ArticleGenome research2010
Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes.
Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 132 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
132 citing papers in PubMed, 219 citations in OpenAlex.
- CASER: A semi-supervised model with multi-omics data integration prioritizes cancer-associated epigenetic regulator genes.PLoS computational biology · 2026Article
- A comparison of genomic methods to assess DNA replication timing.Scientific reports · 2025Article
- Article
- The double life of mammalian DNA replication origins.Genes & development · 2025Review
- R-loops acted on by RNase H1 influence DNA replication timing and genome stability in Leishmania.Nature communications · 2025Article
- Insights into the evolution and regulation of miRNAs from the view of their DNA replication temporal domains.Frontiers in genetics · 2025Article
- Refinement of the Antarctic fur seal (Arctocephalus gazella) reference genome increases continuity and completeness.G3 (Bethesda, Md.) · 2024Article
- Emergence of enhancers at late DNA replicating regions.Nature communications · 2024Article
- Review
- Topography of mutational signatures in human cancer.Cell reports · 2023Article
- Article
- Cell-type specificity of the human mutation landscape with respect to DNA replication dynamics.Cell genomics · 2023Article
- Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths.PLoS computational biology · 2023Article
- Genome-wide measurement of DNA replication fork directionality and quantification of DNA replication initiation and termination with Okazaki fragment sequencing.Nature protocols · 2023Review
- The evolution of the human DNA replication timing program.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- OKseqHMM: a genome-wide replication fork directionality analysis toolkit.Nucleic acids research · 2023Article
- Differences in CpG island distribution between exogenous and endogenous jaagsiekte sheep retrovirus strains.Veterinary research forum : an international quarterly journal · 2023Article
- 3'untranslated regions of tumor suppressor genes evolved specific features to favor cancer resistance.Oncogene · 2022Article
- Human activation-induced deaminase lacks strong replicative strand bias or preference for cytosines in hairpin loops.Nucleic acids research · 2022Article
- Breaking the paradigm: early insights from mammalian DNA breakomes.The FEBS journal · 2022Review
72 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Neutral nucleotide substitutions occur at varying rates along genomes, and it remains a major issue to unravel the mechanisms that cause these variations and to analyze their evolutionary consequences. Here, we study the role of replication in the neutral substitution pattern. We obtained a high-resolution replication timing profile of the whole human genome by massively parallel sequencing of nascent BrdU-labeled replicating DNA. These data were compared to the neutral substitution rates along the human genome, obtained by aligning human and chimpanzee genomes using macaque and orangutan as outgroups. All substitution rates increase monotonously with replication timing even after controlling for local or regional nucleotide composition, crossover rate, distance to telomeres, and chromatin compaction. The increase in non-CpG substitution rates might result from several mechanisms including the increase in mutation-prone activities or the decrease in efficiency of DNA repair during the S phase. In contrast, the rate of C --> T transitions in CpG dinucleotides increases in later-replicating regions due to increasing DNA methylation level that reflects a negative correlation between timing and gene expression. Similar results are observed in the mouse, which indicates that replication timing is a main factor affecting nucleotide substitution dynamics at non-CpG sites and constitutes a major neutral process driving mammalian genome evolution.
Indexed as
Identifiers
What OpenQuestion holds
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.