1. Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development
- Author
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Catherine S. Novak, Quan T. Pham, Bo Ding, Diane Trout, Ingrid Plajzer-Frick, Yuan Zhao, J. Seth Strattan, Elizabeth Lee, Jee Yun Han, Bin Li, Jennifer A. Akiyama, Veena Afzal, Hongbo Yang, Ah Young Lee, Joseph R. Ecker, Sebastian Preissl, Kyle J. Gaulton, Anne N. Harrington, Momoe Kato, Andre Wildberg, Yupeng He, Diane E. Dickel, Tyler H. Garvin, Jean M. Davidson, Joshua Chiou, Bo Zhang, Len A. Pennacchio, Hui Huang, Yoko Fukuda-Yuzawa, Iros Barozzi, Brian A. Williams, Yanxiao Zhang, Yunjiang Qiu, Sora Chee, Axel Visel, Henry Amrhein, Bing Ren, J. Michael Cherry, Wei Wang, Mengchi Wang, David U. Gorkin, Yin Shen, and Brandon J. Mannion
- Subjects
Male ,Epigenomics ,0301 basic medicine ,General Science & Technology ,media_common.quotation_subject ,Datasets as Topic ,Transposases ,Regulatory Sequences, Nucleic Acid ,Fetal Development ,Histones ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Animals ,Humans ,Disease ,Author Correction ,media_common ,Multidisciplinary ,Gene Expression Regulation, Developmental ,Genetic Variation ,Reproducibility of Results ,Molecular Sequence Annotation ,Art ,Chromatin ,Mice, Inbred C57BL ,Enhancer Elements, Genetic ,030104 developmental biology ,Organ Specificity ,Differentiation ,Chromatin Immunoprecipitation Sequencing ,Female ,Humanities ,030217 neurology & neurosurgery - 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.
- Published
- 2021
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