Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Histone lysine acetylation, butyrylation, and crotonylation dynamics and functional interplay in rice under starvation and submergence

ABSTRACT: Histone lysine acylations are regulated by primary metabolism in animal cells. However, histone non-acetyl acylation is not yet studied in plants that have distinct primary metabolic pathways. In this work, we detected rice histone lysine butyrylation (Kbu) and crotonylation (Kcr) sites by mass spectrometry, and found both similar and specific acylation patterns compared with that in mammalian cells.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Oryza Sativa (rice)

TISSUE(S): Leaf

SUBMITTER: qiutao xu

LAB HEAD: Dao-Xiu Zhou

PROVIDER: PXD009091 | Pride | 2018-09-06

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	6627PI-results.zip	Other
	rep1_6627PICrR1-.raw	Raw
	rep1_6627PICrR1.raw	Raw
	rep2_6627PICrR1-.raw	Raw
	rep2_6627PICrR1.raw	Raw

Items per page:

1 - 5 of 5

Publications

Dynamics and functional interplay of histone lysine butyrylation, crotonylation, and acetylation in rice under starvation and submergence.

Lu Yue Y Xu Qiutao Q Liu Yuan Y Yu Yue Y Cheng Zhong-Yi ZY Zhao Yu Y Zhou Dao-Xiu DX

Genome biology 20180925 1

<h4>Background</h4>Histone lysine acylations by short-chain fatty acids are distinct from the widely studied histone lysine acetylation in chromatin, although both modifications are regulated by primary metabolism in mammalian cells. It remains unknown whether and how histone acylation and acetylation interact to regulate gene expression in plants that have distinct regulatory pathways of primary metabolism.<h4>Results</h4>We identify 4 lysine butyrylation (Kbu) sites (H3K14, H4K12, H2BK42, and ...[more]

PMID: 30253806

Similar Datasets

Global involvement of lysine crotonylation in protein modification and transcription regulation in rice

Project description: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.

2018-09-20 | PXD010376 | Pride

Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification

Project description:We report the identification of 67 previously undescribed histone modifications, increasing the current number of known histone marks by about 70%. We further investigated one of the marks, lysine crotonylation (Kcr), confirming that it represents an evolutionarily-conserved histone posttranslational modification. The unique structure and genomic localization of histone Kcr suggest that it is mechanistically and functionally different from histone lysine acetylation (Kac). Specifically, in both human somatic and mouse male germ cell genomes, histone Kcr marks either active promoters or potential enhancers. In male germinal cells immediately following meiosis, Kcr is enriched on sex chromosomes and specifically marks testis-specific genes, including a significant proportion of X-linked genes that escape sex chromosome inactivation in haploid cells. These results therefore dramatically extend the repertoire of histone PTM sites and designate Kcr as a specific mark of active sex chromosome-linked genes in postmeiotic male germ cells. 2 histone marks (pan-lysine acetylation and pan-lysine crotonylation) were studied in 1 human cell type and 2 mouse cell types using ChIP-Seq. Input was sequenced for each cell type as a control. Pan-anti_Kac and pan-anti_Kcr antibodies were custom developed with PTM BioLab, Co., Ltd (Chicago, IL).

2011-10-06 | E-GEOD-32663 | biostudies-arrayexpress

First comprehensive proteome analysis of lysine crotonylation in Streptococcus agalactiae, a pathogen causing meningoencephalitis in teleosts

Project description:In Homo sapiens, Streptococcus agalactiae is a common colonizer of the rectovaginal tract and a fundamental cause of neonatal and non-pregnant adults infectious diseases. It also causes infectious disease in fish which compromises food safety as well as possesses a zoonotic risk. Lysine crotonylation (Kcr) is a type of histone post-translational modifications discovered in 2011. Kcr dynamics are involved in active gene promoters and potential enhancers in yeast and mammalian. However, lysine crotonylation in S. agalactiae has not yet been studied. In the present study, we conducted the first proteome-wide profiling of Kcr in S. agalactiae and identified 241 Kcr sites on 675 proteins, representing the Kcr event in S. agalactiae. Bioinformatics analysis showed that 164 sequences were matched to a total of six definitively conserved motifs, and many of them were significantly enriched in metabolic processes, cellular process, and single-organism processes. Moreover, we found four crotonylation modified proteins predicted as quorum sensing system and virulence factors, which indicate the important role of PTM on bacterial QS system and virulence. These data represent the first report of a global crotonylation proteome and provide a promising starting point for further functional research of crotonylation in bacterial virulence in S. agalactiae.

2021-12-30 | PXD026445 | Pride

Dynamics and functional interplay of histone lysine butyrylation, crotonylation, and acetylation in rice under starvation and submergence

Project description:In this work, we detected lysinebutyrylation (Kbu) and crotonylation(Kcr) sites in rice histone proteins by mass spectrometry, and found both similar and specific acylation patterns compared with that in mammalian cells. Comparative analysis of genome-wide histone Kbu, Kcr, and H3K9ac in combination of RNA-sequencing revealed that a large number of rice genes are marked by both Kbu and Kcr, most of which overlap with H3K9ac and are active genes. Under starvation and submergence, Kbu andKcr appeared to be less dynamic than H3K9ac and the three marks displayed changes in different sets of genes. Kbu and Kcr seemed to have a function to poise stress-induced gene activation. The results suggest that histone Kbu and Kcr provide a platform for histone acetylation during gene activation and that the proportional mixture of distinct histone lysine acylations which are regulated by environmental cues and has functionally consequence in chromatin modification and gene expression in plants.

