PXD050443

PXD050443 is an original dataset announced via ProteomeXchange.

Title	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”)
Description	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.
HostingRepository	PRIDE
AnnounceDate	2025-02-07
AnnouncementXML	Submission_2025-02-06_23:27:52.033.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Richard Imre
SpeciesList	scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702; scientific name: Spirodela polyrhiza; NCBI TaxID: 29656;
ModificationList	methylated residue; phosphorylated residue; acetylated residue; monohydroxylated residue; trimethyl-L-arginine; dimethylated residue; deamidated residue
Instrument	Q Exactive HF; Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-03-07 06:58:18	ID requested
⏵ 1	2025-02-06 23:27:52	announced

10.1101/2024.04.03.587901;

submitter keyword: Plants,Histone PTMs, epigenetics, Transposons

Arturo Mari-Ordonez
contact affiliation	Gregor Mendel Institute of the Austrian Academy of Sciences
contact email	arturo.mari-ordonez@gmi.oeaw.ac.at
lab head
Richard Imre
contact affiliation	IMBA Vienna
contact email	richard.imre@imba.oeaw.ac.at
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/02/PXD050443

PRIDE project URI

• PRIDE
  1. PXD050443
     1. Label: PRIDE project
     2. Name: 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”)