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Volumn 22, Issue 5, 2015, Pages 370-376

A lncRNA regulates alternative splicing via establishment of a splicing-specific chromatin signature

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY RNA; FIBROBLAST GROWTH FACTOR RECEPTOR 2; HISTONE DEMETHYLASE; HISTONE DEMETHYLASE KDM2A; LONG UNTRANSLATED RNA; POLYCOMB GROUP PROTEIN; RIBONUCLEASE A; RNA POLYMERASE II; UNCLASSIFIED DRUG; ARGONAUTE PROTEIN; CELL CYCLE PROTEIN; CHROMATIN; DEAD BOX PROTEIN; DICER1 PROTEIN, HUMAN; EIF2C1 PROTEIN, HUMAN; EIF2C2 PROTEIN, HUMAN; EZH1 PROTEIN, HUMAN; EZH2 PROTEIN, HUMAN; F BOX PROTEIN; FGFR2 PROTEIN, HUMAN; HISTONE; INITIATION FACTOR; KDM2A PROTEIN, HUMAN; POLYCOMB REPRESSIVE COMPLEX 2; POLYPYRIMIDINE TRACT BINDING PROTEIN; RIBONUCLEASE III; RNA PRECURSOR; SMALL INTERFERING RNA; SUZ12 PROTEIN, HUMAN;

EID: 84929270304     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.3005     Document Type: Article
Times cited : (214)

References (34)
  • 1
    • 56749098074 scopus 로고    scopus 로고
    • Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
    • Pan, Q., Shai, O., Lee, L.J., Frey, B.J. & Blencowe, B.J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 40, 1413-1415 (2008).
    • (2008) Nat. Genet. , vol.40 , pp. 1413-1415
    • Pan, Q.1    Shai, O.2    Lee, L.J.3    Frey, B.J.4    Blencowe, B.J.5
  • 2
    • 56549101959 scopus 로고    scopus 로고
    • Alternative isoform regulation in human tissue transcriptomes
    • Wang, E.T. et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470-476 (2008).
    • (2008) Nature , vol.456 , pp. 470-476
    • Wang, E.T.1
  • 3
    • 77952029221 scopus 로고    scopus 로고
    • Deciphering the splicing code
    • Barash, Y. et al. Deciphering the splicing code. Nature 465, 53-59 (2010).
    • (2010) Nature , vol.465 , pp. 53-59
    • Barash, Y.1
  • 4
    • 67650299463 scopus 로고    scopus 로고
    • Control of alternative splicing through siRNA-mediated transcriptional gene silencing
    • Alló, M. et al. Control of alternative splicing through siRNA-mediated transcriptional gene silencing. Nat. Struct. Mol. Biol. 16, 717-724 (2009).
    • (2009) Nat. Struct. Mol. Biol. , vol.16 , pp. 717-724
    • Alló, M.1
  • 5
    • 80455176999 scopus 로고    scopus 로고
    • CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
    • Shukla, S. et al. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 479, 74-79 (2011).
    • (2011) Nature , vol.479 , pp. 74-79
    • Shukla, S.1
  • 6
    • 79952364016 scopus 로고    scopus 로고
    • Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons
    • Saint-André, V., Batsche, E., Rachez, C. & Muchardt, C. Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons. Nat. Struct. Mol. Biol. 18, 337-344 (2011).
    • (2011) Nat. Struct. Mol. Biol. , vol.18 , pp. 337-344
    • Saint-André, V.1    Batsche, E.2    Rachez, C.3    Muchardt, C.4
  • 7
    • 84863654457 scopus 로고    scopus 로고
    • Psip1/Ledgf p52 binds methylated histone H3K36 and splicing factors and contributes to the regulation of alternative splicing
    • Pradeepa, M.M., Sutherland, H.G., Ule, J., Grimes, G.R. & Bickmore, W.A. Psip1/Ledgf p52 binds methylated histone H3K36 and splicing factors and contributes to the regulation of alternative splicing. PLoS Genet. 8, e1002717 (2012).
    • (2012) PLoS Genet. , vol.8 , pp. e1002717
    • Pradeepa, M.M.1    Sutherland, H.G.2    Ule, J.3    Grimes, G.R.4    Bickmore, W.A.5
  • 8
    • 0037064150 scopus 로고    scopus 로고
    • Coordinate regulation of transcription and splicing by steroid receptor coregulators
    • Auboeuf, D., Honig, A., Berget, S.M. & O'Malley, B.W. Coordinate regulation of transcription and splicing by steroid receptor coregulators. Science 298, 416-419 (2002).
    • (2002) Science , vol.298 , pp. 416-419
    • Auboeuf, D.1    Honig, A.2    Berget, S.M.3    O'Malley, B.W.4
  • 10
    • 84898632029 scopus 로고    scopus 로고
    • The transcription factor FBI-1 inhibits SAM68-mediated BCL-X alternative splicing and apoptosis
    • Bielli, P. et al. The transcription factor FBI-1 inhibits SAM68-mediated BCL-X alternative splicing and apoptosis. EMBO Rep. 15, 419-427 (2014).
