Long Noncoding RNAs with snoRNA Ends

Molecular Cell

Volumn 48, Issue 2, 2012, Pages 219-230

  Yin, Qing Fei ^a   Yang, Li ^b   Zhang, Yang ^a   Xiang, Jian Feng ^a   Wu, Yue Wei ^a   Carmichael, Gordon G ^c   Chen, Ling Ling ^a  

^a INSTITUTE OF BIOCHEMISTRY AND CELL BIOLOGY   (China)

^b Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^c UNIVERSITY OF CONNECTICUT HEALTH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SMALL NUCLEOLAR RNA; UNTRANSLATED RNA;

ARTICLE; COILED BODY; GENOME; HUMAN; HUMAN CELL; NUCLEOLUS; NUCLEOTIDE SEQUENCE; PATHOGENESIS; PRADER WILLI SYNDROME; PROTEIN FAMILY; PROTEIN LOCALIZATION; PROTEIN SYNTHESIS; RNA SEQUENCE; RNA SPLICING;

BASE SEQUENCE; CELL LINE; CELL NUCLEOLUS; COILED BODIES; GENE EXPRESSION REGULATION; HUMANS; INTRONS; MOLECULAR SEQUENCE DATA; PRADER-WILLI SYNDROME; REPRESSOR PROTEINS; RNA SPLICING; RNA, LONG UNTRANSLATED; RNA, SMALL NUCLEOLAR; RNA-BINDING PROTEINS;

EID: 84868152631     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2012.07.033     Document Type: Article

References (51)

