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Volumn 16, Issue 1, 2015, Pages

Comparison of the three-dimensional organization of sperm and fibroblast genomes using the Hi-C approach

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; ARTICLE; CELL COMPARTMENTALIZATION; CELL DENSITY; CHROMATIN; CHROMOSOME 19; CONTROLLED STUDY; DNA BASE COMPOSITION; DNA PACKAGING; EMBRYO; EMBRYONIC STEM CELL; FIBROBLAST; GENE FREQUENCY; GENE INTERACTION; GENETIC DISTANCE; GENOME ANALYSIS; MALE; MOUSE; NONHUMAN; SPERM; SPERMATOZOON; ANIMAL; C57BL MOUSE; CHROMOSOME; COMPARATIVE STUDY; CONFORMATION; CYTOLOGY; GENE LOCUS; GENETIC ASSOCIATION STUDY; GENETICS; GENOME; GENOMICS; METABOLISM; PROCEDURES; THEORETICAL MODEL;

EID: 84939154060     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-015-0642-0     Document Type: Article
Times cited : (96)

References (34)
  • 1
    • 33846283384 scopus 로고    scopus 로고
    • Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions
    • Lanctôt C, Cheutin T, Cremer M, Cavalli G, Cremer T. Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat Rev Genet. 2007;8:104-15.
    • (2007) Nat Rev Genet , vol.8 , pp. 104-115
    • Lanctôt, C.1    Cheutin, T.2    Cremer, M.3    Cavalli, G.4    Cremer, T.5
  • 2
    • 77956651480 scopus 로고    scopus 로고
    • Differentiation and large scale spatial organization of the genome
    • Joffe B, Leonhardt H, Solovei I. Differentiation and large scale spatial organization of the genome. Curr Opin Genet Dev. 2010;20:562-9.
    • (2010) Curr Opin Genet Dev , vol.20 , pp. 562-569
    • Joffe, B.1    Leonhardt, H.2    Solovei, I.3
  • 3
    • 80052409661 scopus 로고    scopus 로고
    • Functional nuclear organization of transcription and DNA replication: a topographical marriage between chromatin domains and the interchromatin compartment
    • Markaki Y, Gunkel M, Schermelleh L, Beichmanis S, Neumann J, Heidemann M, et al. Functional nuclear organization of transcription and DNA replication: a topographical marriage between chromatin domains and the interchromatin compartment. Cold Spring Harb Symp Quant Biol. 2010;75:475-92.
    • (2010) Cold Spring Harb Symp Quant Biol , vol.75 , pp. 475-492
    • Markaki, Y.1    Gunkel, M.2    Schermelleh, L.3    Beichmanis, S.4    Neumann, J.5    Heidemann, M.6
  • 4
    • 0035316574 scopus 로고    scopus 로고
    • Chromosome territories, nuclear architecture and gene regulation in mammalian cells
    • Cremer T, Cremer C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet. 2001;2:292-301.
    • (2001) Nat Rev Genet , vol.2 , pp. 292-301
    • Cremer, T.1    Cremer, C.2
  • 5
    • 25844496592 scopus 로고    scopus 로고
    • The role of chromatin structure in regulating the expression of clustered genes
    • Sproul D, Gilbert N, Bickmore WA. The role of chromatin structure in regulating the expression of clustered genes. Nat Rev Genet. 2005;6:775-81.
    • (2005) Nat Rev Genet , vol.6 , pp. 775-781
    • Sproul, D.1    Gilbert, N.2    Bickmore, W.A.3
  • 7
    • 33750203582 scopus 로고    scopus 로고
    • Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions
    • Zhao Z, Tavoosidana G, Sjölinder M, Göndör A, Mariano P, Wang S, et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat Genet. 2006;38:1341-7.
