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Read-through transcription as a general mechanism mediating methylation and silencing of intragenic CGIs

ABSTRACT: Read-through transcription as a general mechanism mediating methylation and silencing of intragenic CGIs

PROVIDER: PRJNA328975 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3894180_1.fastq.gz	Fastqsanger.gz
	SRR3894180_2.fastq.gz	Fastqsanger.gz
	SRR3894181_1.fastq.gz	Fastqsanger.gz
	SRR3894181_2.fastq.gz	Fastqsanger.gz
	SRR3894042_1.fastq.gz	Fastqsanger.gz

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Read-through transcription as a general mechanism mediating methylation and silencing of intragenic CGIs [CAP-Seq]

Project description:Read-through transcription as a general mechanism mediating methylation and silencing of intragenic CGIs [CAP-Seq]

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Read-through transcription as a general mechanism mediating methylation and silencing of intragenic CGIs [CAP-Seq]

Project description:The human genome contains approximately 27,700 CpG islands (CGIs). Most are associated with promoters and their DNA is nearly always unmethylated. By contrast, CGIs lying within the bodies of genes usually become methylated during differentiation and development. CGIs also normally become methylated at X-inactivated and imprinted genes and abnormally methylated in genome rearrangements and in malignancy. In such circumstances, methylation of CGIs is often associated with RNA transcripts reading through these elements but the relationship of this RNA to methylation of CGIs is not clear. Here we investigated a previously described form of α-thalassemia caused by a genome rearrangement leading to abnormal transcription and DNA methylation of the CGI at the promoter of the α-globin gene. We show that transcription per se is responsible for DNMT3B-mediated methylation of the globin CGI, and that this is a general mechanism responsible for methylation of most intragenic CpG islands.

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Read-through transcription as a general mechanism mediating methylation and silencing of intragenic CGIs [H3K36me3_ChIP-seq]

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Read-through transcription as a general mechanism mediating methylation and silencing of intragenic CGIs [small RNA-seq]

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Homo sapiens

Project description:Read-through transcription as a general mechanism mediating methylation and silencing of intragenic CGIs [H3K36me3_ChIP-seq]

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Read-through transcription as a general mechanism mediating methylation and silencing of intragenic CGIs

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

2017-08-10 | GSE84355 | GEO

Mus musculus

Project description:Read-through transcription as a general mechanism mediating methylation and silencing of intragenic CGIs [small RNA-seq]

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Intragenic DNA inversions expand bacterial coding capacity

Project description:Bacteria can generate heterogeneity through phase variation, including enzyme-mediated inversion of specific intergenic regions of genomic DNA. We developed a computation tool that identifies invertible elements using long-read datasets, PhaVa. We identified over 300 ‘intragenic invertons,’ a new class of invertible elements entirely within genes, in both bacteria and archaea. In the gut commensal Bacteroides thetaiotaomicron, we experimentally characterized an intragenic inverton in the thiamine biosynthesis protein thiC. We used mass spectrometry in data-independent acquisition mode to identify and quantify B. theta proteins, including thiC inverton expression at the protein level.

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Cell Type-Specific DNA Methylation at Intragenic CpG Islands in the Immune System (gene expression data)

Project description:Human and mouse genomes contain a similar number of CpG islands (CGIs), which are discrete CpG-rich DNA sequences associated with transcription start sites. In both species, about 50% of all CGIs are remote from annotated promoters, but nevertheless often have promoter-like features. To document the role of CGI methylation in cell differentiation, we analysed DNA methylation at a comprehensive CGI set in cells of the mouse hematopoietic lineage. Using a method that potentially detects ~33% of genomic CpGs in the methylated state (>7 million) we found that large differences in gene expression were accompanied by surprisingly few DNA methylation changes. There were, however, many DNA methylation differences between hematopoietic cells and a distantly related tissue, brain. Altered DNA methylation occurred predominantly at CGIs within gene bodies, which have the properties of cell type-restricted promoters, but infrequently at annotated gene promoters or CGI flanking sequences. Elevated intragenic CGI methylation correlated with silencing of the associated gene. Differentially methylated intragenic CGIs tended to lack H3K4me3 and associate with a transcriptionally repressive environment regardless of methylation state. Our results indicate that DNA methylation changes play a relatively minor role in the late stages of differentiation, but point to a distinct role for intragenic CGIs.

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Cell Type-Specific DNA Methylation at Intragenic CpG Islands in the Immune System (gene expression data)

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