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A pipeline for the identification and characterization of chromatin modifications derived from ChIP-Seq datasets

journal contribution
posted on 2012-11-01, 00:00 authored by Antony Kaspi, Mark Ziemann, Haloom Rafehi, Ross Lazarus, Assam El-Osta
The advent of massive parallel sequencing of immunopurified chromatin and its determinants has provided new avenues for researchers to map epigenome-wide changes and there is tremendous interest to uncover regulatory signatures to understand fundamental questions associated with chromatin structure and function. Indeed, the rapid development of large genome annotation projects has seen a resurgence in chromatin immunoprecipitation (ChIP) based protocols which are used to distinguish protein interactions coupled with large scale sequencing (Seq) to precisely map epigenome-wide interactions. Despite some of the great advances in our understanding of chromatin modifying complexes and their determinants, the development of ChIP-Seq technologies also pose specific demands on the integration of data for visualization, manipulation and analysis. In this article we discuss some of the considerations for experimental design planning, quality control, and bioinformatic analysis. The key aspects of post sequencing analysis are the identification of regions of interest, differentiation between biological conditions and the characterization of sequence differences for chromatin modifications. We provide an overview of best-practise approaches with background information and considerations of integrative analysis from ChIP-Seq experiments.

History

Journal

Biochimie

Volume

94

Issue

11

Pagination

2353 - 2359

Publisher

Elsevier

Location

Amsterdam, The Netherlands

eISSN

1638-6183

Language

eng

Publication classification

C1.1 Refereed article in a scholarly journal; C Journal article

Copyright notice

2012, Elsevier Masson SAS