Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/21376
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dc.contributor.authorTang, Zhonghui-
dc.contributor.authorLuo, Oscar Junhong-
dc.contributor.authorLi, Xingwang-
dc.contributor.authorZheng, Meizhen-
dc.contributor.authorJufen Zhu, Jacqueline-
dc.contributor.authorSZALAJ, Przemek-
dc.contributor.authorTrzaskoma, Pawel-
dc.contributor.authorMagalska, Adriana-
dc.contributor.authorWlodarczyk, Jakub-
dc.contributor.authorRuszczycki, Blazej-
dc.contributor.authorMichalski, Paul-
dc.contributor.authorPiecuch, Emaly-
dc.contributor.authorWang, Ping-
dc.contributor.authorWang, Danjuan-
dc.contributor.authorZhongyuan Tian, Simon-
dc.contributor.authorPenrad-Mobayed, May-
dc.contributor.authorSachs, Laurent M.-
dc.contributor.authorRuan, Xiaoan-
dc.contributor.authorWe, Chia-Lin-
dc.contributor.authorLiu, Edison T.-
dc.contributor.authorWilczynski, Grzegorz M.-
dc.contributor.authorPlewczynski, Dariusz-
dc.contributor.authorLi, Guoliang-
dc.contributor.authorRuan, Yijun-
dc.date.accessioned2016-06-01T12:04:55Z-
dc.date.available2016-06-01T12:04:55Z-
dc.date.issued2015-
dc.identifier.citationCELL, 163 (7), p. 1611-1627-
dc.identifier.issn0092-8674-
dc.identifier.urihttp://hdl.handle.net/1942/21376-
dc.description.abstractSpatial genome organization and its effect on transcription remains a fundamental question. We applied an advanced chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) strategy to comprehensively map higher-order chromosome folding and specific chromatin interactions mediated by CCCTC-binding factor (CTCF) and RNA polymerase II (RNAPII) with haplotype specificity and nucleotide resolution in different human cell lineages. We find that CTCF/cohesin-mediated interaction anchors serve as structural foci for spatial organization of constitutive genes concordant with CTCF-motif orientation, whereas RNAPII interacts within these structures by selectively drawing cell-type-specific genes toward CTCF foci for coordinated transcription. Furthermore, we show that haplotype variants and allelic interactions have differential effects on chromosome configuration, influencing gene expression, and may provide mechanistic insights into functions associated with disease susceptibility. 3D genome simulation suggests a model of chromatin folding around chromosomal axes, where CTCF is involved in defining the interface between condensed and open compartments for structural regulation. Our 3D genome strategy thus provides unique insights in the topological mechanism of human variations and diseases.-
dc.description.sponsorshipY.R. is supported by the Director Innovation Fund of The Jackson Laboratory, NCI R01 CA186714, NHGRI R25HG007631, NIDDK U54DK107967 (4DN), and the Roux family as the Florine Roux Endowed Chair in Genomics and Computational Biology. X.L. is supported in part by China "111 project'' (B07041). Polish National Science Centre supports G.M.W. [UMO-2012/05/E/NZ4/02997]; D.P. and P.S. [2014/15/B/ST6/05082; UMO-2013/09/B/NZ2/00121]; and J.W. [DEC-2012/06/M/NZ3/00163]. D.P. and P.S. are also supported by National Leading Research Centre in Bialystok and the European Union under the European Social Fund. The authors thank C.Z. Zhang for initial DNA-FISH, Agnieszka Walczak and Katarzyna Krawczyk for FISH discussion, Rafael Casellas, Michael Stitzel, and Duygu Ucar for manuscript discussion, and Gosia Popiel for help on preparing Figure S7. Some of the genome sequences described in this research were derived from a HeLa cell line. Henrietta Lacks, and the HeLa cell line that was established from her tumor cells without her knowledge or consent in 1951, have made significant contributions to scientific progress and advances in human health. We are grateful to Henrietta Lacks, now deceased, and to her surviving family members for their contributions to biomedical research. The request to use HeLa data for this research was approved by the NIH Director based on the recommendations of the Advisory Committee to the Director and the evaluation by its HeLa Genome Data Access Working Group (http://acd.od.nih.gov/hlgda.htm). The HeLa genomic datasets used for analysis described in this manuscript were obtained from the database of Genotypes and Phenotypes (dbGaP) through dbGaP: phs000640.-
dc.language.isoen-
dc.rights© 2015 Elsevier Inc. Published by Elsevier Inc. All rights reserved.-
dc.titleCTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription-
dc.typeJournal Contribution-
dc.identifier.epage1627-
dc.identifier.issue7-
dc.identifier.spage1611-
dc.identifier.volume163-
local.bibliographicCitation.jcatA1-
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local.type.refereedRefereed-
local.type.specifiedArticle-
dc.identifier.doi10.1016/j.cell.2015.11.024-
dc.identifier.isi000366854200010-
item.contributorTang, Zhonghui-
item.contributorLuo, Oscar Junhong-
item.contributorLi, Xingwang-
item.contributorZheng, Meizhen-
item.contributorJufen Zhu, Jacqueline-
item.contributorSZALAJ, Przemek-
item.contributorTrzaskoma, Pawel-
item.contributorMagalska, Adriana-
item.contributorWlodarczyk, Jakub-
item.contributorRuszczycki, Blazej-
item.contributorMichalski, Paul-
item.contributorPiecuch, Emaly-
item.contributorWang, Ping-
item.contributorWang, Danjuan-
item.contributorZhongyuan Tian, Simon-
item.contributorPenrad-Mobayed, May-
item.contributorSachs, Laurent M.-
item.contributorRuan, Xiaoan-
item.contributorWe, Chia-Lin-
item.contributorLiu, Edison T.-
item.contributorWilczynski, Grzegorz M.-
item.contributorPlewczynski, Dariusz-
item.contributorLi, Guoliang-
item.contributorRuan, Yijun-
item.accessRightsRestricted Access-
item.fullcitationTang, Zhonghui; Luo, Oscar Junhong; Li, Xingwang; Zheng, Meizhen; Jufen Zhu, Jacqueline; SZALAJ, Przemek; Trzaskoma, Pawel; Magalska, Adriana; Wlodarczyk, Jakub; Ruszczycki, Blazej; Michalski, Paul; Piecuch, Emaly; Wang, Ping; Wang, Danjuan; Zhongyuan Tian, Simon; Penrad-Mobayed, May; Sachs, Laurent M.; Ruan, Xiaoan; We, Chia-Lin; Liu, Edison T.; Wilczynski, Grzegorz M.; Plewczynski, Dariusz; Li, Guoliang & Ruan, Yijun (2015) CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. In: CELL, 163 (7), p. 1611-1627.-
item.validationecoom 2017-
item.fulltextWith Fulltext-
crisitem.journal.issn0092-8674-
crisitem.journal.eissn1097-4172-
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