ArticleBMC genomics2006
Genome-wide sequence and functional analysis of early replicating DNA in normal human fibroblasts.
Article in BMC genomics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed, 17 citations in OpenAlex.
- R-loops acted on by RNase H1 influence DNA replication timing and genome stability in Leishmania.Nature communications · 2025Article
- Replication Timing Aberration ofGlobal medical genetics · 2023Article
- Submegabase copy number variations arise during cerebral cortical neurogenesis as revealed by single-cell whole-genome sequencing.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Distinct mutational behaviors differentiate short tandem repeats from microsatellites in the human genome.Genome biology and evolution · 2013Article
- Temporal and functional analysis of DNA replicated in early S phase.Advances in enzyme regulation · 2011Review
- Replication factory activation can be decoupled from the replication timing program by modulating Cdk levels.The Journal of cell biology · 2010Article
- Temporal differences in DNA replication during the S phase using single fiber analysis of normal human fibroblasts and glioblastoma T98G cells.Cell cycle (Georgetown, Tex.) · 2009Article
- EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data.Genome biology · 2009Article
- Replication-timing-correlated spatial chromatin arrangements in cancer and in primate interphase nuclei.Journal of cell science · 2008Article
- DNA replication in early S phase pauses near newly activated origins.Cell cycle (Georgetown, Tex.) · 2008Article
- Vascular injury during elevated glucose can be mitigated by erythropoietin and Wnt signaling.Current neurovascular research · 2007Article
- Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.Nature · 2007Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundThe 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.
resultsBy 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.
conclusionAn 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.