Co-dependency of H2B monoubiquitination and nucleosome re-assembly on Chd1
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE36334 | GEO | 2012/05/02
SECONDARY ACCESSION(S): PRJNA153387
REPOSITORIES: GEO
Similar Datasets
Project description:Monoubiquitination of histone H2B on lysine 123 (H2BK123ub) is a transient histone modification considered to be essential for establishing H3K4 and H3K79 trimethylation by Set1/COMPASS and Dot1, respectively. Many of the factors such as Rad6/Bre1, the Paf1 complex, and the Bur1/Bur2 complex were identified to be required for proper histone H3K4 and H3K79 trimethylation, and were shown to function by regulating H2BK123ub levels. Here, we have identified Chd1 as a factor that is required for proper maintenance of H2B monoubiquitination levels, but not for H3K4 and H3K79 trimethylation. Loss of Chd1 results in a substantial loss of H2BK123ub levels with little to no effect on the genome-wide pattern of H3K4 and H3K79 trimethylation. Our data shows that nucleosomal occupancy is reduced in gene bodies in both CHD1 null and K123A backgrounds. We have also demonstrated that Chd1’s function in maintaining H2BK123ub levels is conserved from yeast to human. Our study provides evidence that only small levels of H2BK123ub are necessary for full levels of H3K4 and H3K79 trimethylation in vivo, and points to a role for Chd1 in positively regulating gene expression through promoting nucleosome re-assembly coupled with H2B monoubiquitination. Examination of two histone modifications in wild-type and Chd1 null yeast strains using ChIP-seq. Expression profiling in wild-type and Chd1 null yeast strains using RNA-seq.
2012-05-01 | E-GEOD-36334 | biostudies-arrayexpress
Project description:To define the molecular regulators required for differential pattern of H3K79 methylation by Dot1, we performed a GPS screen and discovered that the components of the cell cycle-regulated SBF complex were required for normal levels of H3K79 di- but not trimethylation. Genome-wide mapping revealed that H3K79 di- and trimethylation to present a mutually exclusive pattern on chromatin with M/G1 cell-cycle-regulated genes significantly enriched for H3K79 dimethylation. Since H3K79 trimethylation requires prior monoubiquitination of H2B, we performed genome-wide profiling of H2BK123 monoubiquitination and showed that H2BK123 monoubiquitination is excluded from cell cycle regulated genes and sites containing H3K79me2 but not from H3K79me3 containing regions. A genome-wide screen for factors responsible for the establishment/removal of H3K79 dimethylation resulted in the identification of several genes including NRM1 and WHI3, which both impact the transcription by the SBF, and MBF complexes, further linking the regulation of H3K79's methylation status to the cell cycle.
2009-10-19 | E-MEXP-2273 | biostudies-arrayexpress
Project description:The stimulation of trimethylation of histone H3 lysine 4 (H3K4) by H2B monoubiquitination (H2Bub) has been widely studied with multiple mechanisms proposed for this form of histone crosstalk. Cps35/Swd2 within COMPASS is considered to bridge these processes. However, a truncated form of Set1 (762-Set1) is reported to function in H3K4 trimethylation without interacting with Cps35/Swd2, and such crosstalk is attributed to the n-SET domain of Set1 and its interaction with the Cps40/Spp1 subunit of COMPASS. Here, we use biochemical, structural, in vivo, and ChIP-seq approaches to demonstrate that Cps40/Spp1 and the n-SET domain of Set1 are required for the stability of Set1 and not the crosstalk. Furthermore, the apparent wild-type levels of H3K4 trimethylation (H3K4me3) in the 762-Set1 strain is due to rogue methylase activity of this mutant resulting in the mislocalization of H3K4me3 from the promoter-proximal regions to gene bodies and intergenic regions. We have also performed detailed screens and identified yeast strains lacking H2Bub, but containing intact H2Bub enzymes, that have normal levels of H3K4me3, suggesting that ubiquitination may not directly stimulate COMPASS, but rather works in a context of the PAF and Rad6/Bre1 complexes. Our study demonstrates that the ubiquitination machinery and Cps35/Swd2 function to focus COMPASS’ H3K4me3 activity at promoter-proximal regions in a context dependent manner. ChIP-Seq for H3K4ME3 in S. cerevisie wild-type strains and strains expressing a truncated form of Set1: aa762-1080 Set1. H3K4ME3 ChIP-Seq was also compared for wild-type, leo1 knockout, and chd1 knockout strains
