Kcnq1ot1: A chromatin regulatory RNA

Seminars in Cell and Developmental Biology

Volumn 22, Issue 4, 2011, Pages 343-350

  Kanduri, Chandrasekhar ^a,b  

^a UPPSALA UNIVERSITY   (Sweden)

^b UNIVERSITY OF GOTHENBURG   (Sweden)

Author keywords

Airn; Chromatin; Epigenetics; Genomic imprinting; Heterochromatin; Kcnq1ot1; Noncoding RNA; Polycomb proteins; X chromosome inactivation; Xist

Indexed keywords

CYCLIN DEPENDENT KINASE INHIBITOR 1C; DNA METHYLTRANSFERASE 1; HYGROMYCIN; KCNQ1OT1 NONCODING RNA; RNA POLYMERASE II; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; BINDING SITE; CELL NUCLEUS; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CHROMATIN STRUCTURE; CHROMOSOME; CPG ISLAND; EPIGENETICS; GENE; GENE DELETION; GENE EXPRESSION REGULATION; GENE MUTATION; GENE SILENCING; HISTONE ACETYLATION; HISTONE MODIFICATION; HUMAN; INTRON; KCNQ1 GENE; NONHUMAN; PROMOTER REGION; REVIEW; RNA INTERFERENCE; RNA SEQUENCE; RNA STRUCTURE; RNA SYNTHESIS; RNA TRANSLATION; TRANSCRIPTION REGULATION; TRANSCRIPTION TERMINATION;

EID: 79957552432     PISSN: 10849521     EISSN: 10963634     Source Type: Journal    
DOI: 10.1016/j.semcdb.2011.02.020     Document Type: Review

References (54)

