L, Paro R. Polycomb/Trithorax response elements and epigenetic memory of cell identity. Development 2007; 134(2):223-232.
36. Schuettengruber B, Cavalli G. Recruitment of polycomb group complexes and their role in the dynamic regulation ofcell fate choice. Development 2009; 136(21):3531-3542.
37. Sessa L, Breiling A, Lavorgna G et al. Noncoding RNA synthesis and loss of Polycomb group repression accompanies the colinear activation of the human HOXA cluster. RNA 2007; 13(2):223-239. (Pubitemid 46147898)
38. Sanchez-Eisner T, Gou D, Kremmer E et al. Noncoding RNAs of trithorax response elements recruit Drosophila Ash1 to Ultrabithorax. Science 2006; 311(5764):1118-1123.
39. Petruk S, Sedkov Y, Riley KM et al. Transcription of bxd noncoding RNAs promoted by trithorax represses Ubx in cis by transcriptional interference. Cell 2006; 127(6):1209-1221. (Pubitemid 44894524)
40. Dinger ME, Amaral PP, Mercer TR et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 2008; 18(9):1433-1445.
41. Kelley RL, Kuroda MI. Noncoding RNA genes in dosage compensation and imprinting. Cell 2000; 103(1):9-12.
42. Hallacli E, Akhtar A. X chromosomal regulation in flies: when less is more. Chromosome Res 2009; 17(5):603-619.
43. Heard E, Clerc P, Avner P. X-chromosome inactivation in mammals. Annu Rev Genet 1997; 31:571-610. (Pubitemid 28023720)
44. Ilik I, Akhtar A. roX RNAs: noncoding regulators of the male X chromosome in flies. RNA Biol 2009; 6(2):113-121.
45. Wutz A, Gribnau J. X inactivation Xplained. Curr Opin Genet Dev 2007; 17(5):387-393. (Pubitemid 350016894)
46. Brockdorff N, Ashworth A, Kay GF et al. The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus. Cell 1992; 71:515-526.
47. Lee JT, Davidow LS, Warshawsky D. Tsix, a gene antisense to Xist at the X-inactivation centre. Nat Genet 1999; 21(4):400-404. (Pubitemid 29159577)
48. Lee JT. Regulation of X-chromosome counting by Tsix and Xite sequences. Science 2005; 309(5735):768-771. (Pubitemid 41077322)
49. Zhao J, Sun BK, Erwin JA et al. Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science 2008; 322(5902):750-756.
50. Cohen DE, Davidow LS, Erwin JA et al. The DXPas34 repeat regulates random and imprinted X inactivation. Dev Cell 2007; 12(1):57-71. (Pubitemid 46002600)
51. Vigneau S, Augui S, Navarro P et al. An essential role for the DXPas34 tandem repeat and Tsix transcription in the counting process of X chromosome inactivation. Proc Natl Acad Sci USA 2006; 103(19):7390-7395. (Pubitemid 43727843)
52. Ogawa Y, Sun BK, Lee JT. Intersection of the RNA interference and X-inactivation pathways. Science 2008; 320(5881):1336-1341. (Pubitemid 351929469)
53. Rougeulle C, Avner P. Controlling X-inactivation in mammals: what does the centre hold?. Semin Cell Dev Biol 2003; 14(6):331-340. (Pubitemid 38172999)
54. Kalantry S, Purushothaman S, Bowen RB et al. Evidence of Xist RNA-independent initiation of mouse imprinted X-chromosome inactivation. Nature 2009; 460(7255):647-651.
55. Navarro P, Chambers I, Karwacki-Neisius Vet al. Molecular coupling ofXist regulation and pluripotency. Science 2008; 321(5896):1693-1695.
56. Navarro P, Pichard S, Ciaudo C et al. Tsixtranscription across the Xist gene alters chromatin conformation without affecting Xist transcription: implications for X-chromosome inactivation. Genes Dev 2005; 19(12):1474-1484. (Pubitemid 41003014)
57. Navarro P, Chantalat S, Foglio M et al. A role for noncoding Tsix transcription in partitioning chromatin domains within the mouse X-inactivation centre. Epigenetics Chromatin 2009; 2(1):8.
