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Enhancer hubs and loop collisions identified from single-allele topologies. / Allahyar, Amin; Vermeulen, Carlo; Bouwman, Britta A.M.; Krijger, Peter H.L.; Verstegen, Marjon J.A.M.; Geeven, Geert; van Kranenburg, Melissa; Pieterse, Mark; Straver, Roy; Haarhuis, Judith H.I.; Jalink, Kees; More Authors.

In: Nature Genetics, Vol. 50, 2018, p. 1151-1160.

Research output: Contribution to journalArticleScientificpeer-review

Harvard

Allahyar, A, Vermeulen, C, Bouwman, BAM, Krijger, PHL, Verstegen, MJAM, Geeven, G, van Kranenburg, M, Pieterse, M, Straver, R, Haarhuis, JHI, Jalink, K & More Authors 2018, 'Enhancer hubs and loop collisions identified from single-allele topologies' Nature Genetics, vol. 50, pp. 1151-1160. https://doi.org/10.1038/s41588-018-0161-5

APA

Allahyar, A., Vermeulen, C., Bouwman, B. A. M., Krijger, P. H. L., Verstegen, M. J. A. M., Geeven, G., ... More Authors (2018). Enhancer hubs and loop collisions identified from single-allele topologies. Nature Genetics, 50, 1151-1160. https://doi.org/10.1038/s41588-018-0161-5

Vancouver

Allahyar A, Vermeulen C, Bouwman BAM, Krijger PHL, Verstegen MJAM, Geeven G et al. Enhancer hubs and loop collisions identified from single-allele topologies. Nature Genetics. 2018;50:1151-1160. https://doi.org/10.1038/s41588-018-0161-5

Author

Allahyar, Amin ; Vermeulen, Carlo ; Bouwman, Britta A.M. ; Krijger, Peter H.L. ; Verstegen, Marjon J.A.M. ; Geeven, Geert ; van Kranenburg, Melissa ; Pieterse, Mark ; Straver, Roy ; Haarhuis, Judith H.I. ; Jalink, Kees ; More Authors. / Enhancer hubs and loop collisions identified from single-allele topologies. In: Nature Genetics. 2018 ; Vol. 50. pp. 1151-1160.

BibTeX

@article{f2719fbbd94a4ca797510697ffb85167,
title = "Enhancer hubs and loop collisions identified from single-allele topologies",
abstract = "Chromatin folding contributes to the regulation of genomic processes such as gene activity. Existing conformation capture methods characterize genome topology through analysis of pairwise chromatin contacts in populations of cells but cannot discern whether individual interactions occur simultaneously or competitively. Here we present multi-contact 4C (MC-4C), which applies Nanopore sequencing to study multi-way DNA conformations of individual alleles. MC-4C distinguishes cooperative from random and competing interactions and identifies previously missed structures in subpopulations of cells. We show that individual elements of the β-globin superenhancer can aggregate into an enhancer hub that can simultaneously accommodate two genes. Neighboring chromatin domain loops can form rosette-like structures through collision of their CTCF-bound anchors, as seen most prominently in cells lacking the cohesin-unloading factor WAPL. Here, massive collision of CTCF-anchored chromatin loops is believed to reflect ‘cohesin traffic jams’. Single-allele topology studies thus help us understand the mechanisms underlying genome folding and functioning.",
author = "Amin Allahyar and Carlo Vermeulen and Bouwman, {Britta A.M.} and Krijger, {Peter H.L.} and Verstegen, {Marjon J.A.M.} and Geert Geeven and {van Kranenburg}, Melissa and Mark Pieterse and Roy Straver and Haarhuis, {Judith H.I.} and Kees Jalink and {More Authors}",
year = "2018",
doi = "10.1038/s41588-018-0161-5",
language = "English",
volume = "50",
pages = "1151--1160",
journal = "Nature Genetics",
issn = "1061-4036",
publisher = "Nature Publishing Group",

}

RIS

TY - JOUR

T1 - Enhancer hubs and loop collisions identified from single-allele topologies

AU - Allahyar, Amin

AU - Vermeulen, Carlo

AU - Bouwman, Britta A.M.

AU - Krijger, Peter H.L.

AU - Verstegen, Marjon J.A.M.

AU - Geeven, Geert

AU - van Kranenburg, Melissa

AU - Pieterse, Mark

AU - Straver, Roy

AU - Haarhuis, Judith H.I.

AU - Jalink, Kees

AU - More Authors, null

PY - 2018

Y1 - 2018

N2 - Chromatin folding contributes to the regulation of genomic processes such as gene activity. Existing conformation capture methods characterize genome topology through analysis of pairwise chromatin contacts in populations of cells but cannot discern whether individual interactions occur simultaneously or competitively. Here we present multi-contact 4C (MC-4C), which applies Nanopore sequencing to study multi-way DNA conformations of individual alleles. MC-4C distinguishes cooperative from random and competing interactions and identifies previously missed structures in subpopulations of cells. We show that individual elements of the β-globin superenhancer can aggregate into an enhancer hub that can simultaneously accommodate two genes. Neighboring chromatin domain loops can form rosette-like structures through collision of their CTCF-bound anchors, as seen most prominently in cells lacking the cohesin-unloading factor WAPL. Here, massive collision of CTCF-anchored chromatin loops is believed to reflect ‘cohesin traffic jams’. Single-allele topology studies thus help us understand the mechanisms underlying genome folding and functioning.

AB - Chromatin folding contributes to the regulation of genomic processes such as gene activity. Existing conformation capture methods characterize genome topology through analysis of pairwise chromatin contacts in populations of cells but cannot discern whether individual interactions occur simultaneously or competitively. Here we present multi-contact 4C (MC-4C), which applies Nanopore sequencing to study multi-way DNA conformations of individual alleles. MC-4C distinguishes cooperative from random and competing interactions and identifies previously missed structures in subpopulations of cells. We show that individual elements of the β-globin superenhancer can aggregate into an enhancer hub that can simultaneously accommodate two genes. Neighboring chromatin domain loops can form rosette-like structures through collision of their CTCF-bound anchors, as seen most prominently in cells lacking the cohesin-unloading factor WAPL. Here, massive collision of CTCF-anchored chromatin loops is believed to reflect ‘cohesin traffic jams’. Single-allele topology studies thus help us understand the mechanisms underlying genome folding and functioning.

UR - http://www.scopus.com/inward/record.url?scp=85049622310&partnerID=8YFLogxK

U2 - 10.1038/s41588-018-0161-5

DO - 10.1038/s41588-018-0161-5

M3 - Article

VL - 50

SP - 1151

EP - 1160

JO - Nature Genetics

T2 - Nature Genetics

JF - Nature Genetics

SN - 1061-4036

ER -

ID: 45772232