Genome-wide sequence and functional analysis of early replicating DNA in normal human fibroblasts.
BACKGROUND
The replication of mammalian genomic DNA during the S phase is a highly coordinated process that occurs in a programmed manner. Recent studies have begun to elucidate the pattern of replication timing on a genomic scale. Using a combination of experimental and computational techniques, we identified a genome-wide set of the earliest replicating sequences. This was accomplished by first creating a cosmid library containing DNA enriched in sequences that replicate early in the S phase of normal human fibroblasts. Clone ends were then sequenced and aligned to the human genome.


RESULTS
By clustering adjacent or overlapping early replicating clones, we identified 1759 "islands" averaging 100 kb in length, allowing us to perform the most detailed analysis to date of DNA characteristics and genes contained within early replicating DNA. Islands are enriched in open chromatin, transcription related elements, and Alu repetitive elements, with an underrepresentation of LINE elements. In addition, we found a paucity of LTR retroposons, DNA transposon sequences, and an enrichment in all classes of tandem repeats, except for dinucleotides.


CONCLUSIONS
An analysis of genes associated with islands revealed that nearly half of all genes in the WNT family, and a number of genes in the base excision repair pathway, including four of ten DNA glycosylases, were associated with island sequences. Also, we found an overrepresentation of members of apoptosis-associated genes in very early replicating sequences from both fibroblast and lymphoblastoid cells. These data suggest that there is a temporal pattern of replication for some functionally related genes.
Cohen
Stephanie M
SM
Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, USA. stepmi@med.unc.edu
Furey
Terrence S
TS
Doggett
Norman A
NA
Kaufman
David G
DG
D049109:Cell Proliferation; D002478:Cells, Cultured; D002843:Chromatin / Q000737:chemistry; D004247:DNA / Q000096:biosynthesis*; D042522:DNA Replication Timing / Q000502:physiology*; D005347:Fibroblasts / Q000166:cytology / Q000378:metabolism*; D005796:Genes; D015894:Genome, Human; D044404:Genomic Islands / Q000502:physiology; D015698:Genomic Library; D006801:Humans; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA / Q000379:methods*; D014158:Transcription, Genetic
D002843:Chromatin; D004247:DNA