Differential association of chromatin proteins identifies BAF60a/SMARCD1 as a regulator of embryonic stem cell differentiation

Adi Alajem; Alva Biran; Arigela Harikumar; Badi Sri Sailaja; Yair Aaronson; Ilana Livyatan; Malka Nissim-Rafinia; Andreia Gianotti Sommer; Gustavo Mostoslavsky; Vincent R. Gerbasi; Daniel E. Golden; Arnab Datta; Siu Kwan Sze; Eran Meshorer

doi:10.1016/j.celrep.2015.02.064

Differential association of chromatin proteins identifies BAF60a/SMARCD1 as a regulator of embryonic stem cell differentiation

Adi Alajem, Alva Biran, Arigela Harikumar, Badi Sri Sailaja, Yair Aaronson, Ilana Livyatan, Malka Nissim-Rafinia, Andreia Gianotti Sommer, Gustavo Mostoslavsky, Vincent R. Gerbasi, Daniel E. Golden, Arnab Datta, Siu Kwan Sze, Eran Meshorer^*

^*Corresponding author for this work

PCE - Proteomics Center of Excellence

Research output: Contribution to journal › Article › peer-review

44 Scopus citations

Abstract

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 arepressor and is enriched at developmental regulators and that its chromatin binding coincides withH3K27me3. 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.

Original language	English (US)
Pages (from-to)	2019-2031
Number of pages	13
Journal	Cell reports
Volume	10
Issue number	12
DOIs	https://doi.org/10.1016/j.celrep.2015.02.064
State	Published - Mar 31 2015

Funding

We thank Amichay Afriat and Tal Cohen for help with experiments, Shai Melcer for helpful discussions, and Abed A. Mansour and Jacob Hanna for kindly providing reagents. Microarray hybridization and high-throughput sequencing was carried out at The Center for Genomic Technologies, Institute of Life Sciences, The Hebrew University. This work was supported by the Israel Science Foundation (ISF 1252/12 and 657/12 to E.M.); the Israel Ministry of Science (E.M.), and the European Research Council (ERC-281781 to E.M.). A.B. is a Clore Fellow.

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology

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10.1016/j.celrep.2015.02.064

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Alajem, A., Biran, A., Harikumar, A., Sailaja, B. S., Aaronson, Y., Livyatan, I., Nissim-Rafinia, M., Sommer, A. G., Mostoslavsky, G., Gerbasi, V. R., Golden, D. E., Datta, A., Sze, S. K., & Meshorer, E. (2015). Differential association of chromatin proteins identifies BAF60a/SMARCD1 as a regulator of embryonic stem cell differentiation. Cell reports, 10(12), 2019-2031. https://doi.org/10.1016/j.celrep.2015.02.064

@article{7afe7462c8554ffd9ed3e395fce9ada5,

title = "Differential association of chromatin proteins identifies BAF60a/SMARCD1 as a regulator of embryonic stem cell differentiation",

abstract = "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 arepressor and is enriched at developmental regulators and that its chromatin binding coincides withH3K27me3. 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.",

author = "Adi Alajem and Alva Biran and Arigela Harikumar and Sailaja, {Badi Sri} and Yair Aaronson and Ilana Livyatan and Malka Nissim-Rafinia and Sommer, {Andreia Gianotti} and Gustavo Mostoslavsky and Gerbasi, {Vincent R.} and Golden, {Daniel E.} and Arnab Datta and Sze, {Siu Kwan} and Eran Meshorer",

note = "Funding Information: We thank Amichay Afriat and Tal Cohen for help with experiments, Shai Melcer for helpful discussions, and Abed A. Mansour and Jacob Hanna for kindly providing reagents. Microarray hybridization and high-throughput sequencing was carried out at The Center for Genomic Technologies, Institute of Life Sciences, The Hebrew University. This work was supported by the Israel Science Foundation (ISF 1252/12 and 657/12 to E.M.); the Israel Ministry of Science (E.M.), and the European Research Council (ERC-281781 to E.M.). A.B. is a Clore Fellow. Publisher Copyright: {\textcopyright} 2015 The Authors.",

year = "2015",

month = mar,

day = "31",

doi = "10.1016/j.celrep.2015.02.064",

language = "English (US)",

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Alajem, A, Biran, A, Harikumar, A, Sailaja, BS, Aaronson, Y, Livyatan, I, Nissim-Rafinia, M, Sommer, AG, Mostoslavsky, G, Gerbasi, VR, Golden, DE, Datta, A, Sze, SK & Meshorer, E 2015, 'Differential association of chromatin proteins identifies BAF60a/SMARCD1 as a regulator of embryonic stem cell differentiation', Cell reports, vol. 10, no. 12, pp. 2019-2031. https://doi.org/10.1016/j.celrep.2015.02.064

TY - JOUR

T1 - Differential association of chromatin proteins identifies BAF60a/SMARCD1 as a regulator of embryonic stem cell differentiation

AU - Alajem, Adi

AU - Biran, Alva

AU - Harikumar, Arigela

AU - Sailaja, Badi Sri

AU - Aaronson, Yair

AU - Livyatan, Ilana

AU - Nissim-Rafinia, Malka

AU - Sommer, Andreia Gianotti

AU - Mostoslavsky, Gustavo

AU - Gerbasi, Vincent R.

AU - Golden, Daniel E.

AU - Datta, Arnab

AU - Sze, Siu Kwan

AU - Meshorer, Eran

N1 - Funding Information: We thank Amichay Afriat and Tal Cohen for help with experiments, Shai Melcer for helpful discussions, and Abed A. Mansour and Jacob Hanna for kindly providing reagents. Microarray hybridization and high-throughput sequencing was carried out at The Center for Genomic Technologies, Institute of Life Sciences, The Hebrew University. This work was supported by the Israel Science Foundation (ISF 1252/12 and 657/12 to E.M.); the Israel Ministry of Science (E.M.), and the European Research Council (ERC-281781 to E.M.). A.B. is a Clore Fellow. Publisher Copyright: © 2015 The Authors.

PY - 2015/3/31

Y1 - 2015/3/31

N2 - 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 arepressor and is enriched at developmental regulators and that its chromatin binding coincides withH3K27me3. 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.

AB - 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 arepressor and is enriched at developmental regulators and that its chromatin binding coincides withH3K27me3. 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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AN - SCOPUS:84925946317

SN - 2211-1247

VL - 10

SP - 2019

EP - 2031

JO - Cell reports

JF - Cell reports

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ER -

Differential association of chromatin proteins identifies BAF60a/SMARCD1 as a regulator of embryonic stem cell differentiation

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