biostudies-literatureChatterjee AU.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)U.S. Department of Defense (United States Department of Defense)NCI NIH HHSNIH HHS9037https://www.ebi.ac.uk/biostudies/studies/S-EPMC11490551biostudies-literatureUnknown15(1)The CUT and homeodomain are ubiquitous DNA binding elements often tandemly arranged in multiple transcription factor families. However, how the CUT and homeodomain work concertedly to bind DNA remains unknown. Using ONECUT2, a driver and therapeutic target of advanced prostate cancer, we show that while the CUT initiates DNA binding, the homeodomain thermodynamically stabilizes the ONECUT2-DNA complex through allosteric modulation of CUT. We identify an arginine pair in the ONECUT family homeodomain that can adapt to DNA sequence variations. Base interactions by this ONECUT family-specific arginine pair as well as the evolutionarily conserved residues are critical for optimal DNA binding and ONECUT2 transcriptional activity in a prostate cancer model. The evolutionarily conserved base inteNature communicationsThe homeodomain regulates stable DNA binding of prostate cancer target ONECUT2.PMC11490551T32 CA240172R01 CA2203271R01CA2203272P50CA092131S10 OD016234PC210486P50 CA092131Harter MRFreeman MRMurali RQian CKatiki MKomives EAChatterjee ASilletti SGallent BfalseThe homeodomain regulates stable DNA binding of prostate cancer target ONECUT2.The CUT and homeodomain are ubiquitous DNA binding elements often tandemly arranged in multiple transcription factor families. However, how the CUT and homeodomain work concertedly to bind DNA remains unknown. Using ONECUT2, a driver and therapeutic target of advanced prostate cancer, we show that while the CUT initiates DNA binding, the homeodomain thermodynamically stabilizes the ONECUT2-DNA complex through allosteric modulation of CUT. We identify an arginine pair in the ONECUT family homeodomain that can adapt to DNA sequence variations. Base interactions by this ONECUT family-specific arginine pair as well as the evolutionarily conserved residues are critical for optimal DNA binding and ONECUT2 transcriptional activity in a prostate cancer model. The evolutionarily conserved base inte2024-01-01T00:00:00Z2024 Oct2026-07-15T17:49:06.226Z2025-04-04T02:57:28.49ZS-EPMC114905513942695310.1038/s41467-024-53159-8