Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus (scRNA-Seq)

ABSTRACT: Long non-coding RNAs (lncRNAs) are diverse transcription products emanating from thousands of loci in mammalian genomes, implicated in a wide array of cellular processes including transcriptional regulation, differentiation, cellular reprogramming, and many others. While a large majority of functional lncRNAs have been proposed to act in cis to their sites of transcription, an in-depth understanding of the functional features within such lncRNA loci, as well as their mechanisms of action, is currently lacking. Further insights are hindered by the heavy dependencies of observed phenotypes on the perturbation techniques employed. Here, we study Meteor, a lncRNA transcribed nearby the gene encoding for Eomes, a pleiotropic transcription factor with highly regulated spatiotemporal expression patterns throughout early development and in adult tissues. Using a wide array of perturbation techniques, we show that transcription elongation through the Meteor locus is required for Eomes activation in naive mouse embryonic stem cells (mESCs), with Meteor repression linked to a reduction in cells potentiated to differentiate to the mesoderm lineage. We further demonstrate that a distinct functional feature of the locus – namely, the underlying DNA element – is required for suppressing Eomes expression following neuronal differentiation of mESCs. Our results demonstrate the complex regulation that can be conferred by a single lncRNA locus, and emphasize the importance of careful selection of perturbation techniques for the study of lncRNA loci.

ORGANISM(S): Mus musculus

PROVIDER: GSE223452 | GEO | 2023/04/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus (3' RNA-Seq)

Project description:Long non-coding RNAs (lncRNAs) are diverse transcription products emanating from thousands of loci in mammalian genomes, implicated in a wide array of cellular processes including transcriptional regulation, differentiation, cellular reprogramming, and many others. While a large majority of functional lncRNAs have been proposed to act in cis to their sites of transcription, an in-depth understanding of the functional features within such lncRNA loci, as well as their mechanisms of action, is currently lacking. Further insights are hindered by the heavy dependencies of observed phenotypes on the perturbation techniques employed. Here, we study Meteor, a lncRNA transcribed nearby the gene encoding for Eomes, a pleiotropic transcription factor with highly regulated spatiotemporal expression patterns throughout early development and in adult tissues. Using a wide array of perturbation techniques, we show that transcription elongation through the Meteor locus is required for Eomes activation in naive mouse embryonic stem cells (mESCs), with Meteor repression linked to a reduction in cells potentiated to differentiate to the mesoderm lineage. We further demonstrate that a distinct functional feature of the locus – namely, the underlying DNA element – is required for suppressing Eomes expression following neuronal differentiation of mESCs. Our results demonstrate the complex regulation that can be conferred by a single lncRNA locus, and emphasize the importance of careful selection of perturbation techniques for the study of lncRNA loci.

2023-04-23 | GSE223449 | GEO

Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus (ChIP-Seq)

2023-04-23 | GSE223447 | GEO

Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus (4C)

2023-04-23 | GSE223451 | GEO

Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus (CUT&RUN)

2023-04-23 | GSE223448 | GEO

Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus (RNA-Seq)

2023-04-21 | GSE223445 | GEO

Dicer-microRNA-Myc circuit promotes transcription of hundreds of long noncoding RNAs

Project description:Long noncoding RNAs (lncRNAs) are important regulators of cell fate, and their mis-expression has been implicated in many diseases. While distinct polymerases generate messenger vs. noncoding ribosomal or tRNAs3, little is known about distinct mechanisms controlling lncRNA expression. Here we show that transcription of lncRNAs is quantitatively different from that of messenger RNAs (mRNAs)--as revealed by deficiency of Dicer (Dcr), a key ribonuclease that generates microRNAs (miRNAs). Loss of Dcr in mouse embryonic stem cells (mESCs) led surprisingly to decreased level of the majority of lncRNAs. The canonical Dgcr8-Dcr-miRNA pathway is required for robust lncRNA expression, at the level of transcriptional initiation and elongation of lncRNA genes rather than at the level of their stability. cMyc, an oncogenic transcription factor, whose expression is indirectly regulated by Dcr-miRNA in mESCs, is partly responsible for lncRNA transcription. Loss of cMyc led to a more dramatic decrease of lncRNAs than mRNAs, and cMyc overexpression rescues lncRNA expression in Dcr KO cells. A quantitative metric of “mRNA-lncRNA decoupling” revealed that Dcr and cMyc differentially regulate lncRNAs vs. mRNAs in diverse cell types and in vivo, as evidenced by hundreds of microarray experiments. Thus, Dcr and cMyc may allow numerous lncRNAs to be activated or deactivated as a class, implicating lncRNAs to potential regulatory roles in development and disease states where Dcr and cMyc have been associated with. RNA was sequenced from WT and Dcr KO mESCs and the expression of lncRNAs and mRNAs are compared between WT and Dcr KO mESCs.

