The genomic binding sites of a noncoding RNA

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 51, 2011, Pages 20497-20502

  Simon, Matthew D ^a   Wang, Charlotte I ^b   Kharchenko, Peter V ^c   West, Jason A ^a   Chapman, Brad A ^a   Alekseyenko, Artyom A ^b   Borowsky, Mark L ^a   Kuroda, Mitzi I ^b   Kingston, Robert E ^a  

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b BRIGHAM AND WOMEN S HOSPITAL   (United States)

^c BOSTON CHILDREN S HOSPITAL   (United States)

Author keywords

Chromatin associated RNAs; Chromatin modifying complexes; RNase H mapping

Indexed keywords

GENOMIC RNA; UNTRANSLATED RNA;

ARTICLE; BINDING SITE; CHROMATIN IMMUNOPRECIPITATION; CHROMATIN STRUCTURE; CROSS LINKING; DROSOPHILA; GENE EXPRESSION REGULATION; GENE LOCUS; GENETIC ASSOCIATION; NONHUMAN; PRIORITY JOURNAL; RNA HYBRIDIZATION; RNA SEQUENCE;

AMINO ACID MOTIFS; ANIMALS; BINDING SITES; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; DOSAGE COMPENSATION, GENETIC; DROSOPHILA; DROSOPHILA PROTEINS; GENOMICS; MALE; MODELS, GENETIC; NUCLEIC ACID HYBRIDIZATION; RIBONUCLEASE H; RNA, UNTRANSLATED; RNA-BINDING PROTEINS;

EID: 84862908875     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1113536108     Document Type: Article

References (66)

