PXD020608

PXD020608 is an original dataset announced via ProteomeXchange.

Title	Proteome of rice shoot apical meristem
Description	DNA methylation is an epigenetic modification that specifies the basic state of pluripotent stem cells and regulates the developmental transition from stem cells to various cell types. In flowering plants, the shoot apical meristem (SAM) contains a pluripotent stem cell population which generates the aerial part of plants including the germ cells. Under appropriate conditions, the SAM undergoes a developmental transition from a leaf-forming vegetative SAM to an inflorescence- and flower-forming reproductive SAM. While SAM characteristics are largely altered in this transition, the complete picture of DNA methylation remains elusive. Here, by analyzing whole-genome DNA methylation of isolated rice SAMs in the vegetative and reproductive stages, we found that methylation at CHH sites is kept high, particularly at transposable elements (TEs), in the vegetative SAM relative to the differentiated leaf, and increases in the reproductive SAM via the RNA-dependent DNA methylation pathway. We also found that half of the TEs that were highly methylated in gametes had already undergone CHH hypermethylation in the SAM. Our results indicate that changes in DNA methylation begin in the SAM long before germ cell differentiation to protect the genome from harmful TEs.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:10:51.391.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD020608
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Hiroyuki Tsuji
SpeciesList	scientific name: Oryza sativa (Rice); NCBI TaxID: 4530;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2020-07-28 04:59:50	ID requested
1	2020-08-13 22:20:01	announced
⏵ 2	2024-10-22 05:10:51	announced	2024-10-22: Updated project metadata.

10.6019/PXD020608;

submitter keyword: SAM, rice,shoot apical meristem, flowering

Hiroyuki Tsuji
contact affiliation	Kihara Institute for Biological Research, Yokohama City University
contact email	tsujih@yokohama-cu.ac.jp
lab head
Hiroyuki Tsuji
contact affiliation	Kihara Institute for Biological Research, Yokohama City University
contact email	tsujih@yokohama-cu.ac.jp
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/2020/08/PXD020608

PRIDE project URI

• PRIDE
  1. PXD020608
     1. Label: PRIDE project
     2. Name: Proteome of rice shoot apical meristem