CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

Cell

Volumn 163, Issue 7, 2015, Pages 1611-1627

  Tang, Zhonghui ^a   Luo, Oscar Junhong ^a   Li, Xingwang ^a,b   Zheng, Meizhen ^a   Zhu, Jacqueline Jufen ^a,c   Szalaj, Przemyslaw ^d,e,f   Trzaskoma, Pawel ^g   Magalska, Adriana ^g   Wlodarczyk, Jakub ^g   Ruszczycki, Blazej ^g   Michalski, Paul ^a   Piecuch, Emaly ^a,c   Wang, Ping ^a   Wang, Danjuan ^a   Tian, Simon Zhongyuan ^a   Penrad Mobayed, May ^h   Sachs, Laurent M ⁱ   Ruan, Xiaoan ^a   Wei, Chia Lin ^j   Liu, Edison T ^a   Wilczynski, Grzegorz M ^g   Plewczynski, Dariusz ^f   Li, Guoliang ^b   Ruan, Yijun ^a,b,c   more..

^a JACKSON LABORATORY   (United States)

^b HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^c UNIVERSITY OF CONNECTICUT HEALTH CENTER   (United States)

^d MEDICAL UNIVERSITY OF BIALYSTOK   (Poland)

^e HASSELT UNIVERSITY   (Belgium)

^f UNIVERSITY OF WARSAW   (Poland)

^g NENCKI INSTITUTE OF EXPERIMENTAL BIOLOGY   (Poland)

^h UNIVERSITÉ PARIS DESCARTES   (France)

ⁱ CNRS   (France)

^j DOE JOINT GENOME INSTITUTE   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

COHESIN; PROTEIN; RAD21 PROTEIN; RNA POLYMERASE II; TRANSCRIPTION FACTOR CTCF; UNCLASSIFIED DRUG; ZNF143 PROTEIN; CCCTC-BINDING FACTOR; CELL CYCLE PROTEIN; CHROMATIN; NONHISTONE PROTEIN; REPRESSOR PROTEIN;

ALLELE; ANALYTIC METHOD; ARTICLE; AUTOSOME; BINDING SITE; CELL INTERACTION; CELL LINEAGE; CHROMATIN INTERACTION ANALYSIS; CHROMATIN STRUCTURE; CHROMOSOME; CRISPR CAS SYSTEM; DIMERIZATION; DISEASE PREDISPOSITION; ENHANCER REGION; FEMALE; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENE FUNCTION; GENE MAPPING; GENE SEQUENCE; GENE STRUCTURE; GENETIC ANALYZER; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOME ANALYSIS; GENOME IMPRINTING; HAPLOTYPE; HETEROCHROMATIN; HUMAN; HUMAN CELL; HUMAN GENOME; MOLECULAR INTERACTION; PAIRED END TAG SEQUENCING; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN MOTIF; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION REGULATION; ANIMAL; CELL LINE; CHEMISTRY; CHROMATIN; DNA PACKAGING; GENETICS; METABOLISM; SALAMANDRIDAE;

ANIMALS; CELL CYCLE PROTEINS; CELL LINE; CHROMATIN; CHROMOSOMAL PROTEINS, NON-HISTONE; CHROMOSOMES; DNA PACKAGING; GENOME, HUMAN; HUMANS; REPRESSOR PROTEINS; RNA POLYMERASE II; SALAMANDRIDAE; TRANSCRIPTION, GENETIC;

EID: 84951567954     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2015.11.024     Document Type: Article

References (32)

