title: Cell cycle regulation of human DNA repair and chromatin remodeling genes.
abstract: Maintenance of a genome requires DNA repair integrated with chromatin remodeling. We have analyzed six transcriptome data sets and one data set on translational regulation of known DNA repair and remodeling genes in synchronized human cells. These data are available through our new database: www.dnarepairgenes.com. Genes that have similar transcription profiles in at least two of our data sets generally agree well with known protein profiles. In brief, long patch base excision repair (BER) is enriched for S phase genes, whereas short patch BER uses genes essentially equally expressed in all cell cycle phases. Furthermore, most genes related to DNA mismatch repair, Fanconi anemia and homologous recombination have their highest expression in the S phase. In contrast, genes specific for direct repair, nucleotide excision repair, as well as non-homologous end joining do not show cell cycle-related expression. Cell cycle regulated chromatin remodeling genes were most frequently confined to G1/S and S. These include e.g. genes for chromatin assembly factor 1 (CAF-1) major subunits CHAF1A and CHAF1B; the putative helicases HELLS and ATAD2 that both co-activate E2F transcription factors central in G1/S-transition and recruit DNA repair and chromatin-modifying proteins and DNA double strand break repair proteins; and RAD54L and RAD54B involved in double strand break repair. TOP2A was consistently most highly expressed in G2, but also expressed in late S phase, supporting a role in regulating entry into mitosis. Translational regulation complements transcriptional regulation and appears to be a relatively common cell cycle regulatory mechanism for DNA repair genes. Our results identify cell cycle phases in which different pathways have highest activity, and demonstrate that periodically expressed genes in a pathway are frequently co-expressed. Furthermore, the data suggest that S phase expression and over-expression of some multifunctional chromatin remodeling proteins may set up feedback loops driving cancer cell proliferation.
authors.affiliation: Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.
authors.forename: Robin
authors.initials: R
authors.lastname: Mjelle
authors.affiliation: Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.
authors.forename: Siv Anita
authors.initials: SA
authors.lastname: Hegre
authors.affiliation: Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.
authors.forename: Per Arne
authors.initials: PA
authors.lastname: Aas
authors.affiliation: Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.
authors.forename: Geir
authors.initials: G
authors.lastname: Slupphaug
authors.affiliation: Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.
authors.forename: Finn
authors.initials: F
authors.lastname: Drabløs
authors.affiliation: Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway; Department of Computer and Information Science, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway. Electronic address: pal.satrom@ntnu.no.
authors.forename: Pål
authors.initials: P
authors.lastname: Saetrom
authors.affiliation: Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway. Electronic address: hans.krokan@ntnu.no.
authors.forename: Hans E
authors.initials: HE
authors.lastname: Krokan
mesh_terms: D002453:Cell Cycle; D042002:Chromatin Assembly and Disassembly / Q000235:genetics* / Q000502:physiology; D004260:DNA Repair / Q000235:genetics* / Q000502:physiology; D015870:Gene Expression; D006801:Humans
keywords: Cell cycle; Chromatin remodeling genes; DNA repair genes