메뉴 건너뛰기




Volumn 42, Issue 5, 2014, Pages 3028-3043

Dissecting the chromatin interactome of microRNA genes

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; RNA POLYMERASE II;

EID: 84898935507     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1294     Document Type: Article
Times cited : (24)

References (81)
  • 2
    • 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
  • 3
    • 81355142141 scopus 로고    scopus 로고
    • Non-coding RNAs in human disease
    • Esteller, M. (2011) Non-coding RNAs in human disease. Nat. Rev. Genet., 12, 861-874.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 861-874
    • Esteller, M.1
  • 4
  • 5
    • 8144225486 scopus 로고    scopus 로고
    • MicroRNA genes are transcribed by RNA polymerase II
    • DOI 10.1038/sj.emboj.7600385
    • Lee, Y., Kim, M., Han, J., Yeom, K.H., Lee, S., Baek, S.H. and Kim, V.N. (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J., 23, 4051-4060. (Pubitemid 39472426
    • (2004) EMBO Journal , vol.23 , Issue.20 , pp. 4051-4060
    • Lee, Y.1    Kim, M.2    Han, J.3    Yeom, K.-H.4    Lee, S.5    Baek, S.H.6    Kim, V.N.7
  • 7
    • 77952988986 scopus 로고    scopus 로고
    • Defining the RNA polymerase III transcriptome: Genomewide localization of the RNA polymerase III transcription machinery in human cells
    • Canella, D., Praz, V., Reina, J.H., Cousin, P. and Hernandez, N. (2010) Defining the RNA polymerase III transcriptome: Genomewide 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
  • 13
    • 78649377553 scopus 로고    scopus 로고
    • A miRNA-TRNA mix-up: TRNA origin of proposed miRNA
    • Schopman, N.C., Heynen, S., Haasnoot, J. and Berkhout, B. (2010) A miRNA-TRNA mix-up: TRNA origin of proposed miRNA. RNA Biol., 7, 573-576.
    • (2010) RNA Biol. , vol.7 , pp. 573-576
    • Schopman, N.C.1    Heynen, S.2    Haasnoot, J.3    Berkhout, B.4
  • 14
    • 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. and Cavaille, J. (2009) C19MC microRNAs are processed from introns of large Pol-II, non-protein-coding transcripts. Nucleic Acids Res., 37, 3464-3473.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 3464-3473
    • Bortolin-Cavaille, M.L.1    Dance, M.2    Weber, M.3    Cavaille, J.4
  • 16
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: Genomics, biogenesis, mechanism, and function
    • Bartel, D.P. (2004) MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell, 116, 281-297.
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 17
    • 9344235449 scopus 로고    scopus 로고
    • Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs
    • DOI 10.1261/rna.7135204
    • Cai, X., Hagedorn, C.H. and Cullen, B.R. (2004) Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA, 10, 1957-1966. (Pubitemid 39557833
    • (2004) RNA , vol.10 , Issue.12 , pp. 1957-1966
    • Cai, X.1    Hagedorn, C.H.2    Cullen, B.R.3
  • 18
    • 6344281172 scopus 로고    scopus 로고
    • Identification of mammalian microRNA host genes and transcription units
    • A DOI 10.1101/gr.2722704
    • Rodriguez, A., Griffiths-Jones, S., Ashurst, J.L. and Bradley, A. (2004) Identification of mammalian microRNA host genes and transcription units. Genome Res., 14, 1902-1910. (Pubitemid 39386503
    • (2004) Genome Research , vol.14 , Issue.10 , pp. 1902-1910
    • Rodriguez, A.1    Griffiths-Jones, S.2    Ashurst, J.L.3    Bradley, A.4
  • 19
    • 84859579687 scopus 로고    scopus 로고
    • The context of gene expression regulation
    • Gibcus, J.H. and Dekker, J. (2012) The context of gene expression regulation. F1000 Biol. Rep., 4, 8.
    • (2012) F1000 Biol. Rep. , vol.4 , pp. 8
    • Gibcus, J.H.1    Dekker, J.2
  • 20
    • 84855297335 scopus 로고    scopus 로고
    • A decade of 3C technologies: Insights into nuclear organization
    • de Wit, E. and de Laat, W. (2012) A decade of 3C technologies: Insights into nuclear organization. Genes Dev., 26, 11-24.
    • (2012) Genes Dev. , vol.26 , pp. 11-24
    • De Wit, E.1    De Laat, W.2
  • 21
    • 77956918460 scopus 로고    scopus 로고
    • The yin and yang of chromatin spatial organization
    • Cope, N.F., Fraser, P. and Eskiw, C.H. (2010) The yin and yang of chromatin spatial organization. Genome Biol., 11, 204.