1. Augui S., Nora E.P., Heard E. Regulation of X-chromosome inactivation by the X-inactivation centre. Nat. Rev. Genet. 2011, 12:429-442.
2. Bazeley P.S., Shepelev V., Talebizadeh Z., Butler M.G., Fedorova L., Filatov V., Fedorov A. snoTARGET shows that human orphan snoRNA targets locate close to alternative splice junctions. Gene 2008, 408:172-179.
3. Boisvert F.M., van Koningsbruggen S., Navascués J., Lamond A.I. The multifunctional nucleolus. Nat. Rev. Mol. Cell Biol. 2007, 8:574-585.
4. Cabianca D.S., Casa V., Bodega B., Xynos A., Ginelli E., Tanaka Y., Gabellini D. A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy. Cell 2012, 149:819-831.
5. Cassidy S.B., Schwartz S., Miller J.L., Driscoll D.J. Prader-Willi syndrome. Genet. Med. 2012, 14:10-26.
6. Cavaillé J., Buiting K., Kiefmann M., Lalande M., Brannan C.I., Horsthemke B., Bachellerie J.P., Brosius J., Hüttenhofer A. Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization. Proc. Natl. Acad. Sci. USA 2000, 97:14311-14316.
7. Chen L.L., Carmichael G.G. Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol. Cell 2009, 35:467-478.
8. Chen L.L., Carmichael G.G. Long noncoding RNAs in mammalian cells: what, where, and why?. Wiley Interdiscip Rev RNA 2010, 1:2-21.
9. de Haro M., Al-Ramahi I., De Gouyon B., Ukani L., Rosa A., Faustino N.A., Ashizawa T., Cooper T.A., Botas J. MBNL1 and CUGBP1 modify expanded CUG-induced toxicity in a Drosophila model of myotonic dystrophy type 1. Hum. Mol. Genet. 2006, 15:2138-2145.
10. de Smith A.J., Purmann C., Walters R.G., Ellis R.J., Holder S.E., Van Haelst M.M., Brady A.F., Fairbrother U.L., Dattani M., Keogh J.M., et al. A deletion of the HBII-85 class of small nucleolar RNAs (snoRNAs) is associated with hyperphagia, obesity and hypogonadism. Hum. Mol. Genet. 2009, 18:3257-3265.
11. Duker A.L., Ballif B.C., Bawle E.V., Person R.E., Mahadevan S., Alliman S., Thompson R., Traylor R., Bejjani B.A., Shaffer L.G., et al. Paternally inherited microdeletion at 15q11.2 confirms a significant role for the SNORD116 C/D box snoRNA cluster in Prader-Willi syndrome. Eur. J. Hum. Genet. 2010, 18:1196-1201.
12. Fardaei M., Larkin K., Brook J.D., Hamshere M.G. In vivo co-localisation of MBNL protein with DMPK expanded-repeat transcripts. Nucleic Acids Res. 2001, 29:2766-2771.
13. Filipowicz W., Pogacić V. Biogenesis of small nucleolar ribonucleoproteins. Curr. Opin. Cell Biol. 2002, 14:319-327.
14. Guttman M., Amit I., Garber M., French C., Lin M.F., Feldser D., Huarte M., Zuk O., Carey B.W., Cassady J.P., et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009, 458:223-227.
15. Hao Y., Sekine K., Kawabata A., Nakamura H., Ishioka T., Ohata H., Katayama R., Hashimoto C., Zhang X., Noda T., et al. Apollon ubiquitinates SMAC and caspase-9, and has an essential cytoprotection function. Nat. Cell Biol. 2004, 6:849-860.
16. Hirose T., Steitz J.A. Position within the host intron is critical for efficient processing of box C/D snoRNAs in mammalian cells. Proc. Natl. Acad. Sci. USA 2001, 98:12914-12919.
17. Hirose T., Shu M.D., Steitz J.A. Splicing-dependent and -independent modes of assembly for intron-encoded box C/D snoRNPs in mammalian cells. Mol. Cell 2003, 12:113-123.
18. Hung T., Wang Y., Lin M.F., Koegel A.K., Kotake Y., Grant G.D., Horlings H.M., Shah N., Umbricht C., Wang P., et al. Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat. Genet. 2011, 43:621-629.
19. Jolly C., Lakhotia S.C. Human sat III and Drosophila hsr omega transcripts: a common paradigm for regulation of nuclear RNA processing in stressed cells. Nucleic Acids Res. 2006, 34:5508-5514.
20. Khalil A.M., Guttman M., Huarte M., Garber M., Raj A., Rivea Morales D., Thomas K., Presser A., Bernstein B.E., van Oudenaarden A., et al. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc. Natl. Acad. Sci. USA 2009, 106:11667-11672.
21. Kim K.K., Adelstein R.S., Kawamoto S. Identification of neuronal nuclei (NeuN) as Fox-3, a new member of the Fox-1 gene family of splicing factors. J. Biol. Chem. 2009, 284:31052-31061.
22. Kim K.K., Kim Y.C., Adelstein R.S., Kawamoto S. Fox-3 and PSF interact to activate neural cell-specific alternative splicing. Nucleic Acids Res. 2011, 39:3064-3078.
23. Kiss T. Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs. EMBO J. 2001, 20:3617-3622.
24. Kiss T., Filipowicz W. Exonucleolytic processing of small nucleolar RNAs from pre-mRNA introns. Genes Dev. 1995, 9:1411-1424.
25. Lamprianou S., Chatzopoulou E., Thomas J.L., Bouyain S., Harroch S. A complex between contactin-1 and the protein tyrosine phosphatase PTPRZ controls the development of oligodendrocyte precursor cells. Proc. Natl. Acad. Sci. USA 2011, 108:17498-17503.
26. Matera A.G., Terns R.M., Terns M.P. Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs. Nat. Rev. Mol. Cell Biol. 2007, 8:209-220.
