Genome-wide maps of H3K9Ac in wild type and sinhcaf mutant zebrafish embryos
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ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE198516 | GEO | 2022/03/15
REPOSITORIES: GEO
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Project description:Both genetic and environmental factors are implicated in Type 1 Diabetes (T1D). Since environmental factors can trigger epigenetic changes, we hypothesized that variations in histone posttranslational modifications (PTMs) at the promoter/enhancer regions of T1D susceptible genes may be associated with T1D. We therefore evaluated histone PTM variations at known T1D susceptible genes in blood cells from T1D patients versus healthy non-diabetic controls, and explored their connections to T1D. We used the chromatin-immunoprecipitation-linked-to-microarray approach to profile key histone PTMs, including H3-lysine-4 trimethylation (H3K4me3), H3K27me3, H3K9me3, H3K9 acetylation (H3K9Ac) and H4K16Ac at genes within the T1D susceptible loci in lymphocytes, and H3K4me3, H3K9me2, H3K9Ac and H4K16Ac at the IDDM1 region in monocytes of T1D patients and healthy controls separately. We screened for potential variations in histone PTMs using computational methods to compare datasets from T1D and controls. Interestingly, we observed marked variations in H3K9Ac levels at the upstream regions of HLA-DRB1 and HLA-DQB1 within the IDDM1 locus in T1D monocytes relative to controls. Additional experiments with THP-1 monocytes demonstrated increased expression of HLA-DRB1 and HLA-DQB1 in response to interferon- and TNF-treatment that were accompanied by changes in H3K9Ac at the same promoter regions as that seen in the patient monocytes. These results suggest that the H3K9Ac status of HLA-DRB1 and HLA-DQB1, two genes highly associated with T1D, may be relevant to their regulation and transcriptional response towards external stimuli. Thus, the promoter/enhancer architecture and chromatin status of key susceptible loci could be important determinants in their functional association to T1D susceptibility. We used ChIP-chip to profile key histone PTMs, including H3K4me3, H3K9me2, H3K9Ac and H4K16Ac, at the IDDM1 region in monocytes of T1D patients and healthy controls.
2012-05-31 | E-GEOD-36397 | biostudies-arrayexpress
Project description:Both genetic and environmental factors are implicated in Type 1 Diabetes (T1D). Since environmental factors can trigger epigenetic changes, we hypothesized that variations in histone posttranslational modifications (PTMs) at the promoter/enhancer regions of T1D susceptible genes may be associated with T1D. We therefore evaluated histone PTM variations at known T1D susceptible genes in blood cells from T1D patients versus healthy non-diabetic controls, and explored their connections to T1D. We used the chromatin-immunoprecipitation-linked-to-microarray approach to profile key histone PTMs, including H3-lysine-4 trimethylation (H3K4me3), H3K27me3, H3K9me3, H3K9 acetylation (H3K9Ac) and H4K16Ac at genes within the T1D susceptible loci in lymphocytes, and H3K4me3, H3K9me2, H3K9Ac and H4K16Ac at the IDDM1 region in monocytes of T1D patients and healthy controls separately. We screened for potential variations in histone PTMs using computational methods to compare datasets from T1D and controls. Interestingly, we observed marked variations in H3K9Ac levels at the upstream regions of HLA-DRB1 and HLA-DQB1 within the IDDM1 locus in T1D monocytes relative to controls. Additional experiments with THP-1 monocytes demonstrated increased expression of HLA-DRB1 and HLA-DQB1 in response to interferon- and TNF-treatment that were accompanied by changes in H3K9Ac at the same promoter regions as that seen in the patient monocytes. These results suggest that the H3K9Ac status of HLA-DRB1 and HLA-DQB1, two genes highly associated with T1D, may be relevant to their regulation and transcriptional response towards external stimuli. Thus, the promoter/enhancer architecture and chromatin status of key susceptible loci could be important determinants in their functional association to T1D susceptibility. We evaluated histone PTM variations at known T1D susceptible genes in blood cells from T1D patients versus healthy non-diabetic controls, and explored their connections to T1D. We used the ChIP-chip approach to profile key histone PTMs, including histone H3K4me3, H3K27me3, H3K9me3, H3K9 acetylation (H3K9Ac) and H4K16Ac, at genes within the T1D susceptible loci in lymphocytes.
