Chapter title |
Eukaryotic Transcriptional and Post-Transcriptional Gene Expression Regulation
|
---|---|
Chapter number | 4 |
Book title |
Eukaryotic Transcriptional and Post-Transcriptional Gene Expression Regulation
|
Published in |
Methods in molecular biology, January 2017
|
DOI | 10.1007/978-1-4939-6518-2_4 |
Pubmed ID | |
Book ISBNs |
978-1-4939-6516-8, 978-1-4939-6518-2
|
Authors |
Giannopoulou, Eugenia, Elemento, Olivier, Eugenia Giannopoulou, Olivier Elemento |
Editors |
Narendra Wajapeyee, Romi Gupta |
Abstract |
Chromatin immunoprecipitation followed by sequencing is an invaluable assay for identifying the genomic binding sites of transcription factors. However, transcription factors rarely bind chromatin alone but often bind together with other cofactors, forming protein complexes. Here, we describe a computational method that integrates multiple ChIP-seq and RNA-seq datasets to discover protein complexes and determine their role as activators or repressors. This chapter outlines a detailed computational pipeline for discovering and predicting binding partners from ChIP-seq data and inferring their role in regulating gene expression. This work aims at developing hypotheses about gene regulation via binding partners and deciphering the combinatorial nature of DNA-binding proteins. |
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