2014-01-09 | E-GEOD-53241 | biostudies-arrayexpress
Project description:The stimulation of trimethylation of histone H3 lysine 4 (H3K4) by H2B monoubiquitination (H2Bub) has been widely studied with multiple mechanisms proposed for this form of histone crosstalk. Cps35/Swd2 within COMPASS is considered to bridge these processes. However, a truncated form of Set1 (762-Set1) is reported to function in H3K4 trimethylation without interacting with Cps35/Swd2, and such crosstalk is attributed to the n-SET domain of Set1 and its interaction with the Cps40/Spp1 subunit of COMPASS. Here, we use biochemical, structural, in vivo, and ChIP-seq approaches to demonstrate that Cps40/Spp1 and the n-SET domain of Set1 are required for the stability of Set1 and not the crosstalk. Furthermore, the apparent wild-type levels of H3K4 trimethylation (H3K4me3) in the 762-Set1 strain is due to rogue methylase activity of this mutant resulting in the mislocalization of H3K4me3 from the promoter-proximal regions to gene bodies and intergenic regions. We have also performed detailed screens and identified yeast strains lacking H2Bub, but containing intact H2Bub enzymes, that have normal levels of H3K4me3, suggesting that ubiquitination may not directly stimulate COMPASS, but rather works in a context of the PAF and Rad6/Bre1 complexes. Our study demonstrates that the ubiquitination machinery and Cps35/Swd2 function to focus COMPASS’ H3K4me3 activity at promoter-proximal regions in a context dependent manner.
2014-01-09 | GSE53241 | GEO
Project description:The functional determinants of histone H3 Lys-4 trimethylation (H3K4me3), their potential dependency on histone H2B monoubiquitination (H2Bub) and their contribution to defining transcriptional regimes are poorly defined in plant systems. Unlike in S. cerevisiae, where a single SET1 protein catalyzes H3 Lys-4 trimethylation as part of COMPASS (COMPlex of proteins ASsociated with Set1), in Arabidopsis thaliana this activity involves multiple histone methyltransferases (HMTs). Among these, the plant-specific SDG2 (SET DOMAIN GROUP2) has a prominent role. We report that SDG2 co-regulates hundreds of genes with SWD2-like b (S2Lb), a plant ortholog of the Swd2 axillary subunit of yeast COMPASS. S2Lb co-purifies with the AtCOMPASS core subunit WDR5 from a high-molecular weight complex, and both S2Lb and SDG2 directly influence H3K4me3 enrichment over highly transcribed genes. S2Lb knockout triggers pleiotropic developmental phenotypes at the vegetative and reproductive stages, including reduced fertility and seed dormancy. Notwithstanding, s2lb seedlings display little transcriptomic defects as compared to the large repertoire of genes targeted by S2Lb, SDG2 or H3 Lys-4 trimethylation, suggesting that H3K4me3 enrichment is important for optimal gene induction during cellular transitions rather than for determining on/off transcriptional status. Moreover, unlike in budding yeast, most of the S2Lb and H3K4me3 genomic distribution does not rely on a trans-histone crosstalk with histone H2B monoubiquitination. Collectively, this study unveils that the evolutionarily conserved COMPASS-like complex has been coopted by the plant-specific SDG2 HMT and mediates H3K4me3 deposition through an H2Bub-independent pathway in Arabidopsis.
2019-04-26 | PXD012292 | Pride
Project description:This SuperSeries is composed of the following subset Series: GSE33049: GlcNAcylation of histone H2B facilitates its monoubiquitination [Illumina Genome Analyzer data] GSE33050: GlcNAcylation of histone H2B facilitates its monoubiquitination [Affymetrix data] Refer to individual Series
2011-10-26 | E-GEOD-33051 | biostudies-arrayexpress
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
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 | GSE124317 | 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 | GSE124311 | 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 | GSE124296 | GEO