CAST-ChIP Maps Cell-Type-Specific Chromatin States in the Drosophila Central Nervous System
Chromatin organization and gene activity are responsive to developmental and environmental cues. Although many genes are transcribed throughout development and across cell types, much of gene regulation is highly cell-type specific. To readily track chromatin features at the resolution of cell types...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2013-10-01
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| Series: | Cell Reports |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2211124713004993 |
| _version_ | 1828413452918456320 |
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| author | Tamás Schauer Petra C. Schwalie Ava Handley Carla E. Margulies Paul Flicek Andreas G. Ladurner |
| author_facet | Tamás Schauer Petra C. Schwalie Ava Handley Carla E. Margulies Paul Flicek Andreas G. Ladurner |
| author_sort | Tamás Schauer |
| collection | DOAJ |
| description | Chromatin organization and gene activity are responsive to developmental and environmental cues. Although many genes are transcribed throughout development and across cell types, much of gene regulation is highly cell-type specific. To readily track chromatin features at the resolution of cell types within complex tissues, we developed and validated chromatin affinity purification from specific cell types by chromatin immunoprecipitation (CAST-ChIP), a broadly applicable biochemical procedure. RNA polymerase II (Pol II) CAST-ChIP identifies ∼1,500 neuronal and glia-specific genes in differentiated cells within the adult Drosophila brain. In contrast, the histone H2A.Z is distributed similarly across cell types and throughout development, marking cell-type-invariant Pol II-bound regions. Our study identifies H2A.Z as an active chromatin signature that is refractory to changes across cell fates. Thus, CAST-ChIP powerfully identifies cell-type-specific as well as cell-type-invariant chromatin states, enabling the systematic dissection of chromatin structure and gene regulation within complex tissues such as the brain. |
| first_indexed | 2024-12-10T13:09:07Z |
| format | Article |
| id | doaj.art-623e9b38cd34431eb0eea0a3706e3b28 |
| institution | Directory Open Access Journal |
| issn | 2211-1247 |
| language | English |
| last_indexed | 2024-12-10T13:09:07Z |
| publishDate | 2013-10-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Cell Reports |
| spelling | doaj.art-623e9b38cd34431eb0eea0a3706e3b282022-12-22T01:47:44ZengElsevierCell Reports2211-12472013-10-015127128210.1016/j.celrep.2013.09.001CAST-ChIP Maps Cell-Type-Specific Chromatin States in the Drosophila Central Nervous SystemTamás Schauer0Petra C. Schwalie1Ava Handley2Carla E. Margulies3Paul Flicek4Andreas G. Ladurner5Department of Physiological Chemistry, Butenandt Institute and LMU Biomedical Center, Ludwig Maximilians University of Munich, Butenandtstrasse 5, 81377 Munich, GermanyEuropean Molecular Biology Laboratory International PhD Program, Meyerhofstrasse 1, 69117 Heidelberg, GermanyDepartment of Physiological Chemistry, Butenandt Institute and LMU Biomedical Center, Ludwig Maximilians University of Munich, Butenandtstrasse 5, 81377 Munich, GermanyDepartment of Physiological Chemistry, Butenandt Institute and LMU Biomedical Center, Ludwig Maximilians University of Munich, Butenandtstrasse 5, 81377 Munich, GermanyEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UKDepartment of Physiological Chemistry, Butenandt Institute and LMU Biomedical Center, Ludwig Maximilians University of Munich, Butenandtstrasse 5, 81377 Munich, GermanyChromatin organization and gene activity are responsive to developmental and environmental cues. Although many genes are transcribed throughout development and across cell types, much of gene regulation is highly cell-type specific. To readily track chromatin features at the resolution of cell types within complex tissues, we developed and validated chromatin affinity purification from specific cell types by chromatin immunoprecipitation (CAST-ChIP), a broadly applicable biochemical procedure. RNA polymerase II (Pol II) CAST-ChIP identifies ∼1,500 neuronal and glia-specific genes in differentiated cells within the adult Drosophila brain. In contrast, the histone H2A.Z is distributed similarly across cell types and throughout development, marking cell-type-invariant Pol II-bound regions. Our study identifies H2A.Z as an active chromatin signature that is refractory to changes across cell fates. Thus, CAST-ChIP powerfully identifies cell-type-specific as well as cell-type-invariant chromatin states, enabling the systematic dissection of chromatin structure and gene regulation within complex tissues such as the brain.http://www.sciencedirect.com/science/article/pii/S2211124713004993 |
| spellingShingle | Tamás Schauer Petra C. Schwalie Ava Handley Carla E. Margulies Paul Flicek Andreas G. Ladurner CAST-ChIP Maps Cell-Type-Specific Chromatin States in the Drosophila Central Nervous System Cell Reports |
| title | CAST-ChIP Maps Cell-Type-Specific Chromatin States in the Drosophila Central Nervous System |
| title_full | CAST-ChIP Maps Cell-Type-Specific Chromatin States in the Drosophila Central Nervous System |
| title_fullStr | CAST-ChIP Maps Cell-Type-Specific Chromatin States in the Drosophila Central Nervous System |
| title_full_unstemmed | CAST-ChIP Maps Cell-Type-Specific Chromatin States in the Drosophila Central Nervous System |
| title_short | CAST-ChIP Maps Cell-Type-Specific Chromatin States in the Drosophila Central Nervous System |
| title_sort | cast chip maps cell type specific chromatin states in the drosophila central nervous system |
| url | http://www.sciencedirect.com/science/article/pii/S2211124713004993 |
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