H2AK121ub and H3K27me3 marks have different effects on nucleosome organization in Arabidopsis
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ABSTRACT:
PROVIDER: PRJNA560876 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10001327_1.fastq.gz | Fastqsanger.gz | |||
| SRR10001327_2.fastq.gz | Fastqsanger.gz | |||
| SRR10001328_1.fastq.gz | Fastqsanger.gz | |||
| SRR10001328_2.fastq.gz | Fastqsanger.gz | |||
| SRR10001329_1.fastq.gz | Fastqsanger.gz |
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Project description:Background: Nucleosome organization within chromatin can be altered through the incorporation of histone modifications that in turn affects gene expression. Accordingly, the Polycomb Group (PcG) complexes PRC1 and PRC2 through the incorporation of H2AK121ub and H3K27me3 marks, respectively, maintain the repression of target genes; however, little is known about the exact function of these modifications in shaping nucleosome array at target genes, especially in plants. Results: By using two different MNase-seq datasets we analyzed the nucleosome occupancy profile of different PcG target genes in Arabidopsis. We found that PcG targets strongly differ in their nucleosome organization depending on the marks that they carry. Our data indicate that H2AK121ub marks play a role in fine-tuning +1 nucleosome position, while H3K27me3 marks impact nucleosome spacing and chromatin accessibility at both promoter and gene regions. Furthermore, analyzing the nucleosome profile of transcriptionally active PcG target genes in WT seedlings we found that their apparent activated state may be actually due to transcriptional heterogeneity across different cells. Conclusion: Our findings show that H2AK121ub and H3K27me3 marks differentially affect nucleosome organization in Arabidopsis, displaying additive effects when co-localizing at target genes.
2022-02-02 | GSE135978 | GEO
Project description:Although it is well established that Polycomb Group (PcG) complexes maintain gene repression through the incorporation of H2AK121ub and H3K27me3, little is known about the effect of these modifications on chromatin, which is fundamental to understand PcG function. Here, by integrating chromatin accessibility, histone marks and expression analyses in different Arabidopsis PcG mutants, we show that H2AK121ub marking favors a less accessible but still permissive chromatin at transcriptional regulation hotspots, which can be further reduced by EMF1 and H3K27me3. We found that when acting concurrently, H2AK121ub and H3K27me3 establish an inaccessible but responsive chromatin to marks levels, allowing gene reprograming. Conversely, when H3K27me3 is alone, chromatin is less responsive, indicating that H2AK121ub-marked hotspots are required for transcriptional responses. Interestingly, despite the loss of H2AK121ub and H3K27me3 leads to increased chromatin accessibility, this is not necessarily accompanied by transcriptional activation, indicating that gene expression is not always predictive of accessible chromatin.
2020-12-02 | GSE154696 | GEO
Project description:Although it is well established that Polycomb Group (PcG) complexes maintain gene repression through the incorporation of H2AK121ub and H3K27me3, little is known about the effect of these modifications on chromatin, which is fundamental to understand PcG function. Here, by integrating chromatin accessibility, histone marks and expression analyses in different Arabidopsis PcG mutants, we show that H2AK121ub marking favors a less accessible but still permissive chromatin at transcriptional regulation hotspots, which can be further reduced by EMF1 and H3K27me3. We found that when acting concurrently, H2AK121ub and H3K27me3 establish an inaccessible but responsive chromatin to marks levels, allowing gene reprograming. Conversely, when H3K27me3 is alone, chromatin is less responsive, indicating that H2AK121ub-marked hotspots are required for transcriptional responses. Interestingly, despite the loss of H2AK121ub and H3K27me3 leads to increased chromatin accessibility, this is not necessarily accompanied by transcriptional activation, indicating that gene expression is not always predictive of accessible chromatin.
2020-12-02 | GSE154695 | GEO
Project description:Although it is well established that Polycomb Group (PcG) complexes maintain gene repression through the incorporation of H2AK121ub and H3K27me3, little is known about the effect of these modifications on chromatin, which is fundamental to understand PcG function. Here, by integrating chromatin accessibility, histone marks and expression analyses in different Arabidopsis PcG mutants, we show that H2AK121ub marking favors a less accessible but still permissive chromatin at transcriptional regulation hotspots, which can be further reduced by EMF1 and H3K27me3. We found that when acting concurrently, H2AK121ub and H3K27me3 establish an inaccessible but responsive chromatin to marks levels, allowing gene reprograming. Conversely, when H3K27me3 is alone, chromatin is less responsive, indicating that H2AK121ub-marked hotspots are required for transcriptional responses. Interestingly, despite the loss of H2AK121ub and H3K27me3 leads to increased chromatin accessibility, this is not necessarily accompanied by transcriptional activation, indicating that gene expression is not always predictive of accessible chromatin.