1. Jacob F, Monod J (1961) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3:318-356.
2. Guttman M, et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458:223-227.
3. Birney E, et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799-816.
4. Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS (2008) Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci USA 105:716-721. (Pubitemid 351171774)
5. Ponting CP, Oliver PL, Reik W (2009) Evolution and functions of long noncoding RNAs. Cell 136:629-641.
6. Clark MB, et al. (2011) The reality of pervasive transcription. PLoS Biol 9:e1000625.
7. van Bakel H, Nislow C, Blencowe BJ, Hughes TR (2010) Most "dark matter" transcripts are associated with known genes. PLoS Biol 8:e1000371.
8. Lee JT (2009) Lessons from X-chromosome inactivation: Long ncRNA as guides and tethers to the epigenome. Genes Dev 23:1831-1842.
9. Gelbart ME, Kuroda MI (2009) Drosophila dosage compensation: A complex voyage to the X chromosome. Development 136:1399-1410.
10. Murakami K, Oshimura M, Kugoh H (2007) Suggestive evidence for chromosomal localization of non-coding RNA from imprinted LIT1. J Hum Genet 52:926-933. (Pubitemid 350112487)
11. Mohammad F, et al. (2008) Kcnq1ot1/Lit1 noncoding RNA mediates transcriptional silencing by targeting to the perinucleolar region. Mol Cell Biol 28:3713-3728. (Pubitemid 351732907)
12. Pandey RR, et al. (2008) Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell 32:232-246.
13. Nagano T, et al. (2008) The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 322:1717-1720.
14. Feng J, et al. (2006) The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Dev 20:1470-1484. (Pubitemid 43830654)
15. Shamovsky I, Ivannikov M, Kandel ES, Gershon D, Nudler E (2006) RNA-mediated response to heat shock in mammalian cells. Nature 440:556-560.
16. Orom UA, et al. (2010) Long noncoding RNAs with enhancer-like function in human cells. Cell 143:46-58.
17. Martianov I, Ramadass A, Serra Barros A, Chow N, Akoulitchev A (2007) Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript. Nature 445:666-670. (Pubitemid 46232888)
18. Schmitz KM, Mayer C, Postepska A, Grummt I (2010) Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes. Genes Dev 24:2264-2269.
19. Rinn JL, et al. (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129:1311-1323. (Pubitemid 46962090)
20. Wang KC, et al. (2011) A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472:120-124.
21. Prasanth KV, Spector DL (2007) Eukaryotic regulatory RNAs: An answer to the 'genome complexity' conundrum. Genes Dev 21:11-42. (Pubitemid 46089704)
22. Taft RJ, Pang KC, Mercer TR, Dinger M, Mattick JS (2010) Non-coding RNAs: Regulators of disease. J Pathol 220:126-139.
23. Gilbert C, Svejstrup JQ (2006) RNA immunoprecipitation for determining RNA-protein associations in vivo. Curr Protoc Mol Biol Chapter 27: Unit 27 24.
24. Darnell RB (2010) HITS-CLIP: Panoramic views of protein-RNA regulation in living cells. Interdiscip Rev RNA, (Wiley, New York), Vol 1, pp 266-286.
25. Ule J, Jensen K, Mele A, Darnell RB (2005) CLIP: A method for identifying protein-RNA interaction sites in living cells. Methods 37:376-386. (Pubitemid 41682508)
26. Ule J, et al. (2003) CLIP identifies Nova-regulated RNA networks in the brain. Science 302:1212-1215. (Pubitemid 37421026)
27. Tsai MC, et al. (2010) Long noncoding RNA as modular scaffold of histone modification complexes. Science 329:689-693.
28. Koziol MJ, Rinn JL (2010) RNA traffic control of chromatin complexes. Curr Opin Genet Dev 20:142-148.
29. Nagano T, Fraser P (2011) No-nonsense functions for long noncoding RNAs. Cell 145:178-181.
30. Levsky JM, Singer RH (2003) Fluorescence in situ hybridization: Past, present and future. J Cell Sci 116:2833-2838. (Pubitemid 36926972)
31. Carter D, Chakalova L, Osborne CS, Dai YF, Fraser P (2002) Long-range chromatin regulatory interactions in vivo. Nat Genet 32:623-626. (Pubitemid 35435174)
32. Mariner PD, et al. (2008) Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol Cell 29:499-509. (Pubitemid 351282533)
33. Dejardin J, Kingston RE (2009) Purification of proteins associatedwith specific genomic Loci. Cell 136:175-186.
34. Rinke J, Appel B, Blocker H, Frank R, Luhrmann R (1984) The 5′-terminal sequence of U1 RNA complementary to the consensus 5′ splice site of hnRNA is single-stranded in intact U1 snRNP particles. Nucleic Acids Res 12:4111-4126.
35. Wassarman DA, Steitz JA (1991) Structural analyses of the 7SK ribonucleoprotein (RNP), the most abundant human small RNP of unknown function. Mol Cell Biol 11:3432-3445. (Pubitemid 21895730)
