ArticleGenome biology and evolution2009
Long-range bidirectional strand asymmetries originate at CpG islands in the human genome.
Article in Genome biology and evolution, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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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.
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Who cites it
11 citing papers in PubMed, 19 citations in OpenAlex.
- Chimeric chromosome landscapes of human somatic cell cultures show dependence on stress and regulation of genomic repeats by CGGBP1.Oncotarget · 2022Article
- Genomic methods for measuring DNA replication dynamics.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2020Review
- Evidence for evolutionary and nonevolutionary forces shaping the distribution of human genetic variants near transcription start sites.PloS one · 2014Article
- GC skew at the 5' and 3' ends of human genes links R-loop formation to epigenetic regulation and transcription termination.Genome research · 2013Article
- Human-specific CpG "beacons" identify loci associated with human-specific traits and disease.Epigenetics · 2012Article
- Linking the DNA strand asymmetry to the spatio-temporal replication program. I. About the role of the replication fork polarity in genome evolution.The European physical journal. E, Soft matter · 2012Article
- Measures of compositional strand bias related to replication machinery and its applications.Current genomics · 2012Article
- Article
- Genome-wide depletion of replication initiation events in highly transcribed regions.Genome research · 2011Article
- Genomic signatures of germline gene expression.Genome research · 2010Article
- The evolution of transcription-associated biases of mutations across vertebrates.BMC evolutionary biology · 2010Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In the human genome, CpG islands (CGIs), which are GC- and CpG-rich sequences, are associated with transcription starting sites (TSSs); in addition, there is evidence that CGIs harbor origins of bidirectional replication (OBRs) and are preferred sites for heteroduplex formation during recombination. Transcription, replication, and recombination processes are known to induce specific mutational patterns in various genomes, and therefore, these patterns are expected to be found around CGIs. We use triple alignments of human, chimp, and macaque to compute the rates of nucleotide substitutions in up to 1 Mbps long intergenic regions on both sides of CGIs. Our analysis revealed that around a CGI there is an asymmetry between complementary substitution rates that is similar to the one that found around the OBR in bacteria. We hypothesize that these asymmetries are induced by differences in the replication of the leading and lagging strand and that a significant number of CGIs overlap OBRs. Within CGIs, we observed a mutational signature of GC-biased gene conversion that is associated with recombination. We suggest that recombination has played a major role in the creation of CGIs.
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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.