H2A monoubiquitination targeting by cohesi n subunits in Arabidopsis
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ABSTRACT:
PROVIDER: PRJNA737632 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14813032_1.fastq.gz | Fastqsanger.gz | |||
| SRR14813032_2.fastq.gz | Fastqsanger.gz | |||
| SRR14813033_1.fastq.gz | Fastqsanger.gz | |||
| SRR14813033_2.fastq.gz | Fastqsanger.gz | |||
| SRR14813034_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Histone H2A monoubiquitination (H2Aub1) is a ubiquitous and conserved post-translational modification, playing a non-degradative role in multiple progresses including transcription regulation. In Arabidopsis thaliana, H2Aub1 is mediated by AtRING1s and AtBMI1s, catalytic subunits of Polycomb repressive complex 1 (PRC1). Despite PRC2-associated repressive role of H2Aub1, the mechanism regarding how H2Aub1 distributed on non-H3K27me3 region need to be explained. In this article, we show that the two cohesin subunits AtSCC3 and AtSYN4 directly interact with AtBMI1A/B/C, and theH2Aub1 levels are significantly reduced in atsyn4orAtSCC3RNAi plants. By ChIP-seq analysis, we found that AtSYN4 and AtSCC3 co-localize with H2Aub1 in genome, and are related to H3K27me3-independent transcription activation. Further, we provide evidences to show that AtSYN4 directly bind to G-box element and regulate H2Aub1 modification in G-box containing loci. These findings reveal that AtSCC3 and AtSYN4 are directly and functionally associated with AtBMI1s. Our study uncovers the mechanism of H2Aub1 targeting modification.
2024-06-08 | GSE178189 | GEO
Project description:Histone H2A monoubiquitination (H2Aub1) function as a conserved post-translational modification in eukaryotes to maintain gene repression and ensure cellular identity. Arabidopsis H2Aub1 is catalyzed by polycomb repressive complex 1 (PRC1) contributed by AtRING1s and AtBMI1s. Because PRC1 components lack known DNA binding domains, how H2Aub1 is established at the specific genomic sites remains a topic of debate. Here we show that the cohesin subunits AtSYN4 and AtSCC3 interact with each other and AtSCC3 binds to AtBMI1s. We find that H2Aub1 levels are significantly reduced in the atsyn4 mutant or AtSCC3 RNAi knockdown plants. ChIP-seq analysis indicated that AtSYN4 and AtSCC3 tend to associate with H2Aub1 in the genome regions of transcription activation independent on H3K27me3. Finally, we show that AtSYN4 binds directly to the G-box element and targets H2Aub1to these sites. Our study thus revealed a mechanism for cohesin-mediated recruitment of AtBMI1s to specific loci to mediate H2Aub1.
2022-06-10 | GSE205736 | GEO
Project description:H2A monoubiquitination in Arabidopsis is generally independent of LHP1 and PRC2 activity
| PRJNA351868 | ENA
Project description:Histone H2A monoubiquitination is associated with transcriptional repression and needs to be removed by deubiquitinases to facilitate gene transcription in eukaryotes. However, the deubiquitinase responsible for genome-wide H2A deubiquitination in plants has yet to be identified. We found that UBP5, an ubiquitin-specific protease, interacts with a previously identified PEAT (PWWP-EPCR-ARID-TRB) complex to form a larger version of PEAT complex in Arabidopsis thaliana. UBP5 functions as an H2A deubiquitinase in a nucleosome substrate-dependent manner in vitro and mediates H2A deubiquitination at the whole-genome level in vivo. Moreover, our results indicated that the histone acetyltransferases HAM1 and HAM2 (HAM1/2), catalytic subunits of the NuA4 histone acetyltransferase complex, are also part of the PEAT complex at PEAT target genomic loci. Within the PEAT complex, the PWWP components (PWWP1, PWWP2 and PWWP3) directly interact with UBP5 and are necessary for UBP5-mediated H2A deubiquitination, while the EPCR components (EPCR1 and EPCR2) directly interact with HAM1/2 and are required for HAM1/2-mediated H4K5 acetylation. This study identifies previously unknown regulators of H2A deubiquitination and H4K5 acetylation and illustrates how these processes collaborate at the whole-genome level.
2023-10-08 | GSE232671 | GEO
Project description:Histone H2A monoubiquitination is associated with transcriptional repression and needs to be removed by deubiquitinases to facilitate gene transcription in eukaryotes. However, the deubiquitinase responsible for genome-wide H2A deubiquitination in plants has yet to be identified. We found that UBP5, an ubiquitin-specific protease, interacts with a previously identified PEAT (PWWP-EPCR-ARID-TRB) complex to form a larger version of PEAT complex in Arabidopsis thaliana. UBP5 functions as an H2A deubiquitinase in a nucleosome substrate-dependent manner in vitro and mediates H2A deubiquitination at the whole-genome level in vivo. Moreover, our results indicated that the histone acetyltransferases HAM1 and HAM2 (HAM1/2), catalytic subunits of the NuA4 histone acetyltransferase complex, are also part of the PEAT complex at PEAT target genomic loci. Within the PEAT complex, the PWWP components (PWWP1, PWWP2 and PWWP3) directly interact with UBP5 and are necessary for UBP5-mediated H2A deubiquitination, while the EPCR components (EPCR1 and EPCR2) directly interact with HAM1/2 and are required for HAM1/2-mediated H4K5 acetylation. This study identifies previously unknown regulators of H2A deubiquitination and H4K5 acetylation and illustrates how these processes collaborate at the whole-genome level.
