title: A diffusion model for the coordination of DNA replication in Schizosaccharomyces pombe.
abstract: The locations of proteins and epigenetic marks on the chromosomal DNA sequence are believed to demarcate the eukaryotic genome into distinct structural and functional domains that contribute to gene regulation and genome organization. However, how these proteins and epigenetic marks are organized in three dimensions remains unknown. Recent advances in proximity-ligation methodologies and high resolution microscopy have begun to expand our understanding of these spatial relationships. Here we use polymer models to examine the spatial organization of epigenetic marks, euchromatin and heterochromatin, and origins of replication within the Schizosaccharomyces pombe genome. These models incorporate data from microscopy and proximity-ligation experiments that inform on the positions of certain elements and contacts within and between chromosomes. Our results show a striking degree of compartmentalization of epigenetic and genomic features and lead to the proposal of a diffusion based mechanism, centred on the spindle pole body, for the coordination of DNA replication in S. pombe.
authors.affiliation: Liggins institute, University of Auckland, Grafton, Auckland 1032, New Zealand.
authors.forename: T
authors.initials: T
authors.lastname: Pichugina
authors.affiliation: Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima, 739-8530, Japan.
authors.forename: T
authors.initials: T
authors.lastname: Sugawara
authors.affiliation: The Rockefeller University, New York, New York 10065, USA.
authors.forename: A
authors.initials: A
authors.lastname: Kaykov
authors.affiliation: Liggins institute, University of Auckland, Grafton, Auckland 1032, New Zealand.
authors.forename: W
authors.initials: W
authors.lastname: Schierding
authors.affiliation: Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8530, Japan.
authors.forename: K
authors.initials: K
authors.lastname: Masuda
authors.affiliation: Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima, 739-8530, Japan.
authors.forename: J
authors.initials: J
authors.lastname: Uewaki
authors.affiliation: Liggins institute, University of Auckland, Grafton, Auckland 1032, New Zealand.
authors.forename: R S
authors.initials: RS
authors.lastname: Grand
authors.affiliation: Centre for Theoretical Chemistry and Physics, Institute of Natural and Mathematical Sciences, Massey University, Albany, Auckland 0632, New Zealand.
authors.forename: J R
authors.initials: JR
authors.lastname: Allison
authors.affiliation: HHMI-GBMF, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA.
authors.forename: R A
authors.initials: RA
authors.lastname: Martienssen
authors.affiliation: The Rockefeller University, New York, New York 10065, USA.|The Francis Crick Institute, Lincoln's Inn Fields Laboratories, London WC2A 3LY, United Kingdom.
authors.forename: P
authors.initials: P
authors.lastname: Nurse
authors.affiliation: Research Center for the Mathematics on Chromatin Live Dynamics (RcMcD), Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima, 739-8530, Japan.|Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, 739-8530, Japan.
authors.forename: M
authors.initials: M
authors.lastname: Ueno
authors.affiliation: Liggins institute, University of Auckland, Grafton, Auckland 1032, New Zealand.|Gravida: National Centre for Growth and Development, University of Auckland, Auckland, New Zealand.
authors.forename: J M
authors.initials: JM
authors.lastname: O'Sullivan
mesh_terms: D018797:Cell Cycle Proteins / Q000235:genetics / Q000378:metabolism; D002467:Cell Nucleus / Q000235:genetics; D004261:DNA Replication; D004271:DNA, Fungal; D022041:Euchromatin / Q000235:genetics; D016193:G1 Phase / Q000235:genetics; D016681:Genome, Fungal; D023281:Genomics; D006570:Heterochromatin / Q000235:genetics; D011495:Histone-Lysine N-Methyltransferase; D008780:Methyltransferases / Q000235:genetics / Q000378:metabolism; D008954:Models, Biological; D018741:Replication Origin; D012568:Schizosaccharomyces / Q000235:genetics* / Q000378:metabolism; D029702:Schizosaccharomyces pombe Proteins / Q000235:genetics / Q000378:metabolism; D017384:Sequence Deletion
chemical_list: D018797:Cell Cycle Proteins; D004271:DNA, Fungal; D022041:Euchromatin; D006570:Heterochromatin; D029702:Schizosaccharomyces pombe Proteins; D008780:Methyltransferases; D011495:Histone-Lysine N-Methyltransferase; C112744:clr4 protein, S pombe