    • (2006) Nat Genet , vol.38 , pp. 1341-1347
    • Zhao, Z.1    Tavoosidana, G.2    Sjölinder, M.3    Göndör, A.4    Mariano, P.5    Wang, S.6
  • 8
    • 33750212321 scopus 로고    scopus 로고
    • Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C)
    • Simonis M, Klous P, Splinter E, Moshkin Y, Willemsen R, de Wit E, et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat Genet. 2006;38:1348-54.
    • (2006) Nat Genet , vol.38 , pp. 1348-1354
    • Simonis, M.1    Klous, P.2    Splinter, E.3    Moshkin, Y.4    Willemsen, R.5    Wit, E.6
  • 9
    • 33749400168 scopus 로고    scopus 로고
    • Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements
    • Dostie J, Richmond TA, Arnaout RA, Selzer RR, Lee WL, Honan TA, et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006;16:1299-309.
    • (2006) Genome Res , vol.16 , pp. 1299-1309
    • Dostie, J.1    Richmond, T.A.2    Arnaout, R.A.3    Selzer, R.R.4    Lee, W.L.5    Honan, T.A.6
  • 10
    • 70349873824 scopus 로고    scopus 로고
    • Comprehensive mapping of long-range interactions reveals folding principles of the human genome
    • Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326:289-93.
    • (2009) Science , vol.326 , pp. 289-293
    • Lieberman-Aiden, E.1    Berkum, N.L.2    Williams, L.3    Imakaev, M.4    Ragoczy, T.5    Telling, A.6
  • 11
    • 84878011578 scopus 로고    scopus 로고
    • Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data
    • Dekker J, Marti-Renom MA, Mirny LA. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet. 2013;14:390-403.
    • (2013) Nat Rev Genet , vol.14 , pp. 390-403
    • Dekker, J.1    Marti-Renom, M.A.2    Mirny, L.A.3
  • 12
    • 77951947926 scopus 로고    scopus 로고
    • Ring1b compacts chromatin structure and represses gene expression independent of histone ubiquitination
    • Eskeland R, Leeb M, Grimes GR, Kress C, Boyle S, Sproul D, et al. Ring1b compacts chromatin structure and represses gene expression independent of histone ubiquitination. Mol Cell. 2010;38:452-64.
    • (2010) Mol Cell , vol.38 , pp. 452-464
    • Eskeland, R.1    Leeb, M.2    Grimes, G.R.3    Kress, C.4    Boyle, S.5    Sproul, D.6
  • 13
    • 84862917808 scopus 로고    scopus 로고
    • Genome architectures revealed by tethered chromosome conformation capture and population-based modeling
    • Kalhor R, Tjong H, Jayathilaka N, Alber F, Chen L. Genome architectures revealed by tethered chromosome conformation capture and population-based modeling. Nat Biotechnol. 2012;30:90-8.
    • (2012) Nat Biotechnol , vol.30 , pp. 90-98
    • Kalhor, R.1    Tjong, H.2    Jayathilaka, N.3    Alber, F.4    Chen, L.5
  • 14
    • 84862778059 scopus 로고    scopus 로고
    • Spatial organization of the mouse genome and its role in recurrent chromosomal translocations
    • Zhang Y, McCord RP, Ho YJ, Lajoie BR, Hildebrand DG, Simon AC, et al. Spatial organization of the mouse genome and its role in recurrent chromosomal translocations. Cell. 2012;148:908-21.
    • (2012) Cell , vol.148 , pp. 908-921
    • Zhang, Y.1    McCord, R.P.2    Ho, Y.J.3    Lajoie, B.R.4    Hildebrand, D.G.5    Simon, A.C.6
  • 16
    • 84861095603 scopus 로고    scopus 로고
    • Topological domains in mammalian genomes identified by analysis of chromatin interactions
    • Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485:376-80.
    • (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
  • 17
    • 84861100147 scopus 로고    scopus 로고
    • Spatial partitioning of the regulatory landscape of the X-inactivation centre
    • Nora EP, Lajoie BR, Schulz EG, Giorgetti L, Okamoto I, Servant N, et al. Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature. 2012;485:381-5.
