⮝ Full datasets listing

PXD020608

PXD020608 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleProteome of rice shoot apical meristem
DescriptionDNA 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.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_05:10:51.391.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD020608
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterHiroyuki Tsuji
SpeciesList scientific name: Oryza sativa (Rice); NCBI TaxID: 4530;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentLTQ Orbitrap
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-07-28 04:59:50ID requested
12020-08-13 22:20:01announced
22024-10-22 05:10:51announced2024-10-22: Updated project metadata.
Publication List
10.6019/PXD020608;
Keyword List
submitter keyword: SAM, rice,shoot apical meristem, flowering
Contact List
Hiroyuki Tsuji
contact affiliationKihara Institute for Biological Research, Yokohama City University
contact emailtsujih@yokohama-cu.ac.jp
lab head
Hiroyuki Tsuji
contact affiliationKihara Institute for Biological Research, Yokohama City University
contact emailtsujih@yokohama-cu.ac.jp
dataset submitter
Full Dataset Link List
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
Repository Record List
[ + ]