Systematic identification of gene family regulators in mouse and human embryonic stem cells.
Nucleic Acids Res
; 44(9): 4080-9, 2016 05 19.
Article
em En
| MEDLINE
| ID: mdl-27084933
ABSTRACT
Pluripotent self-renewing embryonic stem cells (ESCs) have been the focus of a growing number of high-throughput experiments, revealing the genome-wide locations of hundreds of transcription factors and histone modifications. While most of these datasets were used in a specific context, all datasets combined offer a comprehensive view of chromatin characteristics and regulatory elements that govern cell states. Here, using hundreds of datasets in ESCs, we generated colocalization maps of chromatin proteins and modifications, and built a discovery pipeline for regulatory proteins of gene families. By comparing genome-wide binding data with over-expression and knockdown analysis of hundreds of genes, we discovered that the pluripotency-related factor NR5A2 separates mitochondrial from cytosolic ribosomal genes, regulating their expression. We further show that genes with a common chromatin profile are enriched for distinct Gene Ontology (GO) categories. Our approach can be generalized to reveal common regulators of any gene group; discover novel gene families, and identify common genomic elements based on shared chromatin features.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Cromatina
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Receptores Citoplasmáticos e Nucleares
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Células-Tronco Embrionárias Humanas
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Células-Tronco Embrionárias Murinas
Tipo de estudo:
Diagnostic_studies
/
Prognostic_studies
Limite:
Animals
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Humans
Idioma:
En
Ano de publicação:
2016
Tipo de documento:
Article