An atlas of dynamic chromatin landscapes in mouse fetal development

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 systema...

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Published in:	Nature (London) Vol. 583; no. 7818; pp. 744 - 751
Main Authors:	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
Format:	Journal Article
Language:	English
Published:	London Nature Publishing Group UK 30.07.2020 Nature Publishing Group
Subjects:	45/15 45/22 45/23 631/136/142 631/208/177 Accessibility Animals Annotations Assaying BASIC BIOLOGICAL SCIENCES Cell cycle Chromatin Chromatin - chemistry Chromatin - genetics Chromatin - metabolism Chromatin Immunoprecipitation Sequencing Datasets Datasets as Topic Deoxyribonucleic acid Developmental stages Differentiation Disease - genetics DNA Embryos Encyclopedias Enhancer Elements, Genetic - genetics Enhancers Epigenetics Epigenomics Female Fetal Development - genetics Fetuses Gene expression Gene Expression Regulation, Developmental - genetics Gene regulation Genetic Variation Genomes Genomics Histones - chemistry Histones - metabolism Humanities and Social Sciences Humans Immunoprecipitation Male Mammals Mice Mice, Inbred C57BL Molecular Sequence Annotation multidisciplinary Organ Specificity - genetics Regulators Regulatory Sequences, Nucleic Acid - genetics Reproducibility of Results Science Science (multidisciplinary) Transcription Transposase Transposases - metabolism
ISSN:	0028-0836, 1476-4687, 1476-4687
Online Access:	Get full text
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Summary:	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. Analysis of chromatin state and accessibility in mouse tissues from twelve sites and eight developmental stages provides a comprehensive view of chromatin dynamics.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 AC02-05CH11231 USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
ISSN:	0028-0836 1476-4687 1476-4687
DOI:	10.1038/s41586-020-2093-3