2020-12-02 | GSE154697 | GEO
Project description:The position of nucleosomes influences DNA accessibility to DNA-binding proteins. Genome-wide nucleosome profiles often report the observation of a canonical nucleosome organization at gene promoters where arrays of well-positioned nucleosomes emanate from nucleosome-depleted regions. It is unclear how this canonical promoter nucleosome organization forms and how it is related to transcription activation and the establishment of histone marks during development. Here we report the genome-wide organization of nucleosomes during zebrafish embryogenesis and show that well-positioned nucleosome arrays appear in thousands of promoters during the activation of the zygotic genome. The formation of canonical promoter nucleosome organization cannot be explained by DNA sequence preference, and is independent of transcription and the presence of RNA polymerase II, but strongly correlates with the presence of Histone H3 Lysine 4 trimethylation (H3K4me3). Our study further suggests that promoter nucleosome structure primes genes to future transcription activation. To determine whether the occlusions are consistent in mammalian pluripotent cells, we performed the same analyses in mouse embryonic stem cells and found similar relationships. MNase-seq to generate nucleosome organization in mouse embryonic stem cell (J1)
2013-10-29 | E-GEOD-51766 | biostudies-arrayexpress
Project description:The position of nucleosomes influences DNA accessibility to DNA-binding proteins. Genome-wide nucleosome profiles often report the observation of a canonical nucleosome organization at gene promoters where arrays of well-positioned nucleosomes emanate from nucleosome-depleted regions. It is unclear how this canonical promoter nucleosome organization forms and how it is related to transcription activation and the establishment of histone marks during development. Here we report the genome-wide organization of nucleosomes during zebrafish embryogenesis and show that well-positioned nucleosome arrays appear in thousands of promoters during the activation of the zygotic genome. The formation of canonical promoter nucleosome organization cannot be explained by DNA sequence preference, and is independent of transcription and the presence of RNA polymerase II, but strongly correlates with the presence of Histone H3 Lysine 4 trimethylation (H3K4me3). Our study further suggests that promoter nucleosome structure primes genes to future transcription activation. Together, this study reveals that genome activation but not transcription underlies the organization of nucleosome arrays during early embryogenesis. MNase-seq to generate nucleosome organization in two stages of zebrafish development; two biological replicates for each stage. 7 ChIP-seq experiments in three stages.
2013-10-18 | E-GEOD-44269 | biostudies-arrayexpress
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:The organization of nucleosomes influences transcriptional activity by controlling accessibility of DNA binding proteins to the genome. Genome-wide nucleosome binding profiles have identified a canonical nucleosome organization at gene promoters, where arrays of well-positioned nucleosomes emanate from nucleosome-depleted regions. The mechanisms of formation and the function of canonical promoter nucleosome organization remain unclear. Here we analyze the genome-wide location of nucleosomes during zebrafish embryogenesis and show that well-positioned nucleosome arrays appear on thousands of promoters during the activation of the zygotic genome. The formation of canonical promoter nucleosome organization is independent of DNA sequence preference, transcriptional elongation, and robust RNA polymerase II (Pol II) binding. Instead, canonical promoter nucleosome organization correlates with the presence of Histone H3 Lysine 4 trimethylation (H3K4me3) and affects future transcriptional activation. These findings reveal that genome activation is central to the organization of nucleosome arrays during early embryogenesis.
2013-10-29 | GSE51766 | GEO
Project description:The organization of nucleosomes influences transcriptional activity by controlling accessibility of DNA binding proteins to the genome. Genome-wide nucleosome binding profiles have identified a canonical nucleosome organization at gene promoters, where arrays of well-positioned nucleosomes emanate from nucleosome-depleted regions. The mechanisms of formation and the function of canonical promoter nucleosome organization remain unclear. Here we analyze the genome-wide location of nucleosomes during zebrafish embryogenesis and show that well-positioned nucleosome arrays appear on thousands of promoters during the activation of the zygotic genome. The formation of canonical promoter nucleosome organization is independent of DNA sequence preference, transcriptional elongation, and robust RNA polymerase II (Pol II) binding. Instead, canonical promoter nucleosome organization correlates with the presence of Histone H3 Lysine 4 trimethylation (H3K4me3) and affects future transcriptional activation. These findings reveal that genome activation is central to the organization of nucleosome arrays during early embryogenesis.
2013-10-18 | GSE44269 | GEO