2014-06-15 | E-GEOD-55338 | biostudies-arrayexpress

Comprehensive Identification of Soybean Long Non-coding RNAs Reveals a Subset of Small Peptide-Coding Transcripts

Project description:Long non-coding RNAs (lncRNAs) are defined as non-protein-coding transcripts that are at least 200 nucleotides long. They are known to play pivotal roles in regulating gene expression, especially during stress responses in plants. We used a large collection of in-house transcriptome data from various soybean (Glycine max and Glycine soja) tissues treated under different conditions to perform a comprehensive identification of soybean lncRNAs. We also retrieved publicly available soybean transcriptome data that were of sufficient quality and sequencing depth to enrich our analysis. In total, RNA-seq data of 332 samples were used for this analysis. An integrated reference-based, de novo transcript assembly was developed that identified ~69,000 lncRNA gene loci. We showed that lncRNAs are distinct from both protein-coding transcripts and genomic background noise in terms of length, number of exons, transposable element composition, and sequence conservation level across legume species. The tissue-specific and time-specific transcriptional responses of the lncRNA genes under some stress conditions may suggest their biological relevance. The transcription start sites of lncRNA gene loci tend to be close to their nearest protein-coding genes, and they may be transcriptionally related to the protein-coding genes, particularly for antisense and intronic lncRNAs. A previously unreported subset of small peptide-coding transcripts was identified from these lncRNA loci via tandem mass spectrometry, which paved the way for investigating their functional roles. Our results also highlight the current inadequacy of the bioinformatic definition of lncRNA, which excludes those lncRNA gene loci with small open reading frames (ORFs) from being regarded as protein-coding.

2020-01-09 | PXD014553 | Pride

Profiles of Long Noncoding RNAs in Human Naive and Memory T Cells

Project description:We employed whole-genome RNA-sequencing to profile mRNAs and both annotated and novel long noncoding RNAs (lncRNAs) in human naive, central memory, and effector memory CD4+ T cells. Loci transcribing both lineage-specific annotated and novel lncRNA are adjacent to lineage-specific protein-coding genes in the genome. Lineage-specific novel lncRNA loci are transcribed from lineage-specific typical- and supertranscriptional enhancers and are not multiexonic, thus are more similar to enhancer RNAs. Novel enhancer-associated lncRNAs transcribed from the IFNG locus bind the transcription factor NF-κB and enhance binding of NF-κB to the IFNG genomic locus. Depletion of the annotated lncRNA, IFNG-AS1, or one IFNG enhancer-associated lncRNA abrogates IFNG expression by memory T cells, indicating these lncRNAs have biologic function.

2017-06-11 | GSE85294 | GEO

The DNMT1 associated lncRNA Dali is an epigenetic regulator of neural differentiation [1]

Project description:Many intergenic long noncoding RNA (lncRNA) loci regulate the expression of adjacent protein coding genes. Less clear is whether intergenic lncRNAs commonly regulate transcription by modulating chromatin at genomically distant loci. Here, we report both genomically local and distal RNA-dependent roles of Dali, a conserved central nervous system expressed intergenic lncRNA. Dali is transcribed downstream of the Pou3f3 transcription factor gene and its depletion disrupts the differentiation of neuroblastoma cells. Locally, Dali transcript regulates transcription of the Pou3f3 locus. Distally, it preferentially targets active promoters and regulates expression of neural differentiation genes, in part through physical association with the POU3F3 protein. Dali interacts with the DNMT1 DNA methyltransferase in mouse and human and regulates DNA methylation status of CpG island-associated promoters in trans. These results demonstrate, for the first time, that a single intergenic lncRNA controls the activity and methylation of genomically distal regulatory elements to modulate large-scale transcriptional programmes. N2A cells transfected with a non-targeting control vector were compared to N2A cells transfected with a Dali knockdown construct. Three biological replicates of each condition were analysed on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays.

2014-12-03 | E-GEOD-62031 | biostudies-arrayexpress

The DNMT1 associated lncRNA Dali is an epigenetic regulator of neural differentiation [3]

Project description:Many intergenic long noncoding RNA (lncRNA) loci regulate the expression of adjacent protein coding genes. Less clear is whether intergenic lncRNAs commonly regulate transcription by modulating chromatin at genomically distant loci. Here, we report both genomically local and distal RNA-dependent roles of Dali, a conserved central nervous system expressed intergenic lncRNA. Dali is transcribed downstream of the Pou3f3 transcription factor gene and its depletion disrupts the differentiation of neuroblastoma cells. Locally, Dali transcript regulates transcription of the Pou3f3 locus. Distally, it preferentially targets active promoters and regulates expression of neural differentiation genes, in part through physical association with the POU3F3 protein. Dali interacts with the DNMT1 DNA methyltransferase in mouse and human and regulates DNA methylation status of CpG island-associated promoters in trans. These results demonstrate, for the first time, that a single intergenic lncRNA controls the activity and methylation of genomically distal regulatory elements to modulate large-scale transcriptional programmes. N2A cells transfected with a non-targeting control vector were compared to N2A cells transfected with a Pou3f3 knockdown construct. Three biological replicates of each condition were analysed on Affymetrix GeneChip Mouse Gene 1.0 ST Arrays.

2014-12-03 | E-GEOD-62033 | biostudies-arrayexpress

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