Open AccessProteomic analyses reveal distinct chromatin‐associated and soluble transcription factor complexes
Author(s) -
Li Xu,
Wang Wenqi,
Wang Jiadong,
Malovannaya Anna,
Xi Yuanxin,
Li Wei,
Guerra Rudy,
Hawke David H,
Qin Jun,
Chen Junjie
Publication year - 2015
Publication title -
molecular systems biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 8.523
H-Index - 148
ISSN - 1744-4292
DOI - 10.15252/msb.20145504
Subject(s) - biology , transcription factor , chromatin , genetics , computational biology , transcription (linguistics) , evolutionary biology , dna , gene , linguistics , philosophy
The current knowledge on how transcription factors ( TF s), 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 TF s, 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 TF s 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 TF s. Our study offers a valuable resource of protein–protein interaction networks for a large number of TF s and underscores the general principle that TF s form distinct location‐specific protein complexes that are associated with the different regulation and diverse functions of these TF s.