    • (2010) Genome Biol. , vol.11 , pp. 204
    • Cope, N.F.1    Fraser, P.2    Eskiw, C.H.3
  • 22
    • 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
  • 29
    • 84861095603 scopus 로고    scopus 로고
    • Topological domains in mammalian genomes identified by analysis of chromatin interactions
    • Dixon, J.R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J.S. and Ren, B. (2012) Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature, 485, 376-380.
    • (2012) Nature , vol.485 , pp. 376-380
    • Dixon, J.R.1    Selvaraj, S.2    Yue, F.3    Kim, A.4    Li, Y.5    Shen, Y.6    Hu, M.7    Liu, J.S.8    Ren, B.9
  • 30
    • 11844278458 scopus 로고    scopus 로고
    • Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
    • DOI 10.1016/j.cell.2004.12.035, PII S0092867404012607
    • Lewis, B.P., Burge, C.B. and Bartel, D.P. (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell, 120, 15-20. (Pubitemid 40094598
    • (2005) Cell , vol.120 , Issue.1 , pp. 15-20
    • Lewis, B.P.1    Burge, C.B.2    Bartel, D.P.3
  • 31
    • 38549124383 scopus 로고    scopus 로고
    • The microRNA.org resource: Targets and expression
    • DOI 10.1093/nar/gkm995
    • Betel, D., Wilson, M., Gabow, A., Marks, D.S. and Sander, C. (2008) The microRNA.org resource: Targets and expression. Nucleic Acids Res., 36, D149-D153. (Pubitemid 351149712
    • (2008) Nucleic Acids Research , vol.36 , Issue.SUPPL. 1
    • Betel, D.1    Wilson, M.2    Gabow, A.3    Marks, D.S.4    Sander, C.5
  • 32
    • 44149083586 scopus 로고    scopus 로고
    • MiRDB: A microRNA target prediction and functional annotation database with a wiki interface
    • DOI 10.1261/rna.965408
    • Wang, X. (2008) miRDB: A microRNA target prediction and functional annotation database with a wiki interface. RNA, 14, 1012-1017. (Pubitemid 351717482
    • (2008) RNA , vol.14 , Issue.6 , pp. 1012-1017
    • Wang, X.1
  • 38
    • 78249233850 scopus 로고    scopus 로고
    • RNA polymerase II binding patterns reveal genomic regions involved in microRNA gene regulation
    • Wang, G., Wang, Y., Shen, C., Huang, Y.W., Huang, K., Huang, T.H., Nephew, K.P., Li, L. and Liu, Y. (2010) RNA polymerase II binding patterns reveal genomic regions involved in microRNA gene regulation. PLoS One, 5, e13798.
    • (2010) PLoS One , vol.5
    • Wang, G.1    Wang, Y.2    Shen, C.3    Huang, Y.W.4    Huang, K.5    Huang, T.H.6    Nephew, K.P.7    Li, L.8    Liu, Y.9
  • 41
    • 0014054519 scopus 로고
    • The detection of disease clustering and a generalized regression approach
    • Mantel, N. (1967) The detection of disease clustering and a generalized regression approach. Cancer Res., 27, 209-220.
    • (1967) Cancer Res. , vol.27 , pp. 209-220
    • Mantel, N.1
  • 42
    • 79955555195 scopus 로고    scopus 로고
    • Comprehensive long-span paired-end-Tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes
    • Hillmer, A.M., Yao, F., Inaki, K., Lee, W.H., Ariyaratne, P.N., Teo, A.S., Woo, X.Y., Zhang, Z., Zhao, H., Ukil, L. et al. (2011) Comprehensive long-span paired-end-Tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. Genome Res., 21, 665-675.
    • (2011) Genome Res. , vol.21 , pp. 665-675
    • Hillmer, A.M.1    Yao, F.2    Inaki, K.3    Lee, W.H.4    Ariyaratne, P.N.5    Teo, A.S.6    Woo, X.Y.7    Zhang, Z.8    Zhao, H.9    Ukil, L.10
  • 43
    • 12344269924 scopus 로고    scopus 로고
    • GO::TermFinder-Open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes
    • DOI 10.1093/bioinformatics/bth456
    • Boyle, E.I., Weng, S., Gollub, J., Jin, H., Botstein, D., Cherry, J.M. and Sherlock, G. (2004) GO::TermFinder-open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics, 20, 3710-3715. (Pubitemid 40136825
    • (2004) Bioinformatics , vol.20 , Issue.18 , pp. 3710-3715
    • Boyle, E.I.1    Weng, S.2    Gollub, J.3    Jin, H.4    Botstein, D.5    Cherry, J.M.6    Sherlock, G.7
  • 49
    • 39449088572 scopus 로고    scopus 로고
    • Genome-wide approaches to studying chromatin modifications
    • Schones, D.E. and Zhao, K. (2008) Genome-wide approaches to studying chromatin modifications. Nat. Rev. Genet., 9, 179-191.
