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Volumn 22, Issue 4, 2012, Pages 666-680

A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver

(39)  Canella, Donatella a   Bernasconi, David a,b,e   Gilardi, Federica a   LeMartelot, Gwendal c   Migliavacca, Eugenia b   Praz, Viviane a   Cousin, Pascal a   Delorenzi, Mauro b,d,e   Hernandez, Nouria a   Deplancke, Bart f   Desvergne, Béatrice a   Guex, Nicolas b   Herr, Winship a   Naef, Felix f   Rougemont, Jacques f   Schibler, Ueli c   Andersin, Teemu c   Gos, Pascal c   Raghav, Sunil f   Fabbretti, Roberto b   more..


Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED RNA POLYMERASE III; TRANSFER RNA;

EID: 84859558677     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.130286.111     Document Type: Article
Times cited : (53)

References (50)
  • 1
    • 0027491877 scopus 로고
    • Nucleotide sequences of the RNA subunit of RNase P from several mammals
    • DOI 10.1006/geno.1993.1488
    • Altman S, Wesolowski D, Puranam RS. 1993. Nucleotide sequences of the RNA subunit of RNase P from several mammals. Genomics 18: 418-422. (Pubitemid 23339559)
    • (1993) Genomics , vol.18 , Issue.2 , pp. 418-422
    • Altman, S.1    Wesolowski, D.2    Puranam, R.S.3
  • 2
    • 0035815662 scopus 로고    scopus 로고
    • A bidirectional promoter connects the poly(ADP-ribose) polymerase 2 (PARP-2) gene to the gene for RNase P RNA: Structure and expression of the mouse PARP-2 gene
    • DOI 10.1074/jbc.M007870200
    • Ame JC, Schreiber V, Fraulob V, Dolle P, de Murcia G, Niedergang CP. 2001. A bidirectional promoter connects the poly(ADP-ribose) polymerase 2 (PARP-2) gene to the gene for RNase P RNA. Structure and expression of the mouse PARP-2 gene. J Biol Chem 276: 11092-11099. (Pubitemid 38089292)
    • (2001) Journal of Biological Chemistry , vol.276 , Issue.14 , pp. 11092-11099
    • Ame, J.-C.1    Schreiber, V.2    Fraulob, V.3    Dolle, P.4    De Murcia, G.5    Niedergang, C.P.6
  • 3
    • 0022472238 scopus 로고
    • Isolation and sequencing of a genomic clone for mouse brain specific small RNA
    • Anzai K, Kobayashi S, Kitamura N, Kanai Y, Nakajima H, Suehiro Y, Goto S. 1986. Isolation and sequencing of a genomic clone for mouse brain specific small RNA. J Neurochem 47: 673-677. (Pubitemid 16029543)
    • (1986) Journal of Neurochemistry , vol.47 , Issue.3 , pp. 673-677
    • Anzai, K.1    Kobayashi, S.2    Kitamura, N.3
  • 4
    • 34249026300 scopus 로고    scopus 로고
    • High-Resolution Profiling of Histone Methylations in the Human Genome
    • DOI 10.1016/j.cell.2007.05.009, PII S0092867407006009
    • Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. 2007. High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837. (Pubitemid 46802390)
    • (2007) Cell , vol.129 , Issue.4 , pp. 823-837
    • Barski, A.1    Cuddapah, S.2    Cui, K.3    Roh, T.-Y.4    Schones, D.E.5    Wang, Z.6    Wei, G.7    Chepelev, I.8    Zhao, K.9
  • 6
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol 57: 289-300.
    • (1995) J R Stat Soc Ser B Methodol , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 8
    • 0018890841 scopus 로고
    • A control region in the center of the 5S RNA gene directs specific initiation of transcription: II. The 3' border of the region
    • Bogenhagen DF, Sakonju S, Brown DD. 1980. A control region in the center of the 5S RNA gene directs specific initiation of transcription: II. The 3′ border of the region. Cell 19: 27-35. (Pubitemid 10154210)
    • (1980) Cell , vol.19 , Issue.1 , pp. 27-35
    • Bogenhagen, D.F.1    Sakonju, S.2    Brown, D.D.3
  • 9
    • 0025642401 scopus 로고
    • Activating-transcription-factor (ATF) regulates human 7S L RNA transcription by RNA polymerase III in vivo and in vitro
    • Bredow S, Surig D, Muller J, Kleinert H, Benecke BJ. 1990. Activatingtranscription- factor (ATF) regulates human 7S L RNA transcription by RNA polymerase III in vivo and in vitro. Nucleic Acids Res 18: 6779-6784. (Pubitemid 120006057)
    • (1990) Nucleic Acids Research , vol.18 , Issue.23 , pp. 6779-6784
    • Bredow, S.1    Surig, D.2    Muller, J.3    Kleinert, H.4    Benecke, B.-J.5
  • 10
    • 77952988986 scopus 로고    scopus 로고
    • Defining the RNA polymerase III transcriptome: Genome-wide localization of the RNA polymerase III transcription machinery in human cells
    • Canella D, Praz V, Reina JH, Cousin P, Hernandez N. 2010. Defining the RNA polymerase III transcriptome: Genome-wide localization of the RNA polymerase III transcription machinery in human cells. Genome Res 20:710-721.
