An atlas of dynamic chromatin landscapes in mouse fetal development

David U. Gorkin; Iros Barozzi; Yuan Zhao; Yanxiao Zhang; Hui Huang; Ah Young Lee; Bin Li; Joshua Chiou; 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. Novak; 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; Jee Yun Han; Brian A. Williams; Diane Trout; Henry Amrhein; Hongbo Yang; J. Michael Cherry; Wei Wang; Kyle Gaulton; Joseph R. Ecker; Yin Shen; Diane E. Dickel; Axel Visel; Len A. Pennacchio; Bing Ren

doi:10.1038/s41586-020-2093-3

An atlas of dynamic chromatin landscapes in mouse fetal development

David U. Gorkin, Iros Barozzi, Yuan Zhao, Yanxiao Zhang, Hui Huang, Ah Young Lee, Bin Li, Joshua Chiou, 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. Novak, Momoe KatoTyler H. Garvin, Quan T. Pham, Anne N. Harrington, Brandon J. Mannion, Elizabeth A. Lee, Yoko Fukuda-Yuzawa, Yupeng He, Sebastian Preissl, Sora Chee, Jee Yun Han, Brian A. Williams, Diane Trout, Henry Amrhein, Hongbo Yang, J. Michael Cherry, Wei Wang, Kyle Gaulton, Joseph R. Ecker, Yin Shen, Diane E. Dickel, Axel Visel^*, Len A. Pennacchio^*, Bing Ren^*

^*Corresponding author for this work

Biochemistry and Molecular Genetics

Research output: Contribution to journal › Article › peer-review

204 Scopus citations

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.

Original language	English (US)
Pages (from-to)	744-751
Number of pages	8
Journal	Nature
Volume	583
Issue number	7818
DOIs	https://doi.org/10.1038/s41586-020-2093-3
State	Published - Jul 30 2020

Funding

Fraction enhancer–gene pairs supported by 3D interactions

ASJC Scopus subject areas

General

Access to Document

10.1038/s41586-020-2093-3

Cite this

Gorkin, D. U., Barozzi, I., Zhao, Y., Zhang, Y., Huang, H., Lee, A. Y., Li, B., Chiou, J., Wildberg, A., Ding, B., Zhang, B., Wang, M., Strattan, J. S., Davidson, J. M., Qiu, Y., Afzal, V., Akiyama, J. A., Plajzer-Frick, I., Novak, C. S., ... Ren, B. (2020). An atlas of dynamic chromatin landscapes in mouse fetal development. Nature, 583(7818), 744-751. https://doi.org/10.1038/s41586-020-2093-3

@article{799005b381fe406f96ac733cdc70e582,

title = "An atlas of dynamic chromatin landscapes in mouse fetal development",

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.",

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

note = "Publisher Copyright: {\textcopyright} 2020, The Author(s).",

year = "2020",

month = jul,

day = "30",

doi = "10.1038/s41586-020-2093-3",

language = "English (US)",

volume = "583",

pages = "744--751",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

number = "7818",

}

Gorkin, DU, Barozzi, I, Zhao, Y, Zhang, Y, Huang, H, Lee, AY, Li, B, Chiou, J, Wildberg, A, Ding, B, Zhang, B, Wang, M, Strattan, JS, Davidson, JM, Qiu, Y, Afzal, V, Akiyama, JA, Plajzer-Frick, I, Novak, CS, Kato, M, Garvin, TH, Pham, QT, Harrington, AN, Mannion, BJ, Lee, EA, Fukuda-Yuzawa, Y, He, Y, Preissl, S, Chee, S, Han, JY, Williams, BA, Trout, D, Amrhein, H, Yang, H, Cherry, JM, Wang, W, Gaulton, K, Ecker, JR, Shen, Y, Dickel, DE, Visel, A, Pennacchio, LA & Ren, B 2020, 'An atlas of dynamic chromatin landscapes in mouse fetal development', Nature, vol. 583, no. 7818, pp. 744-751. https://doi.org/10.1038/s41586-020-2093-3

TY - JOUR

T1 - An atlas of dynamic chromatin landscapes in mouse fetal development

AU - Gorkin, David U.

AU - Barozzi, Iros

AU - Zhao, Yuan

AU - Zhang, Yanxiao

AU - Huang, Hui

AU - Lee, Ah Young

AU - Li, Bin

AU - Chiou, Joshua

AU - Wildberg, Andre

AU - Ding, Bo

AU - Zhang, Bo

AU - Wang, Mengchi

AU - Strattan, J. Seth

AU - Davidson, Jean M.

AU - Qiu, Yunjiang

AU - Afzal, Veena

AU - Akiyama, Jennifer A.

AU - Plajzer-Frick, Ingrid

AU - Novak, Catherine S.

AU - Kato, Momoe

AU - Garvin, Tyler H.

AU - Pham, Quan T.

AU - Harrington, Anne N.

AU - Mannion, Brandon J.

AU - Lee, Elizabeth A.

AU - Fukuda-Yuzawa, Yoko

AU - He, Yupeng

AU - Preissl, Sebastian

AU - Chee, Sora

AU - Han, Jee Yun

AU - Williams, Brian A.

AU - Trout, Diane

AU - Amrhein, Henry

AU - Yang, Hongbo

AU - Cherry, J. Michael

AU - Wang, Wei

AU - Gaulton, Kyle

AU - Ecker, Joseph R.

AU - Shen, Yin

AU - Dickel, Diane E.

AU - Visel, Axel

AU - Pennacchio, Len A.

AU - Ren, Bing

PY - 2020/7/30

Y1 - 2020/7/30

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85088709765&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85088709765&partnerID=8YFLogxK

U2 - 10.1038/s41586-020-2093-3

DO - 10.1038/s41586-020-2093-3

M3 - Article

C2 - 32728240

AN - SCOPUS:85088709765

SN - 0028-0836

VL - 583

SP - 744

EP - 751

JO - Nature

JF - Nature

IS - 7818

ER -

An atlas of dynamic chromatin landscapes in mouse fetal development

Abstract

Funding

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this