Conserved forkhead dimerization motif controls DNA replication timing and spatial organization of chromosomes in S. cerevisiae

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 114; no. 12; pp. E2411 - E2419
• Main Authors: Ostrow, A. Zachary, Kalhor, Reza, Gan, Yan, Villwock, Sandra K., Linke, Christian, Barberis, Matteo, Chen, Lin, Aparicio, Oscar M.
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 21.03.2017
• Series: PNAS Plus
• Subjects: Amino Acid Motifs; Amino Acid Sequence; Binding sites; Biological Sciences; Cell cycle; Cell Cycle Proteins - chemistry; Cell Cycle Proteins - genetics; Cell Cycle Proteins - metabolism; Chromosomes; Chromosomes, Fungal - genetics; Chromosomes, Fungal - metabolism; Deoxyribonucleic acid; Dimerization; DNA; DNA Replication Timing; Forkhead Transcription Factors - chemistry; Forkhead Transcription Factors - genetics; Forkhead Transcription Factors - metabolism; G1 Phase; Gene Expression Regulation, Fungal; Humans; Molecular Sequence Data; Mutation; PNAS Plus; Proteins; Replication Origin; S Phase; Saccharomyces cerevisiae; Saccharomyces cerevisiae - chemistry; Saccharomyces cerevisiae - cytology; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - chemistry; Saccharomyces cerevisiae Proteins - genetics; Saccharomyces cerevisiae Proteins - metabolism; Sequence Alignment; Yeast; DNA replication timing; nuclear organization; Fox proteins; chromatin; DNA binding protein
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1612422114

Forkhead Box (Fox) proteins share the Forkhead domain, a winged-helix DNA binding module, which is conserved among eukaryotes from yeast to humans. These sequence-specific DNA binding proteins have been primarily characterized as transcription factors regulating diverse cellular processes from cell cycle control to developmental fate, deregulation of which contributes to developmental defects, cancer, and aging. We recently identified Saccharomyces cerevisiae Forkhead 1 (Fkh1) and Forkhead 2 (Fkh2) as required for the clustering of a subset of replication origins in G₁ phase and for the early initiation of these origins in the ensuing S phase, suggesting a mechanistic role linking the spatial organization of the origins and their activity. Here, we show that Fkh1 and Fkh2 share a unique structural feature of human FoxP proteins that enables FoxP2 and FoxP3 to form domain-swapped dimers capable of bridging two DNA molecules in vitro. Accordingly, Fkh1 self-associates in vitro and in vivo in amanner dependent on the conserved domain-swapping region, strongly suggestive of homodimer formation. Fkh1- and Fkh2-domain-swap-minus (dsm) mutations are functional as transcription factors yet are defective in replication origin timing control. Fkh1-dsm binds replication origins in vivo but fails to cluster them, supporting the conclusion that Fkh1 and Fkh2 dimers perform a structural role in the spatial organization of chromosomal elements with functional importance.