    • (2010) Genome Res , vol.20 , pp. 710-721
    • Canella, D.1    Praz, V.2    Reina, J.H.3    Cousin, P.4    Hernandez, N.5
  • 12
    • 0024968185 scopus 로고
    • Mouse RNAase MRP RNA is encoded by a nuclear gene and contains a decamer sequence complementary to a conserved region of mitochondrial RNA substrate
    • Chang DD, Clayton DA. 1989. Mouse RNAase MRP RNA is encoded by a nuclear gene and contains a decamer sequence complementary to a conserved region of mitochondrial RNA substrate. Cell 56: 131-139.
    • (1989) Cell , vol.56 , pp. 131-139
    • Chang, D.D.1    Clayton, D.A.2
  • 13
  • 14
    • 0035827649 scopus 로고    scopus 로고
    • Reconstitution of transcription from the human U6 small nuclear RNA promoter with eight recombinant polypeptides and a partially purified RNA polymerase III complex
    • Chong SS, Hu P, Hernandez N. 2001. Reconstitution of transcription from the human U6 small nuclear RNA promoter with eight recombinant polypeptides and a partially purified RNA polymerase III complex. J Biol Chem 276: 20727-20734.
    • (2001) J Biol Chem , vol.276 , pp. 20727-20734
    • Chong, S.S.1    Hu, P.2    Hernandez, N.3
  • 15
    • 0023955980 scopus 로고
    • Upstreamregulatory elements are necessary and sufficient for transcription of a U6 RNA gene by RNA polymerase III
    • Das G, Henning D, Wright D, Reddy R. 1988. Upstreamregulatory elements are necessary and sufficient for transcription of a U6 RNA gene by RNA polymerase III. EMBO J 7: 503-512.
    • (1988) EMBO J , vol.7 , pp. 503-512
    • Das, G.1    Henning, D.2    Wright, D.3    Reddy, R.4
  • 16
    • 0030034259 scopus 로고    scopus 로고
    • Facilitated recycling pathway for RNA polymerase III
    • DOI 10.1016/S0092-8674(00)80979-4
    • Dieci G, Sentenac A. 1996. Facilitated recycling pathway for RNA polymerase III. Cell 84: 245-252. (Pubitemid 26040844)
    • (1996) Cell , vol.84 , Issue.2 , pp. 245-252
    • Dieci, G.1    Sentenac, A.2
  • 17
    • 0038750923 scopus 로고    scopus 로고
    • Multiple, dispersed human U6 small nuclear RNA genes with varied transcriptional efficiencies
    • DOI 10.1093/nar/gkg331
    • Domitrovich AM, Kunkel GR. 2003. Multiple, dispersed human U6 small nuclear RNA genes with varied transcriptional efficiencies. Nucleic Acids Res 31: 2344-2352. (Pubitemid 37442102)
    • (2003) Nucleic Acids Research , vol.31 , Issue.9 , pp. 2344-2352
    • Domitrovich, A.M.1    Kunkel, G.R.2
  • 18
    • 12744280551 scopus 로고    scopus 로고
    • Novel upstream and intragenic control elements for the RNA polymerase III-dependent transcription of human 7SL RNA genes
    • Englert M, Felis M, Junker V, Beier H. 2004. Novel upstream and intragenic control elements for the RNA polymerase III-dependent transcription of human 7SL RNA genes. Biochimie 86: 867-874.