    • (2008) Nat. Rev. Genet. , vol.9 , pp. 179-191
    • Schones, D.E.1    Zhao, K.2
  • 50
    • 67649766870 scopus 로고    scopus 로고
    • Transcription factories: Gene expression in unions? Nat
    • Sutherland, H. and Bickmore, W.A. (2009) Transcription factories: Gene expression in unions? Nat. Rev. Genet., 10, 457-466.
    • (2009) Rev. Genet. , vol.10 , pp. 457-466
    • Sutherland, H.1    Bickmore, W.A.2
  • 53
    • 72949114887 scopus 로고    scopus 로고
    • Leukaemogenesis: More than mutant genes
    • Chen, J., Odenike, O. and Rowley, J.D. (2010) Leukaemogenesis: More than mutant genes. Nat. Rev. Cancer, 10, 23-36.
    • (2010) Nat. Rev. Cancer , vol.10 , pp. 23-36
    • Chen, J.1    Odenike, O.2    Rowley, J.D.3
  • 54
    • 38349114827 scopus 로고    scopus 로고
    • MicroRNAs show a wide diversity of expression profiles in the developing and mature central nervous system
    • Kapsimali, M., Kloosterman, W.P., de Bruijn, E., Rosa, F., Plasterk, R.H. and Wilson, S.W. (2007) MicroRNAs show a wide diversity of expression profiles in the developing and mature central nervous system. Genome Biol., 8, R173.
    • (2007) Genome Biol. , vol.8
    • Kapsimali, M.1    Kloosterman, W.P.2    De Bruijn, E.3    Rosa, F.4    Plasterk, R.H.5    Wilson, S.W.6
  • 55
    • 84868326494 scopus 로고    scopus 로고
    • A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers
    • Plaisier, C.L., Pan, M. and Baliga, N.S. (2012) A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers. Genome Res., 22, 2302-2314.
    • (2012) Genome Res. , vol.22 , pp. 2302-2314
    • Plaisier, C.L.1    Pan, M.2    Baliga, N.S.3
  • 56
    • 84863147229 scopus 로고    scopus 로고
    • Discovering dysfunction of multiple microRNAs cooperation in disease by a conserved microRNA co-expression network
    • Xiao, Y., Xu, C., Guan, J., Ping, Y., Fan, H., Li, Y., Zhao, H. and Li, X. (2012) Discovering dysfunction of multiple microRNAs cooperation in disease by a conserved microRNA co-expression network. PLoS One, 7, e32201.
    • (2012) PLoS One , vol.7
    • Xiao, Y.1    Xu, C.2    Guan, J.3    Ping, Y.4    Fan, H.5    Li, Y.6    Zhao, H.7    Li, X.8
  • 61
    • 0346727524 scopus 로고    scopus 로고
    • MicroRNAs modulate hematopoietic lineage differentiation
    • DOI 10.1126/science.1091903
    • Chen, C.Z., Li, L., Lodish, H.F. and Bartel, D.P. (2004) MicroRNAs modulate hematopoietic lineage differentiation. Science, 303, 83-86. (Pubitemid 38055775
    • (2004) Science , vol.303 , Issue.5654 , pp. 83-86
    • Chen, C.-Z.1    Li, L.2    Lodish, H.F.3    Bartel, D.P.4
  • 66
    • 77955466130 scopus 로고    scopus 로고
    • MiR-661 expression in SNAI1-induced epithelial to mesenchymal transition contributes to breast cancer cell invasion by targeting Nectin-1 and StarD10 messengers
    • Vetter, G., Saumet, A., Moes, M., Vallar, L., Le Bechec, A., Laurini, C., Sabbah, M., Arar, K., Theillet, C., Lecellier, C.H. et al. (2010) miR-661 expression in SNAI1-induced epithelial to mesenchymal transition contributes to breast cancer cell invasion by targeting Nectin-1 and StarD10 messengers. Oncogene, 29, 4436-4448.
