메뉴 건너뛰기




Volumn 17, Issue 5, 2010, Pages 620-628

Human RNA polymerase III transcriptomes and relationships to Pol II promoter chromatin and enhancer-binding factors

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; BRF1 PROTEIN; BRF2 PROTEIN; DNA DIRECTED RNA POLYMERASE III; MICRORNA; PROTEIN; RNA POLYMERASE II; STAT1 PROTEIN; TRANSCRIPTOME; UNCLASSIFIED DRUG;

EID: 77951943463     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb.1801     Document Type: Article
Times cited : (211)

References (46)
  • 3
    • 56649105133 scopus 로고    scopus 로고
    • RNA polymerases i and III, non-coding RNAs and cancer
    • White, R.J. RNA polymerases I and III, non-coding RNAs and cancer. Trends Genet. 24, 622-629 (2008).
    • (2008) Trends Genet. , vol.24 , pp. 622-629
    • White, R.J.1
  • 4
    • 56749170666 scopus 로고    scopus 로고
    • Non-coding RNA production by RNA polymerase III is implicated in cancer
    • Marshall, L. & White, R.J. Non-coding RNA production by RNA polymerase III is implicated in cancer. Nat. Rev. Cancer 8, 911-914 (2008).
    • (2008) Nat. Rev. Cancer , vol.8 , pp. 911-914
    • Marshall, L.1    White, R.J.2
  • 5
    • 0027475474 scopus 로고
    • RNA polymerase III. Genes, factors and transcriptional specifcity
    • Willis, I.M. RNA polymerase III. Genes, factors and transcriptional specifcity. Eur. J. Biochem. 212, 1-11 (1993).
    • (1993) Eur. J. Biochem. , vol.212 , pp. 1-11
    • Willis, I.M.1
  • 6
    • 0035967858 scopus 로고    scopus 로고
    • The RNA polymerase III transcription apparatus
    • Geiduschek, E.P. & Kassavetis, G.A. The RNA polymerase III transcription apparatus. J. Mol. Biol. 310, 1-26 (2001).
    • (2001) J. Mol. Biol. , vol.310 , pp. 1-26
    • Geiduschek, E.P.1    Kassavetis, G.A.2
  • 7
    • 0037108150 scopus 로고    scopus 로고
    • Recruitment of RNA polymerase III to its target promoters
    • Schramm, L. & Hernandez, N. Recruitment of RNA polymerase III to its target promoters. Genes Dev. 16, 2593-2620 (2002).
    • (2002) Genes Dev. , vol.16 , pp. 2593-2620
    • Schramm, L.1    Hernandez, N.2
  • 8
    • 33646912186 scopus 로고    scopus 로고
    • A role for TFIIIC transcription factor complex in genome organization
    • Noma, K., Cam, H.P., Maraia, R.J. & Grewal, S.I. A role for TFIIIC transcription factor complex in genome organization. Cell 125, 859-872 (2006).
    • (2006) Cell , vol.125 , pp. 859-872
    • Noma, K.1    Cam, H.P.2    Maraia, R.J.3    Grewal, S.I.4
  • 9
    • 57349129792 scopus 로고    scopus 로고
    • TFIIIC binding sites function as both heterochromatin barriers and chromatin insulators in Saccharomyces cerevisiae
    • Simms, T.A. et al. TFIIIC binding sites function as both heterochromatin barriers and chromatin insulators in Saccharomyces cerevisiae. Eukaryot. Cell 7, 2078-2086 (2008).
    • (2008) Eukaryot. Cell , vol.7 , pp. 2078-2086
    • Simms, T.A.1
  • 10
    • 2442606759 scopus 로고    scopus 로고
    • Genome-wide occupancy profle of the RNA polymerase III machinery in Saccharomyces cerevisiae reveals loci with incomplete transcription complexes
    • Moqtaderi, Z. & Struhl, K. Genome-wide occupancy profle of the RNA polymerase III machinery in Saccharomyces cerevisiae reveals loci with incomplete transcription complexes. Mol. Cell. Biol. 24, 4118-4127 (2004).
    • (2004) Mol. Cell. Biol. , vol.24 , pp. 4118-4127
    • Moqtaderi, Z.1    Struhl, K.2
  • 11
    • 70350148258 scopus 로고    scopus 로고
    • Transcription independent insulation at TFIIIC-dependent insulators
    • Valenzuela, L., Dhillon, N. & Kamakaka, R.T. Transcription independent insulation at TFIIIC-dependent insulators. Genetics 183, 131-148 (2009).
