Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Satellite repeat RNA expression in epithelial ovarian cancer is linked to a tumor immunosuppressive phenotype

ABSTRACT: Repeatome profiling across ovarian, pancreatic, and colorectal cell lines identifies distinct clustering that is independent of tissue of origin highlighting differences in repeat co-expression patterns. Deeper analysis of ovarian cancer cell lines demonstrated that HSATII satellite repeat expression was highly associated with epithelial mesenchymal transition (EMT) and anti-correlated with interferon (IFN) response genes indicative of a more aggressive phenotype.

ORGANISM(S): Homo sapiens

PROVIDER: GSE205430 | GEO | 2022/06/06

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer

Project description:Aberrant transcription of the HSATII pericentromeric satellite repeat is present in a wide variety of epithelial cancers. We observed that HSATII expression is induced in colon cancer cells cultured as xenografts or under non-adherent conditions in vitro, but it is rapidly lost in standard 2D cultures. Unexpectedly, physiological induction of endogenous HSATII RNA, as well as introduction of synthetic HSATII transcripts, generate complementary DNA intermediates in the form of DNA:RNA hybrids. Single molecule sequencing of tumor xenografts shows that HSATII RNA-derived DNA (rdDNA) molecules are stably reincorporated within pericentromeric loci, leading to progressive expansion of these regions We analyzed the dynamics of HSATII RNA and DNA level changes using single molecule sequencing (Helicos/SeqLL) in SW620 colon cancer cells transitioned from 2D in vitro culture conditions to growth as mouse xenografts and vice versa.

2015-11-02 | E-GEOD-64471 | biostudies-arrayexpress

Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer

2015-11-02 | GSE64471 | GEO

Satellite repeat RNA expression in epithelial ovarian cancer is linked to a tumor immunosuppressive phenotype

Project description:Satellite repeat RNA expression in epithelial ovarian cancer is linked to a tumor immunosuppressive phenotype

| PRJNA845211 | ENA

m6A RNA methylation of major satellite repeat transcripts facilitates chromatin association and RNA:DNA hybrid formation in mouse heterochromatin

Project description:m6A RNA methylation of major satellite repeat transcripts facilitates chromatin association and RNA:DNA hybrid formation in mouse heterochromatin

2021-04-21 | GSE156481 | GEO

DUX4-induced transcripts from pericentric human satellite II repeats form double-stranded RNA [dsRIPseq]

Project description:The DUX4 transcription factor is normally expressed in the cleavage stage embryo and regulates genes involved in zygotic genome activation. Mis-expression of DUX4 in skeletal muscle, however, is toxic and causes facioscapulohumeral muscular dystrophy (FSHD). We recently showed DUX4-induced toxicity is due, in part, to the accumulation of double-stranded RNAs (dsRNAs) with concomitant activation of the PKR viral response pathway. Here, using dsRNA immunoprecipitation coupled with next-generation sequencing, we determined that DUX4-induced dsRNAs originate from intergenic regions enriched for Alu and LINE-1 elements, endogenous retroviruses, and pericentric human satellite II (HSATII) repeats. DUX4-induced HSATII dsRNAs are formed via temporally controlled bidirectional expression with predominant transcription of one strand preceding the other. Whereas DUX4 activation of dsRNAs derived from intergenic regions such as HSATII contributes to toxicity in FSHD, in the early embryo these dsRNAs might facilitate heterochromatin formation, as has been proposed for cleavage stage expression of mouse major satellites.

2019-10-30 | GSE114936 | GEO

H3K9me2 and BRCA1 cooperate to prevent satellite repeat transcription, R-loop formation and germline sterility [ChIP-seq]

Project description:Repetitive sequences, transposable elements and silent tissue-specific genes in C. elegans are differentially enriched for di- and tri-methyl H3 lysine 9 (H3K9). SET-25 (SUV39h1/h2) catalyzes H3K9me3, while MET-2 (SetDB1) deposits only H3K9me1/me2. RNA-seq and genome-wide H3K9 methylation mapping in met-2 and set-25 single mutants showed that H3K9me2-mediated repression of satellite repeats by MET-2 correlates with germline integrity. Aberrant transcription of repeats and DNA transposons generates R-loops, loss of fertility and hydroxyurea hypersensitivity. In a genome-wide synthetic lethal screen, we identified the BRCA1 complex and factors implicated in the degradation of nuclear RNA as essential for germline integrity in met-2 mutants. Highly additive with met-2, the loss of the BRCA1 complex triggers satellite repeat transcription, generating R-loops on transcribed repeats. Supporting direct causality between satellite repeat transcription and BRCA1-mediated genome integrity, the targeted induction of MSAT1 transcripts at endogenous sites leads to damage-induced loss of fertility in wild-type C. elegans.

2017-07-04 | GSE100724 | GEO

H3K9me2 and BRCA1 cooperate to prevent satellite repeat transcription, R-loop formation and germline sterility [RNA-seq]

2017-07-04 | GSE100723 | GEO

DUX4-induced transcripts from pericentric human satellite II repeats form double-stranded RNA [stranded-RNAseq]

2019-10-30 | GSE114938 | GEO

Demethylated HSATII DNA and aberrant HSATII RNA foci act as sponges for epigenetic factors in cancer

Project description:This study reveals that the millions of satellite II (HSATII) sequences in the human genome can bind and impact distribution of epigenetic regulators, and that this goes awry in cancer. In many cancers master epigenetic factors form two-types of cancer-specific nuclear bodies, caused by locus-specific deregulation of HSATII DNA and RNA, respectively. DNA demethylation at the 1q12 mega-satellite, common in cancer, causes PRC1 aggregation into prominent Cancer-Associated Polycomb (CAP) bodies. These loci remain silent, whereas HSATII loci in regions low in PRC1 become de-repressed, reflecting imbalanced distribution of UbH2A on these and other PcG-regulated loci. Large nuclear foci of HSATII RNA form and sequester copious MeCP2 into Cancer-Associated Satellite Transcript (CAST) bodies. Hence, HSATII DNA and RNA have an exceptional capacity to “sponge” epigenetic factors into abnormal nuclear bodies in cancer. Results support a new concept that demethylation of “junk” repeats can trigger further epigenetic compromise by compartmentalizing regulatory factors within nuclear structure.

2017-03-29 | GSE94973 | GEO

Identification of alpha-satellite RNA interacting proteins

Project description:We set out to identify proteins that bind alpha-satellite ncRNAs in HCT-116 and SW-480 colorectal cancer human cell lines. We performed RNA pulldown followed by mass spectrometry identification of the associated proteins. Among the identified proteins, we observed a statistical overrepresenttion of some ontology ssociated to mitotic progression in HCT-116 cells, but not in SW-480 cells.

2022-08-12 | PXD024582 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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