Investigating the requirement of H3K14 and H3P16 for optimal H3K4me3
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Similar Datasets
Project description:ChIP-seq experiment for histone H3 and H3K4me3 from wild-type Saccharomyces cerevisiae (WT) and strains in which H3K14 has been substituted for alanine (K14A) or H3P16 has been substituted with valine (P16V).
2014-07-22 | E-MTAB-2717 | biostudies-arrayexpress
Project description:Here, we have collapsed multiple analysis problems into two coherent categories, signal detection and signal estimation and adapted linear-optimal solutions from signal processing theory. Our algorithms for detection (DFilter) and estimation (EFilter) extend naturally to integration of multiple datasets. In benchmarking tests, DFilter outperformed assay-specific algorithms at identifying promoters from histone ChIP-seq, binding sites from transcription factor (TF) ChIP-seq and open chromatin regions from DNase- and FAIRE-seq data. EFilter similarly outperformed an existing method for predicting mRNA levels from histone ChIP-seq data (Spearman correlation: 0.81 - 0.89). We performed H3K4me3 and H3K36me3 ChIP-seq on e11.5 mouse forebrain and used DFilter and EFilter to predict promoters and developmental gene expression, uncovering plausible gene targets for SNPs associated with neurodevelopmental disorders. Generated two histone modifiction ChiP-seq in developing embryo mouse forebrain and using them for making bioligical inferences
2013-06-10 | E-GEOD-34073 | biostudies-arrayexpress
Project description:Trimethylation of histone H3 lysine 4 (H3K4me3) is associated with transcriptional start sites and proposed to regulate transcription initiation. However, redundant functions of the H3K4 SET1/COMPASS methyltransferase complexes complicate elucidation of the specific role of H3K4me3 in transcriptional regulation. Here, by using mouse embryonic stem cells (mESCs) as a model system, we show that acute ablation of shared subunits of the SET1/COMPASS complexes leads to complete loss of all H3K4 methylation. H3K4me3 turnover occurs more rapidly than H3K4me1 and H3K4me2 and is dependent on KDM5 demethylases. Surprisingly, acute loss of H3K4me3 does not have detectable effects on transcriptional initiation but leads to a widespread decrease in transcriptional output, an increase in RNA polymerase II (RNAPII) pausing and slower elongation. Notably, we show that H3K4me3 is required for the recruitment of the Integrator Complex Subunit 11 (INTS11), which is essential for the eviction of paused RNAPII and transcriptional elongation. Thus, our study demonstrates a distinct role for H3K4me3 in transcriptional pause-release and elongation rather than transcriptional initiation.
2023-02-10 | PXD039176 | Pride
Project description:The experiment aimed at investigating the profiles of two histone marks (H3K27me3 and H3K4me3) in hypothalamus tissues of 35 days-old control (n=3) and thermally-manipulated (cyclic rise in egg incubation temperature of 1.5°C from days 7 to 16 of embryogenesis; n=3) chickens.
2019-10-31 | E-MTAB-7300 | biostudies-arrayexpress
Project description:The experiment aimed at investigating the profiles of two histone marks (H3K27me3 and H3K4me3) in muscle tissues (Pectoralis major) of 35 days-old control (n=3) and thermally-manipulated (cyclic rise in egg incubation temperature of 1.5°C from days 7 to 16 of embryogenesis; n=3) chickens.
2019-10-31 | E-MTAB-7297 | biostudies-arrayexpress
Project description:Arabidopsis telomeric repeat binding factors (TRBs) can bind telomeric DNA sequences to protect telomeres from degradation. TRBs can also recruit Polycomb Repressive Complex 2 (PRC2) to deposit tri-methylation of H3 lysine 27 (H3K27me3) over certain target loci. Here, we demonstrate that TRBs also associate and colocalize with JUMONJI14 (JMJ14) and trigger H3K4me3 demethylation at some loci. The trb1/2/3 triple mutant and the jmj14-1 mutant show an increased level of H3K4me3 over TRB and JMJ14 binding sites, resulting in up-regulation of their target genes. Furthermore, tethering TRBs to the promoter region of genes with an artificial zinc finger (TRB-ZF) successfully triggers target gene silencing, as well as H3K27me3 deposition, and H3K4me3 removal. Interestingly, JMJ14 is predominantly recruited to ZF off-target sites with low levels of H3K4me3, which is accompanied with TRB-ZFs triggered H3K4me3 removal at these loci. These results suggest that TRB proteins coordinate PRC2 and JMJ14 activities to repress target genes via H3K27me3 deposition and H3K4me3 removal.
