title: Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes.
abstract: The current knowledge on how transcription factors (TFs), the ultimate targets and executors of cellular signalling pathways, are regulated by protein-protein interactions remains limited. Here, we performed proteomics analyses of soluble and chromatin-associated complexes of 56 TFs, including the targets of many signalling pathways involved in development and cancer, and 37 members of the Forkhead box (FOX) TF family. Using tandem affinity purification followed by mass spectrometry (TAP/MS), we performed 214 purifications and identified 2,156 high-confident protein-protein interactions. We found that most TFs form very distinct protein complexes on and off chromatin. Using this data set, we categorized the transcription-related or unrelated regulators for general or specific TFs. Our study offers a valuable resource of protein-protein interaction networks for a large number of TFs and underscores the general principle that TFs form distinct location-specific protein complexes that are associated with the different regulation and diverse functions of these TFs.
authors.affiliation: Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
authors.forename: Xu
authors.initials: X
authors.lastname: Li
authors.affiliation: Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
authors.forename: Wenqi
authors.initials: W
authors.lastname: Wang
authors.affiliation: Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
authors.forename: Jiadong
authors.initials: J
authors.lastname: Wang
authors.affiliation: Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Anna
authors.initials: A
authors.lastname: Malovannaya
authors.affiliation: Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Yuanxin
authors.initials: Y
authors.lastname: Xi
authors.affiliation: Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Li
authors.affiliation: Department of Statistics, Rice University, Houston, TX, USA.
authors.forename: Rudy
authors.initials: R
authors.lastname: Guerra
authors.affiliation: Proteomics Facility, Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
authors.forename: David H
authors.initials: DH
authors.lastname: Hawke
authors.affiliation: Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.
authors.forename: Jun
authors.initials: J
authors.lastname: Qin
authors.affiliation: Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA jchen8@mdanderson.org.
authors.forename: Junjie
authors.initials: J
authors.lastname: Chen
mesh_terms: D002843:Chromatin / Q000235:genetics / Q000378:metabolism*; D019295:Computational Biology; D030541:Databases, Genetic; D057809:HEK293 Cells; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D054730:Protein Interaction Domains and Motifs; D040901:Proteomics / Q000379:methods*; D034741:RNA, Small Interfering / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D053719:Tandem Mass Spectrometry; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D014162:Transfection
chemical_list: D002843:Chromatin; D034741:RNA, Small Interfering; D014157:Transcription Factors
keywords: forkhead box; mass spectrometry; protein–protein interaction; transcriptional factor