2018-09-08 | GSE111308 | GEO

The Role of CDYL-Regulated Crotonylation of RPA1 in Homologous Recombination-Mediated DNA Repair

Project description:Lysine crotonylation (Kcr) is a recently-identified protein short-chain acylation. We have previously reported that chromodomain Y-like transcription corepressor CDYL acts as a crotonyl-CoA hydratase and negatively regulates histone Kcr. However, the global crotonylome of CDYL-regulated Kcr on non-histone substrates remains unclear. Using proteome-wide quantitative Kcr analysis, we identified 14,311 Kcr sites across 3,734 proteins in HeLa cells, providing by far the largest crotonylome data set from a single study. Upon depletion of CDYL, 1,141 Kcr sites from 759 proteins were increased by more than 1.5 fold, and 933 Kcr sites from 528 proteins were decreased by more than 0.67 fold. Upregulated crotonylome alterations upon CDYL depletion include components from diverse cellular pathways such as RNA splicing, DNA replication, and amino acid metabolism. Specifically, CDYL regulates K88 and K379 of crotonylation on RPA1, which affects its binding to other DNA repair factors including BLM, DNA2L, RAD50 and WRN. We showed evidence that CDYL-mediated RPA1 crotonylation is critical for the homologous recombination (HR) repair of camptothecin (CPT)-induced DNA damage. Together, our results provide a broad lysine crotonylome in response to CDYL and shed new light on the role of RPA1 Kcr in DNA repair, implicating functional importance of Kcr on non-histone substrates in diverse cellular processes.

2020-04-02 | PXD013616 | Pride

Crotonylome profiling reveals extensive lysine crotonylation in common wheat

Project description:Histone lysine crotonylation (Kcr) is a newly discovered protein post-translational modification (PTM), which was detected from yeast to humans and is mainly related with active transcription. With the development of proteomics technologies, high abundance of non-histone proteins modified by Kcr was also found recently. Here, we first report that lysine Kcr also occurs on cytoplasmic and mitochondrial proteins in common wheat (Triticum aestivum L.). We identified 4,696 Lys-acetylated sites on 1,726 proteins which involved in a wide variety of biological processes, such as chromatin-associated processes, Calvin-Benson cycle, glycolysis, protein metabolism and transport, which representing the largest dataset of lysine acylation proteome reported in the plant kingdom. Interestingly, 98 proteins were involved in multiple processes of photosynthesis, suggesting an important role of lysine Kcr in processes. In addition, 21 potentially specific Kcr motifs in wheat were detected. The protein interaction network analysis revealed that diverse interactions are modulated by protein Kcr. The overlap between Kcr and acetylation (Kac) indicated that they may coordinately regulate the function of some proteins in common wheat. Futhermore, comparative analysis indicated that lysine Kcr is conserved between common wheat and Nicotiana tabacum. Taken together, this study provided the first global survey of Kcr in wheat, making a promising starting point for further functional analysis of Kcr in plants.

2023-07-20 | PXD008483 | Pride

Global Proteomic Analysis of Lysine crotonylation in The Plant Pathogen Botrytis cinerea

Project description:Lysine crotonylation (Kcr), a recently discovered post-translational modification, plays a key role in the regulation of diverse cellular processes. Botrytis cinerea is a destructive necrotrophic fungal pathogen distributed worldwide with broad ranging hosts. However, the functions of Kcr are unknown in B. cinerea or any other plant fungal pathogens. Here, we comprehensively evaluated the crotonylation proteome of B. cinerea and identified 3967 Kcr sites in 1041 proteins, of which contained in 9 types of modification motifs. Our results show that although the crotonylation were largely conserved, different organisms contained distinct crotonylated proteins with unique functions. Bioinformatic analysis demonstrated that the majority of crotonylated proteins were distributed in cytoplasm (35%), mitochondria (26%) and nucleus (22%). The identified proteins were found to be involved in various metabolic and cellular processes, such as cytoplasmic translation and structural constituent of ribosome. Particularly, 26 crotonylated proteins participated in the pathogenicity of B. cinerea, suggesting a significant role for Kcr in this process. Protein interaction network analysis demonstrated that a mass of protein interactions are regulated by crotonylation. These data represent the ﬁrst report of the crotonylome of B. cinerea and provide a good foundation for further explorations of the role of Kcr in plant fungal pathogens.

2020-09-07 | PXD019358 | Pride

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

Project 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.

2018-07-23 | PXD008716 | Pride

Metabolically controlled histone H4K5 acylation/acetylation ratio drives BRD4 genomic distribution VII

Project description:In addition to acetylation, histones are modified by a series of competing longer chain acylations. Most of these acylation marks are enriched and co-exist with acetylation on active gene regulatory elements. Their seemingly redundant functions have hindered the understanding of histone acylations’ specific roles. Here, by using an acute lymphoblastic leukaemia (ALL) cell model and blasts from B-ALL patients, we demonstrate a role for mitochondrial activity in controlling histone acylation/acetylation ratio, especially at H4K5. An increase of the crotonylation and butyrylation over acetylation on H4K5 weakens BRD4-chromatin interaction and increases BRD4 nuclear mobility and availability for binding transcription start site associated nucleosome free regions of active genes. Our data suggest that, with regard to BRD4 dynamics, histone acylations including acetylation, should be considered collectively. A metabolism dependant control of the histone acetylation/longer chain acylation(s) ratio could constitute a common mechanism regulating bromodomain factors’ “reservoir” pool, availability and functional genomic distribution.

2021-06-25 | GSE174105 | GEO

Metabolically controlled histone H4K5 acylation/acetylation ratio drives BRD4 genomic distribution VI

2021-06-25 | GSE164071 | GEO