Analyzing Transcription Factor Occupancy During Embryo Development Using ChIP-seq

Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 786)

Abstract

Accurately assessing the binding of transcription factors to cis-regulatory elements in vivo is an essential step toward understanding the mechanisms that govern embryonic development. Genome-wide transcription factor location analysis has been facilitated by the development of high-density tiling arrays (ChIP-on-chip), and more recently by next-generation sequencing technologies, which are used to sequence the DNA fragments obtained from chromatin immunoprecipitation experiments (ChIP-seq). This chapter provides a detailed protocol of the different steps required to generate a successful ChIP-seq library, starting from embryo collection and fixation to chromatin preparation, immunoprecipitation, and finally library preparation. The protocol is optimized for Drosophila embryos, but can be adapted to any organism. The obtained library is suitable for sequencing on an Illumina GAIIx platform.

Key words

Drosophila Transcription Development Chromatin immunoprecipitation ChIP-seq Next-generation sequencing 

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Genome Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany

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