    • (2009) Genetics , vol.183 , pp. 131-148
    • Valenzuela, L.1    Dhillon, N.2    Kamakaka, R.T.3
  • 12
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    • Bailey, T.L. & Elkan, C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol. 2, 28-36 (1994).
    • (1994) Proc. Int. Conf. Intell. Syst. Mol. Biol. , vol.2 , pp. 28-36
    • Bailey, T.L.1    Elkan, C.2
  • 13
    • 60149112271 scopus 로고    scopus 로고
    • PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
    • Rozowsky, J. et al. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat. Biotechnol. 27, 66-75 (2009).
    • (2009) Nat. Biotechnol. , vol.27 , pp. 66-75
    • Rozowsky, J.1
  • 14
    • 57149096220 scopus 로고    scopus 로고
    • Genome-wide relationship between histone H3 lysine 4 mono-and tri-methylation and transcription factor binding
    • Robertson, A.G. et al. Genome-wide relationship between histone H3 lysine 4 mono-and tri-methylation and transcription factor binding. Genome Res. 18, 1906-1917 (2008).
    • (2008) Genome Res. , vol.18 , pp. 1906-1917
    • Robertson, A.G.1
  • 15
    • 68149150830 scopus 로고    scopus 로고
    • H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions
    • Jin, C. et al. H3.3/H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions. Nat. Genet. 41, 941-945 (2009).
    • (2009) Nat. Genet. , vol.41 , pp. 941-945
    • Jin, C.1
  • 16
    • 60149095014 scopus 로고    scopus 로고
    • Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains
    • Cuddapah, S. et al. Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res. 19, 24-32 (2009).
    • (2009) Genome Res. , vol.19 , pp. 24-32
    • Cuddapah, S.1
  • 17
    • 34047116826 scopus 로고    scopus 로고
    • Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
    • Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 39, 457-466 (2007).
    • (2007) Nat. Genet. , vol.39 , pp. 457-466
    • Weber, M.1
  • 18
    • 0023731768 scopus 로고
    • Increased expression of CD4 molecules on Jurkat cells mediated by human immunodefciency virus tat protein
    • Koka, P. et al. Increased expression of CD4 molecules on Jurkat cells mediated by human immunodefciency virus tat protein. J. Virol. 62, 4353-4357 (1988).
    • (1988) J. Virol. , vol.62 , pp. 4353-4357
    • Koka, P.1
  • 19
    • 34249026300 scopus 로고    scopus 로고
    • High-resolution profling of histone methylations in the human genome
    • Barski, A. et al. High-resolution profling of histone methylations in the human genome. Cell 129, 823-837 (2007).
    • (2007) Cell , vol.129 , pp. 823-837
    • Barski, A.1
  • 20
    • 46249112085 scopus 로고    scopus 로고
    • Combinatorial patterns of histone acetylations and methylations in the human genome
    • Wang, Z. et al. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat. Genet. 40, 897-903 (2008).
    • (2008) Nat. Genet. , vol.40 , pp. 897-903
    • Wang, Z.1
  • 21
    • 50849090969 scopus 로고    scopus 로고
    • Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
    • Valouev, A. et al. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat. Methods 5, 829-834 (2008).
    • (2008) Nat. Methods , vol.5 , pp. 829-834
    • Valouev, A.1
  • 22
    • 74249118523 scopus 로고    scopus 로고
    • DNA specifcity determinants associate with distinct transcription factor functions
    • Hollenhorst, P.C. et al. DNA specifcity determinants associate with distinct transcription factor functions. PLoS Genet. 5, e1000778 (2009).
    • (2009) PLoS Genet. , vol.5
    • Hollenhorst, P.C.1
  • 23
    • 70349643725 scopus 로고    scopus 로고
    • Chromatin poises miRNA-and protein-coding genes for expression
    • Barski, A. et al. Chromatin poises miRNA-and protein-coding genes for expression. Genome Res. 19, 1742-1751 (2009).
    • (2009) Genome Res. , vol.19 , pp. 1742-1751
    • Barski, A.1
  • 24
    • 34547633677 scopus 로고    scopus 로고
    • Genome-wide profles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
    • Robertson, G. et al. Genome-wide profles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods 4, 651-657 (2007).
    • (2007) Nat. Methods , vol.4 , pp. 651-657
    • Robertson, G.1
  • 25
    • 0141834812 scopus 로고    scopus 로고
    • Direct regulation of RNA polymerase III transcription by RB, p53 and c-Myc
    • Felton-Edkins, Z.A. et al. Direct regulation of RNA polymerase III transcription by RB, p53 and c-Myc. Cell Cycle 2, 181-184 (2003).