    • (2014) EMBO Rep. , vol.15 , pp. 419-427
    • Bielli, P.1
  • 11
    • 84894061484 scopus 로고    scopus 로고
    • Phosphoproteomics screen reveals akt isoform-specific signals linking RNA processing to lung cancer
    • Sanidas, I. et al. Phosphoproteomics screen reveals akt isoform-specific signals linking RNA processing to lung cancer. Mol. Cell 53, 577-590 (2014).
    • (2014) Mol. Cell , vol.53 , pp. 577-590
    • Sanidas, I.1
  • 12
    • 77149175671 scopus 로고    scopus 로고
    • Regulation of alternative splicing by histone modifications
    • Luco, R.F. et al. Regulation of alternative splicing by histone modifications. Science 327, 996-1000 (2010).
    • (2010) Science , vol.327 , pp. 996-1000
    • Luco, R.F.1
  • 13
    • 33845910902 scopus 로고    scopus 로고
    • Structure of human MRG15 chromo domain and its binding to Lys36-methylated histone H3
    • Zhang, P. et al. Structure of human MRG15 chromo domain and its binding to Lys36-methylated histone H3. Nucleic Acids Res. 34, 6621-6628 (2006).
    • (2006) Nucleic Acids Res. , vol.34 , pp. 6621-6628
    • Zhang, P.1
  • 14
    • 42149149895 scopus 로고    scopus 로고
    • Ezh2 requires PHF1 to efficiently catalyze H3 lysine 27 trimethylation in vivo
    • Sarma, K., Margueron, R., Ivanov, A., Pirrotta, V. & Reinberg, D. Ezh2 requires PHF1 to efficiently catalyze H3 lysine 27 trimethylation in vivo. Mol. Cell. Biol. 28, 2718-2731 (2008).
    • (2008) Mol. Cell. Biol. , vol.28 , pp. 2718-2731
    • Sarma, K.1    Margueron, R.2    Ivanov, A.3    Pirrotta, V.4    Reinberg, D.5
  • 15
    • 79957543093 scopus 로고    scopus 로고
    • More than a splicing code: Integrating the role of RNA, chromatin and non-coding RNA in alternative splicing regulation
    • Luco, R.F. & Misteli, T. More than a splicing code: integrating the role of RNA, chromatin and non-coding RNA in alternative splicing regulation. Curr. Opin. Genet. Dev. 21, 366-372 (2011).
    • (2011) Curr. Opin. Genet. Dev. , vol.21 , pp. 366-372
    • Luco, R.F.1    Misteli, T.2
  • 16
    • 77954572735 scopus 로고    scopus 로고
    • Long noncoding RNA as modular scaffold of histone modification complexes
    • Tsai, M.C. et al. Long noncoding RNA as modular scaffold of histone modification complexes. Science 329, 689-693 (2010).
    • (2010) Science , vol.329 , pp. 689-693
    • Tsai, M.C.1
  • 17
    • 54049138948 scopus 로고    scopus 로고
    • Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation
    • Pandey, R.R. et al. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol. Cell 32, 232-246 (2008).
    • (2008) Mol. Cell , vol.32 , pp. 232-246
    • Pandey, R.R.1
  • 18
    • 69249235745 scopus 로고    scopus 로고
    • Lessons from X-chromosome inactivation: Long ncRNA as guides and tethers to the epigenome
    • Lee, J.T. Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome. Genes Dev. 23, 1831-1842 (2009).
    • (2009) Genes Dev. , vol.23 , pp. 1831-1842
    • Lee, J.T.1
  • 19
    • 78650253763 scopus 로고    scopus 로고
    • Genome-wide identification of polycomb-associated RNAs by RIP-seq
    • Zhao, J. et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol. Cell 40, 939-953 (2010).
    • (2010) Mol. Cell , vol.40 , pp. 939-953
    • Zhao, J.1
  • 20
    • 77953096072 scopus 로고    scopus 로고
    • Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a
    • Yap, K.L. et al. Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol. Cell 38, 662-674 (2010).
    • (2010) Mol. Cell , vol.38 , pp. 662-674
    • Yap, K.L.1
  • 21
    • 79953748673 scopus 로고    scopus 로고
    • A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression
    • Wang, K.C. et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472, 120-124 (2011).
    • (2011) Nature , vol.472 , pp. 120-124
    • Wang, K.C.1
  • 22
    • 84860885909 scopus 로고    scopus 로고
    • A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy
    • Cabianca, D.S. et al. A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy. Cell 149, 819-831 (2012).
    • (2012) Cell , vol.149 , pp. 819-831
    • Cabianca, D.S.1
  • 23
    • 61649087689 scopus 로고    scopus 로고
    • ESRP1 and ESRP2 are epithelial cell-type-specific regulators of FGFR2 splicing
    • Warzecha, C.C., Sato, T.K., Nabet, B., Hogenesch, J.B. & Carstens, R.P. ESRP1 and ESRP2 are epithelial cell-type-specific regulators of FGFR2 splicing. Mol. Cell 33, 591-601 (2009).
