Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Macro ncRNAs are abundant in imprinted regions and directly regulated by DNA methylation [tiling array]

ABSTRACT: Imprinted macro ncRNAs such as Airn play an important role in silencing protein-coding genes in cis, macro ncRNAs could be a common feature in all imprinted gene clusters. By applying the RNA Expression on Tiling Array (RETA) technique, macro ncRNAs were found to be abundant in 26 known mouse genomic regions containing imprinted genes were detected. All well-known imprinted macro ncRNAs were up-regulated upon depletion of DNA methylation.

ORGANISM(S): Mus musculus

PROVIDER: GSE26718 | GEO | 2017/02/25

SECONDARY ACCESSION(S): PRJNA136125

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Airn transcriptional overlap but not its lncRNA products induce imprinted Igf2r silencing.

Project description:To test if the imprinted long non-coding RNA (lncRNA) Airn transcription or its product silences the protein-coding Igf2r gene, we shortened the endogenous lncRNA to four different lengths by inserting polyadenylation (polyA) cassettes on the paternal chromosome via homologous recombination in ES cells. ES cell differentiation was used to recapitulate the developmental onset of Airn and Igf2r imprinted expression and polyA cassettes inserted before (T3, T16, T27) or after (T31, T51) the Igf2r promoter successfully truncated Airn, with the exception of T27. RNA hybridization to a tiling array (MIRTA) demonstrated loss of Airn upstream of the Igf2r promoter (except T27) and absence of novel spliced variants in all truncation alleles. To further test the transcriptional overlap model we moved the Airn promoter ~700bp before the Igf2r TSS in ES cells that lack an endogenous paternal Airn promoter and called this cell line FAP (Forward-Airn-Promoter). RNA hybridization to a tiling array (MIRTA) demonstrated that the moved Airn promoter expresses Airn in wildtype orientation and terminates at the wildtype 3' end. ES cell lines expressing different Airn variants were differentiated on gelatinized dishes after feeder cell depletion and LIF withdrawal by 0.27M-BM-5M retinoic acid for 5 days and Airn length was assayed.

2012-12-20 | E-GEOD-41444 | biostudies-arrayexpress

Airn transcriptional overlap but not its lncRNA products induce imprinted Igf2r silencing.

2012-12-20 | GSE41444 | GEO

The Airn RNA does not require any DNA elements within its locus to silence distant imprinted genes

Project description:Long non-coding (lnc) RNAs are numerous and found throughout the mammalian genome, and many are thought to be involved in the regulation of gene expression. However, the majority remain relatively uncharacterised and of uncertain function making the use to model systems to uncover their mode of action valuable. Imprinted lncRNAs target and recruit epigenetic silencing to a cluster of imprinted genes on the same chromosome, making them one of the best characterized lncRNAs to silence distant genes in cis. In this study we examined silencing of the distant imprinted gene Slc22a3 by the lncRNA Airn in the Igf2r imprinted cluster in mouse. Previously we proposed that imprinted lncRNAs may silence distant imprinted genes by disrupting promoter-enhancer interactions by being transcribed through the enhancer, which we called the enhancer interference hypothesis. Here we tested this hypothesis by first using allele-specific chromosome conformation capture (3C) to detect interactions between the Slc22a3 promoter and the locus of the Airn lncRNA that silences it on the paternal chromosome. In agreement with the model we found interactions enriched on the maternal allele, but across the entire Airn gene consistent with multiple enhancer-promoter interactions. Therefore, to further test the enhancer interference hypothesis we devised an approach to delete the entire Airn gene. However, the deletion showed that there are no essential enhancers for Slc22a3 within the Airn gene, strongly indicating that the Airn RNA rather than its transcription is responsible for silencing distant imprinted genes. Therefore we propose an alternative hypothesis whereby the chromosome interactions may initially guide the lncRNA to target imprinted promoters and recruit repressive chromatin, and that these interactions are lost once silencing is established.

2019-07-07 | GSE128513 | GEO

An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs.

