Bubble-seq Analysis of the Human Genome Reveals Distinct Chromatin-Mediated Mechanisms for Regulating Early- and Late-Firing Origins

ABSTRACT: We have devised a method for isolating virtually pure and comprehensive libraries of restriction fragments that contained replication initiation sites (bubbles) in vivo (Mesner et al. 2009). We have now sequenced and mapped the bubble-containing fragments from GM06990, a near-normal EBV-transformed lymphoblastoid cell line, and have compared origin distributions to a comprehensive replication timing study recently published for this cell line. We find that early-firing origins overwhelmingly represent zones, associate only marginally with active transcription units, are localized within large domains of open chromatin, and are significantly associated with DNAseI hypersensitivity. Origin density falls from early- to mid-S-phase, but, surprisingly, rises again in late-S-phase to density levels only 17% lower than in early S-phase. Strikingly, late origin density calculated on the 1Mb scale is robustly correlated with measures of increasing chromatin compaction. While origin efficiency decreases with replication time, the median efficiency in late-replicating, heterochromatic domains is only 25% lower than in early-replicating, euchromatic loci. Thus, the activation of early- and late-firing origins must be regulated by quintessentially different mechanisms. The aggregate data can be unified into a model in which initiation site selection is driven almost entirely by epigenetic factors that fashion both the long-range and local chromatin environments, with underlying DNA sequence and local transcriptional activity playing only minor roles. Importantly, the comprehensive origin map we have prepared for GM06990 overlaps only modestly with origin maps recently reported for the genomes of four different human cell lines based on distributions of small nascent strands.

ORGANISM(S): Homo sapiens

PROVIDER: GSE38809 | GEO | 2013/07/09

SECONDARY ACCESSION(S): PRJNA169029

REPOSITORIES: GEO