58. Monkhorst K, Jonkers I, Rentmeester E et al. X inactivation counting and choice is a stochastic process: evidence for involvement of an X-linked activator. Cell 2008; 132(3):410-421. (Pubitemid 351191999)
59. Donohoe ME, Silva SS, Pinter SF et al. The pluripotency factor Oct4 interacts with Ctcf and also controls X-chromosome pairing and counting. Nature 2009; 460(7251):128-132.
60. XuN, Donohoe ME, Silva SS et al. Evidence thathomologous X-chromosome pairing requires transcription and Ctcfprotein. Nat Genet 2007; 39(11):1390-1396. (Pubitemid 350035004)
61. Augui S, FilionGJ, Huart S et al. Sensing X chromosome pairs before X inactivation via a novel X-pairing region ofthe Xic. Science 2007; 318(5856):1632-1636. (Pubitemid 350233663)
62. Sun BK, Deaton AM, Lee JT. A transient heterochromatic state in Xist preempts X inactivation choice without RNA stabilization. Mol Cell 2006; 21(5):617-628. (Pubitemid 43290729)
63. Gilfillan GD, Dahlsveen IK, Becker PB. Lifting a chromosome: dosage compensation in Drosophila melanogaster. FEBS Lett 2004; 567(1):8-14. (Pubitemid 38686416)
64. Franke A, Baker BS. The roxl and rox2 RNAs are essential components of the compensasome, which mediates dosage compensation in Drosophila. Mol Cell 1999; 4(1):117-122. (Pubitemid 29386137)
65. Alekseyenko AA, Peng S, Larschan E et al. A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome. Cell 2008; 134(4):599-609.
66. Kind J, Vaquerizas JM, Gebhardt P et al. Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila. Cell 2008; 133(5):813-828. (Pubitemid 351707688)
67. LinCH, Jackson AL, Guo Jet al. Myc-regulatedmicroRNAs attenuate embryonic stem cell differentiation. EMBO J 2009; 28(20):3157-3170.
68. Xu N, Papagiannakopoulos T, Pan G et al. MicroRNA-145 regulates OCT4, SOX2 and KLF4 and represses pluripotency in human embryonic stem cells. Cell 2009; 137(4):647-658.
69. Sheik Mohamed J, Gaughwin PM, Lim B et al. Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells. RNA 2009.
70. Peters J, Robson JE. Imprinted noncoding RNAs. Mamm Genome 2008; 19(7-8):493-502.
71. Royo H, Cavaille J. Non-coding RNAs in imprinted gene clusters. Biol Cell 2008; 100(3):149-166. (Pubitemid 351372674)
72. Lewis A, Reik W. How imprinting centres work. Cytogenet Genome Res 2006; 113(1-4):81-89.
73. Kanduri C, Pant V, Loukinov D et al. Functional interaction of CTCF with the insulator upstream of the H19 gene is parent of origin-specific and methylation-sensitive. Curr Biol 2000; 10:853-856. (Pubitemid 30597205)
74. Kanduri C, Holmgren C, Franklin G et al. The 5'-flank of the murine H19 gene in an unusual chromatin conformation unidirectionally blocks enhancer-promoter communication. Curr Biol 2000; 10:449-457. (Pubitemid 30247332)
75. Pandey RR, Mondal T, Mohammad F et al. Kcnqlotl antisense noncoding RNAmediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell 2008; 32(2):232-246.
76. Pandey RR, Ceribelli M, Singh PB et al. NF-Y regulates the antisense promoter, bidirectional silencing and differential epigenetic marks of the Kcnql imprinting control region. J Biol Chem 2004; 279(50):52685-52693. (Pubitemid 39656644)
77. Thakur N, Tiwari VK, Thomassin H et al. An antisense RNA regulates the bidirectional silencing property ofthe kcnql imprinting control region. Mol Cell Biol 2004; 24(18):7855-7862. (Pubitemid 39167437)
78. Kanduri C, Thakur N, Pandey RR. The length of the transcript encoded from the Kcnqlotl antisense promoter determines the degree of silencing. EMBO J 2006; 25(10):2096-2106.
