The USR domain of USF1 mediates NF-Y interactions and cooperative DNA binding.

International journal of biological macromolecules 2021 Dec 15

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The trimeric CCAAT-binding NF-Y is a "pioneer" Transcription Factor -TF- known to cooperate with neighboring TFs to regulate gene expression. Genome-wide analyses detected a precise stereo-alignment -10/12 bp- of CCAAT with E-box elements and corresponding colocalization of NF-Y with basic-Helix-Loop-Helix (bHLH) TFs. We dissected here NF-Y interactions with USF1 and MAX. USF1, but not MAX, cooperates in DNA binding with NF-Y. NF-Y and USF1 synergize to activate target promoters. Reconstruction of complexes by structural means shows independent DNA binding of MAX, whereas USF1 has extended contacts with NF-Y, involving the USR, a USF-specific amino acid sequence stretch required for trans-activation. The USR is an intrinsically disordered domain and adopts different conformations based on E-box-CCAAT distances. Deletion of the USR abolishes cooperative DNA binding with NF-Y. Our data indicate that the functionality of certain unstructured domains involves adapting to small variation in stereo-alignments of the multimeric TFs sites. Copyright © 2021. Published by Elsevier B.V.

Citation

Andrea Bernardini, Mariangela Lorenzo, Antonio Chaves-Sanjuan, Paolo Swuec, Matteo Pigni, Dana Saad, Petr V Konarev, Melissa Ann Graewert, Erica Valentini, Dmitri I Svergun, Marco Nardini, Roberto Mantovani, Nerina Gnesutta. The USR domain of USF1 mediates NF-Y interactions and cooperative DNA binding. International journal of biological macromolecules. 2021 Dec 15;193(Pt A):401-413