Arabidopsis and Spirodela Histone PTMs (In case it fits better, the title of the paper will be: “Investigating the transposon silencing landscape of the aquatic monocot Spirodela polyrhiza during clonal growth unveils atypical epigenetic and small RNA patterns”)

ABSTRACT: In flowering plants, silencing of transposable elements (TEs) is achieved by the installation of DNA methylation and histone modifications. 24-nt long small-interfering RNAs (siRNAs) guide the deposition of DNA methylation through RNA-directed DNA methylation (RdDM), which can be maintained independently of siRNAs in coordination with H3K9me2. In most angiosperms, RdDM is ubiquitously expressed in vegetative and sexual reproductive tissues. Spirodela polyrhiza (Lemnaceae), represents an exception with low levels of DNA methylation, very low expression of RdDM and near absence of 24-nt siRNAs during its clonal vegetative propagation. Moreover, some components of RdDM, DNA methylation maintenance and RNA silencing are absent from the genome. By investigating the distribution of epigenetic marks on TEs, we show that Spirodela epigenome is shaped by the loss of DNA methylation and H3K9me2 as TEs decay. Nonetheless, such abundant TE remnants remain silenced and marked by H3K9me1. In contrast, scarce, relatively intact TEs display high levels of DNA methylation, H3K9me2 and siRNAs whose patterns resemble those of TEs subjected to RdDM in other angiosperms. Furthermore, despite the absence of DCL2 in duckweeds, Spirodela can produce 22-nt siRNAs, not only from TEs, but from diverse sources of double-stranded (ds)RNA. Our data suggests that RdDM might still be functional during vegetative clonal growth, albeit tissue or developmentally regulated, and highlights the use of alternative models to further understand and explore the diversity of silencing pathways in plants.

INSTRUMENT(S): Orbitrap Exploris 480, Q Exactive HF

ORGANISM(S): Spirodela Polyrhiza Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Seedling, Whole Plant

SUBMITTER: Richard Imre  

LAB HEAD: Arturo Mari-Ordonez

PROVIDER: PXD050443 | Pride | 2025-02-07

REPOSITORIES: pride