ChIP-Enriched in Silico Targets (ChEST), a ChIP-on-Chip Approach Applied to Analyzing Skeletal Muscle Genes

• DOI: 10.1007/978-1-61779-343-1_33
• Publication Date: 2011-12-02T06:27:47Z
• Authors: Guillaume Junion; Krzysztof Jagla
• Keywords: 0301 basic medicine; 0303 health sciences; Chromatin Immunoprecipitation; Embryo, Nonmammalian; Gene Expression Profiling; Computational Biology; Gene Expression Regulation, Developmental; Nucleic Acid Hybridization; Regulatory Sequences, Nucleic Acid; 03 medical and health sciences; Enhancer Elements, Genetic; Animals; Drosophila; DNA Probes; Muscle, Skeletal; Nucleic Acid Amplification Techniques; Oligonucleotide Array Sequence Analysis

Mapping the cis-regulatory modules (CRMs) to which bind myogenic transcription factors is an -obligatory step towards understanding gene regulatory networks governing muscle development and function. This can be achieved in silico or by chromatin immunoprecipitation (ChIP) approaches. We have developed a ChIP-enriched in silico targets (ChEST) strategy designed for mapping the CRMs by combining in silico and ChIP methods. ChEST involves a software-assisted prediction of transcription factor (TF) - specific CRMs, which are spotted to produce a computed genomic CRM microarray. In parallel, the in vivo pool of targets of a given TF is isolated by ChIP and used as a probe for hybridization with the array generated. Here we describe ChEST strategy applied to identify direct targets of Myogenic Enhancer Factor, Dmef2 in Drosophila embryos.