Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE84352 | GEO | 2017/08/10

SECONDARY ACCESSION(S): PRJNA328979

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

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.

2017-08-10 | GSE84353 | GEO

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

2017-08-10 | GSE84354 | GEO

Cell Type-Specific DNA Methylation at Intragenic CpG Islands in the Immune System (MAP-Seq and ChIP-Seq 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.

2011-05-23 | GSE25688 | GEO

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

2011-05-23 | GSE25578 | GEO

Smchd1 dependent and independent pathways determine developmental dynamics of CpG island methylation on the inactive X chromosome.

Project description:X chromosome inactivation involves multiple levels of chromatin modification, established progressively and in a stepwise manner during early development. The chromosomal protein Smchd1 has recently been shown to play an important role in DNA methylation of CpG islands (CGIs), a late step in the X inactivation pathway required for long-term stability of gene silencing. Here we show that inactive X chromosome (Xi) CGI methylation can occur via either Smchd1 dependent or independent pathways. Smchd1 dependent CGI methylation, the primary pathway, is acquired gradually over an extended period, whereas Smchd1 independent CGI methylation occurs rapidly after the onset of X inactivation. The de novo methyltransferase Dnmt3b is required for methylation of both classes of CGI, whereas Dnmt3a and Dnmt3L are dispensable. Xi CGIs methylated by these distinct pathways differ in respect to their sequence characteristics and immediate chromosomal environment. We discuss the implications of these results for understanding CGI methylation during development. Examination of CpG methylated DNA from wild type and smchd1 null male and female somatic cells and female ES cells differentiated for either 7 or 10 days. Duplicate samples of each type were generated.

2012-10-15 | E-GEOD-37333 | biostudies-arrayexpress

BANP is an essential transcription factor that opens chromatin and activates CpG island regulated genes

Project description:While the majority of RNA polymerase II initiation events in mammalian genomes take place within CpG island (CGI) promoters, our understanding of their regulation remains limited. Here we combine single-molecule footprinting with interaction proteomics to identify BANP as a critical CGI regulator and the long sought-after TF that binds the orphan CGCG element in mouse and human. We show that BANP drives the activity of essential metabolic genes in the mouse genome in pluripotent and terminally differentiated cells. However, BANP binding is strongly repelled by DNA methylation of its motif in vitro and in vivo, which epigenetically restricts most binding to CGIs and accounts for its absence at aberrantly methylated CGIs in cancer cells. Upon binding to an unmethylated motif, BANP opens chromatin and phases nucleosomes. Our results establish Banp as a critical activator and put forth a model whereby CGI promoter activity relies on methylation-sensitive TFs capable of chromatin opening.

2021-06-16 | PXD024794 | Pride

Cell Type-Specific DNA Methylation at Intragenic CpG Islands in the Immune System (MAP-Seq and ChIP-Seq data)

2011-05-23 | E-GEOD-25688 | biostudies-arrayexpress

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

2011-05-23 | E-GEOD-25578 | biostudies-arrayexpress

Genome-wide methylation analysis of AOM/DSS-induced colon tumors

Project description:Genome-wide methylation analysis was performed by methylated DNA immunoprecipitation (MeDIP)-CpG island (CGI) microarray analysis to identify candidate CGIs specifically methylated in mouse colon tumors associated with colitis. We sucessfully identified 23 candidate CGIs methylated in tumors.

2011-06-30 | GSE21333 | GEO

LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation

Project description:De novo DNA methylation (DNAme) occurs coincident with transcription during mouse oogenesis. As many oocyte transcripts originate in Long Terminal Repeats (LTRs), which are divergent across species, we examined whether polymorphic LTR-initiated transcription units (LITs) shape the oocyte methylome. We identified thousands of syntenic regions in mouse, rat and human, including CpG islands (CGIs), that show divergent DNAme associated with polymorphic LITs. Notably, many CGI promoters methylated exclusively in mouse and/or rat are embedded within rodent-specific LITs, and show persistent maternal methylation in the blastocyst. Polymorphic LITs are also responsible for divergent methylation of CGI promoters in distantly related mouse strains, revealing that LITs also promote intra-species diversification of promoter DNAme.

2018-07-06 | GSE112622 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data