H2A.Z Acidic Patch Couples Chromatin Dynamics to Regulation of Gene Expression Programs during ESC Differentiation
The histone H2A variant H2A.Z is essential for embryonic development and for proper control of developmental gene expression programs in embryonic stem cells (ESCs). Divergent regions of amino acid sequence of H2A.Z likely determine its functional specialization compared to core histone H2A. For exa...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | en_US |
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Public Library of Science
2013
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| Online Access: | http://hdl.handle.net/1721.1/81237 https://orcid.org/0000-0002-9608-6464 https://orcid.org/0000-0002-2902-7288 https://orcid.org/0000-0002-6199-6855 https://orcid.org/0000-0003-3491-4962 |
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| author | Subramanian, Vidya Mazumder, Aprotim Fields, Paul A. Torrey, Lillian Levine, Stuart S. Bathe, Mark Surface, Lauren Elizabeth Alwan, Allison M. Thai, Kevin Kinh Boyer, Laurie Ann Butty, Vincent L G |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Subramanian, Vidya Mazumder, Aprotim Fields, Paul A. Torrey, Lillian Levine, Stuart S. Bathe, Mark Surface, Lauren Elizabeth Alwan, Allison M. Thai, Kevin Kinh Boyer, Laurie Ann Butty, Vincent L G |
| author_sort | Subramanian, Vidya |
| collection | MIT |
| description | The histone H2A variant H2A.Z is essential for embryonic development and for proper control of developmental gene expression programs in embryonic stem cells (ESCs). Divergent regions of amino acid sequence of H2A.Z likely determine its functional specialization compared to core histone H2A. For example, H2A.Z contains three divergent residues in the essential C-terminal acidic patch that reside on the surface of the histone octamer as an uninterrupted acidic patch domain; however, we know little about how these residues contribute to chromatin structure and function. Here, we show that the divergent amino acids Gly92, Asp97, and Ser98 in the H2A.Z C-terminal acidic patch (H2A.Z[superscript AP3]) are critical for lineage commitment during ESC differentiation. H2A.Z is enriched at most H3K4me3 promoters in ESCs including poised, bivalent promoters that harbor both activating and repressive marks, H3K4me3 and H3K27me3 respectively. We found that while H2A.Z[superscript AP3] interacted with its deposition complex and displayed a highly similar distribution pattern compared to wild-type H2A.Z, its enrichment levels were reduced at target promoters. Further analysis revealed that H2A.Z[superscript AP3] was less tightly associated with chromatin, suggesting that the mutant is more dynamic. Notably, bivalent genes in H2A.Z[superscript AP3] ESCs displayed significant changes in expression compared to active genes. Moreover, bivalent genes in H2A.Z[superscript AP3] ESCs gained H3.3, a variant associated with higher nucleosome turnover, compared to wild-type H2A.Z. We next performed single cell imaging to measure H2A.Z dynamics. We found that H2A.Z[superscript AP3] displayed higher mobility in chromatin compared to wild-type H2A.Z by fluorescent recovery after photobleaching (FRAP). Moreover, ESCs treated with the transcriptional inhibitor flavopiridol resulted in a decrease in the H2A.Z[superscript AP3] mobile fraction and an increase in its occupancy at target genes indicating that the mutant can be properly incorporated into chromatin. Collectively, our work suggests that the divergent residues in the H2A.Z acidic patch comprise a unique domain that couples control of chromatin dynamics to the regulation of developmental gene expression patterns during lineage commitment. |
| first_indexed | 2024-09-23T14:44:18Z |
| format | Article |
| id | mit-1721.1/81237 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T14:44:18Z |
| publishDate | 2013 |
| publisher | Public Library of Science |
| record_format | dspace |
| spelling | mit-1721.1/812372022-09-29T10:14:56Z H2A.Z Acidic Patch Couples Chromatin Dynamics to Regulation of Gene Expression Programs during ESC Differentiation Subramanian, Vidya Mazumder, Aprotim Fields, Paul A. Torrey, Lillian Levine, Stuart S. Bathe, Mark Surface, Lauren Elizabeth Alwan, Allison M. Thai, Kevin Kinh Boyer, Laurie Ann Butty, Vincent L G Massachusetts Institute of Technology. Department of Biological Engineering Massachusetts Institute of Technology. Department of Biology Massachusetts Institute of Technology. Laboratory for Computational Cell Biology & Biophysics Subramanian, Vidya Surface, Lauren Elizabeth Fields, Paul A. Alwan, Allison M. Thai, Kevin Kinh Boyer, Laurie Mazumder, Aprotim Levine, Stuart S. Butty, Vincent Bathe, Mark Torrey, Lillian The histone H2A variant H2A.Z is essential for embryonic development and for