Human transcription factor protein interaction networks

Helka Göös, Matias Kinnunen, Kari Salokas, Zenglai Tan, Xiaonan Liu, Leena Yadav, Qin Zhang, Gong-Hong Wei and Markku Varjosalo ()
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Helka Göös: Institute of Biotechnology, HiLIFE, University of Helsinki
Matias Kinnunen: Institute of Biotechnology, HiLIFE, University of Helsinki
Kari Salokas: Institute of Biotechnology, HiLIFE, University of Helsinki
Zenglai Tan: Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu
Xiaonan Liu: Institute of Biotechnology, HiLIFE, University of Helsinki
Leena Yadav: Institute of Biotechnology, HiLIFE, University of Helsinki
Qin Zhang: Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu
Gong-Hong Wei: Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu
Markku Varjosalo: Institute of Biotechnology, HiLIFE, University of Helsinki

Nature Communications, 2022, vol. 13, issue 1, 1-16

Abstract: Abstract Transcription factors (TFs) interact with several other proteins in the process of transcriptional regulation. Here, we identify 6703 and 1536 protein–protein interactions for 109 different human TFs through proximity-dependent biotinylation (BioID) and affinity purification mass spectrometry (AP-MS), respectively. The BioID analysis identifies more high-confidence interactions, highlighting the transient and dynamic nature of many of the TF interactions. By performing clustering and correlation analyses, we identify subgroups of TFs associated with specific biological functions, such as RNA splicing or chromatin remodeling. We also observe 202 TF-TF interactions, of which 118 are interactions with nuclear factor 1 (NFI) family members, indicating uncharacterized cross-talk between NFI signaling and other TF signaling pathways. Moreover, TF interactions with basal transcription machinery are mainly observed through TFIID and SAGA complexes. This study provides a rich resource of human TF interactions and also act as a starting point for future studies aimed at understanding TF-mediated transcription.

Date: 2022
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DOI: 10.1038/s41467-022-28341-5

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