    • (2003) Cell Cycle , vol.2 , pp. 181-184
    • Felton-Edkins, Z.A.1
  • 26
    • 0347721764 scopus 로고    scopus 로고
    • Direct activation of RNA polymerase III transcription by c-Myc
    • Gomez-Roman, N., Grandori, C., Eisenman, R.N. & White, R.J. Direct activation of RNA polymerase III transcription by c-Myc. Nature 421, 290-294 (2003).
    • (2003) Nature , vol.421 , pp. 290-294
    • Gomez-Roman, N.1    Grandori, C.2    Eisenman, R.N.3    White, R.J.4
  • 27
    • 65549104157 scopus 로고    scopus 로고
    • Histone modifcations at human enhancers refect global cell-type-specifc gene expression
    • Heintzman, N.D. et al. Histone modifcations at human enhancers refect global cell-type-specifc gene expression. Nature 459, 108-112 (2009).
    • (2009) Nature , vol.459 , pp. 108-112
    • Heintzman, N.D.1
  • 29
    • 67249136441 scopus 로고    scopus 로고
    • C19MC microRNAs are processed from introns of large Pol-II, non-protein-coding transcripts
    • Bortolin-Cavaille, M.L., Dance, M., Weber, M. & Cavaille, J. C19MC microRNAs are processed from introns of large Pol-II, non-protein-coding transcripts. Nucleic Acids Res. 37, 3464-3473 (2009).
    • (2009) Nucleic Acids Res. , vol.37 , pp. 3464-3473
    • Bortolin-Cavaille, M.L.1    Dance, M.2    Weber, M.3    Cavaille, J.4
  • 30
    • 34250891308 scopus 로고    scopus 로고
    • Subtractive hybridization identifes novel differentially expressed ncRNA species in EBV-infected human B cells
    • Mrazek, J., Kreutmayer, S.B., Grasser, F.A., Polacek, N. & Huttenhofer, A. Subtractive hybridization identifes novel differentially expressed ncRNA species in EBV-infected human B cells. Nucleic Acids Res. 35, e73 (2007).
    • (2007) Nucleic Acids Res. , vol.35
    • Mrazek, J.1    Kreutmayer, S.B.2    Grasser, F.A.3    Polacek, N.4    Huttenhofer, A.5
  • 31
    • 35548996309 scopus 로고    scopus 로고
    • Novel rapidly evolving hominid RNAs bind nuclear factor 90 and display tissue-restricted distribution
    • Parrott, A.M. & Mathews, M.B. Novel rapidly evolving hominid RNAs bind nuclear factor 90 and display tissue-restricted distribution. Nucleic Acids Res. 35, 6249-6258 (2007).
    • (2007) Nucleic Acids Res. , vol.35 , pp. 6249-6258
    • Parrott, A.M.1    Mathews, M.B.2
  • 32
    • 34250877841 scopus 로고    scopus 로고
    • A mammalian microRNA expression atlas based on small RNA library sequencing
    • Landgraf, P. et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129, 1401-1414 (2007).
    • (2007) Cell , vol.129 , pp. 1401-1414
    • Landgraf, P.1
  • 34
    • 37349006883 scopus 로고    scopus 로고
    • Extragenic accumulation of RNA polymerase II enhances transcription by RNA polymerase III
    • Listerman, I., Bledau, A.S., Grishina, I. & Neugebauer, K.M. Extragenic accumulation of RNA polymerase II enhances transcription by RNA polymerase III. PLoS Genet. 3, e212 (2007).
    • (2007) PLoS Genet. , vol.3
    • Listerman, I.1    Bledau, A.S.2    Grishina, I.3    Neugebauer, K.M.4
  • 35
    • 37549003250 scopus 로고    scopus 로고
    • CHD8 associates with human Staf and contributes to effcient U6 RNA polymerase III transcription
    • Yuan, C.C. et al. CHD8 associates with human Staf and contributes to effcient U6 RNA polymerase III transcription. Mol. Cell. Biol. 27, 8729-8738 (2007).
    • (2007) Mol. Cell. Biol. , vol.27 , pp. 8729-8738
    • Yuan, C.C.1
  • 36
    • 66149147557 scopus 로고    scopus 로고
    • Developmental programming of CpG island methylation profles in the human genome
    • Straussman, R. et al. Developmental programming of CpG island methylation profles in the human genome. Nat. Struct. Mol. Biol. 16, 564-571 (2009).
