Mapping Dmef2-Binding Regulatory Modules by Using a ChIP-Enriched in Silico Targets Approach

Mapping the regulatory modules to which transcription factors bind in vivo is a key step toward understanding of global gene expression programs. We have developed a chromatin immunoprecipitation (ChIP)-chip strategy for identifying factor-specific regulatory regions acting in vivo. This method, cal...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2005-12, Vol.102 (51), p.18479-18484
Main Authors: Guillaume Junion, Teresa Jagla, Sebastien Duplant, Romain Tapin, Da Ponte, Jean-Philippe, Jagla, Krzysztof, Olson, Eric N.
Format: Article
Language:English
Subjects:
Animals
Biological Sciences
Chromatin Immunoprecipitation
Computational Biology
DNA
Drosophila
Drosophila melanogaster - genetics
Drosophila melanogaster - metabolism
Embryos
Gene expression
Gene Expression Regulation, Developmental
Genes
Genome
Genomes
Genomics
Insects
Introns
MEF2 Transcription Factors
Muscle development
Muscular system
Myogenic Regulatory Factors - genetics
Myogenic Regulatory Factors - metabolism
Protein Binding
Transcription factors
Transcriptional regulatory elements
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Summary:Mapping the regulatory modules to which transcription factors bind in vivo is a key step toward understanding of global gene expression programs. We have developed a chromatin immunoprecipitation (ChIP)-chip strategy for identifying factor-specific regulatory regions acting in vivo. This method, called the ChIP-enriched in silico targets (ChEST) approach, combines immunoprecipitation of cross-linked protein-DNA complexes (X-ChIP) with in silico prediction of targets and generation of computed DNA microarrays. We report the use of ChEST in Drosophila to identify several previously unknown targets of myocyte enhancer factor 2 (MEF2), a key regulator of myogenic differentiation. Our approach was validated by demonstrating that the identified sequences act as enhancers in vivo and are able to drive reporter gene expression specifically in MEF2-positive muscle cells. Presented here, the ChEST strategy was originally designed to identify regulatory modules in Drosophila, but it can be adapted for any sequenced and annotated genome.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0507030102