2012-05-31 | E-GEOD-36402 | biostudies-arrayexpress
Project description:OCI-AML3 Acute myeloid leukemia cell line was used for ChIP-sequencing profiling of H3K4me3, H3K4me1, H3K9ac and H3K27ac histone post-translational modifications to identify active promoter and enhancer regions.
2022-04-04 | GSE199964 | GEO
Project description:This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains ChIP-chip data on Agilent 244K dual-color arrays for antibody: H3K9Ac at 12 different time-points of Drosophila development. Current Dataset: [GSM386138..GSM386146]: ChIP-chip of H3K9AC in Drosophila embryos at 12-16 hours of development [GSM386148..GSM386156]: ChIP-chip of H3K9AC in Drosophila L1 larvae [GSM386158..GSM386166]: ChIP-chip of H3K9AC in Drosophila L2 larvae [GSM386168..GSM386176]: ChIP-chip of H3K9AC in Adult female Drosophila [GSM418290..GSM418298]: ChIP-chip of H3K9AC in Adult male Drosophila [GSM442311..GSM442316]: ChIP-chip of H3K9AC in Drosophila embryos at 8-12 hours of development [GSM442317..GSM442325]: ChIP-chip of H3K9AC in Adult male Drosophila - Set2 [GSM442326..GSM442334]: ChIP-chip of H3K9AC in Pupae [GSM442335..GSM442343]: ChIP-chip of H3K9AC in L3 [GSM442344..GSM442352]: ChIP-chip of H3K9AC in Drosophila embryos at 20-24 hours of development [GSM442353..GSM442361]: ChIP-chip of H3K9AC in Drosophila embryos at 4-8 hours of development [GSM442362..GSM442370]: ChIP-chip of H3K9AC in Drosophila embryos at 0-4 hours of development For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
2009-03-28 | GSE15426 | GEO
Project description:Purpose: Exploring the alteration in histone acetylation colocalized with CREB/CRTC binding, which are important for long-term memory maintenance Methods: The nuclei of Drosophila mushroom bodies were purified and the histone acetylation and CREB/CRTC binding were examined by ChIP-seq using specific antibodies. The sequencing was performed using SOLiD, and aligned to dm3 using Lifescope..The sequence reads that passed quality filters were analyzed by peak calling using PICS and ERD equipped on Strand NGS software. This method using two algorisms excludes false-positive calling of peaks. The PICS and ERD were run using a default setting except for the following parameters; for PICS, 120 bp as an average fragment length, 10 bp as a minimum distance between forward and reverse reads, 200 bp as a minimum distance between forward and reverse reads, 100 bp as a window width, with 5% false discovery rate; for ERD, 2 as an enrichment factor, 100 bp as a window size, 10 bp as a window slide size, 100 bp as a minimum region size. The peaks obtained by ERD analysis were filtered by an enrichment factor of 1.5, and a density of reads at 0.3 for H3K9Ac, 0.15 for H4K16Ac, 0.18 for CREB and 0.15 for CRTC. To determine the histone acetylation-increased sites, the peaks determined from 3 replicates of the trained samples were summed to analyze all peaks. Then the centers of the H3K9Ac and H4K16Ac peaks were extracted, and then used to create neighboring 400 bp windows. The mapped reads were counted in these 400 bp windows for each biological replicate of ChIP-seq analysis. The counted read numbers in individual regions were normalized by elav for H3K9Ac ChIP-seq, and gapdh2 for H4K16Ac ChIP. The normalized read numbers in individual windows obtained from the spaced trained flies and the naïve flies were analyzed by Student’s t test (p < 0.05). Standard deviations of the normalized read numbers in individual windows from 3 replicates of naïve flies were 0.07 in H3K9Ac-ChIP-seq and 0.10 in H4K16Ac-ChIP-seq. Significantly increased peaks showing a more than 1.2-fold increase (>2SD) were determined as sites with an increase in H3K9Ac or H4K16Ac. Results: Using an optimized data analysis workflow, the filtered reads amounted to 12-15 million reads for H3K9Ac in each of 3 replicates, 5-7 million reads for H4K16 in each of 3 replicates, 2.4 million reads for CREB, 2 million reads for CRTC, and 2.9 million reads for input. Using anti-H3K9Ac antibody, we found significant increases in H3K9Ac 1 day after training, and 75.0% of these mapped within 500bps of the transcriptional start sites (TSSs) of 1766 genes. Using anti-H4K16Ac antibody, we found significant