79. Mancini-Dinardo D, Steele SJ, Levorse JM et al. Elongation of the Kcnqlotl transcript is required for genomic imprinting of neighboring genes. Genes Dev 2006; 20(10):1268-1282. (Pubitemid 43727588)
80. Shin JY, Fitzpatrick GV, Higgins MJ. Two distinct mechanisms of silencing by the KvDMRl imprinting control region. EMBO J 2008; 27(1):168-178.
81. Koerner MV, Pauler FM, Huang R et al. The function of noncoding RNAs in genomic imprinting. Development 2009; 136(11):1771-1783.
82. Sleutels F, Zwart R, Barlow DP. The noncoding Air RNA is required for silencing autosomal imprinted genes. Nature 2002; 415(6873):810-813. (Pubitemid 34150505)
83. Nagano T, Mitchell JA, Sanz LA et al. The Air Noncoding RNA Epigenetically Silences Transcription by Targeting G9a to Chromatin. Science. 2008.
84. Williamson CM, Ball ST, Nottingham WT et al. A cis-acting control region is required exclusively for the tissue-specific imprinting ofGnas. Nat Genet 2004; 36(8):894-899. (Pubitemid 39014110)
85. Landers M, Bancescu DL, Le Meur E et al. Regulation of the large (approximately 1000 kb) imprinted murine Ube3a antisense transcript by alternative exons upstream of Snurf/Snrpn. Nucleic Acids Res 2004; 32(11):3480-3492. Print 2004. (Pubitemid 39117465)
86. Vitali P, Royo H, Marty V et al. Long nuclear-retained noncoding RNAs and allele-specific higher-order chromatin organization at imprinted snoRNA gene arrays. J Cell Sci 123(Pt 1):70-83.
87. Lin SP, Youngson N, Takada S et al. Asymmetric regulation of imprinting on the maternal and paternal chromosomes at the Dlk1-Gtl2 imprinted cluster on mouse chromosome 12. Nat Genet 2003; 35(1):97-102. (Pubitemid 37048602)
88. Davis E, Caiment F, Tordoir X et al. RNAi-mediated allelic trans-interaction at the imprinted Rtll/Pegll locus. Curr Biol 2005; 15(8):743-749. (Pubitemid 40599929)
89. Bernstein E, Allis CD. RNA meets chromatin. Genes Dev 2005; 19(14):1635-1655. (Pubitemid 41058358)
90. Pezer Z, Ugarkovic D. Role of noncoding RNA and heterochromatin in aneuploidy and cancer. Semin Cancer Biol 2008; 18(2):123-130.
91. Chen ES, Zhang K, Nicolas E et al. Cell cycle control of centromeric repeat transcription and heterochromatin assembly. Nature 2008; 451(7179):734-737. (Pubitemid 351220568)
92. Bouzinba-Segard H, Guais A, Francastel C. Accumulation of small murine minor satellite transcripts leads to impaired centromeric architecture and function. Proc Natl Acad Sci USA 2006; 103(23):8709-8714. (Pubitemid 43878084)
93. Djupedal I, Ekwall K. Epigenetics: heterochromatinmeets RNAi. Cell Res 2009; 19(3):282-295.
94. Motamedi MR, Verdel A, Colmenares SU et al. Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell 2004; 119(6):789-802. (Pubitemid 40017686)
95. Verdel A, Jia S, Gerber S et al. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 2004; 303(5658):672-676. (Pubitemid 38141633)
96. Kagansky A, Folco HD, Almeida R et al. Synthetic heterochromatin bypasses RNAi and centromeric repeats to establish functional centromeres. Science 2009; 324(5935):1716-1719.
97. Fukagawa T, Nogami M, Yoshikawa M et al. Dicer is essential for formation of the heterochromatin structure in vertebrate cells. Nat Cell Biol 2004; 6(8):784-791. (Pubitemid 39144485)
98. Sinkkonen L, Hugenschmidt T, Berninger P et al. MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. Nat Struct Mol Biol 2008; 15(3):259-267. (Pubitemid 351654045)