Project description: Not available

| S-EPMC3213133 | biostudies-literature

Transcriptome high-throughput sequencing derived from mouse blastocysts with artificial oocyte activation treatment

Project description:Intracytoplasmic sperm injection (ICSI) has been an effective infertility treatment. Nevertheless, ICSI failures still occurred. One of the factors associated with ICSI failure is oocyte activation deficiency (AOD). The most commonly applied method of artificial oocyte activation (AOA) in humans includes ionophore. Although AOA is performed as a routine process in many assisted reproduction centers, up to date, there is no relevant study to expound whether AOA procedures increase developmental risks by disturbing subsequent gene expression during the embryonic development stages. Our results for the first time provide a profile of the changes in the global patterns of gene expression in AOA treatment versus ICSI generated mouse early embryos. In particular, we focus on the expression changes of imprinted genes. Another key observation in this study is that AOA treatment affects imprinted gene Igf2r expression and mehtylation, which is regulated by the imprinted Airn macro long non-coding (lnc) RNA.

2021-11-10 | GSE155948 | GEO

ATAC-seq of Thp1-mono, Thp1-macro, and Thp1-M.tb

Project description:Next Generation Sequencing data of ATAC-Seq library of Thp1-mono, Thp1-macro, and Thp1-M.tb

2022-09-06 | GSE208044 | GEO

ChIP-seq of Thp1-mono, Thp1-macro, and Thp1-M.tb

Project description:Next Generation Sequencing data of ChIP-seq library of Thp1-mono, Thp1-macro, and Thp1-M.tb

2022-09-06 | GSE208043 | GEO

Differential ncRNAs of oxaliplatin-resistant versus parental HCT116 cells

Project description:Oxaliplatin resistance frequently leads to therapeutic failure in colorectal cancer (CRC). Increasing evidence has shown that noncoding RNAs (ncRNAs) play pivotal roles in chemoresistance of CRC. However, the roles and mechanisms of ncRNAs in oxaliplatin resistance are not well understood. In this study, to identify the ncRNAs induced by oxaliplatin, we profile the expression of ncRNAs in oxaliplatin-resistant HCT116 CRC cells (HCT116oxR) and parental HCT116 cells using next-generation sequencing technology.

2023-08-31 | GSE119603 | GEO

Prolonged T–DC macro-clustering in lymph nodes initiates site-specific Th2 differentiation

Project description:T helper 2 (Th2) responses protect against pathogens while also driving allergic inflammation, yet how large-scale Th2 responses are generated in tissue context remains unclear. Here, we used quantitative imaging to investigate early Th2 differentiation within lymph nodes (LNs) following cutaneous allergen administration. Contrary to current models, we observed extensive activation and ‘macro-clustering’ of early Th2 cells with migratory type-2 dendritic cells (cDC2s) generating specialized Th2-promoting microenvironments. Macro-clustering was integrin mediated and promoted localized cytokine exchange among T cells to reinforce differentiation, which contrasted behavior during Th1 responses. Unexpectedly, formation of Th2 macro-clusters was dependent on the site of skin sensitization. Differences between sites were driven by divergent activation states of migratory cDC2 from different dermal tissues, with enhanced costimulatory molecule expression by cDC2 in Th2-generating LNs promoting prolonged T cell activation, macro-clustering, and cytokine sensing. Thus, generation of dedicated Th2 priming microenvironments through enhanced costimulatory molecule signaling initiates Th2 responses in vivo and occurs in a skin site-specific manner.

2024-01-29 | GSE254473 | GEO

Expression of 50-500nt ncRNAs in silkworm Bombyx mori during development

Project description:With an experimental RNomics, we identified 194 novel ncRNAs in silkworm through four developmental stages (egg, larva, pupa and adult). Oligos of 132 ncRNAs were sucessfully designed, the expression of these ncRNAs were analyzed by dual-channel microarray, results showed that 36 ncRNAs had significantly differential expression during development.

2010-12-22 | GSE22911 | 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