An atlas of dynamic chromatin landscapes in mouse fetal development

作者：David U. Gorkin, Iros Barozzi, Yuan Zhao, Yanxiao Zhang, Hui Huang, Ah Young Lee, Bin Li, Joshua Chiou, André 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, Y. Fukuda, Yupeng He, Sebastian Preißl, Sora Chee, Jee Yun Han, Brian A. Williams, Diane E. Trout, Henry Amrhein, Hongbo Yang, J. Michael Cherry, Wei Wang, Kyle J. Gaulton, Joseph R. Ecker, Yin Shen, Diane E. Dickel, Axel Visel, Len A. Pennacchio, Bing Ren · 发表于：Nature · 年份：2020 · DOI：10.1038/s41586-020-2093-3 · 被引用次数：452 · 研究领域：Genomics and Chromatin Dynamics、RNA Research and Splicing、Cancer-related molecular mechanisms research

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.