IDEAS home Printed from https://ideas.repec.org/a/nat/nature/v583y2020i7818d10.1038_s41586-020-2093-3.html
   My bibliography  Save this article

An atlas of dynamic chromatin landscapes in mouse fetal development

Author

Listed:
  • David U. Gorkin

    (Ludwig Institute for Cancer Research
    University of California, San Diego School of Medicine)

  • Iros Barozzi

    (Lawrence Berkeley National Laboratory
    Imperial College London)

  • Yuan Zhao

    (Ludwig Institute for Cancer Research
    University of California, San Diego)

  • Yanxiao Zhang

    (Ludwig Institute for Cancer Research)

  • Hui Huang

    (Ludwig Institute for Cancer Research
    University of California, San Diego School of Medicine)

  • Ah Young Lee

    (Ludwig Institute for Cancer Research)

  • Bin Li

    (Ludwig Institute for Cancer Research)

  • Joshua Chiou

    (University of California, San Diego School of Medicine
    University of California, San Diego School of Medicine)

  • Andre Wildberg

    (University of California, San Diego School of Medicine)

  • Bo Ding

    (University of California, San Diego School of Medicine)

  • Bo Zhang

    (Penn State School of Medicine)

  • Mengchi Wang

    (University of California, San Diego School of Medicine)

  • J. Seth Strattan

    (Stanford University School of Medicine, Department of Genetics)

  • Jean M. Davidson

    (Stanford University School of Medicine, Department of Genetics)

  • Yunjiang Qiu

    (Ludwig Institute for Cancer Research
    University of California, San Diego)

  • Veena Afzal

    (Lawrence Berkeley National Laboratory)

  • Jennifer A. Akiyama

    (Lawrence Berkeley National Laboratory)

  • Ingrid Plajzer-Frick

    (Lawrence Berkeley National Laboratory)

  • Catherine S. Novak

    (Lawrence Berkeley National Laboratory)

  • Momoe Kato

    (Lawrence Berkeley National Laboratory)

  • Tyler H. Garvin

    (Lawrence Berkeley National Laboratory)

  • Quan T. Pham

    (Lawrence Berkeley National Laboratory)

  • Anne N. Harrington

    (Lawrence Berkeley National Laboratory)

  • Brandon J. Mannion

    (Lawrence Berkeley National Laboratory)

  • Elizabeth A. Lee

    (Lawrence Berkeley National Laboratory)

  • Yoko Fukuda-Yuzawa

    (Lawrence Berkeley National Laboratory)

  • Yupeng He

    (University of California, San Diego
    Salk Institute for Biological Studies)

  • Sebastian Preissl

    (Ludwig Institute for Cancer Research
    University of California, San Diego School of Medicine)

  • Sora Chee

    (Ludwig Institute for Cancer Research)

  • Jee Yun Han

    (University of California, San Diego School of Medicine)

  • Brian A. Williams

    (California Institute of Technology)

  • Diane Trout

    (California Institute of Technology)

  • Henry Amrhein

    (California Institute of Technology)

  • Hongbo Yang

    (Penn State School of Medicine)

  • J. Michael Cherry

    (Stanford University School of Medicine, Department of Genetics)

  • Wei Wang

    (University of California, San Diego School of Medicine)

  • Kyle Gaulton

    (University of California, San Diego School of Medicine)

  • Joseph R. Ecker

    (Salk Institute for Biological Studies
    Salk Institute for Biological Studies)

  • Yin Shen

    (Institute for Human Genetics and University of California, San Francisco
    University of California, San Francisco)

  • Diane E. Dickel

    (Lawrence Berkeley National Laboratory)

  • Axel Visel

    (Lawrence Berkeley National Laboratory
    US Department of Energy Joint Genome Institute
    University of California, Merced)

  • Len A. Pennacchio

    (Lawrence Berkeley National Laboratory
    US Department of Energy Joint Genome Institute
    University of California, Berkeley)

  • Bing Ren

    (Ludwig Institute for Cancer Research
    University of California, San Diego School of Medicine
    University of California, San Diego School of Medicine
    University of California, San Diego School of Medicine)

Abstract

The Encyclopedia of DNA Elements (ENCODE) project has established a genomic resource for mammalian development, profiling a diverse panel of mouse tissues at 8 developmental stages from 10.5 days after conception until birth, including transcriptomes, methylomes and chromatin states. Here we systematically examined the state and accessibility of chromatin in the developing mouse fetus. In total we performed 1,128 chromatin immunoprecipitation with sequencing (ChIP–seq) assays for histone modifications and 132 assay for transposase-accessible chromatin using sequencing (ATAC–seq) assays for chromatin accessibility across 72 distinct tissue-stages. We used integrative analysis to develop a unified set of chromatin state annotations, infer the identities of dynamic enhancers and key transcriptional regulators, and characterize the relationship between chromatin state and accessibility during developmental gene regulation. We also leveraged these data to link enhancers to putative target genes and demonstrate tissue-specific enrichments of sequence variants associated with disease in humans. The mouse ENCODE data sets provide a compendium of resources for biomedical researchers and achieve, to our knowledge, the most comprehensive view of chromatin dynamics during mammalian fetal development to date.