2023-10-08 | GSE232670 | GEO
Project description:BACKGROUND: Polycomb group complexes PRC1 and PRC2 repress gene expression at the chromatin level in eukaryotes. The classic recruitment model of Polycomb group complexes in which PRC2-mediated H3K27 trimethylation recruits PRC1 for H2A monoubiquitination was recently challenged by data showing that PRC1 activity can also recruit PRC2. However, the prevalence of these two mechanisms is unknown, especially in plants as H2AK121ub marks were examined at only a handful of Polycomb group targets. RESULTS: By using genome-wide analyses, we show that H2AK121ub marks are surprisingly widespread in Arabidopsis thaliana, often co-localizing with H3K27me3 but also occupying a set of transcriptionally active genes devoid of H3K27me3. Furthermore, by profiling H2AK121ub and H3K27me3 marks in atbmi1a/b/c, clf/swn, and lhp1 mutants we found that PRC2 activity is not required for H2AK121ub marking at most genes. In contrast, loss of AtBMI1 function impacts the incorporation of H3K27me3 marks at most Polycomb group targets. CONCLUSIONS: Our findings show the relationship between H2AK121ub and H3K27me3 marks across the A. thaliana genome and unveil that ubiquitination by PRC1 is largely independent of PRC2 activity in plants, while the inverse is true for H3K27 trimethylation.
2017-03-21 | GSE89356 | GEO
Project description:BACKGROUND: Polycomb group complexes PRC1 and PRC2 repress gene expression at the chromatin level in eukaryotes. The classic recruitment model of Polycomb group complexes in which PRC2-mediated H3K27 trimethylation recruits PRC1 for H2A monoubiquitination was recently challenged by data showing that PRC1 activity can also recruit PRC2. However, the prevalence of these two mechanisms is unknown, especially in plants as H2AK121ub marks were examined at only a handful of Polycomb group targets. RESULTS: By using genome-wide analyses, we show that H2AK121ub marks are surprisingly widespread in Arabidopsis thaliana, often co-localizing with H3K27me3 but also occupying a set of transcriptionally active genes devoid of H3K27me3. Furthermore, by profiling H2AK121ub and H3K27me3 marks in atbmi1a/b/c, clf/swn, and lhp1 mutants we found that PRC2 activity is not required for H2AK121ub marking at most genes. In contrast, loss of AtBMI1 function impacts the incorporation of H3K27me3 marks at most Polycomb group targets. CONCLUSIONS: Our findings show the relationship between H2AK121ub and H3K27me3 marks across the A. thaliana genome and unveil that ubiquitination by PRC1 is largely independent of PRC2 activity in plants, while the inverse is true for H3K27 trimethylation.
2017-03-21 | GSE89357 | GEO
Project description:Histone H2A monoubiquitination (H2Aub1) functions as a conserved posttranslational modification in eukaryotes to maintain gene expression and guarantee cellular identity. Arabidopsis H2Aub1 is catalyzed by the core components AtRING1s and AtBMI1s of polycomb repressive complex 1 (PRC1). Because PRC1 components lack known DNA binding domains, it is unclear how H2Aub1 is established at specific genomic locations. Here, we show that the Arabidopsis cohesin subunits AtSYN4 and AtSCC3 interact with each other, and AtSCC3 binds to AtBMI1s. H2Aub1 levels are reduced in atsyn4 mutant or AtSCC3 artificial microRNA knockdown plants. ChIP-seq assays indicate that most binding events of AtSYN4 and AtSCC3 are associated with H2Aub1 along the genome where transcription is activated independently of H3K27me3. Finally, we show that AtSYN4 binds directly to the G-box motif and directs H2Aub1 to these sites. Our study thus reveals a mechanism for cohesin-mediated recruitment of AtBMI1s to specific genomic loci to mediate H2Aub1.
| S-EPMC9984397 | biostudies-literature
Project description:Binding by the Polycomb complex component BMI1 and H2A monoubiquitination shape local and long-range interactions in the Arabidopsis genome
| PRJEB52473 | ENA
Project description:Polycomb Repressive Complexes (PRCs) control gene expression through the incorporation of H2Aub and H3K27me3. In recent years, there is increasing evidence of the complexity of PRCs’ interaction networks and the interplay of these interactors with PRCs in epigenome reshaping, which is fundamental to understand gene regulatory mechanisms. Here, we identified UBIQUITIN SPECIFIC PROTEASE 5 (UBP5) as a chromatin player able to counteract the deposition of the two PRCs epigenetic hallmarks in Arabidopsis thaliana. We demonstrated that UBP5 is a plant developmental regulator based on functional analyses of ubp5-CRISPR Cas9 mutant plants. UBP5 promotes H2A monoubiquitination erasure, leading to transcriptional de-repression. Furthermore, preferential association of UBP5 at PRC2 recruiting motifs and local H3K27me3 gaining in ubp5 mutant plants suggest the existence of functional interplays between UBP5 and PRC2 in regulating epigenome dynamics. In summary, acting as an antagonist of the pivotal epigenetic repressive marks H2Aub and H3K27me3, UBP5 provides novel insights to disentangle the complex regulation of PRCs’ activities.
2023-12-01 | GSE209707 | GEO