ArticleGenetics2023
Somatic mutations inferred from RNA-seq data highlight the contribution of replication timing to mutation rate variation in a model plant.
Article in Genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- The annotated blueprint: integrated functional genomic resources for a model tetraploid wheat Triticum turgidum cv Kronos.The New phytologist · 2026Article
- Nanorate sequencing reveals theProceedings of the National Academy of Sciences of the United States of America · 2025Article
- The Potential of NGTs to Overcome Constraints in Plant Breeding and Their Regulatory Implications.International journal of molecular sciences · 2025Review
- The Annotated Blueprint: Integrated Functional Genomic Resources for a model Tetraploid WheatbioRxiv : the preprint server for biology · 2025Article
- The resistance awakens: Diversity at the DNA, RNA, and protein levels informs engineering of plant immune receptors from Arabidopsis to crops.The Plant cell · 2025Review
- Exploring the Relationship Between Gene Expression and Low-Frequency Somatic Mutations in Arabidopsis with Duplex Sequencing.Genome biology and evolution · 2024Article
- Chromatin dynamics and RNA metabolism are double-edged swords for the maintenance of plant genome integrity.Nature plants · 2024Review
- H3K4me1 recruits DNA repair proteins in plants.The Plant cell · 2024Article
- High allelic diversity in Arabidopsis NLRs is associated with distinct genomic features.EMBO reports · 2024Article
- Investigating low frequency somatic mutations inbioRxiv : the preprint server for biology · 2024Article
- High intraspecies allelic diversity inbioRxiv : the preprint server for biology · 2023Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors.
Funding
Abstract
Variation in the rates and characteristics of germline and somatic mutations across the genome of an organism is informative about DNA damage and repair processes and can also shed light on aspects of organism physiology and evolution. We adapted a recently developed method for inferring somatic mutations from bulk RNA-seq data and applied it to a large collection of Arabidopsis thaliana accessions. The wide range of genomic data types available for A. thaliana enabled us to investigate the relationships of multiple genomic features with the variation in the somatic mutation rate across the genome of this model plant. We observed that late replicated regions showed evidence of an elevated rate of somatic mutation compared to genomic regions that are replicated early. We identified transcriptional strand asymmetries, consistent with the effects of transcription-coupled damage and/or repair. We also observed a negative relationship between the inferred somatic mutation count and the H3K36me3 histone mark which is well documented in the literature of human systems. In addition, we were able to support previous reports of an inverse relationship between inferred somatic mutation count and guanine-cytosine content as well as a positive relationship between inferred somatic mutation count and DNA methylation for both cytosine and noncytosine mutations.
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