    • (2009) Mol. Cell , vol.33 , pp. 591-601
    • Warzecha, C.C.1    Sato, T.K.2    Nabet, B.3    Hogenesch, J.B.4    Carstens, R.P.5
  • 24
    • 0036810248 scopus 로고    scopus 로고
    • RNAi-mediated PTB depletion leads to enhanced exon definition
    • Wagner, E.J. & Garcia-Blanco, M.A. RNAi-mediated PTB depletion leads to enhanced exon definition. Mol. Cell 10, 943-949 (2002).
    • (2002) Mol. Cell , vol.10 , pp. 943-949
    • Wagner, E.J.1    Garcia-Blanco, M.A.2
  • 25
    • 84867230570 scopus 로고    scopus 로고
    • Argonaute proteins couple chromatin silencing to alternative splicing
    • Ameyar-Zazoua, M. et al. Argonaute proteins couple chromatin silencing to alternative splicing. Nat. Struct. Mol. Biol. 19, 998-1004 (2012).
    • (2012) Nat. Struct. Mol. Biol. , vol.19 , pp. 998-1004
    • Ameyar-Zazoua, M.1
  • 26
    • 84874279332 scopus 로고    scopus 로고
    • Two new and distinct roles for Drosophila Argonaute-2 in the nucleus: Alternative pre-mRNA splicing and transcriptional repression
    • Taliaferro, J.M. et al. Two new and distinct roles for Drosophila Argonaute-2 in the nucleus: alternative pre-mRNA splicing and transcriptional repression. Genes Dev. 27, 378-389 (2013).
    • (2013) Genes Dev. , vol.27 , pp. 378-389
    • Taliaferro, J.M.1
  • 27
    • 77952212771 scopus 로고    scopus 로고
    • RNA traffic control of chromatin complexes
    • Koziol, M.J. & Rinn, J.L. RNA traffic control of chromatin complexes. Curr. Opin. Genet. Dev. 20, 142-148 (2010).
    • (2010) Curr. Opin. Genet. Dev. , vol.20 , pp. 142-148
    • Koziol, M.J.1    Rinn, J.L.2
  • 28
    • 0028318228 scopus 로고
    • Sequence specific thermodynamic and structural properties for DNA.RNA duplexes
    • Ratmeyer, L., Vinayak, R., Zhong, Y.Y., Zon, G. & Wilson, W.D. Sequence specific thermodynamic and structural properties for DNA.RNA duplexes. Biochemistry 33, 5298-5304 (1994).
    • (1994) Biochemistry , vol.33 , pp. 5298-5304
    • Ratmeyer, L.1    Vinayak, R.2    Zhong, Y.Y.3    Zon, G.4    Wilson, W.D.5
  • 29
    • 79960521632 scopus 로고    scopus 로고
    • Extensive relationship between antisense transcription and alternative splicing in the human genome
    • Morrissy, A.S., Griffith, M. & Marra, M.A. Extensive relationship between antisense transcription and alternative splicing in the human genome. Genome Res. 21, 1203-1212 (2011).
    • (2011) Genome Res. , vol.21 , pp. 1203-1212
    • Morrissy, A.S.1    Griffith, M.2    Marra, M.A.3
  • 30
    • 80052978224 scopus 로고    scopus 로고
    • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    • Cabili, M.N. et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25, 1915-1927 (2011).
    • (2011) Genes Dev. , vol.25 , pp. 1915-1927
    • Cabili, M.N.1
  • 31
    • 0036064136 scopus 로고    scopus 로고
    • Clonal heterogeneity in differentiation potential of immortalized human mesenchymal stem cells
    • Okamoto, T. et al. Clonal heterogeneity in differentiation potential of immortalized human mesenchymal stem cells. Biochem. Biophys. Res. Commun. 295, 354-361 (2002).
    • (2002) Biochem. Biophys. Res. Commun. , vol.295 , pp. 354-361
    • Okamoto, T.1
  • 32
    • 84891022708 scopus 로고    scopus 로고
    • Dynamic chromatin modification sustains epithelial-mesenchymal transition following inducible expression of Snail-1
    • Javaid, S. et al. Dynamic chromatin modification sustains epithelial-mesenchymal transition following inducible expression of Snail-1. Cell Reports 5, 1679-1689 (2013).
    • (2013) Cell Reports , vol.5 , pp. 1679-1689
    • Javaid, S.1
  • 33
    • 23744458086 scopus 로고    scopus 로고
    • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
    • Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034-1050 (2005).
    • (2005) Genome Res. , vol.15 , pp. 1034-1050
    • Siepel, A.1
  • 34
    • 39049191299 scopus 로고    scopus 로고
    • fjoin: Simple and efficient computation of feature overlaps
    • Richardson, J.E. fjoin: simple and efficient computation of feature overlaps. J. Comput. Biol. 13, 1457-1464 (2006).
    • (2006) J. Comput. Biol. , vol.13 , pp. 1457-1464
    • Richardson, J.E.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.