    • (2004) Biochimie , vol.86 , pp. 867-874
    • Englert, M.1    Felis, M.2    Junker, V.3    Beier, H.4
  • 19
    • 0030603243 scopus 로고    scopus 로고
    • Genes for murine Y1 and Y3 Ro RNAs have class 3 RNA polymerase III promoter structures and are unlinked on mouse chromosome 6
    • DOI 10.1016/0378-1119(96)00279-X
    • Farris AD, Gross JK, Hanas JS, Harley JB. 1996. Genes for murine Y1 and Y3 Ro RNAs have class 3 RNA polymerase III promoter structures and are unlinked on mouse chromosome 6. Gene 174: 35-42. (Pubitemid 26326848)
    • (1996) Gene , vol.174 , Issue.1 , pp. 35-42
    • Farris, A.D.1    Gross, J.K.2    Hanas, J.S.3    Harley, J.B.4
  • 20
    • 73249137562 scopus 로고    scopus 로고
    • 4.5SI RNA genes and the role of their 59-flanking sequences in the gene transcription
    • Gogolevskaya IK, Kramerov DA. 2010. 4.5SI RNA genes and the role of their 59-flanking sequences in the gene transcription. Gene 451: 32-37.
    • (2010) Gene , vol.451 , pp. 32-37
    • Gogolevskaya, I.K.1    Kramerov, D.A.2
  • 21
    • 0025334286 scopus 로고
    • The gene for the RNA component of the mitochondrial RNA-processing endoribonuclease is located on human chromosome 9p and on mouse chromosome 4
    • DOI 10.1016/0888-7543(90)90483-B
    • Hsieh CL, Donlon TA, Darras BT, Chang DD, Topper JN, Clayton DA, Francke U. 1990. The gene for the RNA component of the mitochondrial RNA-processing endoribonuclease is located on human chromosome 9p and on mouse chromosome 4. Genomics 6: 540-544. (Pubitemid 20168686)
    • (1990) Genomics , vol.6 , Issue.3 , pp. 540-544
    • Hsieh, C.-L.1    Donlon, T.A.2    Darras, B.T.3    Chang, D.D.4    Topper, J.N.5    Clayton, D.A.6    Francke, U.7
  • 22
    • 52649132425 scopus 로고    scopus 로고
    • Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
    • Jothi R, Cuddapah S, Barski A, Cui K, Zhao K. 2008. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res 36: 5221-5231.
    • (2008) Nucleic Acids Res , vol.36 , pp. 5221-5231
    • Jothi, R.1    Cuddapah, S.2    Barski, A.3    Cui, K.4    Zhao, K.5
  • 24
    • 0037986643 scopus 로고    scopus 로고
    • Identification of conserved vault RNA expression elements and a non-expressed mouse vault RNA gene
    • DOI 10.1016/S0378-1119(03)00507-9
    • Kickhoefer VA, Emre N, Stephen AG, Poderycki MJ, Rome LH. 2003. Identification of conserved vault RNA expression elements and a non-expressed mouse vault RNA gene. Gene 309: 65-70. (Pubitemid 36577502)
    • (2003) Gene , vol.309 , Issue.2 , pp. 65-70
    • Kickhoefer, V.A.1    Emre, N.2    Stephen, A.G.3    Poderycki, M.J.4    Rome, L.H.5
  • 25
    • 16244384503 scopus 로고    scopus 로고
    • A novel domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation
    • DOI 10.1128/MCB.25.8.3305-3316.2005
    • Kizer KO, Phatnani HP, Shibata Y, Hall H, Greenleaf AL, Strahl BD. 2005. A novel domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation. Mol Cell Biol 25: 3305-3316. (Pubitemid 40464330)
    • (2005) Molecular and Cellular Biology , vol.25 , Issue.8 , pp. 3305-3316
    • Kizer, K.O.1    Phatnani, H.P.2    Shibata, Y.3    Hall, H.4    Greenleaf, A.L.5    Strahl, B.D.6
  • 26
    • 33847076849 scopus 로고    scopus 로고
    • Chromatin Modifications and Their Function
    • DOI 10.1016/j.cell.2007.02.005, PII S0092867407001845
    • Kouzarides T. 2007. Chromatin modifications and their function. Cell 128: 693-705. (Pubitemid 46273577)
    • (2007) Cell , vol.128 , Issue.4 , pp. 693-705
    • Kouzarides, T.1
  • 28
    • 80053383499 scopus 로고    scopus 로고
    • Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes
    • Kutter C, Brown GD, Goncalves A, Wilson MD, Watt S, Brazma A, White RJ, Odom DT. 2011. Pol III binding in six mammals shows conservation among amino acid isotypes despite divergence among tRNA genes. Nat Genet 43: 948-955.