proper control of developmental gene expression programs in embryonic stem cells (ESCs). Divergent regions of amino acid sequence of H2A.Z likely determine its functional specialization compared to core histone H2A. For example, H2A.Z contains three divergent residues in the essential C-terminal acidic patch that reside on the surface of the histone octamer as an uninterrupted acidic patch domain; however, we know little about how these residues contribute to chromatin structure and function. Here, we show that the divergent amino acids Gly92, Asp97, and Ser98 in the H2A.Z C-terminal acidic patch (H2A.Z[superscript AP3]) are critical for lineage commitment during ESC differentiation. H2A.Z is enriched at most H3K4me3 promoters in ESCs including poised, bivalent promoters that harbor both activating and repressive marks, H3K4me3 and H3K27me3 respectively. We found that while H2A.Z[superscript AP3] interacted with its deposition complex and displayed a highly similar distribution pattern compared to wild-type H2A.Z, its enrichment levels were reduced at target promoters. Further analysis revealed that H2A.Z[superscript AP3] was less tightly associated with chromatin, suggesting that the mutant is more dynamic. Notably, bivalent genes in H2A.Z[superscript AP3] ESCs displayed significant changes in expression compared to active genes. Moreover, bivalent genes in H2A.Z[superscript AP3] ESCs gained H3.3, a variant associated with higher nucleosome turnover, compared to wild-type H2A.Z. We next performed single cell imaging to measure H2A.Z dynamics. We found that H2A.Z[superscript AP3] displayed higher mobility in chromatin compared to wild-type H2A.Z by fluorescent recovery after photobleaching (FRAP). Moreover, ESCs treated with the transcriptional inhibitor flavopiridol resulted in a decrease in the H2A.Z[superscript AP3] mobile fraction and an increase in its occupancy at target genes indicating that the mutant can be properly incorporated into chromatin. Collectively, our work suggests that the divergent residues in the H2A.Z acidic patch comprise a unique domain that couples control of chromatin dynamics to the regulation of developmental gene expression patterns during lineage commitment. Massachusetts Life Sciences Center (David H. Koch Institute for Integrative Cancer Research at MIT Core Grant P30-CA14051) National Science Foundation (U.S.). Emergent Behaviors of Integrated Cellular Systems (Grant CBET-0939511) MIT Faculty Start-up Fund Massachusetts Institute of Technology. Computational and Systems Biology Initiative (Merck & Co. Postdoctoral Fellowship) 2013-09-30T15:28:10Z 2013-09-30T15:28:10Z 2013-08 2013-01 Article http://purl.org/eprint/type/JournalArticle 1553-7404 1553-7390 http://hdl.handle.net/1721.1/81237 Subramanian, Vidya, Aprotim Mazumder, Lauren E. Surface, Vincent L. Butty, Paul A. Fields, Allison Alwan, Lillian Torrey, et al. “H2A.Z Acidic Patch Couples Chromatin Dynamics to Regulation of Gene Expression Programs during ESC Differentiation.” Edited by Hiten D. Madhani. PLoS Genetics 9, no. 8 (August 22, 2013): e1003725. https://orcid.org/0000-0002-9608-6464 https://orcid.org/0000-0002-2902-7288 https://orcid.org/0000-0002-6199-6855 https://orcid.org/0000-0003-3491-4962 en_US http://dx.doi.org/10.1371/journal.pgen.1003725 PLoS Genetics Creative Commons Attribution http://creativecommons.org/licenses/by/2.5/ application/pdf Public Library of Science PLoS |
| spellingShingle | Subramanian, Vidya Mazumder, Aprotim Fields, Paul A. Torrey, Lillian Levine, Stuart S. Bathe, Mark Surface, Lauren Elizabeth Alwan, Allison M. Thai, Kevin Kinh Boyer, Laurie Ann Butty, Vincent L G H2A.Z Acidic Patch Couples Chromatin Dynamics to Regulation of Gene Expression Programs during ESC Differentiation |
| title | H2A.Z Acidic Patch Couples Chromatin Dynamics to Regulation of Gene Expression Programs during ESC Differentiation |
| title_full | H2A.Z Acidic Patch Couples Chromatin Dynamics to Regulation of Gene Expression Programs during ESC Differentiation |
| title_fullStr | H2A.Z Acidic Patch Couples Chromatin Dynamics to Regulation of Gene Expression Programs during ESC Differentiation |
| title_full_unstemmed | H2A.Z Acidic Patch Couples Chromatin Dynamics to Regulation of Gene Expression Programs during ESC Differentiation |
| title_short | H2A.Z Acidic Patch Couples Chromatin Dynamics to Regulation of Gene Expression Programs during ESC Differentiation |
| title_sort | h2a z acidic patch couples chromatin dynamics to regulation of gene expression programs during esc differentiation |
| url | http://hdl.handle.net/1721.1/81237 https://orcid.org/0000-0002-9608-6464 https://orcid.org/0000-0002-2902-7288 https://orcid.org/0000-0002-6199-6855 https://orcid.org/0000-0003-3491-4962 |
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