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Interactome of vertebrate GAF/ThPOK reveals its diverse functions in gene regulation and DNA repair

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Abstract

GAGA associated factor (GAF) is a sequence-specific DNA binding transcription factor that is evolutionarily conserved from flies to humans. Emerging evidence shows a context-dependent function of vertebrate GAF (vGAF, a.k.a. ThPOK) in multiple processes like gene activation, repression, and enhancer-blocking. We hypothesize that context-dependent interaction of vGAF with a diverse set of proteins forms the basis for the multifunctional nature of vGAF. To this end, we deciphered the protein–protein interactome of vGAF and show that vGAF interacts with chromatin remodelers, RNA metabolic machinery, transcriptional activators/repressors, and components of DNA repair machinery. We further validated the biological significance of our protein–protein interaction data with functional studies and established a novel role of vGAF in DNA repair and cell-survival after UV-induced DNA damage. One of the major risk factors for skin cutaneous melanoma is prolonged exposure of UV and subsequent DNA damage. vGAF is highly expressed in normal skin tissue. Interestingly, our analysis of high-throughput RNA-sequencing data shows that vGAF is heavily downregulated across all major stages of skin cutaneous melanoma suggesting its potential as a diagnostic biomarker. Taken together, our study provides a plausible explanation for the diverse gene regulatory functions of vGAF and unravels its novel role in DNA repair.

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Acknowledgements

AS acknowledge GATE-SRF fellowship from CSIR. The authors thank CCMB-Proteomics facility members for performing the mass-spectrometry. Research in RKM lab is supported by CSIR and DBT, India.

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Correspondence to Rakesh K Mishra.

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Corresponding editor: BJ Rao

Communicated by BJ Rao.

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Srivastava, A., Mishra, R.K. Interactome of vertebrate GAF/ThPOK reveals its diverse functions in gene regulation and DNA repair. J Biosci 45, 38 (2020). https://doi.org/10.1007/s12038-020-0014-0

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Keywords

  • Vertebrate GAF
  • ThPOK
  • DNA repair
  • protein-interactome
  • skin cutaneous melanoma