1. Amaral P.P., Mattick J.S. Noncoding RNA in development. Mamm Genome 2008, 19:454-492.
2. Prasanth K.V., Spector D.L. Eukaryotic regulatory RNAs: an answer to the 'genome complexity' conundrum. Genes Dev 2007, 21:11-42.
3. Pauli A., Rinn J.L., Schier A.F. Non-coding RNAs as regulators of embryogenesis. Nat Rev Genet 2011, 12:136-149.
4. Mercer T.R., Dinger M.E., Mattick J.S. Long non-coding RNAs: insights into functions. Nat Rev Genet 2009, 10:155-159.
5. Wilusz J.E., Sunwoo H., Spector D.L. Long noncoding RNAs: functional surprises from the RNA world. Genes Dev 2009, 23:1494-1504.
6. Bernstein E., Allis C.D. RNA meets chromatin. Genes Dev 2005, 19:1635-1655.
7. Faghihi M.A., Wahlestedt C. Regulatory roles of natural antisense transcripts. Nat Rev Mol Cell Biol 2009, 10:637-643.
8. Bracken A.P., Helin K. Polycomb group proteins: navigators of lineage pathways led astray in cancer. Nat Rev Cancer 2009, 9:773-784.
9. Whitehead J., Pandey G.K., Kanduri C. Regulation of the mammalian epigenome by long noncoding RNAs. Biochim Biophys Acta 2009, 1790:936-947.
10. Royo H., Cavaille J. Non-coding RNAs in imprinted gene clusters. Biol Cell 2008, 100:149-166.
11. Mohammad F., Mondal T., Kanduri C. Epigenetics of imprinted long noncoding RNAs. Epigenetics 2009, 4:277-286.
12. Koerner M.V., Pauler F.M., Huang R., Barlow D.P. The function of non-coding RNAs in genomic imprinting. Development 2009, 136:1771-1783.
13. Wu H.A., Bernstein E. Partners in imprinting: noncoding RNA and polycomb group proteins. Dev Cell 2008, 15:637-638.
14. Paulsen M., Davies K., Bowden L., Villar A., Franck O., Fuermann M., et al. Syntenic organization of the mouse distal chromosome 7 imprinting cluster and the Beckwith-Wiedemann syndrome region in chromosome 11p15.5. Hum Mol Genet 2000, 7:1149-1159.
15. Thakur N., Tiwari V.K., Thomassin H., Pandey R.R., Kanduri M., Gondor A., et al. An antisense RNA regulates the bidirectional silencing property of the kcnq1 imprinting control region. Mol Cell Biol 2004, 24:7855-7862.
16. Pandey R.R., Ceribelli M., Singh P.B., Ericsson J., Mantovani R., Kanduri C. NF-Y regulates the antisense promoter, bidirectional silencing, and differential epigenetic marks of the Kcnq1 imprinting control region. J Biol Chem 2004, 279:52685-52693.
17. Shin J.Y., Fitzpatrick G.V., Higgins M.J. Two distinct mechanisms of silencing by the KvDMR1 imprinting control region. EMBO J 2008, 27:168-178.
18. Mancini-Dinardo D., Steele S.J., Levorse J.M., Ingram R.S., Tilghman S.M. Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes. Genes Dev 2006, 20:1268-1282.
19. Pandey R.R., 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. Mol Cell 2008, 32:232-246.
20. Paulsen M., Khare T., Burgard C., Tierling S., Walter J. Evolution of the Beckwith-Wiedemann syndrome region in vertebrates. Genome Res 2005, 15:146-153. [Epub 2004 Dec 8].
21. Fitzpatrick G.V., Soloway P.D., Higgins M.J. Regional loss of imprinting and growth deficiency in mice with a targeted deletion of KvDMR1. Nat Genet 2002, 32:426-431. [Epub 2002 Sep 9].
22. Horike S., Mitsuya K., Meguro M., Kotobuki N., Kashiwagi A., Notsu T., et al. Targeted disruption of the human LIT1 locus defines a putative imprinting control element playing an essential role in Beckwith-Wiedemann syndrome. Hum Mol Genet 2000, 9:2075-2083.
23. Mohammad F., Pandey R.R., Nagano T., Chakalova L., Mondal T., Fraser P., et al. Kcnq1ot1/Lit1 noncoding RNA mediates transcriptional silencing by targeting to the perinucleolar region. Mol Cell Biol 2008, 28:3713-3728.
24. Mohammad F., Mondal T., Guseva N., Pandey G.K., Kanduri C. Kcnq1ot1 noncoding RNA mediates transcriptional gene silencing by interacting with Dnmt1. Development 2010, 137:2493-2499.
25. Redrup L., Branco M.R., Perdeaux E.R., Krueger C., Lewis A., Santos F., et al. The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing. Development 2009, 136:525-530.
26. Murakami K., Oshimura M., Kugoh H. Suggestive evidence for chromosomal localization of non-coding RNA from imprinted LIT1. J Hum Genet 2007, 52:926-933.
27. Terranova R., Yokobayashi S., Stadler M.B., Otte A.P., van Lohuizen M., Orkin S.H., et al. Polycomb group proteins Ezh2 and Rnf2 direct genomic contraction and imprinted repression in early mouse embryos. Dev Cell 2008, 15:668-679.
