Molecular basis for DNA recognition by the maternal pioneer transcription factor FoxH1

Radoslaw Pluta, Eric Aragón, Nicholas A. Prescott, Lidia Ruiz, Rebeca A. Mees, Blazej Baginski, Julia R. Flood, Pau Martin-Malpartida, Joan Massagué, Yael David and Maria J. Macias ()
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Radoslaw Pluta: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST)
Eric Aragón: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST)
Nicholas A. Prescott: Tri-Institutional PhD Program in Chemical Biology
Lidia Ruiz: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST)
Rebeca A. Mees: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST)
Blazej Baginski: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST)
Julia R. Flood: Chemical Biology Program, Memorial Sloan Kettering Cancer Center
Pau Martin-Malpartida: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST)
Joan Massagué: Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center
Yael David: Chemical Biology Program, Memorial Sloan Kettering Cancer Center
Maria J. Macias: Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST)

Nature Communications, 2022, vol. 13, issue 1, 1-15

Abstract: Abstract Forkhead box H1 (FoxH1) is an essential maternal pioneer factor during embryonic development that binds to specific GG/GT-containing DNA target sequences. Here we have determined high-resolution structures of three FoxH1 proteins (from human, frog and fish species) and four DNAs to clarify the way in which FoxH1 binds to these sites. We found that the protein-DNA interactions extend to both the minor and major DNA grooves and are thus almost twice as extensive as those of other FOX family members. Moreover, we identified two specific amino acid changes in FoxH1 that allowed the recognition of GG/GT motifs. Consistent with the pioneer factor activity of FoxH1, we found that its affinity for nucleosomal DNA is even higher than for linear DNA fragments. The structures reported herein illustrate how FoxH1 binding to distinct DNA sites provides specificity and avoids cross-regulation by other FOX proteins that also operate during the maternal-zygotic transition and select canonical forkhead sites.

Date: 2022
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DOI: 10.1038/s41467-022-34925-y

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