Epigenomic Landscape of Human Fetal Brain, Heart, and Liver

The epigenetic regulation of spatiotemporal gene expression is crucial for human development. Here, we present whole-genome chromatin immunoprecipitation followed by high throughput DNA sequencing (ChIP-seq) analyses of a wide variety of histone markers in the brain, heart, and liver of early human...

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Published in	The Journal of biological chemistry Vol. 291; no. 9; pp. 4386 - 4398
Main Authors	Yan, Liying, Guo, Hongshan, Hu, Boqiang, Li, Rong, Yong, Jun, Zhao, Yangyu, Zhi, Xu, Fan, Xiaoying, Guo, Fan, Wang, Xiaoye, Wang, Wei, Wei, Yuan, Wang, Yan, Wen, Lu, Qiao, Jie, Tang, Fuchou
Format	Journal Article
Language	English
Published	United States Elsevier Inc 26.02.2016 American Society for Biochemistry and Molecular Biology
Subjects	Aborted Fetus - metabolism Biomarkers - metabolism Brain - embryology Brain - metabolism China Chromatin - chemistry Chromatin - metabolism Databases, Nucleic Acid development Developmental Biology Epigenesis, Genetic epigenetics Gene Expression Regulation, Developmental Gene Ontology gene regulation Genomic Library genomics Heart - embryology high throughput screening High-Throughput Nucleotide Sequencing Histones - genetics Histones - metabolism Humans Liver - embryology Liver - metabolism Lysine - metabolism Methylation Myocardium - metabolism Organ Specificity Protein Processing, Post-Translational Sequence Analysis, DNA Species Specificity China genomics development gene regulation high throughput screening epigenetics
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Abstract	The epigenetic regulation of spatiotemporal gene expression is crucial for human development. Here, we present whole-genome chromatin immunoprecipitation followed by high throughput DNA sequencing (ChIP-seq) analyses of a wide variety of histone markers in the brain, heart, and liver of early human embryos shortly after their formation. We identified 40,181 active enhancers, with a large portion showing tissue-specific and developmental stage-specific patterns, pointing to their roles in controlling the ordered spatiotemporal expression of the developmental genes in early human embryos. Moreover, using sequential ChIP-seq, we showed that all three organs have hundreds to thousands of bivalent domains that are marked by both H3K4me3 and H3K27me3, probably to keep the progenitor cells in these organs ready for immediate differentiation into diverse cell types during subsequent developmental processes. Our work illustrates the potentially critical roles of tissue-specific and developmental stage-specific epigenomes in regulating the spatiotemporal expression of developmental genes during early human embryonic development.
AbstractList	The epigenetic regulation of spatiotemporal gene expression is crucial for human development. Here, we present whole-genome chromatin immunoprecipitation followed by high throughput DNA sequencing (ChIP-seq) analyses of a wide variety of histone markers in the brain, heart, and liver of early human embryos shortly after their formation. We identified 40,181 active enhancers, with a large portion showing tissue-specific and developmental stage-specific patterns, pointing to their roles in controlling the ordered spatiotemporal expression of the developmental genes in early human embryos. Moreover, using sequential ChIP-seq, we showed that all three organs have hundreds to thousands of bivalent domains that are marked by both H3K4me3 and H3K27me3, probably to keep the progenitor cells in these organs ready for immediate differentiation into diverse cell types during subsequent developmental processes. Our work illustrates the potentially critical roles of tissue-specific and developmental stage-specific epigenomes in regulating the spatiotemporal expression of developmental genes during early human embryonic development. The epigenetic regulation of spatiotemporal gene expression is crucial for human development. Here, we present whole-genome chromatin immunoprecipitation followed by high throughput DNA sequencing (ChIP-seq) analyses of a wide variety of histone markers in the brain, heart, and liver of early human embryos shortly after their formation. We identified 40,181 active enhancers, with a large portion showing tissue-specific and developmental stage-specific patterns, pointing to their roles in controlling the ordered spatiotemporal expression of the developmental genes in early human embryos. Moreover, using sequential ChIP-seq, we showed that all three organs have hundreds to thousands of bivalent domains that are marked by both H3K4me3 and H3K27me3, probably to keep the progenitor cells in these organs ready for immediate differentiation into diverse cell types during subsequent developmental processes. Our work illustrates the potentially critical roles of tissue-specific and developmental stage-specific epigenomes in regulating the spatiotemporal expression of developmental genes during early human embryonic development.The epigenetic regulation of spatiotemporal gene expression is crucial for human development. Here, we present whole-genome chromatin immunoprecipitation followed by high throughput DNA sequencing (ChIP-seq) analyses of a wide variety of histone markers in the brain, heart, and liver of early human embryos shortly after their formation. We identified 40,181 active enhancers, with a large portion showing tissue-specific and developmental stage-specific patterns, pointing to their roles in controlling the ordered spatiotemporal expression of the developmental genes in early human embryos. Moreover, using sequential ChIP-seq, we showed that all three organs have hundreds to thousands of bivalent domains that are marked by both H3K4me3 and H3K27me3, probably to keep the progenitor cells in these organs ready for immediate differentiation into diverse cell types during subsequent developmental processes. Our work illustrates the potentially critical roles of tissue-specific and developmental stage-specific epigenomes in regulating the spatiotemporal expression of developmental genes during early human embryonic development.
