Lysine Degradation Reprograms Tumour Immunity through Histone Crotonylation [ChIP-seq]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA860227 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Lysine Degradation Reprograms Tumour Immunity through Histone Crotonylation [RNA-seq]
| PRJNA860228 | ENA
Project description:Lysine Catabolism Reprograms Tumour Immunity through Histone Crotonylation.
| PRJNA860225 | ENA
Project description:To understand how GCDH enhances the oncogenic traits in GSCs, we carried out comparative transcriptomic analysis in two patient-derived GSCs (GSC23, GSC3028) with or without GCDH depletion to identify the driving events. To further examine the connection between lysine catabolism and GSC functions, we controlled L-lysine culture concentrations (0.2 and 2 mM) of GSCs in lysine-deprived media and performed RNA-seq. To address the functional significance of ECHS1 loss in tumour biology, we carried out RNA-seq in two early-passage DGCs (DGC23, DGC3028) with or without ECHS1 depletion. Kcr, H3K27ac or H3K9me3 ChIP-seq was performed in GSC23 to understand the molecular basis of how GCDH loss or lysine restriction affects chromatin landscape.
2023-03-16 | GSE208616 | GEO
Project description:To understand how GCDH enhances the oncogenic traits in GSCs, we carried out comparative transcriptomic analysis in two patient-derived GSCs (GSC23, GSC3028) with or without GCDH depletion to identify the driving events. To further examine the connection between lysine catabolism and GSC functions, we controlled L-lysine culture concentrations (0.2 and 2 mM) of GSCs in lysine-deprived media and performed RNA-seq. To address the functional significance of ECHS1 loss in tumour biology, we carried out RNA-seq in two early-passage DGCs (DGC23, DGC3028) with or without ECHS1 depletion. Kcr, H3K27ac or H3K9me3 ChIP-seq was performed in GSC23 to understand the molecular basis of how GCDH loss or lysine restriction affects chromatin landscape.
2023-03-16 | GSE208617 | GEO
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
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:Histone Lysine Crotonylation Regulates Long-Term Memory Storage
| PRJNA1181824 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2023-03-15 | GSE208618 | GEO
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
Project description:Histone lysine acetylation and methylation regulate gene transcription through coordination of chromatin structure and transcriptional activity. However, our understanding of the role of histones in gene regulation is far from complete, in part due to newly discovered novel histone modifications, whose functions are yet to be uncovered1. Here we report that histone H3 lysine 27 crotonylation (H3K27cr) is selectively recognized by the YEATS domain of GAS41 in association with SIN3a-HDAC1/2 co-repressor complex for gene transcriptional repression. The GAS41 YEATS domain dimer binds proto-oncogenic transcription factor c-Myc, which recruits GAS41/SIN3a-HDAC1/2 complex to target gene loci in chromatin such as cell cycle inhibitor p21. Transcriptional de-repression of p21, directed by tumor suppressor p53 upon doxorubicin stimulation, entails dissociation of c-Myc/GAS41/SIN3a-HDAC1/2 complex from chromatin, reduced H3K27 crotonylation, and consequentially increased H3K27 acetylation at p21 locus. GAS41 knockout or H3K27cr binding depletion with CRISPR/Cas9 results in p21 activation, cell cycle arrest and tumor growth inhibition in mice. Our study explains mechanistically causal effect of GAS41 and c-Myc gene amplification on down-regulation of p21 in human colorectal cancer, and suggests GAS41 as an anti-cancer target. We propose that H3K27 crotonylation represents a previously unrecognized, distinct chromatin state for gene transcriptional repression in contrast to H3K27 trimethylation for long-term transcriptional silencing and H3K27 acetylation for transcriptional activation.
2023-10-03 | GSE128590 | GEO