increases in H4K16Ac 1 day after spaced training, and 61.6% of these mapped within 500bps of the TSSs of 1320 genes. Epigenetic changes in the vicinity of TSSs suggests that expression of these genes may be increased in LTM maintenance. We also examined CRTC and CREB binding 1 day after training. We identified 2390 CRTC binding sites, of which 79.6% of these were close to CREB binding sites. These CREB/CRTC binding sites mapped to 1394 genes, and were predominately located within 500bp from TSSs (55.4%). Of the 1394 CREB/CRTC target genes, 346 genes showed increases in H3K9Ac, 319 showed increases in H4K16Ac, and 135 showed increases in both. Conclusions: Our study represents the first detailed analysis of chromatin state related to memory in Drosophila mushroom bodied. The optimized data analysis workflows reported here should provide a framework for comparative investigations of tissue-specific epigenetic alterations.
2017-02-09 | GSE73386 | GEO
Project description:Both genetic and environmental factors are implicated in Type 1 Diabetes (T1D). Since environmental factors can trigger epigenetic changes, we hypothesized that variations in histone posttranslational modifications (PTMs) at the promoter/enhancer regions of T1D susceptible genes may be associated with T1D. We therefore evaluated histone PTM variations at known T1D susceptible genes in blood cells from T1D patients versus healthy non-diabetic controls, and explored their connections to T1D. We used the chromatin-immunoprecipitation-linked-to-microarray approach to profile key histone PTMs, including H3-lysine-4 trimethylation (H3K4me3), H3K27me3, H3K9me3, H3K9 acetylation (H3K9Ac) and H4K16Ac at genes within the T1D susceptible loci in lymphocytes, and H3K4me3, H3K9me2, H3K9Ac and H4K16Ac at the IDDM1 region in monocytes of T1D patients and healthy controls separately. We screened for potential variations in histone PTMs using computational methods to compare datasets from T1D and controls. Interestingly, we observed marked variations in H3K9Ac levels at the upstream regions of HLA-DRB1 and HLA-DQB1 within the IDDM1 locus in T1D monocytes relative to controls. Additional experiments with THP-1 monocytes demonstrated increased expression of HLA-DRB1 and HLA-DQB1 in response to interferon- and TNF-treatment that were accompanied by changes in H3K9Ac at the same promoter regions as that seen in the patient monocytes. These results suggest that the H3K9Ac status of HLA-DRB1 and HLA-DQB1, two genes highly associated with T1D, may be relevant to their regulation and transcriptional response towards external stimuli. Thus, the promoter/enhancer architecture and chromatin status of key susceptible loci could be important determinants in their functional association to T1D susceptibility.
2012-06-01 | GSE36397 | GEO
Project description:This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains ChIP-chip data on Agilent 244K dual-color arrays for antibody: H3K9Ac at 12 different time-points of Drosophila development. Current Dataset: [GSM386138..GSM386146]: ChIP-chip of H3K9AC in Drosophila embryos at 12-16 hours of development [GSM386148..GSM386156]: ChIP-chip of H3K9AC in Drosophila L1 larvae [GSM386158..GSM386166]: ChIP-chip of H3K9AC in Drosophila L2 larvae [GSM386168..GSM386176]: ChIP-chip of H3K9AC in Adult female Drosophila [GSM418290..GSM418298]: ChIP-chip of H3K9AC in Adult male Drosophila [GSM442311..GSM442316]: ChIP-chip of H3K9AC in Drosophila embryos at 8-12 hours of development [GSM442317..GSM442325]: ChIP-chip of H3K9AC in Adult male Drosophila - Set2 [GSM442326..GSM442334]: ChIP-chip of H3K9AC in Pupae [GSM442335..GSM442343]: ChIP-chip of H3K9AC in L3 [GSM442344..GSM442352]: ChIP-chip of H3K9AC in Drosophila embryos at 20-24 hours of development [GSM442353..GSM442361]: ChIP-chip of H3K9AC in Drosophila embryos at 4-8 hours of development [GSM442362..GSM442370]: ChIP-chip of H3K9AC in Drosophila embryos at 0-4 hours of development For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf For each combination of time-point and antibody, triplicate ChIP experiments have been performed and hybridized on Agilent 244K arrays. 3 arrays per genome have been used so that each time-point is a set of 9 tiling arrays.
