An atlas of dynamic chromatin landscapes in mouse fetal development

David U. Gorkin(University of California San Diego), Iros Barozzi(Lawrence Berkeley National Laboratory), Yuan Zhao(University of California San Diego), Yanxiao Zhang(Ludwig Cancer Research), Hui Huang(University of California San Diego), Ah Young Lee(Ludwig Cancer Research), Bin Li(Ludwig Cancer Research), Joshua Chiou(University of California San Diego), André Wildberg(University of California San Diego), Bo Ding(University of California San Diego), Bo Zhang(Penn State Milton S. Hershey Medical Center), Mengchi Wang(University of California San Diego), J. Seth Strattan(Stanford University), Jean M. Davidson(Stanford University), Yunjiang Qiu(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 Pham(Lawrence Berkeley National Laboratory), Anne Harrington(Lawrence Berkeley National Laboratory), Brandon J. Mannion(Lawrence Berkeley National Laboratory), Elizabeth A. Lee(Lawrence Berkeley National Laboratory), Y. Fukuda(Lawrence Berkeley National Laboratory), Yupeng He(Salk Institute for Biological Studies), Sebastian Preißl(University of California San Diego), Sora Chee(Ludwig Cancer Research), Jee Yun Han(University of California San Diego), Brian A. Williams(California Institute of Technology), Diane Trout(California Institute of Technology), Henry Amrhein(California Institute of Technology), Hongbo Yang(Penn State Milton S. Hershey Medical Center), J. Michael Cherry(Stanford University), Wei Wang(University of California San Diego), Kyle J. Gaulton(University of California San Diego), Joseph R. Ecker(Salk Institute for Biological Studies), Yin Shen(University of California, San Francisco), Diane E. Dickel(Lawrence Berkeley National Laboratory), Axel Visel(Lawrence Berkeley National Laboratory), L Pennacchio(Lawrence Berkeley National Laboratory), Bing Ren(Ludwig Cancer Research)
Nature
July 29, 2020
10.1038/s41586-020-2093-3
Cited by 435Open Access
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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.

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