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Arabidopsis thaliana

ABSTRACT: H2A monoubiquitination in Arabidopsis is generally independent of LHP1 and PRC2 activity [ChIP-seq]

PROVIDER: PRJNA351870 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4734660.fastq.gz	Fastqsanger.gz
	SRR4734670.fastq.gz	Fastqsanger.gz
	SRR4734661.fastq.gz	Fastqsanger.gz
	SRR4734671.fastq.gz	Fastqsanger.gz
	SRR4734662.fastq.gz	Fastqsanger.gz

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Project description:H2A monoubiquitination in Arabidopsis is generally independent of LHP1 and PRC2 activity [RNA-seq]

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H2A monoubiquitination in Arabidopsis is generally independent of LHP1 and PRC2 activity

Project description:H2A monoubiquitination in Arabidopsis is generally independent of LHP1 and PRC2 activity

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H2A monoubiquitination in Arabidopsis is generally independent of LHP1 and PRC2 activity [ChIP-seq]

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.

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H2A monoubiquitination in Arabidopsis is generally independent of LHP1 and PRC2 activity [RNA-seq]

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RNA-seq analysis of emf1, lhp1, ebs shl and ebs shl lhp1 transcriptomes in Arabidopsis thaliana

Project description:By RNA deep sequencing, around 11,000 genes were found to be differentially expressed in ebs shl lhp1 compared with wild type, and SHL and EBS, together with LHP1 and EMF1, co-regulate the expression of thousands of gene in Arabidopsis

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H2A monoubiquitination targeting by cohesi n subunits in Arabidopsis

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.

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The Arabidopsis chromodomain-containing LHP1 colocalizes with histone H3 lysine27 trimethylation

Project description:The POLYCOMB proteins are required for maintenance of silent chromatin states mediated by H3K27 trimethylation in animals, but POLYCOMB homologues are not found in plant genomes. Using DamID-chip, we found that the Arabidopsis chromodomain-containing protein LHP1 localizes to chromatin associated with H3K27me3 genome-wide. Furthermore, the LHP1 chromodomain binds H3K27me3 with high affinity. These results suggest that LHP1 shares similar functions with POLYCOMB. Keywords: DamID-Chip

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Project description:Polycomb repressive complex 1 (PRC1) catalyzes H2A monoubiquitination (uH2A) and regulates pluripotency in embryonic stem cells (ESCs). However the mechanisms controlling PRC1 recruitment and activity are largely unknown. Here we show that Fbxl10 interacts with Ring1B and Nspc1, forming a non-canonical PRC1. We demonstrate that Fbxl10-PRC1 is essential for H2A ubiquitination in mouse ESCs. Genome-wide analyses reveal that Fbxl10 preferentially binds to CpG islands and co-localizes with Ring1B on Polycomb target genes. Notably, Fbxl10 depletion causes modest dissociation of Ring1B but a major loss of uH2A on target genes. Furthermore rescue experiments for Fbxl10 reveal that its DNA binding capability and integration into PRC1 are required for proper H2A ubiquitination. ES cells lacking Fbxl10, like previously characterized Polycomb mutants, show a severely compromised capacity for successful differentiation. Our results shed light on a novel mechanism how CpG islands regulate chromatin function by affecting polycomb recruitment and activity. All ChIP-seq reactions were performed in either untransfected cells, cells expressing scrambled shRNA or Fbxl10 shRNA, Ring1b-/- or Suz12-/- mouse ES cells

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ChIP-seq of LHP1 and H3K27me3 distribution in Arabidopsis thaliana

Project description:ChIP-seq of LHP1 and H3K27me3 distribution in Arabidopsis thaliana

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