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Human transcription factor protein interaction networks

Author

Listed:
  • Helka Göös

    (Institute of Biotechnology, HiLIFE, University of Helsinki
    Finnish Red Cross Blood Service)

  • 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
    School of Basic Medical Sciences, Fudan University Shanghai Cancer Center, Shanghai Medical College of Fudan University)

  • Markku Varjosalo

    (Institute of Biotechnology, HiLIFE, University of Helsinki)

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.

Suggested Citation

  • Helka Göös & Matias Kinnunen & Kari Salokas & Zenglai Tan & Xiaonan Liu & Leena Yadav & Qin Zhang & Gong-Hong Wei & Markku Varjosalo, 2022. "Human transcription factor protein interaction networks," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-28341-5
    DOI: 10.1038/s41467-022-28341-5
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    References listed on IDEAS

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    2. Ho Sung Rhee & B. Franklin Pugh, 2012. "Erratum: Genome-wide structure and organization of eukaryotic pre-initiation complexes," Nature, Nature, vol. 487(7405), pages 128-128, July.
    3. Rajagopal, 2014. "The Human Factors," Palgrave Macmillan Books, in: Architecting Enterprise, chapter 9, pages 225-249, Palgrave Macmillan.
    4. Tong Ihn Lee & Helen C. Causton & Frank C. P. Holstege & Wu-Cheng Shen & Nancy Hannett & Ezra G. Jennings & Fred Winston & Michael R. Green & Richard A. Young, 2000. "Redundant roles for the TFIID and SAGA complexes in global transcription," Nature, Nature, vol. 405(6787), pages 701-704, June.
    5. Xiaonan Liu & Kari Salokas & Fitsum Tamene & Yaming Jiu & Rigbe G. Weldatsadik & Tiina Öhman & Markku Varjosalo, 2018. "An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations," Nature Communications, Nature, vol. 9(1), pages 1-16, December.
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