PXD008716-1

PXD008716 is an original dataset announced via ProteomeXchange.

Title	GlobaGlobal involvement of lysine crotonylation in protein modification and transcription regulation in ricel involvement of lysine crotonylation in protein modification and transcription regulation in rice
Description	Lysine crotonylation (Kcr) is a newly discovered post-translational modification (PTM) existing in mammalian. Here, we performed a global crotonylome analysis of rice (Oryza sativa L. japonica) using high accuracy nano-LC-MS/MS in combination with crotonylated peptide enrichment. A total of 1,265 lysine crotonylation sites were identified on 690 proteins in rice seedlings. Subcellular localization analysis revealed that 51% of the crotonylated proteins identified were predicted to be associated with chloroplasts. The photosynthesis-associated proteins were also mostly enriched in total crotonylated proteins. Furthermore, to assess the relevance between histone Kcr and the genome, we performed a genomic localization analysis of histone Kcr by ChIP-seq analysis. Of the 10,923 identified peak regions, the majority (86.7%) of the enriched peaks were located in genes, especially exons. Furthermore, the degree of histone Kcr modification was positively correlated with gene expression in genic regions. Compared with other published histone modification data, the Kcr was co-located with the active histone modifications. Interestingly, histone Kcr facilitated expression of genes with existing active histone modifications. In addition, 77% of histone Kcr modifications overlapped with DNase hypersensitive sites (DHSs) in intergenic regions of the rice genome, and might mark other cis-regulatory DNA elements which are different from IPA1, a transcription activator in rice seedling. Overall, our results provide a comprehensive understanding of the biological functions of the crotonylome and new active histone modification in transcriptional regulation in plants.
HostingRepository	PRIDE
AnnounceDate	2018-07-23
AnnouncementXML	Submission_2018-07-23_07:15:35.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chenyu Lu
SpeciesList	scientific name: Rice(O. sativa); NCBI TaxID: 4530;
ModificationList	N6-crotonyl-L-lysine
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-01-19 02:42:12	ID requested
⏵ 1	2018-07-23 07:15:36	announced
2	2024-10-22 04:04:09	announced	2024-10-22: Updated project metadata.

Liu S, Xue C, Fang Y, Chen G, Peng X, Zhou Y, Chen C, Liu G, Gu M, Wang K, Zhang W, Wu Y, Gong Z, Global Involvement of Lysine Crotonylation in Protein Modification and Transcription Regulation in Rice. Mol Cell Proteomics, 17(10):1922-1936(2018) [pubmed]

curator keyword: Biological

submitter keyword: Oryza sativa, post-translational modification, crotonyl lysine, histone lysine

Zhiyun Gong
contact affiliation	Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
contact email	zygong@yzu.edu.cn
lab head
Chenyu Lu
contact affiliation	Zhejiang University
contact email	lcyyz@hotmail.com
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/2018/07/PXD008716

PRIDE project URI

• PRIDE
  1. PXD008716
     1. Label: PRIDE project
     2. Name: GlobaGlobal involvement of lysine crotonylation in protein modification and transcription regulation in ricel involvement of lysine crotonylation in protein modification and transcription regulation in rice