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Landscape of cohesin-mediated chromatin loops in the human genome

Author

Listed:
  • Fabian Grubert

    (Stanford University School of Medicine
    Stanford University School of Medicine)

  • Rohith Srivas

    (Stanford University School of Medicine)

  • Damek V Spacek

    (Stanford University School of Medicine)

  • Maya Kasowski

    (Stanford University School of Medicine
    Stanford University School of Medicine)

  • Mariana Ruiz-Velasco

    (European Molecular Biology Laboratory)

  • Nasa Sinnott-Armstrong

    (Stanford University School of Medicine)

  • Peyton Greenside

    (Stanford University School of Medicine)

  • Anil Narasimha

    (Stanford University School of Medicine)

  • Qing Liu

    (Stanford University School of Medicine)

  • Benjamin Geller

    (Stanford University School of Medicine)

  • Akshay Sanghi

    (Stanford University School of Medicine)

  • Michael Kulik

    (University of Georgia
    University of Georgia)

  • Silin Sa

    (Stanford University School of Medicine
    Stanford University School of Medicine
    Stanford University School of Medicine)

  • Marlene Rabinovitch

    (Stanford University School of Medicine
    Stanford University School of Medicine
    Stanford University School of Medicine)

  • Anshul Kundaje

    (Stanford University School of Medicine
    Stanford University)

  • Stephen Dalton

    (University of Georgia
    University of Georgia)

  • Judith B. Zaugg

    (European Molecular Biology Laboratory)

  • Michael Snyder

    (Stanford University School of Medicine)

Abstract

Physical interactions between distal regulatory elements have a key role in regulating gene expression, but the extent to which these interactions vary between cell types and contribute to cell-type-specific gene expression remains unclear. Here, to address these questions as part of phase III of the Encyclopedia of DNA Elements (ENCODE), we mapped cohesin-mediated chromatin loops, using chromatin interaction analysis by paired-end tag sequencing (ChIA-PET), and analysed gene expression in 24 diverse human cell types, including core ENCODE cell lines. Twenty-eight per cent of all chromatin loops vary across cell types; these variations modestly correlate with changes in gene expression and are effective at grouping cell types according to their tissue of origin. The connectivity of genes corresponds to different functional classes, with housekeeping genes having few contacts, and dosage-sensitive genes being more connected to enhancer elements. This atlas of chromatin loops complements the diverse maps of regulatory architecture that comprise the ENCODE Encyclopedia, and will help to support emerging analyses of genome structure and function.

Suggested Citation

  • Fabian Grubert & Rohith Srivas & Damek V Spacek & Maya Kasowski & Mariana Ruiz-Velasco & Nasa Sinnott-Armstrong & Peyton Greenside & Anil Narasimha & Qing Liu & Benjamin Geller & Akshay Sanghi & Micha, 2020. "Landscape of cohesin-mediated chromatin loops in the human genome," Nature, Nature, vol. 583(7818), pages 737-743, July.
  • Handle: RePEc:nat:nature:v:583:y:2020:i:7818:d:10.1038_s41586-020-2151-x
    DOI: 10.1038/s41586-020-2151-x
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    Cited by:

    1. Konstantin Okonechnikov & Aylin Camgöz & Owen Chapman & Sameena Wani & Donglim Esther Park & Jens-Martin Hübner & Abhijit Chakraborty & Meghana Pagadala & Rosalind Bump & Sahaana Chandran & Katerina K, 2023. "3D genome mapping identifies subgroup-specific chromosome conformations and tumor-dependency genes in ependymoma," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    2. Youngsook Lucy Jung & Wenping Zhao & Ian Li & Dhawal Jain & Charles B. Epstein & Bradley E. Bernstein & Sareh Parangi & Richard Sherwood & Cassianne Robinson-Cohen & Yi-Hsiang Hsu & Peter J. Park & Mi, 2024. "Epigenetic profiling reveals key genes and cis-regulatory networks specific to human parathyroids," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    3. Julia Minderjahn & Alexander Fischer & Konstantin Maier & Karina Mendes & Margit Nuetzel & Johanna Raithel & Hanna Stanewsky & Ute Ackermann & Robert Månsson & Claudia Gebhard & Michael Rehli, 2022. "Postmitotic differentiation of human monocytes requires cohesin-structured chromatin," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    4. 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.
    5. 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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