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
Affiliations
Adi Alajem
Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
Alva Biran
Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
Arigela Harikumar
Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
Badi Sri Sailaja
Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
Yair Aaronson
Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
Ilana Livyatan
Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
Malka Nissim-Rafinia
Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
Andreia Gianotti Sommer
Section of Gastroenterology, Department of Medicine, Center for Regenerative Medicine (CReM), Boston University School of Medicine, 670 Albany Street, Suite 209, Boston, MA 02118, USA
Gustavo Mostoslavsky
Section of Gastroenterology, Department of Medicine, Center for Regenerative Medicine (CReM), Boston University School of Medicine, 670 Albany Street, Suite 209, Boston, MA 02118, USA
Vincent R. Gerbasi
Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
Daniel E. Golden
Merial Inc., a Sanofi Company, Duluth, GA 30096, USA
Arnab Datta
School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
Siu Kwan Sze
School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
Eran Meshorer
Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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.
