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Single-cell expression noise and gene-body methylation in Arabidopsis thaliana
Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Science for Life Laboratory (SciLifeLab).ORCID iD: 0000-0002-3221-8835
Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Science for Life Laboratory (SciLifeLab).
Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Stockholm University, Science for Life Laboratory (SciLifeLab).
Number of Authors: 42019 (English)In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 123, no 2, p. 81-91Article in journal (Refereed) Published
Abstract [en]

Gene-body methylation (gbM) refers to an increased level of methylated cytosines specifically in a CG sequence context within genes. gbM is found in plant genes with intermediate expression level, which evolve slowly, and is often broadly conserved across millions of years of evolution. Intriguingly however, some plants lack gbM, and thus it remains unclear whether gbM has a function. In animals, there is support for a role of gbM in reducing erroneous transcription and transcription noise, but so far most studies in plants have tested for an effect of gbM on expression level, not noise. Here, we therefore tested whether gbM was associated with reduced expression noise in Arabidopsis thaliana, using single-cell transcriptome sequencing data from root quiescent centre cells. We find that gbM genes have lower expression noise levels than unmethylated genes. However, an analysis of covariance revealed that, if other genomic features are taken into account, this association disappears. Nonetheless, gbM genes were more consistently expressed across single-cell samples, supporting previous inference that gbM genes are constitutively expressed. Finally, we observed that fewer RNAseq reads map to introns of gbM genes than to introns of unmethylated genes, which indicates that gbM might be involved in reducing erroneous transcription by reducing intron retention.

Place, publisher, year, edition, pages
2019. Vol. 123, no 2, p. 81-91
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:su:diva-171987DOI: 10.1038/s41437-018-0181-zISI: 000474747800001PubMedID: 30651589OAI: oai:DiVA.org:su-171987DiVA, id: diva2:1347256
Available from: 2019-08-30 Created: 2019-08-30 Last updated: 2019-08-30Bibliographically approved

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Horvath, RobertLaenen, BenjaminSlotte, Tanja
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