An atlas of dynamic chromatin landscapes in mouse fetal development

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, Yunjiang Qiu, Veena Afzal, Jennifer A. Akiyama, Ingrid Plajzer-Frick, Catherine S. Novak, Momoe Kato, Tyler H. Garvin, Quan T. Pham, Anne N. Harrington, Brandon J. Mannion, Elizabeth A. Lee, Yoko Fukuda-Yuzawa, Yupeng He, Sebastian Preissl, Sora Chee, Jee Yun Han, Brian A. Williams, Diane Trout, Henry Amrhein, Hongbo Yang, J. Michael Cherry, Wei Wang, Kyle Gaulton, Joseph R. Ecker, Yin Shen, Diane E. Dickel, Axel Visel (), Len A. Pennacchio () and Bing Ren ()
Additional contact information
David U. Gorkin: Ludwig Institute for Cancer Research
Iros Barozzi: Lawrence Berkeley National Laboratory
Yuan Zhao: Ludwig Institute for Cancer Research
Yanxiao Zhang: Ludwig Institute for Cancer Research
Hui Huang: Ludwig Institute for Cancer Research
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
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
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
Sebastian Preissl: Ludwig Institute for Cancer Research
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
Yin Shen: Institute for Human Genetics and University of California, San Francisco
Diane E. Dickel: Lawrence Berkeley National Laboratory
Axel Visel: Lawrence Berkeley National Laboratory
Len A. Pennacchio: Lawrence Berkeley National Laboratory
Bing Ren: Ludwig Institute for Cancer Research

Nature, 2020, vol. 583, issue 7818, 744-751

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41586-020-2093-3

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