2023-02-22 | MSV000091349 | MassIVE
Project description:The functional determinants of histone H3 Lys-4 trimethylation (H3K4me3), their potential dependency on histone H2B monoubiquitination (H2Bub) and their contribution in defining gene expression programs are poorly defined in plant systems. Differently from S. cerevisiae in which a single SET1 protein catalyzes H3 Lys-4 trimethylation as part of COMPASS (COMPlex of proteins ASsociated with SET1), this activity involves multiple histone methyltransferases (HMTs) in Arabidopsis thaliana, among which the plant-specific SDG2 (SET DOMAIN GROUP2) has a prominent role. Here we report that SDG2 co-regulates hundreds genes with SWD2-like b (S2Lb), a plant ortholog of the Swd2 axillary subunit of the evolutionarily conserved COMPASS complex. Accordingly, S2Lb associates with the AtCOMPASS core subunit WDR5a within a high-molecular weight complex and is required for proper H3K4me3 enrichment over genes highly occupied by RNA Polymerase II. S2Lb knock-out plants display little transcriptomic defects, suggesting that H3K4me3 deposition is important for optimal gene induction rather than for determining on/off transcriptional states. We further report that S2Lb and H3K4me3 are accurately targeted over most genes in hub1 mutant plants lacking histone H2B monoubiquitination. Collectively, our study indicates that a plant-specific COMPASS-like complex acting mainly through an H2Bub-independent mechanism is a major determinant of H3K4me3 deposition in Arabidopsis.
2019-05-04 | GSE124296 | GEO
Project description:Here, we have collapsed multiple analysis problems into two coherent categories, signal detection and signal estimation and adapted linear-optimal solutions from signal processing theory. Our algorithms for detection (DFilter) and estimation (EFilter) extend naturally to integration of multiple datasets. In benchmarking tests, DFilter outperformed assay-specific algorithms at identifying promoters from histone ChIP-seq, binding sites from transcription factor (TF) ChIP-seq and open chromatin regions from DNase- and FAIRE-seq data. EFilter similarly outperformed an existing method for predicting mRNA levels from histone ChIP-seq data (Spearman correlation: 0.81 - 0.89). We performed H3K4me3 and H3K36me3 ChIP-seq on e11.5 mouse forebrain and used DFilter and EFilter to predict promoters and developmental gene expression, uncovering plausible gene targets for SNPs associated with neurodevelopmental disorders.
2013-06-10 | GSE34073 | GEO
Project description:The functional determinants of histone H3 Lys-4 trimethylation (H3K4me3), their potential dependency on histone H2B monoubiquitination (H2Bub) and their contribution in defining gene expression programs are poorly defined in plant systems. Differently from S. cerevisiae in which a single SET1 protein catalyzes H3 Lys-4 trimethylation as part of COMPASS (COMPlex of proteins ASsociated with SET1), this activity involves multiple histone methyltransferases (HMTs) in Arabidopsis thaliana, among which the plant-specific SDG2 (SET DOMAIN GROUP2) has a prominent role. Here we report that SDG2 co-regulates hundreds genes with SWD2-like b (S2Lb), a plant ortholog of the Swd2 axillary subunit of the evolutionarily conserved COMPASS complex. Accordingly, S2Lb associates with the AtCOMPASS core subunit WDR5a within a high-molecular weight complex and is required for proper H3K4me3 enrichment over genes highly occupied by RNA Polymerase II. S2Lb knock-out plants display little transcriptomic defects, suggesting that H3K4me3 deposition is important for optimal gene induction rather than for determining on/off transcriptional states. We further report that S2Lb and H3K4me3 are accurately targeted over most genes in hub1 mutant plants lacking histone H2B monoubiquitination. Collectively, our study indicates that a plant-specific COMPASS-like complex acting mainly through an H2Bub-independent mechanism is a major determinant of H3K4me3 deposition in Arabidopsis.
2019-05-04 | GSE124318 | GEO