    • (2011) Nat Genet , vol.43 , pp. 948-955
    • Kutter, C.1    Brown, G.D.2    Goncalves, A.3    Wilson, M.D.4    Watt, S.5    Brazma, A.6    White, R.J.7    Odom, D.T.8
  • 29
    • 0028808110 scopus 로고
    • Cloning and characterization of three new murine genes encoding short homologues of RNase P RNA
    • Li K, Williams RS. 1995. Cloning and characterization of three new murine genes encoding short homologues of RNase P RNA. J Biol Chem 270:25281-25285.
    • (1995) J Biol Chem , vol.270 , pp. 25281-25285
    • Li, K.1    Williams, R.S.2
  • 30
    • 0037147121 scopus 로고    scopus 로고
    • Association of the histone methyltransferase Set2 with RNA polymerase II plays a role in transcription elongation
    • DOI 10.1074/jbc.M209294200
    • Li J, Moazed D, Gygi SP. 2002. Association of the histone methyltransferase Set2 with RNA polymerase II plays a role in transcription elongation. J Biol Chem 277: 49383-49388. (Pubitemid 36014370)
    • (2002) Journal of Biological Chemistry , vol.277 , Issue.51 , pp. 49383-49388
    • Li, J.1    Moazed, D.2    Gygi, S.P.3
  • 31
    • 37349006883 scopus 로고    scopus 로고
    • Extragenic accumulation of RNA polymerase II enhances transcription by RNA polymerase III
    • doi: 10.1371/journal.pgen.0030212.
    • Listerman I, Bledau AS, Grishina I, Neugebauer KM. 2007. Extragenic accumulation of RNA polymerase II enhances transcription by RNA polymerase III. PLoS Genet 3: e212. doi: 10.1371/journal.pgen.0030212.
    • (2007) PLoS Genet , vol.3
    • Listerman, I.1    Bledau, A.S.2    Grishina, I.3    Neugebauer, K.M.4
  • 32
    • 0026480738 scopus 로고
    • ATBP complex essential for transcription from TATA-less but not TATA-containing RNA polymerase III promoters is part of the TFIIIB fraction
    • Lobo SM, Tanaka M, Sullivan ML, Hernandez N. 1992. ATBP complex essential for transcription from TATA-less but not TATA-containing RNA polymerase III promoters is part of the TFIIIB fraction. Cell 71: 1029-1040.
    • (1992) Cell , vol.71 , pp. 1029-1040
    • Lobo, S.M.1    Tanaka, M.2    Sullivan, M.L.3    Hernandez, N.4
  • 33
    • 0028876868 scopus 로고
    • BC1 RNA: Transcriptional analysis of a neural cell-specific RNA polymerase III transcript
    • Martignetti JA, Brosius J. 1995. BC1 RNA: transcriptional analysis of a neural cell-specific RNA polymerase III transcript. Mol Cell Biol 15: 1642-1650.
    • (1995) Mol Cell Biol , vol.15 , pp. 1642-1650
    • Martignetti, J.A.1    Brosius, J.2
  • 34
    • 0026096482 scopus 로고
    • Common RNA polymerase I, II, and III upstream elements in mouse 7SK gene locus revealed by the inverse polymerase chain reaction
    • Moon IS, Krause MO. 1991. Common RNA polymerase I, II, and III upstream elements in mouse 7SK gene locus revealed by the inverse polymerase chain reaction. DNA Cell Biol 10: 23-32.
    • (1991) DNA Cell Biol , vol.10 , pp. 23-32
    • Moon, I.S.1    Krause, M.O.2
  • 35
    • 77951962545 scopus 로고    scopus 로고
    • Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells
    • Moqtaderi Z, Wang J, Raha D, White RJ, Snyder M, Weng Z, Struhl K. 2010. Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nat Struct Mol Biol 17: 635-640.
    • (2010) Nat Struct Mol Biol , vol.17 , pp. 635-640
    • Moqtaderi, Z.1    Wang, J.2    Raha, D.3    White, R.J.4    Snyder, M.5    Weng, Z.6    Struhl, K.7
  • 39
    • 34249660747 scopus 로고    scopus 로고
    • Ro-associated Y RNAs in metazoans: Evolution and diversification
    • DOI 10.1093/molbev/msm084
    • Perreault J, Perreault JP, Boire G. 2007. Ro-associated Y RNAs in metazoans: evolution and diversification. Mol Biol Evol 24: 1678-1689. (Pubitemid 47236684)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.8 , pp. 1678-1689
    • Perreault, J.1    Perreault, J.-P.2    Boire, G.3
  • 40
    • 0023657449 scopus 로고
    • The 5S gene internal control region is composed of three distinct sequence elements, organized as two functional domains with variable spacing
    • Pieler T, Hamm J, Roeder RG. 1987. The 5S gene internal control region is composed of three distinct sequence elements, organized as two functional domains with variable spacing. Cell 48: 91-100.