28. Umlauf D., Goto Y., Cao R., Cerqueira F., Wagschal A., Zhang Y., et al. Imprinting along the Kcnq1 domain on mouse chromosome 7 involves repressive histone methylation and recruitment of Polycomb group complexes. Nat Genet 2004, 36:1296-1300. [Epub 2004 Oct 31].
29. Lewis A., Mitsuya K., Umlauf D., Smith P., Dean W., Walter J., et al. Imprinting on distal chromosome 7 in the placenta involves repressive histone methylation independent of DNA methylation. Nat Genet 2004, 36:1291-1295. [Epub 2004 Oct 31].
30. Lewis A., Green K., Dawson C., Redrup L., Huynh K.D., Lee J.T., et al. Epigenetic dynamics of the Kcnq1 imprinted domain in the early embryo. Development 2006, 133:4203-4210.
31. Wagschal A., Sutherland H.G., Woodfine K., Henckel A., Chebli K., Schulz R., et al. G9a histone methyltransferase contributes to imprinting in the mouse placenta. Mol Cell Biol 2008, 28:1104-1113.
32. Kanduri C., Thakur N., Pandey R.R. The length of the transcript encoded from the Kcnq1ot1 antisense promoter determines the degree of silencing. EMBO J 2006, 25:2096-2106.
33. Lei H., Oh S.P., Okano M., Juttermann R., Goss K.A., Jaenisch R., et al. De novo DNA cytosine methyltransferase activities in mouse embryonic stem cells. Development 1996, 122:3195-3205.
34. Li E., Bestor T.H., Jaenisch R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 1992, 69:915-926.
35. Caspary T., Cleary M.A., Baker C.C., Guan X.J., Tilghman S.M. Multiple mechanisms regulate imprinting of the mouse distal chromosome 7 gene cluster. Mol Cell Biol 1998, 18:3466-3474.
36. Weaver J.R., Sarkisian G., Krapp C., Mager J., Mann M.R., Bartolomei M.S. Domain-specific response of imprinted genes to reduced DNMT1. Mol Cell Biol 2010, 30:3916-3928.
37. Tanaka M., Puchyr M., Gertsenstein M., Harpal K., Jaenisch R., Rossant J., et al. Parental origin-specific expression of Mash2 is established at the time of implantation with its imprinting mechanism highly resistant to genome-wide demethylation. Mech Dev 1999, 87:129-142.
38. Cirio M.C., Martel J., Mann M., Toppings M., Bartolomei M., Trasler J., et al. DNA methyltransferase 1o functions during preimplantation development to preclude a profound level of epigenetic variation. Dev Biol 2008, 324:139-150.
39. Green K., Lewis A., Dawson C., Dean W., Reinhart B., Chaillet J.R., et al. A developmental window of opportunity for imprinted gene silencing mediated by DNA methylation and the Kcnq1ot1 noncoding RNA. Mamm Genome 2007, 18:32-42.
40. Mager J., Montgomery N.D., de Villena F.P., Magnuson T. Genome imprinting regulated by the mouse Polycomb group protein Eed. Nat Genet 2003, 33:502-507.
41. Gupta R.A., Shah N., Wang K.C., Kim J., Horlings H.M., Wong D.J., et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 2010, 464:1071-1076.
42. Margueron R., Reinberg D. The Polycomb complex PRC2 and its mark in life. Nature 2011, 469:343-349.
43. Mondal T., Rasmussen M., Pandey G.K., Isaksson A., Kanduri C. Characterization of the RNA content of chromatin. Genome Res 2010, 20:899-907.
44. Rinn J.L., Kertesz M., Wang J.K., Squazzo S.L., Xu X., Brugmann S.A., et al. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 2007, 129:1311-1323.
45. Kanduri C. Functional insights into long antisense noncoding RNA Kcnq1ot1 mediated bidirectional silencing. RNA Biol 2008, 5:208-211.
46. Lee J.T. Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome. Genes Dev 2009, 23:1831-1842.
47. 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, 583:857-864.
48. Wutz A., Rasmussen T.P., Jaenisch R. Chromosomal silencing and localization are mediated by different domains of Xist RNA. Nat Genet 2002, 30:167-174.
49. Chaumeil J., Le Baccon P., Wutz A., Heard E. A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silenced. Genes Dev 2006, 20:2223-2237.
50. Chow J.C., Ciaudo C., Fazzari M.J., Mise N., Servant N., Glass J.L., et al. LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation. Cell 2010, 141:956-969.
51. Nagano T., Mitchell J.A., Sanz L.A., Pauler F.M., Ferguson-Smith A.C., Feil R., et al. The air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 2008.
52. Sleutels F., Zwart R., Barlow D.P. The non-coding air RNA is required for silencing autosomal imprinted genes. Nature 2002, 415:810-813.
53. Carrel L., Willard H.F. X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature 2005, 434:400-404.
54. Tsai M.C., Manor O., Wan Y., Mosammaparast N., Wang J.K., Lan F., et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science 2010, 329:689-693.