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An oestrogen-receptor-α-bound human chromatin interactome

Author

Listed:
  • Melissa J. Fullwood

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Mei Hui Liu

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • You Fu Pan

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Jun Liu

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Han Xu

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Yusoff Bin Mohamed

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Yuriy L. Orlov

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Stoyan Velkov

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Andrea Ho

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Poh Huay Mei

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Elaine G. Y. Chew

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Phillips Yao Hui Huang

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Willem-Jan Welboren

    (Nijmegen Centre for Molecular Life Sciences, Radboud University)

  • Yuyuan Han

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Hong Sain Ooi

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Pramila N. Ariyaratne

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Vinsensius B. Vega

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Yanquan Luo

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Peck Yean Tan

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Pei Ye Choy

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • K. D. Senali Abayratna Wansa

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Bing Zhao

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Kar Sian Lim

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Shi Chi Leow

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Jit Sin Yow

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Roy Joseph

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Haixia Li

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Kartiki V. Desai

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Jane S. Thomsen

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Yew Kok Lee

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • R. Krishna Murthy Karuturi

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Thoreau Herve

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Guillaume Bourque

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Hendrik G. Stunnenberg

    (Nijmegen Centre for Molecular Life Sciences, Radboud University)

  • Xiaoan Ruan

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Valere Cacheux-Rataboul

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Wing-Kin Sung

    (Genome Institute of Singapore, Agency for Science, Technology and Research
    School of Computing, National University of Singapore)

  • Edison T. Liu

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Chia-Lin Wei

    (Genome Institute of Singapore, Agency for Science, Technology and Research)

  • Edwin Cheung

    (Genome Institute of Singapore, Agency for Science, Technology and Research
    Yong Loo Lin School of Medicine, National University of Singapore
    School of Biological Sciences, Nanyang Technological University)

  • Yijun Ruan

    (Genome Institute of Singapore, Agency for Science, Technology and Research
    Yong Loo Lin School of Medicine, National University of Singapore)

Abstract

Genomes are organized into high-level three-dimensional structures, and DNA elements separated by long genomic distances can in principle interact functionally. Many transcription factors bind to regulatory DNA elements distant from gene promoters. Although distal binding sites have been shown to regulate transcription by long-range chromatin interactions at a few loci, chromatin interactions and their impact on transcription regulation have not been investigated in a genome-wide manner. Here we describe the development of a new strategy, chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) for the de novo detection of global chromatin interactions, with which we have comprehensively mapped the chromatin interaction network bound by oestrogen receptor α (ER-α) in the human genome. We found that most high-confidence remote ER-α-binding sites are anchored at gene promoters through long-range chromatin interactions, suggesting that ER-α functions by extensive chromatin looping to bring genes together for coordinated transcriptional regulation. We propose that chromatin interactions constitute a primary mechanism for regulating transcription in mammalian genomes.

Suggested Citation

  • Melissa J. Fullwood & Mei Hui Liu & You Fu Pan & Jun Liu & Han Xu & Yusoff Bin Mohamed & Yuriy L. Orlov & Stoyan Velkov & Andrea Ho & Poh Huay Mei & Elaine G. Y. Chew & Phillips Yao Hui Huang & Willem, 2009. "An oestrogen-receptor-α-bound human chromatin interactome," Nature, Nature, vol. 462(7269), pages 58-64, November.
  • Handle: RePEc:nat:nature:v:462:y:2009:i:7269:d:10.1038_nature08497
    DOI: 10.1038/nature08497
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    Citations

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    Cited by:

    1. Jose M. Ramos-Pittol & Isabel Fernandes-Freitas & Alexandra Milona & Stephen M. Manchishi & Kara Rainbow & Brian Y. H. Lam & John A. Tadross & Anthony Beucher & William H. Colledge & Inês Cebola & Kev, 2023. "Dax1 modulates ERα-dependent hypothalamic estrogen sensing in female mice," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    2. Laureano Tomás-Daza & Llorenç Rovirosa & Paula López-Martí & Andrea Nieto-Aliseda & François Serra & Ainoa Planas-Riverola & Oscar Molina & Rebecca McDonald & Cedric Ghevaert & Esther Cuatrecasas & Do, 2023. "Low input capture Hi-C (liCHi-C) identifies promoter-enhancer interactions at high-resolution," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    3. Beatriz del Blanco & Sergio Niñerola & Ana M. Martín-González & Juan Paraíso-Luna & Minji Kim & Rafael Muñoz-Viana & Carina Racovac & Jose V. Sanchez-Mut & Yijun Ruan & Ángel Barco, 2024. "Kdm1a safeguards the topological boundaries of PRC2-repressed genes and prevents aging-related euchromatinization in neurons," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    4. Hao Wang & Jiaxin Yang & Yu Zhang & Jianliang Qian & Jianrong Wang, 2022. "Reconstruct high-resolution 3D genome structures for diverse cell-types using FLAMINGO," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    5. Vianne R. Gao & Rui Yang & Arnav Das & Renhe Luo & Hanzhi Luo & Dylan R. McNally & Ioannis Karagiannidis & Martin A. Rivas & Zhong-Min Wang & Darko Barisic & Alireza Karbalayghareh & Wilfred Wong & Yi, 2024. "ChromaFold predicts the 3D contact map from single-cell chromatin accessibility," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    6. Patricia A. Clow & Menghan Du & Nathaniel Jillette & Aziz Taghbalout & Jacqueline J. Zhu & Albert W. Cheng, 2022. "CRISPR-mediated multiplexed live cell imaging of nonrepetitive genomic loci with one guide RNA per locus," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    7. Haoxi Chai & Harianto Tjong & Peng Li & Wei Liao & Ping Wang & Chee Hong Wong & Chew Yee Ngan & Warren J. Leonard & Chia-Lin Wei & Yijun Ruan, 2023. "ChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    8. Jia-Yong Zhong & Longjian Niu & Zhuo-Bin Lin & Xin Bai & Ying Chen & Feng Luo & Chunhui Hou & Chuan-Le Xiao, 2023. "High-throughput Pore-C reveals the single-allele topology and cell type-specificity of 3D genome folding," Nature Communications, Nature, vol. 14(1), pages 1-18, December.
    9. Katelyn L. Mortenson & Courtney Dawes & Emily R. Wilson & Nathan E. Patchen & Hailey E. Johnson & Jason Gertz & Swneke D. Bailey & Yang Liu & Katherine E. Varley & Xiaoyang Zhang, 2024. "3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    10. Yufan Zhou & Tian Li & Lavanya Choppavarapu & Kun Fang & Shili Lin & Victor X. Jin, 2024. "Integration of scHi-C and scRNA-seq data defines distinct 3D-regulated and biological-context dependent cell subpopulations," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    11. Shuai Liu & Yaqiang Cao & Kairong Cui & Qingsong Tang & Keji Zhao, 2022. "Hi-TrAC reveals division of labor of transcription factors in organizing chromatin loops," Nature Communications, Nature, vol. 13(1), pages 1-17, December.

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