1. An atlas of dynamic chromatin landscapes in mouse fetal development
- Author
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Axel Visel, Catherine S. Novak, Tyler H. Garvin, Hongbo Yang, Anne N. Harrington, Diane E. Dickel, Yin Shen, Kyle J. Gaulton, J. Michael Cherry, Bin Li, Quan T. Pham, Yunjiang Qiu, Mengchi Wang, Jean M. Davidson, Bo Ding, Elizabeth Lee, Ingrid Plajzer-Frick, Sora Chee, Sebastian Preissl, Jee Yun Han, Diane Trout, Henry Amrhein, Yupeng He, Jennifer A. Akiyama, Momoe Kato, Joseph R. Ecker, Veena Afzal, J. Seth Strattan, Yuan Zhao, Bo Zhang, Wei Wang, Len A. Pennacchio, David U. Gorkin, Brian A. Williams, Iros Barozzi, Ah Young Lee, Hui Huang, Yoko Fukuda-Yuzawa, Yanxiao Zhang, Brandon J. Mannion, Bing Ren, Andre Wildberg, and Joshua Chiou
- Subjects
Epigenomics ,Male ,Transposases ,Datasets as Topic ,Regulatory Sequences, Nucleic Acid ,Inbred C57BL ,ACCESSIBLE CHROMATIN ,Histones ,Fetal Development ,Mice ,Disease ,Developmental ,TRANSCRIPTION FACTOR ,ENCODE ,Regulation of gene expression ,Multidisciplinary ,biology ,Gene Expression Regulation, Developmental ,CELL IDENTITY ,STATE ,Chromatin ,Multidisciplinary Sciences ,Enhancer Elements, Genetic ,Histone ,Organ Specificity ,Differentiation ,Science & Technology - Other Topics ,Chromatin Immunoprecipitation Sequencing ,Female ,Biotechnology ,EXPRESSION ,DOMAINS ,Enhancer Elements ,General Science & Technology ,1.1 Normal biological development and functioning ,Computational biology ,Article ,Vaccine Related ,Genetic ,Genetics ,Animals ,Humans ,Enhancer ,Vaccine Related (AIDS) ,Gene ,Science & Technology ,Nucleic Acid ,Prevention ,Human Genome ,GENOME-WIDE ,Reproducibility of Results ,Genetic Variation ,Molecular Sequence Annotation ,SUPER-ENHANCERS ,GENE ,Mice, Inbred C57BL ,Gene Expression Regulation ,biology.protein ,Immunization ,Generic health relevance ,Chromatin immunoprecipitation ,Regulatory Sequences - 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., Analysis of chromatin state and accessibility in mouse tissues from twelve sites and eight developmental stages provides a comprehensive view of chromatin dynamics.
- Published
- 2020