2010-10-08 | E-GEOD-15426 | biostudies-arrayexpress
Project description:Both genetic and environmental factors are implicated in Type 1 Diabetes (T1D). Since environmental factors can trigger epigenetic changes, we hypothesized that variations in histone posttranslational modifications (PTMs) at the promoter/enhancer regions of T1D susceptible genes may be associated with T1D. We therefore evaluated histone PTM variations at known T1D susceptible genes in blood cells from T1D patients versus healthy non-diabetic controls, and explored their connections to T1D. We used the chromatin-immunoprecipitation-linked-to-microarray approach to profile key histone PTMs, including H3-lysine-4 trimethylation (H3K4me3), H3K27me3, H3K9me3, H3K9 acetylation (H3K9Ac) and H4K16Ac at genes within the T1D susceptible loci in lymphocytes, and H3K4me3, H3K9me2, H3K9Ac and H4K16Ac at the IDDM1 region in monocytes of T1D patients and healthy controls separately. We screened for potential variations in histone PTMs using computational methods to compare datasets from T1D and controls. Interestingly, we observed marked variations in H3K9Ac levels at the upstream regions of HLA-DRB1 and HLA-DQB1 within the IDDM1 locus in T1D monocytes relative to controls. Additional experiments with THP-1 monocytes demonstrated increased expression of HLA-DRB1 and HLA-DQB1 in response to interferon- and TNF-treatment that were accompanied by changes in H3K9Ac at the same promoter regions as that seen in the patient monocytes. These results suggest that the H3K9Ac status of HLA-DRB1 and HLA-DQB1, two genes highly associated with T1D, may be relevant to their regulation and transcriptional response towards external stimuli. Thus, the promoter/enhancer architecture and chromatin status of key susceptible loci could be important determinants in their functional association to T1D susceptibility.
2012-06-01 | GSE36402 | GEO
Project description:We presented a genome-wide characterization for H3K9 acetylation (H3K9ac) binding regions in normal temperature and heat-stress conditions via ChIP-seq. The results revealed H3K9ac was an extensive epigenetic modulation in A. japonicus. We further identified differentially acetylated regions (DARs) under heat stress.
2022-11-03 | GSE186066 | GEO
Project description:We report the high-throughput profiling of H3K9ac and SRT1 in MH63 and SRT1 RNAi. By obtaining about 8 million pair-end reads from H3K9ac and 6 million pair-end reads from SRT1, we find that about 45% of rice genes are marked by H3K9ac in 11 day-old seedlings. There are 1824 genes may be bound directly by OsSRT1. OsSRT1 is a site-specific deacetylase involved in deacetylation of H3K9 over specific genes. Overlapping between increased H3K9ac peaks in the RNAi plants and that of OsSRT1-binding was found over 37 genes, suggesting that OsSRT1 directly targeted to these genes for H3K9 deacetylation. The observations that H3K9ac was enriched at the 5M-bM-^@M-^Y end of genes larger than 1.5 kb and OsSRT1 RNAi enhanced the enrichment at that position. However, the OsSRT1-binding was found to be enriched over gene bodies. While the meaning of this binding profile is not yet clear, it is speculated that OsSRT1 may contribute to maintain the low level of H3K9ac in the gene body. In addition, this work revealed that OsSRT1 is enriched over retrotransposons. Examination of H3K9ac in MH63(WT) and SRT1-RNAi, OsSRT1 in MH63.
2013-02-10 | E-GEOD-40054 | biostudies-arrayexpress