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An atlas of dynamic chromatin landscapes in mouse fetal development

Gorkin, David U. and Williams, Brian A. and Trout, Diane and Amrhein, Henry (2020) An atlas of dynamic chromatin landscapes in mouse fetal development. Nature, 583 (7818). pp. 744-751. ISSN 0028-0836. PMCID PMC7398618. https://resolver.caltech.edu/CaltechAUTHORS:20181031-110727092

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1038/s41586-020-2093-3DOIArticle
https://doi.org/10.1038/s41586-020-2841-4DOIAuthor Correction
https://doi.org/10.1101/166652DOIDiscussion Paper
https://github.com/ENCODE-DCC/ChIP-seq-pipelineRelated ItemCode
http://www.ncbi.nlm.nih.gov/pmc/articles/pmc7398618/PubMed CentralArticle
ORCID:
AuthorORCID
Gorkin, David U.0000-0003-4944-4107
Trout, Diane0000-0002-4928-5532
Amrhein, Henry0000-0002-4264-140X
Alternate Title:Systematic mapping of chromatin state landscapes during mouse development
Additional Information:© 2020 The Author(s). This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. Received 08 August 2017; Accepted 11 June 2019; Published 29 July 2020. This study was funded by the National Human Genome Research Institute as part of the Encyclopedia of DNA Elements (ENCODE) project (U54HG006997), and was performed in compliance with all relevant ethical regulations. D.U.G. was supported by the NIH Institutional Research and Academic Career Development Awards (IRACDA) program, and an A. P. Giannini Foundation fellowship. D.E.D, A.V., and L.A.P. were also supported by UM1HG009421, and research conducted at the E. O. Lawrence Berkeley National Laboratory was performed under Department of Energy Contract DE-AC02-05CH11231, University of California. I.B. is funded through an Imperial College Research Fellowship. Y.H. is supported by the H.A. and Mary K. Chapman Charitable Trust. J.R.E. is an Investigator of the Howard Hughes Medical Institute. The embryo image second from the right in Fig. 1a was adapted from ref. 89, an Open Access article distributed under the terms of the Creative Commons Attribution License. Data availability: All raw and processed data can be accessed via the ENCODE Data Collection and Coordination (DCC) website: https://www.encodedcc.org via the experiment IDs listed in Supplementary Table 13. Code availability: The ENCODE histone ChIP–seq pipeline is among the collection of ENCODE Uniform Processing Pipelines that can be found here: https://github.com/ENCODE-DCC/ChIP-seq-pipeline. Author Contributions: These authors contributed equally: David U. Gorkin, Iros Barozzi, Yuan Zhao, Yanxiao Zhang, Hui Huang. Study conceived and overseen by B.R., D.U.G., L.A.P., A.V., D.E.D., Y.S., K.G., H.Y., J.R.E., W.W., and J.M.C. Tissue collections performed by V.A., J.A.A., I.P.-F., C.S.N., and M.K. ChIP–seq experiments performed by A.Y.L. and S.C. ATAC–seq experiments performed by H.H. and J.Y.H. Data curation and processing by J.S.S., J.M.D., B.L., B.A.W., D.T., H.A., and D.U.G. Analysis performed by I.B., D.U.G., Y. Zhao., Y. Zhang, Y.F.-Y., J.C., A.W., B.D., B.Z., M.W., Y.Q., Y.H., and S.P. Transgenic assays performed by V.A., J.A.A., I.P.-F., C.S.N, M.K., T.H.G., Q.T.P., A.N.H., B.J.M., and E.A.L. Manuscript written by D.U.G., I.B., Y. Zhao., Y. Zhang, D.E.D., and B.R. with input from all authors. Competing interests: B.R. is co-founder and share holder of Arima Genomics. The other authors declare no competing interests.
Errata:Gorkin, D.U., Barozzi, I., Zhao, Y. et al. Author Correction: An atlas of dynamic chromatin landscapes in mouse fetal development. Nature (2020). https://doi.org/10.1038/s41586-020-2841-4
Funders:
Funding AgencyGrant Number
NIHU54HG006997
A. P. Giannini FoundationUNSPECIFIED
NIHUM1HG009421
Department of Energy (DOE)DE-AC02-05CH11231
Imperial College LondonUNSPECIFIED
H. A. and Mary K. Chapman Charitable TrustUNSPECIFIED
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Subject Keywords:Differentiation; Epigenomics
Issue or Number:7818
PubMed Central ID:PMC7398618
Record Number:CaltechAUTHORS:20181031-110727092
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20181031-110727092
Official Citation:Systematic mapping of chromatin state landscapes during mouse development. David Gorkin, Iros Barozzi, Yanxiao Zhang, Ah Young Lee, Bin Lee, Yuan Zhao, Andre 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. Pickle, Momoe Kato, Tyler H. Garvin, Quan T. Pham, Anne N. Harrington, Brandon J. Mannion, Elizabeth A. Lee, Yoko Fukuda-Yuzawa, Yupeng He, Sebastian Preissl, Sora Chee, Brian A. Williams, Diane Trout, Henry Amrhein, Hongbo Yang, J. Michael Cherry, Yin Shen, Joseph R. Ecker, Wei Wang, Diane E. Dickel, Axel Visel, Len A. Pennacchio, Bing Ren. bioRxiv 166652; doi: https://doi.org/10.1101/166652
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:90544
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:01 Nov 2018 17:49
Last Modified:20 Oct 2020 17:28

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