Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE32663 | GEO | 2011/10/06

SECONDARY ACCESSION(S): PRJNA147047

REPOSITORIES: GEO

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

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

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

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

| PRJNA147047 | ENA

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

Dynamic profiling of histone Kcr and Kla during neural differentiation in vivo

Project description:To gain a deeper insight into dynamic changes of histone lysine crotonylation and lactylation during embryonic neurogenesis, ChIP-seq, ATAC-seq and RNA-seq were performed to analyze the genome-wide changes of histone Kcr and Kla in the developing telencephalon.

2022-06-30 | GSE171088 | GEO

Dynamic profiling of histone Kcr and Kla during neural differentiation in P19 embryonal carcinoma cells

2022-06-30 | GSE171832 | GEO

Lysine 2-hydroxyisobutyrylatome profiling reveals extensive lysine 2-hydroxyisobutyrylation in common wheat

Project description:In this work, we first analyzed wheat (Triticum aestivum L.) lysine Khib sites by mass spectrometry. A total of 3,348 lysine modification sites from 1,047 proteins were identified in wheat seedlings. The identified Kcr proteins were discovered to be widespread. Bioinformatic data indicated these Kcr proteins involved in diverse biology and metabolic processes. Our data indicated that Khib is as dynamic as Kac and Khib changes in response to the deacetylase inhibitors Trichostatin A (TSA) and nicotinamide (NAM). We tested histone Khib and deacylation activities of several wheat HATs and HDACs using wheat Krnose EMS mutants. Finally, we confirmed lysine Khib on K206 of PGK was a regulatory modification using mustagenesis experiments and found that de-Khib impaired protein interactions of PGK. Our data demonstrate that the regulatory scope of lysine Khib is broad and comparable with that of other major PTMs. Wheat histone Khib are dynamically regulated by environmental cues and are likely to be removed by different mechanisms.

2022-12-31 | PXD012666 | Pride

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

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

ChIP-seq and RNA-seq analysis of histone Kcr in the embryonic forebrain and neural stem/progenitor cells.

Project description:To gain a deeper insight into how histone lysine crotonylation regulates embryonic neural stem/progenitor cells (NSPCs) proliferation and differentiation, ChIP-seq and RNA-seq were performed to analyze the genome-wide changes of histone Kcr and transcriptiome changes stimulated with crotonate and MS-275 in E13.5 NSPCs.

2021-06-22 | GSE124540 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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