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Structural bases for Nuclear Factor 1-X activation and DNA recognition. Prototypic insight into the NFI transcription factor family

Tiberi, M.; Lapi, M.; Gourlay, L. J.; Chaves-Sanjuan, A.; Polentarutti, M.; Demitri, N.; Cavinato, M.; Bonnet, D. M. V. J.; Taglietti, V.; Righetti, A.; Sala, R.; Cauteruccio, S.; Kumawat, A.; Russo, R.; Barbiroli, A. G.; Gnesutta, N.; Camilloni, C.; Bolognesi, M.; Messina, G.; Nardini, M.

2025-03-21 biochemistry
10.1101/2025.03.21.644642 bioRxiv
Show abstract

Nuclear Factor I (NFI) proteins were first identified in adenovirus DNA replication and later as regulators of gene transcription, stem cell proliferation, and differentiation. They play key roles in development, cancer and congenital disorders. Within the NFI family, NFI-X is critical for neural stem cell biology, hematopoiesis, muscle development, muscular dystrophies and oncogenesis. Here, we present the first structural characterization of the NFI transcription factor, NFI-X, both alone and bound to its consensus palindromic DNA site. Our analyses reveal a novel, MH1-like fold within NFI-X DNA-binding domain (DBD) and identify crucial structural determinants for activity, such as a Zn{superscript 2} binding site, dimeric assembly, activation mechanism and DNA-binding specificity. Given the >95% sequence identity within the NFI DBDs, our structural data are prototypic for the entire family; a NFI Rosetta Stone that allows decoding a wealth of biochemical and functional data and provides a precise target for drug design in a wider disease context.

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