    • (2012) Nature , vol.485 , pp. 381-385
    • Nora, E.P.1    Lajoie, B.R.2    Schulz, E.G.3    Giorgetti, L.4    Okamoto, I.5    Servant, N.6
  • 18
    • 84866978321 scopus 로고    scopus 로고
    • Organization of chromosomes during spermatogenesis and in mature sperm
    • Rousseaux S, Khochbin S, editors. Berlin, Heidelberg: Springer
    • Mudrak O, Zalenskaya I, Zalensky A. Organization of chromosomes during spermatogenesis and in mature sperm. In: Rousseaux S, Khochbin S, editors. Epigenetics and human reproduction. Berlin, Heidelberg: Springer; 2011. p. 261-77.
    • (2011) Epigenetics and human reproduction , pp. 261-277
    • Mudrak, O.1    Zalenskaya, I.2    Zalensky, A.3
  • 23
    • 84919949716 scopus 로고    scopus 로고
    • A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping
    • Rao SSP, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014;159:1665-80.
    • (2014) Cell , vol.159 , pp. 1665-1680
    • Rao, S.S.P.1    Huntley, M.H.2    Durand, N.C.3    Stamenova, E.K.4    Bochkov, I.D.5    Robinson, J.T.6
  • 24
  • 25
    • 84905401266 scopus 로고    scopus 로고
    • Genome-wide mapping and characterization of notch-regulated long noncoding RNAs in acute leukemia
    • Trimarchi T, Bilal E, Ntziachristos P, Fabbri G, Dalla-Favera R, Tsirigos A, et al. Genome-wide mapping and characterization of notch-regulated long noncoding RNAs in acute leukemia. Cell. 2014;158:593-606.
    • (2014) Cell , vol.158 , pp. 593-606
    • Trimarchi, T.1    Bilal, E.2    Ntziachristos, P.3    Fabbri, G.4    Dalla-Favera, R.5    Tsirigos, A.6
  • 26
    • 84908352990 scopus 로고    scopus 로고
    • Depletion of the chromatin looping proteins CTCF and cohesin causes chromatin compaction: insight into chromatin folding by polymer modelling
    • Tark-Dame M, Jerabek H, Manders EMM, Heermann DW, van Driel R. Depletion of the chromatin looping proteins CTCF and cohesin causes chromatin compaction: insight into chromatin folding by polymer modelling. PLoS Comput Biol. 2014;10, e1003877.
    • (2014) PLoS Comput Biol , vol.10
    • Tark-Dame, M.1    Jerabek, H.2    Manders, E.M.M.3    Heermann, D.W.4    Driel, R.5
  • 27
    • 77953292127 scopus 로고    scopus 로고
    • Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa
    • Brykczynska U, Hisano M, Erkek S, Ramos L, Oakeley EJ, Roloff TC, et al. Repressive and active histone methylation mark distinct promoters in human and mouse spermatozoa. Nat Struct Mol Biol. 2010;17:679-87.
    • (2010) Nat Struct Mol Biol , vol.17 , pp. 679-687
    • Brykczynska, U.1    Hisano, M.2    Erkek, S.3    Ramos, L.4    Oakeley, E.J.5    Roloff, T.C.6
  • 30
    • 84939205612 scopus 로고    scopus 로고
    • Hi-C data analysis tools by Leonid Mirny lab. http://mirnylab.bitbucket.org/hiclib/ .
  • 31
    • 84939182315 scopus 로고    scopus 로고
    • MINE tool. http://minepy.sourceforge.net/ .
  • 33
    • 0041758569 scopus 로고
    • Two rules of thumb for the approximation of the binomial distribution by the normal distribution
    • Schader M, Schmid F. Two rules of thumb for the approximation of the binomial distribution by the normal distribution. Am Stat. 1989;43:23-4.
    • (1989) Am Stat , vol.43 , pp. 23-24
    • Schader, M.1    Schmid, F.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.