    • (2010) Oncogene , vol.29 , pp. 4436-4448
    • Vetter, G.1    Saumet, A.2    Moes, M.3    Vallar, L.4    Le Bechec, A.5    Laurini, C.6    Sabbah, M.7    Arar, K.8    Theillet, C.9    Lecellier, C.H.10
  • 70
    • 20444479428 scopus 로고    scopus 로고
    • C-Myc-regulated microRNAs modulate E2F1 expression
    • DOI 10.1038/nature03677
    • O'Donnell, K.A., Wentzel, E.A., Zeller, K.I., Dang, C.V. and Mendell, J.T. (2005) c-Myc-regulated microRNAs modulate E2F1 expression. Nature, 435, 839-843. (Pubitemid 40839736
    • (2005) Nature , vol.435 , Issue.7043 , pp. 839-843
    • O'Donnell, K.A.1    Wentzel, E.A.2    Zeller, K.I.3    Dang, C.V.4    Mendell, J.T.5
  • 72
    • 22444437609 scopus 로고    scopus 로고
    • Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis
    • DOI 10.1038/nature03817
    • Zhao, Y., Samal, E. and Srivastava, D. (2005) Serum response factor regulates a muscle-specific microRNA that targets Hand2 during cardiogenesis. Nature, 436, 214-220. (Pubitemid 41021266
    • (2005) Nature , vol.436 , Issue.7048 , pp. 214-220
    • Zhao, Y.1    Samal, E.2    Srivastava, D.3
  • 75
    • 34047234690 scopus 로고    scopus 로고
    • Characterization and identification of microRNA core promoters in four model species
    • Zhou, X., Ruan, J., Wang, G. and Zhang, W. (2007) Characterization and identification of microRNA core promoters in four model species. PLoS Comput. Biol., 3, e37.
    • (2007) PLoS Comput. Biol. , vol.3
    • Zhou, X.1    Ruan, J.2    Wang, G.3    Zhang, W.4
  • 76
    • 38849151740 scopus 로고    scopus 로고
    • Putative promoter regions of miRNA genes involved in evolutionarily conserved regulatory systems among vertebrates
    • DOI 10.1093/bioinformatics/btm589
    • Fujita, S. and Iba, H. (2008) Putative promoter regions of miRNA genes involved in evolutionarily conserved regulatory systems among vertebrates. Bioinformatics, 24, 303-308. (Pubitemid 351189004
    • (2008) Bioinformatics , vol.24 , Issue.3 , pp. 303-308
    • Fujita, S.1    Iba, H.2
  • 78
    • 65449183132 scopus 로고    scopus 로고
    • Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data
    • Corcoran, D.L., Pandit, K.V., Gordon, B., Bhattacharjee, A., Kaminski, N. and Benos, P.V. (2009) Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PLoS One, 4, e5279.
    • (2009) PLoS One , vol.4
    • Corcoran, D.L.1    Pandit, K.V.2    Gordon, B.3    Bhattacharjee, A.4    Kaminski, N.5    Benos, P.V.6
  • 79
    • 34249819336 scopus 로고    scopus 로고
    • MicroRNAmediated feedback and feedforward loops are recurrent network motifs in mammals
    • Tsang, J., Zhu, J. and van Oudenaarden, A. (2007) MicroRNAmediated feedback and feedforward loops are recurrent network motifs in mammals. Mol. Cell, 26, 753-767.
    • (2007) Mol. Cell , vol.26 , pp. 753-767
    • Tsang, J.1    Zhu, J.2    Van Oudenaarden, A.3
  • 80
    • 34547555796 scopus 로고    scopus 로고
    • Global and local architecture of the mammalian microRNA-Transcription factor regulatory network
    • Shalgi, R., Lieber, D., Oren, M. and Pilpel, Y. (2007) Global and local architecture of the mammalian microRNA-Transcription factor regulatory network. PLoS Comput. Biol., 3, e131.
    • (2007) PLoS Comput. Biol. , vol.3
    • Shalgi, R.1    Lieber, D.2    Oren, M.3    Pilpel, Y.4
  • 81
    • 70349334678 scopus 로고    scopus 로고
    • Genome-wide survey of microRNA-Transcription factor feed-forward regulatory circuits in human
    • Re, A., Cora, D., Taverna, D. and Caselle, M. (2009) Genome-wide survey of microRNA-Transcription factor feed-forward regulatory circuits in human. Mol. Biosyst., 5, 854-867.
    • (2009) Mol. Biosyst. , vol.5 , pp. 854-867
    • Re, A.1    Cora, D.2    Taverna, D.3    Caselle, M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.