Global involvement of lysine crotonylation in protein modification and transcription regulation in rice
- 1Yangzhou University, China
- 2Nanjing Agricultural University, China
- 3Jingjie PTM Biolabs (Hangzhou) Co. Ltd
- 4Fujian Agriculture and Forestry University, China
- ↵* Corresponding Author:
Zhiyun Gong, Yangzhou University, China. E-mail: zygong{at}yzu.edu.cn
Abstract
Lysine crotonylation (Kcr) is a newly discovered post-translational modification (PTM) existing in mammals.
A global crotonylome
analysis was undertaken in 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 localized in chloroplasts.
The photosynthesis-associated proteins were also mostly enriched in
total
crotonylated proteins.
In addition, a genomic
localization analysis of histone Kcr by ChIP-seq was performed to assess
the
relevance between histone Kcr and the genome. Of
the 10,923 identified peak regions, the majority (86.7%) of the enriched
peaks were located in gene body, 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 seedlings.
Overall, our results
provide a comprehensive understanding of the biological functions of the
crotonylome and new active histone modification in
transcriptional regulation in plants.
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