Systematic Discovery of Chromatin-Bound Protein Complexes from ChIP-seq Datasets.

TitleSystematic Discovery of Chromatin-Bound Protein Complexes from ChIP-seq Datasets.
Publication TypeJournal Article
Year of Publication2017
AuthorsGiannopoulou E, Elemento O
JournalMethods Mol Biol
Date Published2017
KeywordsCell Line, Chromatin Immunoprecipitation, Computer Simulation, DNA-Binding Proteins, High-Throughput Nucleotide Sequencing, Humans, Multiprotein Complexes, Protein Interaction Mapping, Regression Analysis, Sequence Analysis, DNA, Transcription Factors

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.

Alternate JournalMethods Mol. Biol.
PubMed ID27832531
Grant ListR01 CA194547 / CA / NCI NIH HHS / United States