    • (2009) Nat. Struct. Mol. Biol. , vol.16 , pp. 564-571
    • Straussman, R.1
  • 37
    • 0345598934 scopus 로고    scopus 로고
    • The RNA polymerase III transcriptome revealed by genome-wide localization and activity-occupancy relationships
    • Roberts, D.N., Stewart, A.J., Huff, J.T. & Cairns, B.R. The RNA polymerase III transcriptome revealed by genome-wide localization and activity-occupancy relationships. Proc. Natl. Acad. Sci. USA 100, 14695-14700 (2003).
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 14695-14700
    • Roberts, D.N.1    Stewart, A.J.2    Huff, J.T.3    Cairns, B.R.4
  • 38
    • 0141625270 scopus 로고    scopus 로고
    • Genome-wide location of yeast RNA polymerase III transcription machinery
    • Harismendy, O. et al. Genome-wide location of yeast RNA polymerase III transcription machinery. EMBO J. 22, 4738-4747 (2003).
    • (2003) EMBO J. , vol.22 , pp. 4738-4747
    • Harismendy, O.1
  • 39
    • 33846659385 scopus 로고    scopus 로고
    • Integration of nutritional and stress signaling pathways by Maf1
    • Willis, I.M. & Moir, R.D. Integration of nutritional and stress signaling pathways by Maf1. Trends Biochem. Sci. 32, 51-53 (2007).
    • (2007) Trends Biochem. Sci. , vol.32 , pp. 51-53
    • Willis, I.M.1    Moir, R.D.2
  • 40
    • 0022555861 scopus 로고
    • Nonviral retroposons: Genes, pseudogenes, and transposable elements generated by the reverse fow of genetic information
    • Weiner, A.M., Deininger, P.L. & Efstratiadis, A. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse fow of genetic information. Annu. Rev. Biochem. 55, 631-661 (1986).
    • (1986) Annu. Rev. Biochem. , vol.55 , pp. 631-661
    • Weiner, A.M.1    Deininger, P.L.2    Efstratiadis, A.3
  • 41
    • 38649099445 scopus 로고    scopus 로고
    • High-resolution mapping and characterization of open chromatin across the genome
    • Boyle, A.P. et al. High-resolution mapping and characterization of open chromatin across the genome. Cell 132, 311-322 (2008).
    • (2008) Cell , vol.132 , pp. 311-322
    • Boyle, A.P.1
  • 42
    • 34347361647 scopus 로고    scopus 로고
    • Genome-wide dynamics of SAPHIRE, an essential complex for gene activation and chromatin boundaries
    • Gordon, M. et al. Genome-wide dynamics of SAPHIRE, an essential complex for gene activation and chromatin boundaries. Mol. Cell. Biol. 27, 4058-4069 (2007).
    • (2007) Mol. Cell. Biol. , vol.27 , pp. 4058-4069
    • Gordon, M.1
  • 43
    • 0038133335 scopus 로고    scopus 로고
    • Purifying mRNAs with a high-affnity eIF4E mutant identifes the short 3′ poly(A) end phenotype
    • Choi, Y.H. & Hagedorn, C.H. Purifying mRNAs with a high-affnity eIF4E mutant identifes the short 3′ poly(A) end phenotype. Proc. Natl. Acad. Sci. USA 100, 7033-7038 (2003).
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 7033-7038
    • Choi, Y.H.1    Hagedorn, C.H.2
  • 44
    • 39749145198 scopus 로고    scopus 로고
    • Dynamic regulation of nucleosome positioning in the human genome
    • Schones, D.E. et al. Dynamic regulation of nucleosome positioning in the human genome. Cell 132, 887-898 (2008).
    • (2008) Cell , vol.132 , pp. 887-898
    • Schones, D.E.1
  • 45
    • 60849117520 scopus 로고    scopus 로고
    • Empirical methods for controlling false positives and estimating confdence in ChIP-Seq peaks
    • Nix, D.A., Courdy, S.J. & Boucher, K.M. Empirical methods for controlling false positives and estimating confdence in ChIP-Seq peaks. BMC Bioinformatics 9, 523 (2008).
    • (2008) BMC Bioinformatics , vol.9 , pp. 523
    • Nix, D.A.1    Courdy, S.J.2    Boucher, K.M.3
  • 46
    • 67749114140 scopus 로고    scopus 로고
    • Distinctive chromatin in human sperm packages genes for embryo development
    • Hammoud, S.S. et al. Distinctive chromatin in human sperm packages genes for embryo development. Nature 460, 473-478 (2009).
    • (2009) Nature , vol.460 , pp. 473-478
    • Hammoud, S.S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.