title: Conserved forkhead dimerization motif controls DNA replication timing and spatial organization of chromosomes inS. cerevisiae.
abstract: 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 identifiedSaccharomyces cerevisiaeForkhead 1 (Fkh1) and Forkhead 2 (Fkh2) as required for the clustering of a subset of replication origins in G1phase 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 a manner 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.
authors.affiliation: Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089-2910.
authors.forename: A Zachary
authors.initials: AZ
authors.lastname: Ostrow
authors.affiliation: Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089-2910.
authors.forename: Reza
authors.identifier: 0000-0002-5558-7545
authors.initials: R
authors.lastname: Kalhor
authors.affiliation: Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089-2910.
authors.forename: Yan
authors.initials: Y
authors.lastname: Gan
authors.affiliation: Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089-2910.
authors.forename: Sandra K
authors.initials: SK
authors.lastname: Villwock
authors.affiliation: Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098 XH, The Netherlands.
authors.forename: Christian
authors.initials: C
authors.lastname: Linke
authors.affiliation: Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam 1098 XH, The Netherlands m.barberis@uva.nl.
authors.forename: Matteo
authors.initials: M
authors.lastname: Barberis
authors.affiliation: Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089-2910.
authors.forename: Lin
authors.initials: L
authors.lastname: Chen
authors.affiliation: Molecular and Computational Biology Program, University of Southern California, Los Angeles, CA 90089-2910; oaparici@usc.edu.
authors.forename: Oscar M
authors.initials: OM
authors.lastname: Aparicio
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D018797:Cell Cycle Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D015825:Chromosomes, Fungal / Q000235:genetics* / Q000378:metabolism; D042522:DNA Replication Timing; D019281:Dimerization; D051858:Forkhead Transcription Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D016193:G1 Phase; D015966:Gene Expression Regulation, Fungal; D006801:Humans; D008969:Molecular Sequence Data; D018741:Replication Origin; D016196:S Phase; D012441:Saccharomyces cerevisiae / Q000737:chemistry / Q000166:cytology / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D016415:Sequence Alignment
chemical_list: D018797:Cell Cycle Proteins; C465448:FOXP2 protein, human; C418974:FOXP3 protein, human; C464906:Fkh1 protein, S cerevisiae; C464958:Fkh2 protein, S cerevisiae; D051858:Forkhead Transcription Factors; D029701:Saccharomyces cerevisiae Proteins
keywords: DNA binding protein; DNA replication timing; Fox proteins; chromatin; nuclear organization