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ASH-1-catalyzed H3K36 methylation drives gene repression and marks H3K27me2/3-competent chromatin

ABSTRACT: ASH-1-catalyzed H3K36 methylation drives gene repression and marks H3K27me2/3-competent chromatin

PROVIDER: PRJNA485801 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7690280.fastq.gz	Fastqsanger.gz
	SRR7690290.fastq.gz	Fastqsanger.gz
	SRR7690271.fastq.gz	Fastqsanger.gz
	SRR7690281.fastq.gz	Fastqsanger.gz
	SRR7690272.fastq.gz	Fastqsanger.gz

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ASH-1-catalyzed H3K36 methylation drives gene repression and marks H3K27me2/3-competent chromatin

Project description:ASH-1 orthologs are H3K36-specific methyltransferases that are conserved from fungi to humans but are poorly understood, in part because they are typically essential for viability. Here we examine the H3K36 methylation pathway of Neurospora crassa, which we find has just two H3K36 methyltransferases, ASH-1 and RNA polymerase II-associated SET-2. Our investigation of the interplay between SET-2 and ASH-1 uncovered a regulatory mechanism connecting ASH-1-catalyzed H3K36 methylation to repression of poorly transcribed genes. Our findings provide new insight into ASH-1 function, H3K27me2/3 establishment, and repression at facultative heterochromatin.

2018-08-14 | GSE118495 | GEO

ASH1-catalyzed H3K36 methylation drives gene repression and marks H3K27me2/3-competent chromatin.

Project description:Methylation of histone H3 at lysine 36 (H3K36me), a widely-distributed chromatin mark, largely results from association of the lysine methyltransferase (KMT) SET-2 with RNA polymerase II (RNAPII), but most eukaryotes also have additional H3K36me KMTs that act independently of RNAPII. These include the orthologs of ASH1, which are conserved in animals, plants, and fungi but whose function and control are poorly understood. We found that Neurospora crassa has just two H3K36 KMTs, ASH1 and SET-2, and were able to explore the function and distribution of each enzyme independently. While H3K36me deposited by SET-2 marks active genes, inactive genes are modified by ASH1 and its activity is critical for their repression. ASH1-marked chromatin can be further modified by methylation of H3K27, and ASH1 catalytic activity modulates the accumulation of H3K27me2/3 both positively and negatively. These findings provide new insight into ASH1 function, H3K27me2/3 establishment, and repression in facultative heterochromatin.

| S-EPMC6251624 | biostudies-literature

Integrative analysis of green ash phloem transcripts and proteins during an emerald ash borer infestation

Project description:We performed RNA-seq and proteomics on naturally infested green ash (F. pennsylvanica) trees at low, medium and high levels of increasing emerald ash borer (A. planipennis) infestation. Our integrative analysis of the RNA-Seq and proteomics data identified 14 proteins and 4 transcripts that contribute most to the difference between highly infested and low infested trees.

2023-03-08 | GSE212332 | GEO

Effects of ash-2, hsf-1, or ash-2 + hsf-1 RNAi on gene expression in Day 1 adult Q40::YFP C. elegans

Project description:To determine how gene expression changes in long-lived ash-2-deficient worms expressing the amyloidogenic Q40::YFP, and to assess how simultaneous depletion of hsf-1 effects these transcriptomic changes.

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Ash genome

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Arsenophonus endosymbiont of Aphis craccivora strain:Ash | isolate:Ash

Project description:Arsenophonus endosymbiont of Aphis craccivora strain:Ash | isolate:Ash Genome sequencing

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Integrative analysis of green ash phloem transcripts and proteins during an emerald ash borer infestation

Project description:We performed proteomics on naturally infested green ash (F. pennsylvanica) trees at low and high levels of emerald ash borer (A. planipennis) infestation. Our integrative analysis of the RNA-Seq and proteomics data identified 14 proteins and 4 transcripts that contribute most to the difference between highly infested and low infested trees.

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Histone post translational modification mass sprectrometry SUZ12 exon 4 cell lines

Project description:We investigate the contribution of each SUZ12 isoform on PRC2 activity on chromatin using our different ESC lines. As an additional comparison for ∆ex4 cells (SUZ12-S), we included an ESC clone in which an unsuccessful CRISPR editing event resulted in a mutant allele with nearly constitutive splicing of exon 4 (herein, CSex4) and normal Suz12 expression levels (expressing only SUZ12-L). First, we profiled H3K27 bulk PTMs by WB and observed that, while CSex4 cells showed no major differences to control cells, ∆ex4 cells displayed lower levels of H3K27me2 and -me3, with higher levels of mono-methylation and acetylation. Similar results were obtained when comparing SUZ12-L and SUZ12-S ESC rescue lines. To validate these findings with an antibody-independent technique, and to additionally profile other histone PTMs, we analysed these cells with histone-MS. In line with the previous estimates26, WT cells displayed approximately 85% of H3K27 methylation. This proportion was largely similar in CSex4 cells, while it dropped to ~50% in ∆ex4 cells, with H3K27me2 and -me3 being the most affected modifications. Notably, H3K27me2/3 loss in ∆ex4 cells occurred at histone peptides regardless of their H3K36 methylation status. Moreover, the global H3K36 methylation rates were not affected in either CSex4 or ∆ex4 cells (Figure S4C), and no major changes in methylation or acetylation levels were observed at other residues. Importantly, reintroduction of SUZ12-L in KO cells rescued a higher degree of methylation compared to SUZ12-S. Overall, these results indicate that SUZ12-S alone is unable to maintain global physiological levels of H3K27 methylation; rather SUZ12-L is also necessary for this task.

2024-03-18 | PXD046640 | Pride

Evolutionary and Functional Insights into the Ski2-like helicase Family in Archaea: A Comparison of Thermococcales ASH-Ski2 and Hel308 Activities

Project description:RNA helicases perform essential housekeeping and regulatory functions in all domains of life by binding and unwinding RNA molecules. The Ski2-like proteins are primordial helicases that play an active role in eukaryotic RNA homeostasis pathways, with multiple homologs having specialized functions. The significance of the expansion and diversity of Ski2-like proteins in Archaea, the third domain of life, has not yet been established. Here, by studying the phylogenetic diversity of Ski2-like helicases among archaeal genomes and the enzymatic activities of those in Thermococcales, we provide further evidence of the function of this protein family in archaeal metabolism of nucleic acids. We show that, in the course of evolution, ASH-Ski2 and Hel308-Ski2, the two main groups of Ski2-like proteins, have diverged in their biological functions. Whereas Hel308 has been shown to mainly act on DNA, we show that ASH-Ski2, previously described to be associated with the 5′-3′ aRNaseJ exonuclease, acts on RNA by supporting an efficient annealing activity, but also an RNA unwinding with a 3′-5′ polarity. To gain insights into the function of Ski2, we also analyse the transcriptome of Thermococcus barophilus ASH-Ski2 mutant strain and provide evidence of the importance of ASH-Ski2 in cellular metabolism pathways related to translation.

2024-03-04 | GSE229955 | GEO

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