Differential association of chromatin proteins identifies BAF60a/SMARCD1 as a regulator of embryonic stem cell differentiation
Embryonic stem cells (ESCs) possess a distinct chromatin conformation maintained by specialized chromatin proteins. To identify chromatin regulators in ESCs, we developed a simple biochemical assay named D-CAP (differential chromatin-associated proteins), using brief micrococcal nuclease digestion o...
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sg-ntu-dr.10356-1072892023-02-28T17:05:08Z Differential association of chromatin proteins identifies BAF60a/SMARCD1 as a regulator of embryonic stem cell differentiation Alajem, Adi Biran, Alva Harikumar, Arigela Sailaja, Badi Sri Aaronson, Yair Livyatan, Ilana Nissim-Rafinia, Malka Sommer, Andreia Gianotti Mostoslavsky, Gustavo Gerbasi, Vincent R. Golden, Daniel E. Datta, Arnab Sze, Siu Kwan Meshorer, Eran School of Biological Sciences DRNTU::Science::Biological sciences Embryonic stem cells (ESCs) possess a distinct chromatin conformation maintained by specialized chromatin proteins. To identify chromatin regulators in ESCs, we developed a simple biochemical assay named D-CAP (differential chromatin-associated proteins), using brief micrococcal nuclease digestion of chromatin, followed by liquid chromatography tandem mass spectrometry (LC-MS/MS). Using D-CAP, we identified several differentially chromatin-associated proteins between undifferentiated and differentiated ESCs, including the chromatin remodeling protein SMARCD1. SMARCD1 depletion in ESCs led to altered chromatin and enhanced endodermal differentiation. Gene expression and chromatin immunoprecipitation sequencing (ChIP-seq) analyses suggested that SMARCD1 is both an activator and a repressor and is enriched at developmental regulators and that its chromatin binding coincides with H3K27me3. SMARCD1 knockdown caused H3K27me3 redistribution and increased H3K4me3 around the transcription start site (TSS). One of the identified SMARCD1 targets was Klf4. In SMARCD1-knockdown clones, KLF4, as well as H3K4me3 at the Klf4 locus, remained high and H3K27me3 was abolished. These results propose a role for SMARCD1 in restricting pluripotency and activating lineage pathways by regulating H3K27 methylation. Published version 2015-04-22T08:58:26Z 2019-12-06T22:28:09Z 2015-04-22T08:58:26Z 2019-12-06T22:28:09Z 2015 2015 Journal Article Alajem, A., Biran, A., Harikumar, A., Sailaja, B., Aaronson, Y., Livyatan, I., et al. (2015). Differential association of chromatin proteins identifies BAF60a/SMARCD1 as a regulator of embryonic stem cell differentiation. Cell reports, 10(12), 2019-2031. 2211-1247 https://hdl.handle.net/10356/107289 http://hdl.handle.net/10220/25451 10.1016/j.celrep.2015.02.064 en Cell reports © 2015 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/). 14 p. application/pdf |
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DRNTU::Science::Biological sciences Alajem, Adi Biran, Alva Harikumar, Arigela Sailaja, Badi Sri Aaronson, Yair Livyatan, Ilana Nissim-Rafinia, Malka Sommer, Andreia Gianotti Mostoslavsky, Gustavo Gerbasi, Vincent R. Golden, Daniel E. Datta, Arnab Sze, Siu Kwan Meshorer, Eran Differential association of chromatin proteins identifies BAF60a/SMARCD1 as a regulator of embryonic stem cell differentiation |
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Embryonic stem cells (ESCs) possess a distinct chromatin conformation maintained by specialized chromatin proteins. To identify chromatin regulators in ESCs, we developed a simple biochemical assay named D-CAP (differential chromatin-associated proteins), using brief micrococcal nuclease digestion of chromatin, followed by liquid chromatography tandem mass spectrometry (LC-MS/MS). Using D-CAP, we identified several differentially chromatin-associated proteins between undifferentiated and differentiated ESCs, including the chromatin remodeling protein SMARCD1. SMARCD1 depletion in ESCs led to altered chromatin and enhanced endodermal differentiation. Gene expression and chromatin immunoprecipitation sequencing (ChIP-seq) analyses suggested that SMARCD1 is both an activator and a repressor and is enriched at developmental regulators and that its chromatin binding coincides with H3K27me3. SMARCD1 knockdown caused H3K27me3 redistribution and increased H3K4me3 around the transcription start site (TSS). One of the identified SMARCD1 targets was Klf4. In SMARCD1-knockdown clones, KLF4, as well as H3K4me3 at the Klf4 locus, remained high and H3K27me3 was abolished. These results propose a role for SMARCD1 in restricting pluripotency and activating lineage pathways by regulating H3K27 methylation. |
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School of Biological Sciences |
author_facet |
School of Biological Sciences Alajem, Adi Biran, Alva Harikumar, Arigela Sailaja, Badi Sri Aaronson, Yair Livyatan, Ilana Nissim-Rafinia, Malka Sommer, Andreia Gianotti Mostoslavsky, Gustavo Gerbasi, Vincent R. Golden, Daniel E. Datta, Arnab Sze, Siu Kwan Meshorer, Eran |
format |
Article |
author |
Alajem, Adi Biran, Alva Harikumar, Arigela Sailaja, Badi Sri Aaronson, Yair Livyatan, Ilana Nissim-Rafinia, Malka Sommer, Andreia Gianotti Mostoslavsky, Gustavo Gerbasi, Vincent R. Golden, Daniel E. Datta, Arnab Sze, Siu Kwan Meshorer, Eran |
author_sort |
Alajem, Adi |
title |
Differential association of chromatin proteins identifies BAF60a/SMARCD1 as a regulator of embryonic stem cell differentiation |
title_short |
Differential association of chromatin proteins identifies BAF60a/SMARCD1 as a regulator of embryonic stem cell differentiation |
title_full |
Differential association of chromatin proteins identifies BAF60a/SMARCD1 as a regulator of embryonic stem cell differentiation |
title_fullStr |
Differential association of chromatin proteins identifies BAF60a/SMARCD1 as a regulator of embryonic stem cell differentiation |
title_full_unstemmed |
Differential association of chromatin proteins identifies BAF60a/SMARCD1 as a regulator of embryonic stem cell differentiation |
title_sort |
differential association of chromatin proteins identifies baf60a/smarcd1 as a regulator of embryonic stem cell differentiation |
publishDate |
2015 |
url |
https://hdl.handle.net/10356/107289 http://hdl.handle.net/10220/25451 |
_version_ |
1759857552147873792 |