    • (1987) Cell , vol.48 , pp. 91-100
    • Pieler, T.1    Hamm, J.2    Roeder, R.G.3
  • 41
    • 33746745499 scopus 로고    scopus 로고
    • Mapping of binding regions for the circadian regulators BMAL1 and CLOCK within the mouse Rev-erba gene
    • Ripperger JA. 2006. Mapping of binding regions for the circadian regulators BMAL1 and CLOCK within the mouse Rev-erba gene. Chronobiol Int 23:135-142.
    • (2006) Chronobiol Int , vol.23 , pp. 135-142
    • Ripperger, J.A.1
  • 42
    • 0018841209 scopus 로고
    • A control region in the center of the 5S RNA gene directs specific initiation of transcription: 1. The 5' border of the region
    • Sakonju S, Bogenhagen DF, Brown DD. 1980. A control region in the center of the 5S RNA gene directs specific initiation of transcription: I. The 5′ border of the region. Cell 19: 13-25. (Pubitemid 10154209)
    • (1980) Cell , vol.19 , Issue.1 , pp. 13-25
    • Sakonju, S.1    Bogenhagen, D.F.2    Brown, D.D.3
  • 44
    • 0030668257 scopus 로고    scopus 로고
    • The largest subunit of human RNA polymerase III is closely related to the largest subunit of yeast and trypanosome RNA polymerase III
    • Sepehri S, Hernandez N. 1997. The largest subunit of human RNA polymerase III is closely related to the largest subunit of yeast and trypanosome RNA polymerase III. Genome Res 7: 1006-1019. (Pubitemid 27487765)
    • (1997) Genome Research , vol.7 , Issue.10 , pp. 1006-1019
    • Sepehri, S.1    Hernandez, N.2
  • 45
    • 0030479536 scopus 로고    scopus 로고
    • The origin of interspersed repeats in the human genome
    • DOI 10.1016/S0959-437X(96)80030-X
    • Smit AF. 1996. The origin of interspersed repeats in the human genome. Curr Opin Genet Dev 6: 743-748. (Pubitemid 27010635)
    • (1996) Current Opinion in Genetics and Development , vol.6 , Issue.6 , pp. 743-748
    • Smit, A.F.A.1
  • 46
    • 0032784908 scopus 로고    scopus 로고
    • Interspersed repeats and other mementos of transposable elements in mammalian genomes
    • Smit AF. 1999. Interspersed repeats and other mementos of transposable elements in mammalian genomes. Curr Opin Genet Dev 9: 657-663.
    • (1999) Curr Opin Genet Dev , vol.9 , pp. 657-663
    • Smit, A.F.1
  • 47
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical bayes methods for assessing differential expression in microarray experiments
    • doi: 10.2202/1544-6115.1027
    • Smyth GK. 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: doi: 10.2202/1544-6115.1027.
    • (2004) Stat Appl Genet Mol Biol , vol.3
    • Smyth, G.K.1
  • 48
    • 0022414359 scopus 로고
    • Upstream sequences modulate the internal promotor of the human 7SL RNA gene
    • DOI 10.1038/318371a0
    • Ullu E, Weiner AM. 1985. Upstream sequences modulate the internal promoter of the human 7SL RNA gene. Nature 318: 371-374. (Pubitemid 16198493)
    • (1985) Nature , vol.318 , Issue.6044 , pp. 371-374
    • Ullu, E.1    Weiner, A.M.2
  • 49
    • 0034671952 scopus 로고    scopus 로고
    • Nuclear factor 1 (NF1) affects accurate termination and multiple-round transcription by human RNA polymerase III
    • DOI 10.1093/emboj/19.24.6823
    • Wang Z, Bai L, Hsieh YJ, Roeder RG. 2000. Nuclear factor 1 (NF1) affects accurate termination and multiple-round transcription by human RNA polymerase III. EMBO J 19: 6823-6832. (Pubitemid 32011675)
    • (2000) EMBO Journal , vol.19 , Issue.24 , pp. 6823-6832
    • Wang, Z.1    Bai, L.2    Hsieh, Y.-J.3    Roeder, R.G.4


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