Suggested Citation

  • David U. Gorkin & Iros Barozzi & Yuan Zhao & Yanxiao Zhang & Hui Huang & Ah Young Lee & Bin Li & Joshua Chiou & Andre Wildberg & Bo Ding & Bo Zhang & Mengchi Wang & J. Seth Strattan & Jean M. Davidson, 2020. "An atlas of dynamic chromatin landscapes in mouse fetal development," Nature, Nature, vol. 583(7818), pages 744-751, July.
    • Handle: RePEc:nat:nature:v:583:y:2020:i:7818:d:10.1038_s41586-020-2093-3
    DOI: 10.1038/s41586-020-2093-3
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41586-020-2093-3
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.
    File URL: https://libkey.io/10.1038/s41586-020-2093-3?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Zhangyuan Pan & Yuelin Yao & Hongwei Yin & Zexi Cai & Ying Wang & Lijing Bai & Colin Kern & Michelle Halstead & Ganrea Chanthavixay & Nares Trakooljul & Klaus Wimmers & Goutam Sahana & Guosheng Su & M, 2021. "Pig genome functional annotation enhances the biological interpretation of complex traits and human disease," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    2. Adriana Arneson & Amin Haghani & Michael J. Thompson & Matteo Pellegrini & Soo Bin Kwon & Ha Vu & Emily Maciejewski & Mingjia Yao & Caesar Z. Li & Ake T. Lu & Marco Morselli & Liudmilla Rubbi & Bret B, 2022. "A mammalian methylation array for profiling methylation levels at conserved sequences," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    3. Phoebe Lut Fei Tam & Ming Fung Cheung & Lu Yan Chan & Danny Leung, 2024. "Cell-type differential targeting of SETDB1 prevents aberrant CTCF binding, chromatin looping, and cis-regulatory interactions," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    4. Sudha Sunil Rajderkar & Kitt Paraiso & Maria Luisa Amaral & Michael Kosicki & Laura E. Cook & Fabrice Darbellay & Cailyn H. Spurrell & Marco Osterwalder & Yiwen Zhu & Han Wu & Sarah Yasmeen Afzal & Ma, 2024. "Dynamic enhancer landscapes in human craniofacial development," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    5. Jennifer P. Nguyen & Timothy D. Arthur & Kyohei Fujita & Bianca M. Salgado & Margaret K. R. Donovan & Hiroko Matsui & Ji Hyun Kim & Agnieszka D’Antonio-Chronowska & Matteo D’Antonio & Kelly A. Frazer, 2023. "eQTL mapping in fetal-like pancreatic progenitor cells reveals early developmental insights into diabetes risk," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
    6. Ze Yan & Ji Yang & Wen-Tian Wei & Ming-Liang Zhou & Dong-Xin Mo & Xing Wan & Rui Ma & Mei-Ming Wu & Jia-Hui Huang & Ya-Jing Liu & Feng-Hua Lv & Meng-Hua Li, 2024. "A time-resolved multi-omics atlas of transcriptional regulation in response to high-altitude hypoxia across whole-body tissues," Nature Communications, Nature, vol. 15(1), pages 1-22, December.
    7. Ye Cai & Huifen Cao & Fang Wang & Yufei Zhang & Philipp Kapranov, 2022. "Complex genomic patterns of abasic sites in mammalian DNA revealed by a high-resolution SSiNGLe-AP method," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
    8. Yael Aylon & Noa Furth & Giuseppe Mallel & Gilgi Friedlander & Nishanth Belugali Nataraj & Meng Dong & Ori Hassin & Rawan Zoabi & Benjamin Cohen & Vanessa Drendel & Tomer Meir Salame & Saptaparna Mukh, 2022. "Breast cancer plasticity is restricted by a LATS1-NCOR1 repressive axis," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
    9. Renata Bordeira-Carriço & Joana Teixeira & Marta Duque & Mafalda Galhardo & Diogo Ribeiro & Rafael D. Acemel & Panos. N. Firbas & Juan J. Tena & Ana Eufrásio & Joana Marques & Fábio J. Ferreira & Telm, 2022. "Multidimensional chromatin profiling of zebrafish pancreas to uncover and investigate disease-relevant enhancers," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    10. Christopher T. Rhodes & Joyce J. Thompson & Apratim Mitra & Dhanya Asokumar & Dongjin R. Lee & Daniel J. Lee & Yajun Zhang & Eva Jason & Ryan K. Dale & Pedro P. Rocha & Timothy J. Petros, 2022. "An epigenome atlas of neural progenitors within the embryonic mouse forebrain," Nature Communications, Nature, vol. 13(1), pages 1-17, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:nature:v:583:y:2020:i:7818:d:10.1038_s41586-020-2093-3. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.