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Volumn 43, Issue 14, 2015, Pages

Dissecting the nascent human transcriptome by analysing the RNA content of transcription factories

Author keywords

[No Author keywords available]

Indexed keywords

CHROMATIN RNA; LONG INTERGENIC NONCODING RNA; MICRORNA PRECUSOR; POLYADENYLATED RNA; RNA; TRANSCRIPTION FACTORY; TRANSCRIPTOME; TUMOR NECROSIS FACTOR; UNCLASSIFIED DRUG; CHROMATIN; LONG UNTRANSLATED RNA; SMALL UNTRANSLATED RNA; UNTRANSLATED RNA;

EID: 84965090069     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv390     Document Type: Article
Times cited : (28)

References (49)
  • 1
    • 84865777822 scopus 로고    scopus 로고
    • Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs
    • Tilgner, H., Knowles, D.G., Johnson, R., Davis, C.A., Chakrabortty, S., Djebali, S., Curado, J., Snyder, M., Gingeras, T.R. and Guigó, R. (2012) Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res., 22, 1616-1625.
    • (2012) Genome Res. , vol.22 , pp. 1616-1625
    • Tilgner, H.1    Knowles, D.G.2    Johnson, R.3    Davis, C.A.4    Chakrabortty, S.5    Djebali, S.6    Curado, J.7    Snyder, M.8    Gingeras, T.R.9    Guigó, R.10
  • 2
    • 77952905505 scopus 로고    scopus 로고
    • Most "dark matter" transcripts are associated with known genes
    • van Bakel, H., Nislow, C., Blencowe, B.J. and Hughes, T.R. (2010) Most "dark matter" transcripts are associated with known genes. PLoS Biol., 8, e1000371.
    • (2010) PLoS Biol. , vol.8 , pp. e1000371
    • Van Bakel, H.1    Nislow, C.2    Blencowe, B.J.3    Hughes, T.R.4
  • 4
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: Target recognition and regulatory functions
    • Bartel, D.P. (2009) MicroRNAs: target recognition and regulatory functions. Cell, 136, 215-233.
    • (2009) Cell , vol.136 , pp. 215-233
    • Bartel, D.P.1
  • 5
  • 6
    • 23844495159 scopus 로고    scopus 로고
    • LINEs, SINEs and processed pseudogenes: Parasitic strategies for genome modeling
    • Dewannieux, M. and Heidmann, T. (2005) LINEs, SINEs and processed pseudogenes: parasitic strategies for genome modeling. Cytogenet. Genome Res., 110, 35-48.
    • (2005) Cytogenet. Genome Res. , vol.110 , pp. 35-48
    • Dewannieux, M.1    Heidmann, T.2
  • 7
    • 84877910548 scopus 로고    scopus 로고
    • Epigenetic regulation of transcription and possible functions of mammalian short interspersed elements, SINEs
    • Ichiyanagi, K. (2013) Epigenetic regulation of transcription and possible functions of mammalian short interspersed elements, SINEs. Genes Genet. Syst., 88, 19-29.
    • (2013) Genes Genet. Syst. , vol.88 , pp. 19-29
    • Ichiyanagi, K.1
  • 8
    • 57849109058 scopus 로고    scopus 로고
    • Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
    • Core, L.J., Waterfall, J.J. and Lis, J.T. (2008) Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science, 322, 1845-1848.
    • (2008) Science , vol.322 , pp. 1845-1848
    • Core, L.J.1    Waterfall, J.J.2    Lis, J.T.3
  • 14
    • 78751659330 scopus 로고    scopus 로고
    • Nascent transcript sequencing visualizes transcription at nucleotide resolution
    • Churchman, L.S. and Weissman, J.S. (2011) Nascent transcript sequencing visualizes transcription at nucleotide resolution. Nature, 469, 368-373.
    • (2011) Nature , vol.469 , pp. 368-373
    • Churchman, L.S.1    Weissman, J.S.2
  • 15
    • 84864251757 scopus 로고    scopus 로고
    • Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions
    • Bhatt, D.M., Pandya-Jones, A., Tong, A.J., Barozzi, I., Lissner, M.M., Natoli, G., Black, D.L. and Smale, S.T. (2012) Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions. Cell, 150, 279-290.
    • (2012) Cell , vol.150 , pp. 279-290
    • Bhatt, D.M.1    Pandya-Jones, A.2    Tong, A.J.3    Barozzi, I.4    Lissner, M.M.5    Natoli, G.6    Black, D.L.7    Smale, S.T.8
  • 16
    • 82955232386 scopus 로고    scopus 로고
    • Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain
    • Ameur, A., Zaghlool, A., Halvardson, J., Wetterbom, A., Gyllensten, U., Cavelier, L. and Feuk, L. (2011) Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain. Nat. Struct. Mol. Biol., 18, 1435-1440.
    • (2011) Nat. Struct. Mol. Biol. , vol.18 , pp. 1435-1440