Author	Li, Rong Tang, Fuchou Wang, Wei Wen, Lu Zhi, Xu Qiao, Jie Yan, Liying Fan, Xiaoying Guo, Hongshan Zhao, Yangyu Guo, Fan Hu, Boqiang Wang, Yan Wei, Yuan Yong, Jun Wang, Xiaoye
Author_xml	– sequence: 1 givenname: Liying surname: Yan fullname: Yan, Liying organization: From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital – sequence: 2 givenname: Hongshan surname: Guo fullname: Guo, Hongshan organization: From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital – sequence: 3 givenname: Boqiang surname: Hu fullname: Hu, Boqiang organization: From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital – sequence: 4 givenname: Rong surname: Li fullname: Li, Rong organization: From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital – sequence: 5 givenname: Jun surname: Yong fullname: Yong, Jun organization: From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital – sequence: 6 givenname: Yangyu surname: Zhao fullname: Zhao, Yangyu organization: From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital – sequence: 7 givenname: Xu surname: Zhi fullname: Zhi, Xu organization: From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital – sequence: 8 givenname: Xiaoying surname: Fan fullname: Fan, Xiaoying organization: From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital – sequence: 9 givenname: Fan surname: Guo fullname: Guo, Fan organization: From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital – sequence: 10 givenname: Xiaoye surname: Wang fullname: Wang, Xiaoye organization: From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital – sequence: 11 givenname: Wei surname: Wang fullname: Wang, Wei organization: From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital – sequence: 12 givenname: Yuan surname: Wei fullname: Wei, Yuan organization: From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital – sequence: 13 givenname: Yan surname: Wang fullname: Wang, Yan organization: From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital – sequence: 14 givenname: Lu surname: Wen fullname: Wen, Lu organization: From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital – sequence: 15 givenname: Jie surname: Qiao fullname: Qiao, Jie email: jie.qiao@263.net organization: From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital – sequence: 16 givenname: Fuchou surname: Tang fullname: Tang, Fuchou email: tangfuchou@pku.edu.cn organization: From the Biodynamic Optical Imaging Center and Center for Reproductive Medicine, College of Life Sciences, Department of Obstetrics and Gynecology, Third Hospital
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ContentType	Journal Article
Copyright	2016 © 2016 ASBMB. Currently published by Elsevier Inc; originally published by American Society for Biochemistry and Molecular Biology. 2016 by The American Society for Biochemistry and Molecular Biology, Inc. 2016 by The American Society for Biochemistry and Molecular Biology, Inc. 2016 The American Society for Biochemistry and Molecular Biology, Inc.
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Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Supported by National Key Technologies Research and Development Program Grant 2012BAI32B01. These authors contributed equally to this work. Supported by National Basic Research Program of China Grants 2011CB944504, 2014CB943200, 2012CB966704, and 2011CB966303, National Natural Science Foundation of China Grants 31230047, 31322037, 31271543, and 81170538, and Beijing Municipal Science and Technology Commission Grant Z131100005213006. Supported by National Natural Science Foundation of China Grant 31440063 and National Basic Research Program of China Grant 2011CB944503.
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Snippet	The epigenetic regulation of spatiotemporal gene expression is crucial for human development. Here, we present whole-genome chromatin immunoprecipitation...
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SubjectTerms	Aborted Fetus - metabolism Biomarkers - metabolism Brain - embryology Brain - metabolism China Chromatin - chemistry Chromatin - metabolism Databases, Nucleic Acid development Developmental Biology Epigenesis, Genetic epigenetics Gene Expression Regulation, Developmental Gene Ontology gene regulation Genomic Library genomics Heart - embryology high throughput screening High-Throughput Nucleotide Sequencing Histones - genetics Histones - metabolism Humans Liver - embryology Liver - metabolism Lysine - metabolism Methylation Myocardium - metabolism Organ Specificity Protein Processing, Post-Translational Sequence Analysis, DNA Species Specificity
Title	Epigenomic Landscape of Human Fetal Brain, Heart, and Liver
URI	https://dx.doi.org/10.1074/jbc.M115.672931 https://www.ncbi.nlm.nih.gov/pubmed/26719341 https://www.proquest.com/docview/1768557413 https://pubmed.ncbi.nlm.nih.gov/PMC4813467
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