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Chen J, Hu Y, Yu Y, Zhang L, Yang P, Jin H. Quantitative analysis of post-translational modifications of histone H3 variants during the cell cycle. Anal Chim Acta 2019; 1080:116-126. [DOI: 10.1016/j.aca.2019.06.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/09/2019] [Accepted: 06/10/2019] [Indexed: 10/26/2022]
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Chen X, Ye Y, Gu L, Sun J, Du Y, Liu WJ, Li W, Zhang X, Jiang C. H3K27me3 Signal in the Cis Regulatory Elements Reveals the Differentiation Potential of Progenitors During Drosophila Neuroglial Development. GENOMICS PROTEOMICS & BIOINFORMATICS 2019; 17:297-304. [PMID: 31195140 PMCID: PMC6818177 DOI: 10.1016/j.gpb.2018.12.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/14/2018] [Accepted: 12/14/2018] [Indexed: 01/24/2023]
Abstract
Drosophila neural development undergoes extensive chromatin remodeling and precise epigenetic regulation. However, the roles of chromatin remodeling in establishment and maintenance of cell identity during cell fate transition remain enigmatic. Here, we compared the changes in gene expression, as well as the dynamics of nucleosome positioning and key histone modifications between the four major neural cell types during Drosophila neural development. We find that the neural progenitors can be separated from the terminally differentiated cells based on their gene expression profiles, whereas nucleosome distribution in the flanking regions of transcription start sites fails to identify the relationships between the progenitors and the differentiated cells. H3K27me3 signal in promoters and enhancers can not only distinguish the progenitors from the differentiated cells but also identify the differentiation path of the neural stem cells (NSCs) to the intermediate progenitor cells to the glial cells. In contrast, H3K9ac signal fails to identify the differentiation path, although it activates distinct sets of genes with neuron-specific and glia-related functions during the differentiation of the NSCs into neurons and glia, respectively. Together, our study provides novel insights into the crucial roles of chromatin remodeling in determining cell type during Drosophila neural development.
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Affiliation(s)
- Xiaolong Chen
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Youqiong Ye
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Liang Gu
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Jin Sun
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Yanhua Du
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Wen-Ju Liu
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Wei Li
- Tongji University Library, Tongji University, Shanghai 200092, China
| | - Xiaobai Zhang
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Cizhong Jiang
- Institute of Translational Research, Tongji Hospital, School of Life Sciences and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China; Research Center of Stem Cells and Ageing, Tsingtao Advanced Research Institute, Tongji University, Tsingtao 266071, China.
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Nucleosome eviction along with H3K9ac deposition enhances Sox2 binding during human neuroectodermal commitment. Cell Death Differ 2017; 24:1121-1131. [PMID: 28475175 PMCID: PMC5442478 DOI: 10.1038/cdd.2017.62] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 03/28/2017] [Accepted: 03/31/2017] [Indexed: 02/06/2023] Open
Abstract
Neuroectoderm is an important neural precursor. However, chromatin remodeling and its epigenetic regulatory roles during the differentiation of human neuroectodermal cells (hNECs) from human embryonic stem cells (hESCs) remain largely unexplored. Here, we obtained hNECs through directed differentiation from hESCs, and determined chromatin states in the two cell types. Upon differentiation, H2A.Z-mediated nucleosome depletion leads to an open chromatin structure in promoters and upregulates expression of neuroectodermal genes. Increase in H3K9ac signals and decrease in H3K27me3 signals in promoters result in an active chromatin state and activate neuroectodermal genes. Conversely, decrease in H3K9ac signals and increase in H3K27me3 signals in promoters repress pluripotency genes. Moreover, H3K9ac signals facilitate the pluripotency factor Sox2 binding to target sites unique to hNECs. Knockdown of the acetyltransferase Kat2b erases H3K9ac signals, disrupts Sox2 binding, and fails the differentiation. Our results demonstrate a hierarchy of epigenetic regulation of gene expression during the differentiation of hNECs from hESCs through chromatin remodeling.
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Ye Y, Li M, Gu L, Chen X, Shi J, Zhang X, Jiang C. Chromatin remodeling during in vivo neural stem cells differentiating to neurons in early Drosophila embryos. Cell Death Differ 2016; 24:409-420. [PMID: 27858939 PMCID: PMC5344203 DOI: 10.1038/cdd.2016.135] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 10/06/2016] [Accepted: 10/18/2016] [Indexed: 12/25/2022] Open
Abstract
Neurons are a key component of the nervous system and differentiate from multipotent neural stem cells (NSCs). Chromatin remodeling has a critical role in the differentiation process. However, its in vivo epigenetic regulatory role remains unknown. We show here that nucleosome depletion regions (NDRs) form in both proximal promoters and distal enhancers during NSCs differentiating into neurons in the early Drosophila embryonic development. NDR formation in the regulatory regions involves nucleosome shift and eviction. Nucleosome occupancy in promoter NDRs is inversely proportional to the gene activity. Genes with promoter NDR formation during differentiation are enriched for functions related to neuron development and maturation. Active histone-modification signals (H3K4me3 and H3K9ac) in promoters are gained in neurons in two modes: de novo establishment to high levels or increase from the existing levels in NSCs. The gene sets corresponding to the two modes have different neuron-related functions. Dynamic changes of H3K27ac and H3K9ac signals in enhancers and promoters synergistically repress genes associated with neural stem or progenitor cell-related pluripotency and upregulate genes associated with neuron projection morphogenesis, neuron differentiation, and so on. Our results offer new insights into chromatin remodeling during in vivo neuron development and lay a foundation for its epigenetic regulatory mechanism study of other lineage specification.
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Affiliation(s)
- Youqiong Ye
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, The Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China
| | - Min Li
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, The Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China
| | - Liang Gu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, The Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China
| | - Xiaolong Chen
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, The Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China
| | - Jiejun Shi
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, The Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China
| | - Xiaobai Zhang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, The Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China
| | - Cizhong Jiang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai Key Laboratory of Signaling and Disease Research, The School of Life Sciences and Technology, The Collaborative Innovation Center for Brain Science, Tongji University, Shanghai 200092, China
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Chromatin remodeling during the in vivo glial differentiation in early Drosophila embryos. Sci Rep 2016; 6:33422. [PMID: 27634414 PMCID: PMC5025732 DOI: 10.1038/srep33422] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 08/26/2016] [Indexed: 12/31/2022] Open
Abstract
Chromatin remodeling plays a critical role in gene regulation and impacts many biological processes. However, little is known about the relationship between chromatin remodeling dynamics and in vivo cell lineage commitment. Here, we reveal the patterns of histone modification change and nucleosome positioning dynamics and their epigenetic regulatory roles during the in vivo glial differentiation in early Drosophila embryos. The genome-wide average H3K9ac signals in promoter regions are decreased in the glial cells compared to the neural progenitor cells. However, H3K9ac signals are increased in a group of genes that are up-regulated in glial cells and involved in gliogenesis. There occurs extensive nucleosome remodeling including shift, loss, and gain. Nucleosome depletion regions (NDRs) form in both promoters and enhancers. As a result, the associated genes are up-regulated. Intriguingly, NDRs form in two fashions: nucleosome shift and eviction. Moreover, the mode of NDR formation is independent of the original chromatin state of enhancers in the neural progenitor cells.
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