    • Ameur, A.1    Zaghlool, A.2    Halvardson, J.3    Wetterbom, A.4    Gyllensten, U.5    Cavelier, L.6    Feuk, L.7
  • 17
    • 82955247079 scopus 로고    scopus 로고
    • Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila
    • Khodor, Y.L., Rodriguez, J., Abruzzi, K.C., Tang, C.H., Marr, M.T. 2nd and Rosbash, M. (2011) Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila. Genes Dev., 25, 2502-2512.
    • (2011) Genes Dev. , vol.25 , pp. 2502-2512
    • Khodor, Y.L.1    Rodriguez, J.2    Abruzzi, K.C.3    Tang, C.H.4    Marr, M.T.5    Rosbash, M.6
  • 20
    • 84860381359 scopus 로고    scopus 로고
    • Transcription factories: Genetic programming in three dimensions
    • Edelman, L.B. and Fraser, P. (2012) Transcription factories: genetic programming in three dimensions. Curr. Opin. Genet. Dev., 22, 110-114.
    • (2012) Curr. Opin. Genet. Dev. , vol.22 , pp. 110-114
    • Edelman, L.B.1    Fraser, P.2
  • 21
    • 84889005653 scopus 로고    scopus 로고
    • Transcription factories: Genome organization and gene regulation
    • Papantonis, A. and Cook, P.R. (2013) Transcription factories: genome organization and gene regulation. Chem. Rev., 113, 8683-86705.
    • (2013) Chem. Rev. , vol.113 , pp. 8683-86705
    • Papantonis, A.1    Cook, P.R.2
  • 22
    • 84899873434 scopus 로고    scopus 로고
    • Imaging RNA Polymerase II transcription sites in living cells
    • Buckley, M.S. and Lis, J.T. (2014) Imaging RNA Polymerase II transcription sites in living cells. Curr. Opin. Genet. Dev., 25, 126-130.
    • (2014) Curr. Opin. Genet. Dev. , vol.25 , pp. 126-130
    • Buckley, M.S.1    Lis, J.T.2
  • 23
    • 67649766870 scopus 로고    scopus 로고
    • Transcription factories: Gene expression in unions?
    • Sutherland, H. and Bickmore, W.A. (2009) Transcription factories: gene expression in unions? Nat. Rev. Genet., 10, 457-466.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 457-466
    • Sutherland, H.1    Bickmore, W.A.2
  • 24
    • 81355146972 scopus 로고    scopus 로고
    • Ultrastructural study of transcription factories in mouse erythroblasts
    • Eskiw, C.H. and Fraser, P. (2011) Ultrastructural study of transcription factories in mouse erythroblasts. J. Cell Sci., 124, 3676-3683.
    • (2011) J. Cell Sci. , vol.124 , pp. 3676-3683
    • Eskiw, C.H.1    Fraser, P.2
  • 27
    • 80255137474 scopus 로고    scopus 로고
    • The proteomes of transcription factories containing RNA polymerases I, II or III
    • Melnik, S., Deng, B., Papantonis, A., Baboo, S., Carr, I.M. and Cook, P.R. (2010) The proteomes of transcription factories containing RNA polymerases I, II or III. Nat. Methods, 8, 963-968.
    • (2010) Nat. Methods , vol.8 , pp. 963-968
    • Melnik, S.1    Deng, B.2    Papantonis, A.3    Baboo, S.4    Carr, I.M.5    Cook, P.R.6
  • 29
    • 84862908850 scopus 로고    scopus 로고
    • Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation
    • Li, G., Ruan, X., Auerbach, R.K., Sandhu, K.S., Zheng, M., Wang, P., Poh, H.M., Goh, Y., Lim, J., Zhang, J. et al. (2012) Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell, 148, 84-98.
    • (2012) Cell , vol.148 , pp. 84-98
    • Li, G.1    Ruan, X.2    Auerbach, R.K.3    Sandhu, K.S.4    Zheng, M.5    Wang, P.6    Poh, H.M.7    Goh, Y.8    Lim, J.9    Zhang, J.10
  • 30
    • 85027929606 scopus 로고    scopus 로고
    • Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization
    • Denholtz, M., Bonora, G., Chronis, C., Splinter, E., de Laat, W., Ernst, J., Pellegrini, M. and Plath, K. (2013) Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization. Cell Stem Cell, 13, 602-616.
    • (2013) Cell Stem Cell , vol.13 , pp. 602-616
    • Denholtz, M.1    Bonora, G.2    Chronis, C.3    Splinter, E.4    De Laat, W.5    Ernst, J.6    Pellegrini, M.7    Plath, K.8
  • 31
    • 84876879622 scopus 로고    scopus 로고
    • Insulators target active genes to transcription factories and polycomb-repressed genes to polycomb bodies
    • Li, H.B., Ohno, K., Gui, H. and Pirrotta, V. (2013) Insulators target active genes to transcription factories and polycomb-repressed genes to polycomb bodies. PLoS Genet., 9, e1003436.
    • (2013) PLoS Genet. , vol.9 , pp. e1003436
    • Li, H.B.1    Ohno, K.2    Gui, H.3    Pirrotta, V.4
  • 32
    • 84901779165 scopus 로고    scopus 로고
