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De novo methylaton of the unmethylated K. phaffii genome by human DNA methyltransferases (DNMTs) [RNA-seq]

ABSTRACT: De novo methylaton of the unmethylated K. phaffii genome by human DNA methyltransferases (DNMTs) [RNA-seq]

PROVIDER: PRJNA578165 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10303413_1.fastq.gz	Fastqsanger.gz
	SRR10303413_2.fastq.gz	Fastqsanger.gz
	SRR10303414_1.fastq.gz	Fastqsanger.gz
	SRR10303414_2.fastq.gz	Fastqsanger.gz
	SRR10303415_1.fastq.gz	Fastqsanger.gz

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De novo methylaton of the unmethylated K. phaffii genome by human DNA methyltransferases (DNMTs)

Project description:De novo methylaton of the unmethylated K. phaffii genome by human DNA methyltransferases (DNMTs)

| PRJNA578169 | ENA

De novo methylaton of the unmethylated K. phaffii genome by human DNA methyltransferases (DNMTs) [BiSulfite-seq]

Project description:De novo methylaton of the unmethylated K. phaffii genome by human DNA methyltransferases (DNMTs) [BiSulfite-seq]

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De novo methylaton of the unmethylated K. phaffii genome by human DNA methyltransferases (DNMTs) [RNA-seq]

Project description:We engineered combinatorial knock-in of human DNMTs in Komagataella phaffii, a yeast species lacking endogenous DNA methylation, to characterize methylation preferences and functional consequences of individual de-novo DNMTs as well as their combinations. Methylation preferences were determined through whole-genome bisulfite sequencing (WGBS) experiments. Effects of knock-in on gene expression were determined by RNA-seq. Measurements of genome-wide methylation produced by distinct de-novo DNMTs permitted determination of methylation preferences and aversions specific to individual DNMTs. Combining methylation and gene expression data provided insight about cellular response to the stress of DNA methylation and about the association between gene methylation patterns and changes in transcriptional output.

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De novo methylaton of the unmethylated K. phaffii genome by human DNA methyltransferases (DNMTs) [BiSulfite-seq]

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De novo methylaton of the unmethylated K. phaffii genome by human DNA methyltransferases (DNMTs)

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-02-28 | GSE139063 | GEO

DNA methyltransferases are complementary in maintaining DNA methylation in embryonic stem cells

Project description:To investigate the cooperative function DNMTs in the maintenance of DNA methylation at the ICRs, we established mutant ES clones lacking three major DNA methyltransferases (DNMTs).

2022-10-21 | GSE208759 | GEO

Linking DNA Methyltransferases (DNMTs) to Epigenetic Marks and Nucleosome Structure Genome-Wide in Human Tumor Cells

Project description:Linking DNA Methyltransferases (DNMTs) to Epigenetic Marks and Nucleosome Structure Genome-Wide in Human Tumor Cells

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Transcriptomic profiling of human pancreatic cell lines hPNE/hTert stably over-expressing DNMTs compared to GFP-hPNE/hTert over-expressing control cells after lentiviral transduction

Project description:The overexpression of DNA methyltransferases (DNMTs) is a common hallmark of numerous cancers. These aberrant changes in DNA methylation profiles are correlated to the overexpression of DNMTs. Although this association is clearly demonstrated, the causal role of DNMT overexpression in pancreatic cancer has not been clearly established. Consequently, we decided to determine whether DNMT overexpression induces diffrent methylation patterns in non-cancerous pancreatic cells.

2023-04-20 | GSE148913 | GEO

Genome-wide roles of DNA methyltransferases in mouse embryos

Project description:Mouse embryos acquire global DNA methylation of their genome during implantation. However the exact roles of DNA methyltransferases (DNMTs) in embryognesis have not been studied comprehensively. Here we systematically analyze the consequences of genetic inactivation of Dnmt1, Dnmt3a and Dnmt3b on the methylome and transcriptome of mouse embryos and fibroblasts.

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CRISPR-Cas9 knockout screen informs efficient reduction of the Komagataella phaffii secretome

Project description:The yeast Komagataella phaffii is a promising alternative host for manufacturing of therapeutic proteins. Deletion of unneeded endogenous proteins could increase the secreted titer of recombinant proteins by redirecting cellular resources. Genetic engineering in non-model hosts is hampered by limited annotation of genes, especially essential genes. In this study, we identified the set of endogenous secreted proteins in K. phaffii and attempted to disrupt these genes. We designed, transformed, and sequenced a pooled CRISPR-Cas9 knockout library to determine which genes are essential. With this knowledge, we rapidly disrupted up to 9 consecutive genes in K. phaffii. Engineered strains exhibited a ~20x increase in the production of human serum albumin and a 2x increase in the production of a monoclonal antibody. The pooled CRISPR-Cas9 library and knowledge of gene essentiality reported here will facilitate future efforts to engineer K. phaffii for production of other recombinant therapeutic proteins and enzymes.

2024-08-08 | GSE252605 | GEO

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