1. W.A. Bickmore The spatial organization of the human genome Annu. Rev. Genomics Hum. Genet. 14 2013 67 84
2. S. Boyle, M.J. Rodesch, H.A. Halvensleben, J.A. Jeddeloh, and W.A. Bickmore Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis Chromosome Res. 19 2011 901 909
3. M. Cremer, F. Grasser, C. Lanctôt, S. Müller, M. Neusser, R. Zinner, I. Solovei, and T. Cremer Multicolor 3D fluorescence in situ hybridization for imaging interphase chromosomes Methods Mol. Biol. 463 2008 205 239
4. K.E. Cullen, M.P. Kladde, and M.A. Seyfred Interaction between transcription regulatory regions of prolactin chromatin Science 261 1993 203 206
5. J.R. Dixon, S. Selvaraj, F. Yue, A. Kim, Y. Li, Y. Shen, M. Hu, J.S. Liu, and B. Ren Topological domains in mammalian genomes identified by analysis of chromatin interactions Nature 485 2012 376 380
6. J.M. Dowen, Z.P. Fan, D. Hnisz, G. Ren, B.J. Abraham, L.N. Zhang, A.S. Weintraub, J. Schuijers, T.I. Lee, K. Zhao, and R.A. Young Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes Cell 159 2014 374 387
7. ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome Nature 489 2012 57 74
8. M.J. Fullwood, M.H. Liu, Y.F. Pan, J. Liu, H. Xu, Y.B. Mohamed, Y.L. Orlov, S. Velkov, A. Ho, P.H. Mei, and et al. An oestrogen-receptor-alpha-bound human chromatin interactome Nature 462 2009 58 64
9. Y. Guo, Q. Xu, D. Canzio, J. Shou, J. Li, D.U. Gorkin, I. Jung, H. Wu, Y. Zhai, Y. Tang, and et al. CRISPR inversion of CTCF sites alters genome topology and enhancer/promoter function Cell 162 2015 900 910
10. M.H. Hall, A. Magalska, M. Malinowska, B. Ruszczycki, I. Czaban, S. Patel, M. Ambrożek-Latecka, E. Zołocińska, H. Broszkiewicz, K. Parobczak, and et al. Localization and regulation of PML bodies in the adult mouse brain Brain Struct. Funct. 2015 10.1007/s00429-015-1053-4
11. Q. He, J. Johnston, and J. Zeitlinger ChIP-nexus enables improved detection of in vivo transcription factor binding footprints Nat. Biotechnol. 33 2015 395 401
12. A.H. Horakova, S.C. Moseley, C.R. McLaughlin, D.C. Tremblay, and B.P. Chadwick The macrosatellite DXZ4 mediates CTCF-dependent long-range intrachromosomal interactions on the human inactive X chromosome Hum. Mol. Genet. 21 2012 4367 4377
13. R. Kalhor, H. Tjong, N. Jayathilaka, F. Alber, and L. Chen Genome architectures revealed by tethered chromosome conformation capture and population-based modeling Nat. Biotechnol. 30 2012 90 98
14. D. Leung, I. Jung, N. Rajagopal, A. Schmitt, S. Selvaraj, A.Y. Lee, C.A. Yen, S. Lin, Y. Lin, Y. Qiu, and et al. Integrative analysis of haplotype-resolved epigenomes across human tissues Nature 518 2015 350 354
15. G. Li, M.J. Fullwood, H. Xu, F.H. Mulawadi, S. Velkov, V. Vega, P.N. Ariyaratne, Y.B. Mohamed, H.S. Ooi, C. Tennakoon, and et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing Genome Biol. 11 2010 R22
16. G. Li, X. Ruan, R.K. Auerbach, K.S. Sandhu, M. Zheng, P. Wang, H.M. Poh, Y. Goh, J. Lim, J. Zhang, and et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation Cell 148 2012 84 98
17. Z. Liang, D. Zickler, M. Prentiss, F.S. Chang, G. Witz, K. Maeshima, and N. Kleckner Chromosomes progress to metaphase in multiple discrete steps via global compaction/expansion cycles Cell 161 2015 1124 1137
18. E. Lieberman-Aiden, N.L. van Berkum, L. Williams, M. Imakaev, T. Ragoczy, A. Telling, I. Amit, B.R. Lajoie, P.J. Sabo, M.O. Dorschner, and et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome Science 326 2009 289 293
19. R. McDaniell, B.K. Lee, L. Song, Z. Liu, A.P. Boyle, M.R. Erdos, L.J. Scott, M.A. Morken, K.S. Kucera, A. Battenhouse, and et al. Heritable individual-specific and allele-specific chromatin signatures in humans Science 328 2010 235 239
20. S.B. Montgomery, M. Sammeth, M. Gutierrez-Arcelus, R.P. Lach, C. Ingle, J. Nisbett, R. Guigo, and E.T. Dermitzakis Transcriptome genetics using second generation sequencing in a Caucasian population Nature 464 2010 773 777
21. G.T. Morgan Lampbrush chromosomes and associated bodies: new insights into principles of nuclear structure and function Chromosome Res. 10 2002 177 200
22. R. Nativio, A. Sparago, Y. Ito, R. Weksberg, A. Riccio, and A. Murrell Disruption of genomic neighbourhood at the imprinted IGF2-H19 locus in Beckwith-Wiedemann syndrome and Silver-Russell syndrome Hum. Mol. Genet. 20 2011 1363 1374
23. C.T. Ong, and V.G. Corces CTCF: an architectural protein bridging genome topology and function Nat. Rev. Genet. 15 2014 234 246
24. M. Penrad-Mobayed, R. Kanhoush, and C. Perrin Tips and tricks for preparing lampbrush chromosome spreads from Xenopus tropicalis oocytes Methods 51 2010 37 44
25. S.S. Rao, M.H. Huntley, N.C. Durand, E.K. Stamenova, I.D. Bochkov, J.T. Robinson, A.L. Sanborn, I. Machol, A.D. Omer, E.S. Lander, and E.L. Aiden A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping Cell 159 2014 1665 1680
26. H.S. Rhee, and B.F. Pugh Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution Cell 147 2011 1408 1419
27. J. Rozowsky, A. Abyzov, J. Wang, P. Alves, D. Raha, A. Harmanci, J. Leng, R. Bjornson, Y. Kong, N. Kitabayashi, and et al. AlleleSeq: analysis of allele-specific expression and binding in a network framework Mol. Syst. Biol. 7 2011 522
28. S. Selvaraj, J. R Dixon, V. Bansal, and B. Ren Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing Nat. Biotechnol. 31 2013 1111 1118
29. R.J. Sims III, S.S. Mandal, and D. Reinberg Recent highlights of RNA-polymerase-II-mediated transcription Curr. Opin. Cell Biol. 16 2004 263 271
30. B.E. Stranger, A.C. Nica, M.S. Forrest, A. Dimas, C.P. Bird, C. Beazley, C.E. Ingle, M. Dunning, P. Flicek, D. Koller, and et al. Population genomics of human gene expression Nat. Genet. 39 2007 1217 1224
31. D.J. Verlaan, S. Berlivet, G.M. Hunninghake, A.M. Madore, M. Larivière, S. Moussette, E. Grundberg, T. Kwan, M. Ouimet, B. Ge, and et al. Allele-specific chromatin remodeling in the ZPBP2/GSDMB/ORMDL3 locus associated with the risk of asthma and autoimmune disease Am. J. Hum. Genet. 85 2009 377 393
32. Y. Zhang, C.H. Wong, R.Y. Birnbaum, G. Li, R. Favaro, C.Y. Ngan, J. Lim, E. Tai, H.M. Poh, E. Wong, and et al. Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations Nature 504 2013 306 310