ArticleBMC genomics2021
Elevated transcription of transposable elements is accompanied by het-siRNA-driven de novo DNA methylation in grapevine embryogenic callus.
Article in BMC genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
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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
6 citing papers in PubMed, 14 citations in OpenAlex.
- Harnessing clonal diversity in grapevine: from genomic insights to modern breeding applications.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- The role of mobile DNA elements in the dynamics of plant genome plasticity.Journal of experimental botany · 2025Review
- Insights into plant regeneration: cellular pathways and DNA methylation dynamics.Plant cell reports · 2024Review
- Emerging Roles of Epigenetics in Grapevine and Winegrowing.Plants (Basel, Switzerland) · 2024Review
- Article
- Epigenetic regulation and beyond in grapevine-pathogen interactions: a biotechnological perspective.Physiologia plantarumReview
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundSomatic variation is a valuable source of trait diversity in clonally propagated crops. In grapevine, which has been clonally propagated worldwide for centuries, important phenotypes such as white berry colour are the result of genetic changes caused by transposable elements. Additionally, epiallele formation may play a role in determining geo-specific ('terroir') differences in grapes and thus ultimately in wine. This genomic plasticity might be co-opted for crop improvement via somatic embryogenesis, but that depends on a species-specific understanding of the epigenetic regulation of transposable element (TE) expression and silencing in these cultures. For this reason, we used whole-genome bisulphite sequencing, mRNA sequencing and small RNA sequencing to study the epigenetic status and expression of TEs in embryogenic callus, in comparison with leaf tissue.
resultsWe found that compared with leaf tissue, grapevine embryogenic callus cultures accumulate relatively high genome-wide CHH methylation, particularly across heterochromatic regions. This de novo methylation is associated with an abundance of transcripts from highly replicated TE families, as well as corresponding 24 nt heterochromatic siRNAs. Methylation in the TE-specific CHG context was relatively low over TEs located within genes, and the expression of TE loci within genes was highly correlated with the expression of those genes.
conclusionsThis multi-'omics analysis of grapevine embryogenic callus in comparison with leaf tissues reveals a high level of genome-wide transcription of TEs accompanied by RNA-dependent DNA methylation of these sequences in trans. This provides insight into the genomic conditions underlying somaclonal variation and epiallele formation in plants regenerated from embryogenic cultures, which is an important consideration when using these tissues for plant propagation and genetic improvement.
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