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Epigenetic Analysis: ChIP-chip and ChIP-seq

  • Matteo PellegriniEmail author
  • Roberto Ferrari
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 802)

Abstract

The access of transcription factors and the replication machinery to DNA is regulated by the epigenetic state of chromatin. In eukaryotes, this complex layer of regulatory processes includes the direct methylation of DNA, as well as covalent modifications to histones. Using next-generation sequencers, it is now possible to obtain profiles of epigenetic modifications across a genome using chromatin immunoprecipitation followed by sequencing (ChIP-seq). This technique permits the detection of the binding of proteins to specific regions of the genome with high resolution. It can be used to determine the target sequences of transcription factors, as well as the positions of histones with specific modification of their N-terminal tails. Antibodies that selectively bind methylated DNA may also be used to determine the position of methylated cytosines. Here, we present a data analysis pipeline for processing ChIP-seq data, and discuss the limitations and idiosyncrasies of these approaches.

Key words

ChIP-seq Chromatin immunoprecipitation Transcription factor binding sites Peak calling Histone modification DNA methylation Next-generation sequencing Poisson statistics 

Notes

Acknowledgments

The authors would like to thank Professor Bernard L. Mirkin for development of the drug-resistant models of human neuroblastoma cells and for his advice and encouragement, and Jesse Moya for technical assistance. This work was supported by Broad Stem Cell Research Center and Institute of Genomics and Proteomics at UCLA.

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Department of Molecular, Cell and DevelopmentalUniversity of CaliforniaLos AngelesUSA
  2. 2.Department of Biological ChemistryUniversity of CaliforniaLos AngelesUSA

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