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PXD008716 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleGlobaGlobal involvement of lysine crotonylation in protein modification and transcription regulation in ricel involvement of lysine crotonylation in protein modification and transcription regulation in rice
DescriptionLysine 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.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterChenyu Lu
SpeciesList scientific name: Rice(O. sativa); NCBI TaxID: 4530;
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02018-01-19 02:42:12ID requested
12018-07-23 07:15:36announced
Publication List
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]
Keyword List
curator keyword: Biological
submitter keyword: Oryza sativa, post-translational modification, crotonyl lysine, histone lysine
Contact List
Zhiyun Gong
contact affiliationJiangsu 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 emailzygong@yzu.edu.cn
lab head
Chenyu Lu
contact affiliationZhejiang University
contact emaillcyyz@hotmail.com
dataset submitter
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