title: Bubble-chip analysis of human origin distributions demonstrates on a genomic scale significant clustering into zones and significant association with transcription.
abstract: We have used a novel bubble-trapping procedure to construct nearly pure and comprehensive human origin libraries from early S- and log-phase HeLa cells, and from log-phase GM06990, a karyotypically normal lymphoblastoid cell line. When hybridized to ENCODE tiling arrays, these libraries illuminated 15.3%, 16.4%, and 21.8% of the genome in the ENCODE regions, respectively. Approximately half of the origin fragments cluster into zones, and their signals are generally higher than those of isolated fragments. Interestingly, initiation events are distributed about equally between genic and intergenic template sequences. While only 13.2% and 14.0% of genes within the ENCODE regions are actually transcribed in HeLa and GM06990 cells, 54.5% and 25.6% of zonal origin fragments overlap transcribed genes, most with activating chromatin marks in their promoters. Our data suggest that cell synchronization activates a significant number of inchoate origins. In addition, HeLa and GM06990 cells activate remarkably different origin populations. Finally, there is only moderate concordance between the log-phase HeLa bubble map and published maps of small nascent strands for this cell line.
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA.
authors.forename: Larry D
authors.initials: LD
authors.lastname: Mesner
authors.forename: Veena
authors.initials: V
authors.lastname: Valsakumar
authors.forename: Neerja
authors.initials: N
authors.lastname: Karnani
authors.forename: Anindya
authors.initials: A
authors.lastname: Dutta
authors.forename: Joyce L
authors.initials: JL
authors.lastname: Hamlin
authors.forename: Stefan
authors.initials: S
authors.lastname: Bekiranov
mesh_terms: D002453:Cell Cycle / Q000235:genetics; D002843:Chromatin / Q000235:genetics / Q000378:metabolism*; D016000:Cluster Analysis; D004261:DNA Replication; D021901:DNA, Intergenic / Q000378:metabolism; D005260:Female; D015723:Gene Library; D015894:Genome, Human; D006367:HeLa Cells; D006801:Humans; D046228:Microarray Analysis / Q000379:methods*; D016366:Open Reading Frames / Q000235:genetics; D011401:Promoter Regions, Genetic; D018741:Replication Origin; D014158:Transcription, Genetic
chemical_list: D002843:Chromatin; D021901:DNA, Intergenic