title: Genomic analysis of Drosophila chromosome underreplication reveals a link between replication control and transcriptional territories.
abstract: In Drosophila polytene chromosomes, most late-replicating regions remain underreplicated. A loss-of-function mutant of the suppressor of underreplication [Su(UR)] gene suppresses underreplication (UR), whereas extra copies of this gene enhance the level and number of regions showing UR. By combining DNA microarray analysis with manipulation of the number of Su(UR) gene copies, we achieved genomic-scale molecular identification of 1,036 genes that are arranged in clusters located in 52 UR chromosomal regions. These regions overlap extensively (96%) but are not completely identical with late-replicating regions of mitotically dividing Kc cells in culture. Reanalysis of published gene expression profiles revealed that genomic regions defined by replication properties include clusters of coordinately expressed genes. Genomic regions that are UR in polytene chromosomes and late replicated in Kc cell chromosomes show a particularly common association with transcriptional territories that are expressed in testis/males but not ovary/females or embryos. An attractive hypothesis for future testing is that factors involved in replication control, such as SU(UR), may interact physically with those involved in epigenetic silencing of transcription territories.
authors.affiliation: Institute of Cytology and Genetics of Siberian Division, Russian Academy of Sciences, Novosibirsk 630090, Russia.
authors.forename: Stepan N
authors.initials: SN
authors.lastname: Belyakin
authors.forename: George K
authors.initials: GK
authors.lastname: Christophides
authors.forename: Artyom A
authors.initials: AA
authors.lastname: Alekseyenko
authors.forename: Evgenia V
authors.initials: EV
authors.lastname: Kriventseva
authors.forename: Elena S
authors.initials: ES
authors.lastname: Belyaeva
authors.forename: Roman A
authors.initials: RA
authors.lastname: Nanayev
authors.forename: Igor V
authors.initials: IV
authors.lastname: Makunin
authors.forename: Fotis C
authors.initials: FC
authors.lastname: Kafatos
authors.forename: Igor F
authors.initials: IF
authors.lastname: Zhimulev
mesh_terms: D000818:Animals; D002460:Cell Line; D002875:Chromosomes / Q000235:genetics*; D004261:DNA Replication / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000235:genetics; D004330:Drosophila / Q000235:genetics*; D029721:Drosophila Proteins / Q000235:genetics; D005260:Female; D018628:Gene Dosage; D005786:Gene Expression Regulation / Q000235:genetics*; D016678:Genome; D023281:Genomics; D008297:Male; D008938:Mitosis; D005810:Multigene Family / Q000235:genetics; D009154:Mutation / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D004268:DNA-Binding Proteins; D029721:Drosophila Proteins; C464850:SuUR protein, Drosophila