27. Nakahata S., Kawamoto S. Tissue-dependent isoforms of mammalian Fox-1 homologs are associated with tissue-specific splicing activities. Nucleic Acids Res. 2005, 33:2078-2089.
28. Ørom U.A., Derrien T., Beringer M., Gumireddy K., Gardini A., Bussotti G., Lai F., Zytnicki M., Notredame C., Huang Q., et al. Long noncoding RNAs with enhancer-like function in human cells. Cell 2010, 143:46-58.
29. Otto E., Kunimoto M., McLaughlin T., Bennett V. Isolation and characterization of cDNAs encoding human brain ankyrins reveal a family of alternatively spliced genes. J. Cell Biol. 1991, 114:241-253.
30. Polymenidou M., Lagier-Tourenne C., Hutt K.R., Huelga S.C., Moran J., Liang T.Y., Ling S.C., Sun E., Wancewicz E., Mazur C., et al. Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43. Nat. Neurosci. 2011, 14:459-468.
31. Rearick D., Prakash A., McSweeny A., Shepard S.S., Fedorova L., Fedorov A. Critical association of ncRNA with introns. Nucleic Acids Res. 2011, 39:2357-2366.
32. Royo H., Cavaillé J. Non-coding RNAs in imprinted gene clusters. Biol. Cell 2008, 100:149-166.
33. Runte M., Hüttenhofer A., Gross S., Kiefmann M., Horsthemke B., Buiting K. The IC-SNURF-SNRPN transcript serves as a host for multiple small nucleolar RNA species and as an antisense RNA for UBE3A. Hum. Mol. Genet. 2001, 10:2687-2700.
34. Sahoo T., del Gaudio D., German J.R., Shinawi M., Peters S.U., Person R.E., Garnica A., Cheung S.W., Beaudet A.L. Prader-Willi phenotype caused by paternal deficiency for the HBII-85 C/D box small nucleolar RNA cluster. Nat. Genet. 2008, 40:719-721.
35. Salzman J., Gawad C., Wang P.L., Lacayo N., Brown P.O. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PLoS ONE 2012, 7:e30733.
36. Shi Y., Di Giammartino D.C., Taylor D., Sarkeshik A., Rice W.J., Yates J.R., Frank J., Manley J.L. Molecular architecture of the human pre-mRNA 3' processing complex. Mol. Cell 2009, 33:365-376.
37. Skryabin B.V., Gubar L.V., Seeger B., Pfeiffer J., Handel S., Robeck T., Karpova E., Rozhdestvensky T.S., Brosius J. Deletion of the MBII-85 snoRNA gene cluster in mice results in postnatal growth retardation. PLoS Genet. 2007, 3:e235.
38. Sokka A.L., Mudo G., Aaltonen J., Belluardo N., Lindholm D., Korhonen L. Bruce/apollon promotes hippocampal neuron survival and is downregulated by kainic acid. Biochem. Biophys. Res. Commun. 2005, 338:729-735.
39. Tollervey J.R., Curk T., Rogelj B., Briese M., Cereda M., Kayikci M., König J., Hortobágyi T., Nishimura A.L., Zupunski V., et al. Characterizing the RNA targets and position-dependent splicing regulation by TDP-43. Nat. Neurosci. 2011, 14:452-458.
40. Tripathi V., Ellis J.D., Shen Z., Song D.Y., Pan Q., Watt A.T., Freier S.M., Bennett C.F., Sharma A., Bubulya P.A., et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol. Cell 2010, 39:925-938.
41. Tycowski K.T., Shu M.D., Steitz J.A. A small nucleolar RNA is processed from an intron of the human gene encoding ribosomal protein S3. Genes Dev. 1993, 7(7A):1176-1190.
42. Underwood J.G., Boutz P.L., Dougherty J.D., Stoilov P., Black D.L. Homologues of the Caenorhabditis elegans Fox-1 protein are neuronal splicing regulators in mammals. Mol. Cell. Biol. 2005, 25:10005-10016.
43. Valgardsdottir R., Chiodi I., Giordano M., Rossi A., Bazzini S., Ghigna C., Riva S., Biamonti G. Transcription of Satellite III non-coding RNAs is a general stress response in human cells. Nucleic Acids Res. 2008, 36:423-434.
44. Voineagu I., Wang X., Johnston P., Lowe J.K., Tian Y., Horvath S., Mill J., Cantor R.M., Blencowe B.J., Geschwind D.H. Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature 2011, 474:380-384.
45. Wang K.C., Chang H.Y. Molecular mechanisms of long noncoding RNAs. Mol. Cell 2011, 43:904-914.
46. Wang Z., Rolish M.E., Yeo G., Tung V., Mawson M., Burge C.B. Systematic identification and analysis of exonic splicing silencers. Cell 2004, 119:831-845.
47. Wang E.T., Sandberg R., Luo S., Khrebtukova I., Zhang L., Mayr C., Kingsmore S.F., Schroth G.P., Burge C.B. Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456:470-476.
48. Won H., Mah W., Kim E., Kim J.W., Hahm E.K., Kim M.H., Cho S., Kim J., Jang H., Cho S.C., et al. GIT1 is associated with ADHD in humans and ADHD-like behaviors in mice. Nat. Med. 2011, 17:566-572.
49. Yang L., Duff M.O., Graveley B.R., Carmichael G.G., Chen L.L. Genomewide characterization of non-polyadenylated RNAs. Genome Biol. 2011, 12:R16.
50. Yeo G.W., Coufal N.G., Liang T.Y., Peng G.E., Fu X.D., Gage F.H. An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat. Struct. Mol. Biol. 2009, 16:130-137.
51. Zhang C., Zhang Z., Castle J., Sun S., Johnson J., Krainer A.R., Zhang M.Q. Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. Genes Dev. 2008, 22:2550-2563.