Integrating ChIP-seq with other functional genomics data

Shan Jiang, Ali Mortazavi
<span title="2018-03-01">2018</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="" style="color: black;">Briefings in Functional Genomics</a> </i> &nbsp;
Transcription is regulated by transcription factor (TF) binding at promoters and distal regulatory elements and histone modifications that control the accessibility of these elements. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become the standard assay for identifying genome-wide protein-DNA interactions in vitro and in vivo. As large-scale ChIPseq data sets have been collected for different TFs and histone modifications, their potential to predict gene expression can
more &raquo; ... used to test hypotheses about the mechanisms of gene regulation. In addition, complementary functional genomics assays provide a global view of chromatin accessibility and long-range cis-regulatory interactions that are being combined with TF binding and histone remodeling to study the regulation of gene expression. Thus, ChIP-seq analysis is now widely integrated with other functional genomics assays to better understand gene regulatory mechanisms. In this review, we discuss advances and challenges in integrating ChIP-seq data to identify context-specific chromatin states associated with gene activity. We describe the overall computational design of integrating ChIP-seq data with other functional genomics assays. We also discuss the challenges of extending these methods to low-input ChIP-seq assays and related single-cell assays.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="">doi:10.1093/bfgp/ely002</a> <a target="_blank" rel="external noopener" href="">pmid:29579165</a> <a target="_blank" rel="external noopener" href="">fatcat:zbfaimtxrvdyvmigeepu5o4cuq</a> </span>
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