GEO DataSets

(Submitter supplied) 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.

Organism:

Oryza sativa Japonica Group

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18525

4 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13834

41 Samples

Download data: TXT, XLSX

(Submitter supplied) 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). more...

Organism:

Homo sapiens; Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13112 GPL11002 GPL9052

9 Samples

Download data: BED

(Submitter supplied) In eukaryotic cells, DNA is tightly packed in the nucleus in chromatin which has histones as its main protein component. Histones are subject to a large number of distinct post-translational modifications, whose sequential or combinatorial action affects genome function. Here, we report the identification of acetylation at lysine 36 in histone H3 (H3K36ac) as a modification in Arabidopsis thaliana. H3K36ac was found to be an evolutionary conserved modification in seed plants. It is highly enriched in euchromatin and very low in heterochromatin. Genome-wide ChIP-seq experiments revealed that H3K36ac is generally found at the 5’ end of genes. Independently of gene length, H3K36ac covers about 500 bp, about two to three nucleosomes, immediately downstream of the transcriptional start. H3K36ac overlaps with H3K4me3 and the H2A.Z histone variant. The histone acetyl transferase GCN5 and the histone deacetylase HDA19 are required for normal steady state levels of H3K36ac in plants. There is negative crosstalk between H3K36ac and H3K36me3, mediated by the histone methyl transferase SDG8 and GCN5. H3K36ac levels are associated with transcriptional activity but show no linear relation. Instead, H3K36ac is a binary indicator of transcription

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13222

29 Samples

Download data: BW

(Submitter supplied) 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 P19 embryonal carcinoma cells.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL24247

28 Samples

Download data: BW, TXT

(Submitter supplied) 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.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

22 Samples

Download data: BW, TXT

(Submitter supplied) We report the application of CHIP-seq technology for high-throughput profiling of histone modifications in HY(Hwayong) and chd1(chr729). By obtaining about 12 million reads of sequence from chromatin immunoprecipitated DNA, we generated genome-wide H3K4me3 and H3k27me3 maps of HY(Hwayong) and chd1(chr729). We find that lysine 4 and lysine 27 trimethylation marked genes effectively losed in chd1 compared to HY.

Organism:

Oryza sativa Japonica Group

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13834

4 Samples

Download data: FA, FASTQ, TXT, WIG

(Submitter supplied) In order to study the function of CHR729 in rice, the T-DNA insertion mutant of CHR729 was obtained and analysed.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

6 Samples

Download data: CEL

(Submitter supplied) To gain a deeper insight into how crotonate regulates embryonic neural stem/progenitor cells (NSPCs) proliferation and differentiation, CUT&Tag was performed to analyze the genome-wide changes of H3K4me3 and H3K27me3 stimulated with crotonate in E13.5 NSPCs.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

6 Samples

Download data: BW, TXT

(Submitter supplied) To gain a deeper insight into how crotonate regulates embryonic neural stem/progenitor cells (NSPCs) proliferation and differentiation, ChIP-seq was performed to analyze the genome-wide changes of H3K4me3, H3K27ac and H3K27me3 stimulated with crotonate in E13.5 NSPCs.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24247

10 Samples

Download data: BW, TXT

(Submitter supplied) 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.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL24247 GPL23479

30 Samples

Download data: BED, BW, TXT

(Submitter supplied) Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene expression allows us to understand the mechanisms underlying cellular differentiation during xylogenesis (wood formation) and identify novel functional regions in plant genomes. However, woody tissue poses unique challenges for using high-throughput chromatin immunoprecipitation (ChIP) techniques for studying genome-wide histone modifications in vivo. more...

Organism:

Eucalyptus grandis

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20030

5 Samples

Download data: BEDGRAPH

(Submitter supplied) We generated genome-wide high-resolution maps of H4K16ac and H3K23ac in Arabidopsis thaliana and Oryza sativa.

Organism:

Arabidopsis thaliana; Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13222 GPL13160

5 Samples

Download data: BW

(Submitter supplied) We conducted genome-wide identification of R-loops followed by integrative analyses of R-loops with relation to gene expressionand epigenetic signatures in the rice genome. We found that the correlation between gene expression levels and profiled R-looppeak levels was dependent on the positions of R-loops within gene structures (hereafter named 'genic position'). Both antisenseonly (ASO)-R-loops and sense/antisense(S/AS)-R-loops sharply peaked around transcription start sites (TSSs), and these peaklevels corresponded positively with transcript levels of overlapping genes. more...

Organism:

Oryza sativa

Type:

Methylation profiling by high throughput sequencing; Other

Platforms:

GPL19290 GPL24468

10 Samples

Download data: BED, TXT

(Submitter supplied) We sought to characterize the genomic localization of the YEATS domain protein AF9 in the macrophage-like cell line RAW 264.7 +/- LPS stimulation and +/- sodium crotonate pretreatment. We performed chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) for endogenous AF9 or for a FLAG-tagged AF9 transgene in RAW264.7 or a RAW264.7 cell line engineered to express FLAG-AF9, respectively.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17021 GPL19057

10 Samples

Download data: TDF

(Submitter supplied) Genome wide chromatin maps have shown that spreading repressive histone modifications such as H3K9me3 and H4K20me3 are present on pericentromeric and telomeric repeats and on the inactive X chromosome where H3K27me3 or H3K9me3 alternately modify megabasepair sized domains. However, only a few regions along an autosome of which Homeobox gene clusters are notable examples, have been shown to display spreading of repressive histone modifications. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9185

1 Sample

Download data: GFF, TXT, WIG

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array; Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL6814 GPL6815 GPL6813

39 Samples

Download data: TXT

(Submitter supplied) Genome wide chromatin maps have shown that spreading repressive histone modifications such as H3K9me3 and H4K20me3 are present on pericentromeric and telomeric repeats and on the inactive X chromosome where H3K27me3 or H3K9me3 alternately modify megabasepair sized domains. However, only a few regions along an autosome of which Homeobox gene clusters are notable examples, have been shown to display spreading of repressive histone modifications. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL6815

5 Samples

Download data: TXT

(Submitter supplied) Genome wide chromatin maps have shown that spreading repressive histone modifications such as H3K9me3 and H4K20me3 are present on pericentromeric and telomeric repeats and on the inactive X chromosome where H3K27me3 or H3K9me3 alternately modify megabasepair sized domains. However, only a few regions along an autosome of which Homeobox gene clusters are notable examples, have been shown to display spreading of repressive histone modifications. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL6815 GPL6814 GPL6813

34 Samples

Download data: TXT

(Submitter supplied) Amino-terminal tails of histones are targets for diverse post-translational modifications whose combinatorial action may constitute a code that will be read and interpreted by cellular proteins to define particular transcriptional states. Here, we describe monomethylation of histone H3 lysine 23 (H3K23me1) as a novel histone modification in plants. H3K23me1 is an evolutionary conserved mark in diverse flowering plant species. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13222

12 Samples

Download data: BW