Author:
Gorkin David U.,Barozzi Iros,Zhao Yuan,Zhang Yanxiao,Huang Hui,Lee Ah Young,Li Bin,Chiou Joshua,Wildberg Andre,Ding Bo,Zhang Bo,Wang Mengchi,Strattan J. Seth,Davidson Jean M.,Qiu Yunjiang,Afzal Veena,Akiyama Jennifer A.,Plajzer-Frick Ingrid,Novak Catherine S.,Kato Momoe,Garvin Tyler H.,Pham Quan T.,Harrington Anne N.,Mannion Brandon J.,Lee Elizabeth A.,Fukuda-Yuzawa Yoko,He Yupeng,Preissl Sebastian,Chee Sora,Han Jee Yun,Williams Brian A.,Trout Diane,Amrhein Henry,Yang Hongbo,Cherry J. Michael,Wang Wei,Gaulton Kyle,Ecker Joseph R.,Shen Yin,Dickel Diane E.,Visel Axel,Pennacchio Len A.,Ren Bing
Abstract
AbstractThe 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.
Publisher
Springer Science and Business Media LLC