Genome-wide profiling of histone lysine crotonylation reveals positive regulation of transcription in rice
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ABSTRACT:
ORGANISM(S): Oryza sativa Japonica Group
PROVIDER: GSE108542 | GEO | 2018/06/01
REPOSITORIES: GEO
Similar Datasets
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
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
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
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.
2011-10-06 | GSE32663 | GEO
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
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
Project description:Toxoplasma gondii (T. gondii) is an obligate intracellular parasite that can infect almost all warm-blooded animals, causing serious public health problems. Lysine crotonylation (Kcr) is a newly discovered posttranslational modification (PTM), which has been proved that is relevant to procreation regulation, active transcription and cell signaling pathway. However, the biological functions of crotonylation have not yet been reported in macrophages infected with T. gondii. In our study, we performed a ChIP-seq analysis of porcine alveolar macrophages infected with T. gondii RH to explore the relationship of histone Kcr with T. gondii infection.
2021-12-31 | GSE167340 | GEO
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
Project description: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.
2018-09-06 | PXD009091 | Pride
Project description:Lysine crotonylation on histones is a recently identified post-translational modification that has been demonstrated to associate with active promoters and to directly stimulate transcription.Given that crotonyl-CoA is essential for the acyl transfer reaction and it is a metabolic intermediate widely localized within the cell, we postulate that lysine crotonylation on non-histone proteins could also widely exist. Using specific antibody to enrich crotonylated lysine(Kcr) peptides followed by high-resolution mass spectrometry analysis reveals that crotonylated proteins and lysine residues. Bioinformatic analysis reveals that crotonylated proteins are particularly enriched in the nuclei, that lysine crotonylation alters level of the modified proteins in the chromatin and that cotonylation of a subset of proteins influences DNA replication and cell cycle. Taken together, our data indicate that lysine crotonylation could be induced in a large number of proteins other than histones and this type of acyl modification could play an important role regulating multiple cellular processes.
2016-06-11 | MSV000079810 | MassIVE