Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PekUSZ_Development of Lysine Crotonyl-mimic Probe to Covalently Identify H3K27Cr Interacting Proteins

ABSTRACT: we developed a novel H3g27Cr peptide probe mimicking Histone lysine crotonylation, which could more effectively recognize Histone Kcr-interacting proteins through covalent proximity-induced bioconjugation. We initially validated the orthogonality and cysteine reactivity of crotonyl-like group through protein-ligand binding models of PDZΔRGS3 and PLCγ1-c SH2, and further showed the feasibility of H3g27Cr to covalently bind the known Kcr “eraser” HDAC1. With the H3g27Cr probe in hands, we successfully identified and validated one unknown H3K27Cr-interacting protein, the transcriptional activator STAT3, from AP-MS experiment in A549 cell lysates. The candidate protein STAT3 was found that directly bound to the Histone H3K27Ac/Cr in XL-MS and pull-down assays, and this interaction might reduce the H3K27Ac/Cr levels.

ORGANISM(S): Homo Sapiens

SUBMITTER: Rui Wang

PROVIDER: PXD039527 | iProX | Tue Jan 17 00:00:00 GMT 2023

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Similar Datasets

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

Genome-wide profiling of histone lysine crotonylation reveals positive regulation of transcription in rice

Project description:Histone lysine crotonylation (Kcr) is a newly discovered post-translational modification (PTM) existing in mammalian. To assess relevance in histone Kcr and genome, we performed on genomic localization analysis of histone Kcr by ChIP-seq analysis.

2018-06-01 | GSE108542 | GEO

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

2011-10-06 | GSE32663 | GEO

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

Nuclear condensation of CDYL links histone crotonylation and cystogenesis in autosomal dominant polycystic kidney disease [RNA-Seq]

Project description:Background:molecular mechanisms coupling cellular metabolisms with the epigenome in cystic cells remains largely unknown Methods:To investigate the molecular mechanisms underlying the suppression of cyst growth by CDYL overexpression, we generated an engineered ADPKD cell line by stably expressing CDYL with TY1 tag in WT 9-12 human ADPKD cells (CDYL OE). We profiled genome-wide distribution of CDYL through chromatin immunoprecipitation coupled with sequencing (ChIP-seq) analysis in both parental WT 9-12 cells (control) and CDYL OE cells. Genetic overexpression of CDYL reduces histone Kcr. We examined histone Kcr on CDYL-target genes by performing ChIP-seq analyses using antibody recognizing PanKcr and H3K18cr in control and CDYL OE cells. Results: Using integrative cistromic and transcriptomic analyses, CDYL-regulated cyst-associated genes are identified, whose downregulation depends on CDYL-mediated suppression of histone Kcr. Conclusions: Thus, through establishing a metabolic niche via nuclear condensation, CDYL connects metabolic changes to transcriptional response via histone Kcr in ADPKD.

2022-05-24 | GSE183510 | GEO

Nuclear condensation of CDYL links histone crotonylation and cystogenesis in autosomal dominant polycystic kidney disease [ChIP-Seq]

2022-05-24 | GSE183511 | GEO

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

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

The Functional Roles of HDAC1 and HDAC2 in Neurodevelopment of the Mouse Brain

Project description:In this study, we explored the roles of histone deacetylases HDAC1 and HDAC2 in the developmental dynamics of the mouse brain. We discovered that these epigenetic regulators, HDAC1/2, are crucial in mediating the transition from neural epithelial cells (NEs) to radial glial cells (RGCs). To probe the epigenomic influence of HDAC1/2 on cortical development, we utilized a suite of techniques including RNA sequencing (RNA-seq), single-cell RNA sequencing (scRNA-seq), and H3K27ac Cleavage Under Targets and Tagmentation (CUT&Tag) in both wild-type (WT) and HDAC1/2-deficient brain samples. Our analysis identified a significant dysregulation of numerous transcription-related genes in the HDAC1 and HDAC2 mutant brains. These findings underscore the critical role of HDAC1/2 as epigenetic modulators in the NE-to-RGC transition.

2024-10-01 | GSE251727 | 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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data