    • Pronounced cohabitation of active immunoglobulin genes from three different chromosomes in transcription factories during maximal antibody synthesis
    • Park, S.K., Xiang, Y., Feng, X. and Garrard, W.T. (2014) Pronounced cohabitation of active immunoglobulin genes from three different chromosomes in transcription factories during maximal antibody synthesis. Genes Dev., 28, 1159-1164.
    • (2014) Genes Dev. , vol.28 , pp. 1159-1164
    • Park, S.K.1    Xiang, Y.2    Feng, X.3    Garrard, W.T.4
  • 34
    • 0029203732 scopus 로고
    • Synthesis and maturation of viral transcripts in herpes simplex virus type 1 infected HeLa cells: The role of interchromatin granules
    • Besse, S., Vigneron, M., Pichard, E. and Puvion-Dutilleul, F. (1995) Synthesis and maturation of viral transcripts in herpes simplex virus type 1 infected HeLa cells: the role of interchromatin granules. Gene Expr., 4, 143-161.
    • (1995) Gene Expr. , vol.4 , pp. 143-161
    • Besse, S.1    Vigneron, M.2    Pichard, E.3    Puvion-Dutilleul, F.4
  • 37
    • 84876842759 scopus 로고    scopus 로고
    • Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells
    • Danko, C.G., Hah, N., Luo, X., Martins, A.L., Core, L., Lis, J.T., Siepel, A. and Kraus, W.L. (2012) Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. Mol. Cell, 50, 212-222.
    • (2012) Mol. Cell , vol.50 , pp. 212-222
    • Danko, C.G.1    Hah, N.2    Luo, X.3    Martins, A.L.4    Core, L.5    Lis, J.T.6    Siepel, A.7    Kraus, W.L.8
  • 38
    • 84896786505 scopus 로고    scopus 로고
    • Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase
    • Weber, C.M., Ramachandran, S. and Henikoff, S. (2014) Nucleosomes are context-specific, H2A.Z-modulated barriers to RNA polymerase. Mol. Cell, 53, 819-830.
    • (2014) Mol. Cell , vol.53 , pp. 819-830
    • Weber, C.M.1    Ramachandran, S.2    Henikoff, S.3
  • 39
    • 0029881045 scopus 로고    scopus 로고
    • Sequences attaching loops of nuclear and mitochondrial DNA to underlying structures in human cells: The role of transcription units
    • Jackson, D.A., Bartlett, J. and Cook, P.R. (1996) Sequences attaching loops of nuclear and mitochondrial DNA to underlying structures in human cells: the role of transcription units. Nucleic Acids Res., 24, 1212-1219.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 1212-1219
    • Jackson, D.A.1    Bartlett, J.2    Cook, P.R.3
  • 40
    • 73949113629 scopus 로고    scopus 로고
    • TNF-induced microRNAs regulate TNF-induced expression of E-selectin and intercellular adhesion molecule-1 on human endothelial cells: Feedback control of inflammation
    • Suárez, Y., Wang, C., Manes, T.D. and Pober, J.S. (2010) TNF-induced microRNAs regulate TNF-induced expression of E-selectin and intercellular adhesion molecule-1 on human endothelial cells: feedback control of inflammation. J. Immunol., 184, 21-25.
    • (2010) J. Immunol. , vol.184 , pp. 21-25
    • Suárez, Y.1    Wang, C.2    Manes, T.D.3    Pober, J.S.4
  • 41
    • 84880361099 scopus 로고    scopus 로고
    • RNA splicing regulates the temporal order of TNF-induced gene expression
    • Hao, S. and Baltimore, D. (2013) RNA splicing regulates the temporal order of TNF-induced gene expression. Proc. Natl. Acad. Sci. U.S.A., 110, 11934-11939.
    • (2013) Proc. Natl. Acad. Sci. U.S.A. , vol.110 , pp. 11934-11939
    • Hao, S.1    Baltimore, D.2
  • 42
  • 45
    • 84938303841 scopus 로고    scopus 로고
    • IRNA-seq: Computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data
    • Madsen, J.G., Schmidt, S.F., Larsen, B.D., Loft, A., Nielsen, R. and Mandrup, S. (2015) iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data. Nucleic Acids Res., 43, e40.
    • (2015) Nucleic Acids Res. , vol.43 , pp. e40
    • Madsen, J.G.1    Schmidt, S.F.2    Larsen, B.D.3    Loft, A.4    Nielsen, R.5    Mandrup, S.6
  • 46
    • 84904735424 scopus 로고    scopus 로고
    • Transcriptional regulatory functions of nuclear long noncoding RNAs
    • Vance, K.W. and Ponting, C.P. (2014) Transcriptional regulatory functions of nuclear long noncoding RNAs. Trends Genet., 30, 348-355.
    • (2014) Trends Genet. , vol.30 , pp. 348-355
    • Vance, K.W.1    Ponting, C.P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.