ArticleGenomics, proteomics & bioinformatics2012
Distinct contributions of replication and transcription to mutation rate variation of human genomes.
Article in Genomics, proteomics & bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 34 citations in OpenAlex.
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- Cell-type specificity of the human mutation landscape with respect to DNA replication dynamics.Cell genomics · 2023Article
- Replication Stress, Genomic Instability, and Replication Timing: A Complex Relationship.International journal of molecular sciences · 2021Review
- Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades.Genomics, proteomics & bioinformatics · 2020Article
- Evolutionary Forces and Codon Bias in Different Flavors of Intrinsic Disorder in the Human Proteome.Journal of molecular evolution · 2020Article
- Germline DNA replication timing shapes mammalian genome composition.Nucleic acids research · 2018Article
- MTD: a mammalian transcriptomic database to explore gene expression and regulation.Briefings in bioinformatics · 2017Article
- Precision Medicine: What Do We Expect in the Scope of Basic Biomedical Sciences?Genomics, proteomics & bioinformatics · 2016Article
- Mutation Detection in an Antibody-Producing Chinese Hamster Ovary Cell Line by Targeted RNA Sequencing.BioMed research international · 2016Article
- Conserved and divergent patterns of DNA methylation in higher vertebrates.Genome biology and evolution · 2014Article
- Translational selection in human: more pronounced in housekeeping genes.Biology direct · 2014Article
- Ribogenomics: the science and knowledge of RNA.Genomics, proteomics & bioinformatics · 2014Article
- Complex correlations: replication timing and mutational landscapes during cancer and genome evolution.Current opinion in genetics & development · 2014Review
- DNA replication timing, genome stability and cancer: late and/or delayed DNA replication timing is associated with increased genomic instability.Seminars in cancer biology · 2013Review
- Does the genetic code have a eukaryotic origin?Genomics, proteomics & bioinformatics · 2013Article
- The pendulum model for genome compositional dynamics: from the four nucleotides to the twenty amino acids.Genomics, proteomics & bioinformatics · 2012Article
- Life on two tracks.Genomics, proteomics & bioinformatics · 2012Article
- Challenges to the common dogma.Genomics, proteomics & bioinformatics · 2012Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Here, we evaluate the contribution of two major biological processes--DNA replication and transcription--to mutation rate variation in human genomes. Based on analysis of the public human tissue transcriptomics data, high-resolution replicating map of Hela cells and dbSNP data, we present significant correlations between expression breadth, replication time in local regions and SNP density. SNP density of tissue-specific (TS) genes is significantly higher than that of housekeeping (HK) genes. TS genes tend to locate in late-replicating genomic regions and genes in such regions have a higher SNP density compared to those in early-replication regions. In addition, SNP density is found to be positively correlated with expression level among HK genes. We conclude that the process of DNA replication generates stronger mutational pressure than transcription-associated biological processes do, resulting in an increase of mutation rate in TS genes while having weaker effects on HK genes. In contrast, transcription-associated processes are mainly responsible for the accumulation of mutations in highly-expressed HK genes.
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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.