36. Lingner J, Hendrick LL, Cech TR (1994) Telomerase RNAs of different ciliates have a common secondary structure and a permuted template. Genes Dev 8:1984-1998. (Pubitemid 24273897)
37. Stein H, Hausen P (1969) Enzyme from calf thymus degrading the RNA moiety of DNA-RNA Hybrids: Effect on DNA-dependent RNA polymerase. Science 166:393-395.
38. Ryder U, Sproat BS, Lamond AI (1990) Sequence-specific affinity selection of mammalian splicing complexes. Nucleic Acids Res 18:7373-7379. (Pubitemid 120006040)
39. Lingner J, Cech TR (1996) Purification of telomerase from Euplotes aediculatus: Requirement of a primer 3′ overhang. Proc Natl Acad Sci USA 93:10712-10717.
40. Hirsch JD, et al. (2002) Easily reversible desthiobiotin binding to streptavidin, avidin, and other biotin-binding proteins: Uses for protein labeling, detection, and isolation. Anal Biochem 308:343-357. (Pubitemid 35177149)
41. Alekseyenko AA, et al. (2008) A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome. Cell 134:599-609.
42. Chen LL, Carmichael GG (2009) Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: Functional role of a nuclear noncoding RNA. Mol Cell 35:467-478.
43. Clemson CM, et al. (2009) An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol Cell 33:717-726.
44. Hutchinson JN, et al. (2007) A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. BMC Genomics 8:39.
45. 2+/calmodulin kinase II inhibitor alpha. Brain Res 1148:38-42.
46. Sasaki YT, Ideue T, Sano M, Mituyama T, Hirose T (2009) MENepsilon/beta noncoding RNAs are essential for structural integrity of nuclear paraspeckles. Proc Natl Acad Sci USA 106:2525-2530.
47. Sunwoo H, et al. (2009) MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res 19:347-359.
48. Wilusz JE, Freier SM, Spector DL (2008) 3′ end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell 135:919-932.
49. Fox AH, Lamond AI (2010) Paraspeckles. Cold Spring Harb Perspect Biol 2:a000687.
50. Spector DL, Lamond AI (2011) Nuclear speckles. Cold Spring Harb Perspect Biol 3:a000646.
51. Mao YS, Sunwoo H, Zhang B, Spector DL (2010) Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs. Nat Cell Biol 13:95-101.
52. Franke A, Baker BS (1999) The rox1 and rox2 RNAs are essential components of the compensasome, which mediates dosage compensation in Drosophila. Mol Cell 4:117-122. (Pubitemid 29386137)
53. Kelley RL, et al. (1999) Epigenetic spreading of the Drosophila dosage compensation complex from roX RNA genes into flanking chromatin. Cell 98:513-522. (Pubitemid 29402488)
54. Meller VH, et al. (2000) Ordered assembly of roX RNAs into MSL complexes on the dosage-compensated X chromosome in Drosophila. Curr Biol 10:136-143. (Pubitemid 30115744)
55. Alekseyenko AA, Larschan E, Lai WR, Park PJ, Kuroda MI (2006) High-resolution ChIP-chip analysis reveals that the Drosophila MSL complex selectively identifies active genes on the male X chromosome. Genes Dev 20:848-857.
56. Gelbart ME, Larschan E, Peng S, Park PJ, Kuroda MI (2009) Drosophila MSL complex globally acetylates H4K16 on the male X chromosome for dosage compensation. Nat Struct Mol Biol 16:825-832.
57. Gilfillan GD, et al. (2006) Chromosome-wide gene-specific targeting of the Drosophila dosage compensation complex. Genes Dev 20:858-870.
58. Kind J, et al. (2008) Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila. Cell 133:813-828. (Pubitemid 351707688)
59. Smith ER, Allis CD, Lucchesi JC (2001) Linking global histone acetylation to the transcription enhancement of X-chromosomal genes in Drosophila males. J Biol Chem 276:31483-31486.
60. Hilfiker A, Hilfiker-Kleiner D, Pannuti A, Lucchesi JC (1997) mof, a putative acetyl transferase gene related to the Tip60 and MOZ human genes and to the SAS genes of yeast, is required for dosage compensation in Drosophila. EMBO J 16:2054-2060. (Pubitemid 27170966)
61. Larschan E, et al. (2011) X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila. Nature 471:115-118.
62. Straub T, Grimaud C, Gilfillan GD, Mitterweger A, Becker PB (2008) The chromosomal high-affinity binding sites for the Drosophila dosage compensation complex. PLoS Genet 4:e1000302.
63. Gorchakov AA, Alekseyenko AA, Kharchenko P, Park PJ, Kuroda MI (2009) Long-range spreading of dosage compensation in Drosophila captures transcribed autosomal genes inserted on X. Genes Dev 23:2266-2271.
64. Mosrin-Huaman C, Canaple L, Locker D, Decoville M (1998) DSP1 gene of Drosophila melanogaster encodes an HMG-domain protein that plays multiple roles in development. Dev Genet 23:324-334. (Pubitemid 29019101)
65. Kharchenko PV, et al. (2011) Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 471:480-485.
66. Chu C, et al. (2011) Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions. Mol Cell 44:667-648.