Systematic Discovery of Chromatin-Bound Protein Complexes from ChIP-seq Datasets.
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.
Biological Sciences Department, New York City College of Technology, City University of New York, New York, NY, USA. egiannopoulou@citytech.cuny.edu.|Arthritis and Tissue Degeneration Program and the David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA. egiannopoulou@citytech.cuny.edu.
Eugenia
E
Giannopoulou
HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine and Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA.
Olivier
O
Elemento
D002460:Cell Line; D047369:Chromatin Immunoprecipitation; D003198:Computer Simulation; D004268:DNA-Binding Proteins / Q000302:isolation & purification*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D046912:Multiprotein Complexes / Q000302:isolation & purification; D025941:Protein Interaction Mapping; D012044:Regression Analysis; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000302:isolation & purification
D004268:DNA-Binding Proteins; D046912:Multiprotein Complexes; D014157:Transcription Factors
ChIP-seq; Combinatorial transcription factor binding; ENCODE datasets; Protein complexes; Protein-protein interactions; RNA-seq