Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

57 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MRNA-seq of neuronal compartments in shRNA-mediated + small-molecule knockdown of Mettl3 in mouse primary cortical neurons (mPCN)

ABSTRACT: To study the effect of m6A modifications on subcellular mRNA localization we depleted m6A writer Mettl3 with shRNA and small molecule from mouse primary cortical neurons (mPCN) and sequenced neuritic and somatic compartments in parallel with scrambled shRNA control.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mus musculus

SUBMITTER: Marina Chekulaeva

PROVIDER: E-MTAB-11570 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

mRNA-seq of neuronal compartments in shRNA-mediated knockdown of Ythdf1, -2 and -3 in mouse primary cortical neurons (mPCN)

Project description:To study the effect of m6A modifications on subcellular mRNA localization we depleted m6A readers Ythdf1, -2 and -3 with shRNAs from mouse primary cortical neurons (mPCN) and sequenced neuritic and somatic compartments in parallel with scrambled shRNA control.

2023-07-12 | E-MTAB-11569 | biostudies-arrayexpress

Sequencing of a human Orfeome in subcellular compartments of mouse primary cortical neurons (mPCN)

Project description:To study how the codon composition of the coding sequence affects subcellular localization of mRNA in an unbiased way, mouse primary cortical neurons were transfected with a collection of human open reading frames (ORFs) with identical untranslated regions, separated into soma and neurites, and subjected to RNA sequencing with specific amplification of the ORFs.

2023-07-12 | E-MTAB-11571 | biostudies-arrayexpress

mRNA-seq of neuronal compartments with perturbed mRNA degradation machinery in mouse primary cortical neurons (mPCN)

Project description:We have perturbed mRNA degradation machinery and investigated the change in subcellular localization of mRNA in mouse primary cortical neurons (mPCNs). Mutant mPCN line harbouring a ponasteroneA-inducible heterozygous dominant-negative Caf1 (dnCaf1) was generated, separated into neuronal compartments (soma and neurites) and sequenced in parallel with compartments from the GFP-transfected cells (GFP, negative control).

2022-11-14 | E-MTAB-11572 | biostudies-arrayexpress

Slamseq of whole mouse primary cortical neurons (mPCN) with perturbed mRNA degradation machinery

Project description:We perturbed mRNA degradation machinery in mouse primary cortical neurons (mPCN) and investigated the change in mRNA half-lives. We performed SLAMseq Metabolic RNA Labeling on Mutant mPCN line harbouring a ponasteroneA-inducible heterozygous dominant-negative Caf1 (dnCaf1) and on GFP-transfected mPCNs. The Slamseq technique provided snapshots of mRNA kinetics allowing to estimate mRNA half-lives.

2022-11-14 | E-MTAB-11575 | biostudies-arrayexpress

Mass spectrometry analysis of METTL3 phosphorylation in extracellular growth factor signaling

Project description:A fundamental facet of cell signaling is the conversion of extracellular signals into adaptive transcriptional responses. The role of RNA modifications in this process is poorly understood. We found that epidermal growth factor (EGF) promotes ERK-dependent phosphorylation of the m6A writer enzyme METTL3 at serine-43. Serine-43 phosphorylation increased METTL3-mediated methylation of the small nuclear RNA 7SK. Here we performed of phosphorylation mass spectrometry based on Data independent acquisition (DIA) of Hela cells stimulated with EGF in the absence or presence of the inhibitor U0126. Additionally, we validated known interactions between the 7SK-associated protein LARP7. Our findings establish a novel function for the m6A modification in converting growth-factor signaling events to a transcriptional elongation regulatory response via an RNA-methylation-dependent switch mediated by ERK signaling.

2023-06-27 | PXD036344 | Pride

m6A-RIP-seq of mRNA in yw, Mettl3, Mettl14 and Hakai flies

Project description:In order to obtain a stringent m6A methylome in Drosophila adults, we performed m6A-RIP-seq in yw control (male and female), Mettl3 (male), Mettl14 (male) and Hakai (male) mutant flies. We find that the effective m6A modification, which depends on the writer complex, is mostly distributed in 5’ UTR and near start codon in Drosophila, in contrast to the mammalian system. We define a set of high-confident m6A methylation sites shared by Mettl3, Mettl14 and Hakai, indicating that Hakai is a core component of the m6A writer complex. We also find differential methylation pattern in certain loci between male and female flies.

2021-03-01 | GSE155662 | GEO

Two zinc finger proteins with functions in m6A writing interact with HAKAI

Project description:The methyltransferase complex (m6A writer), which catalyzes the deposition of N6-methyladenosine (m6A) in mRNAs, is highly conserved across most eukaryotic organisms, but its components and interactions between them are still far from fully understood. Using in vivo interaction proteomics, two HAKAI-interacting zinc finger proteins, HIZ1 and HIZ2, were discovered as novel components of the Arabidopsis m6A writer complex. HAKAI is required for the interaction between HIZ1 and MTA. Whilst HIZ1 knockout plants have normal levels of m6A, plants in which it is overexpressed show reduced methylation. In addition, HIZ1 was found to be involved in root hair development upon auxin transport inhibition in a HAKAI-dependent manner. Mutant plants lacking HIZ2 are viable but have an 85% reduction in m6A abundance and show severe developmental defects. Our findings suggest that HIZ1 appears to be a HAKAI-dependent negative regulator of m6A deposition and HIZ2 is a novel and essential member of the Arabidopsis m6A writer complex.

2022-02-09 | PXD026287 | Pride

Porcine Rotavirus VP6 Protein Wrests IPEC-J2 METTL3-Mediated M6A Modification to Fight Antiviral Immune Response

Project description:N6-methyladenosine (m6A), the most abundant mRNA modification, can regulate various mRNA metabolism to affect numerous physiological and pathophysiological processes, including immune function. However, the regulation of m6A methylation and its role in immune defense against virus infections remain unexplored. Here, we found that Porcine rotavirus (PoRV) infection decreased global m6A levels in host cells by downregulating m6A writer METTL3. Remarkably, knockdown of Mettl3 or m6A reader Ythdf2 enhances antiviral resistance in IPEC-J2 cells. Through RNA-seq and m6A -seq, we identified interferon regulatory factor 2 (IRF2) and interferon induced protein 44-like (IFI44L) as key m6A targets during PoRV infection. Silencing Mettl3 or Ythdf2 elevated mRNA stability of Irf2 and Ifi44l to restricting viral replication. Conversely, depletion of Irf2 and Ifi44l rendered host cells more susceptible to PoRV infection. Our findings uncover a novel m6A-mediated antiviral mechanism targeting the interferon response factors IRF2 and IFI44L, shedding new light on the epitranscriptomic regulation of host-pathogen interactions.

2024-04-19 | GSE264016 | GEO

Effects of Mettl3 and Alkbh5 knockdown on total RNA

Project description:Understanding the functional role of RNA modifications and to what extent they might regulate mature miRNA function and their secretion in extracellular vesicles (EVs) is unknown. Analysis of RNA content across a variety of EVs has shown differential miRNA enrichment when compared to parental cell expression patterns. Whether this is due to differential stability, specific regulation of miRNA export, or other mechanisms is unclear. Here, we tested whether RNA base modifications and recognition of those modifications might underlie differential miRNA export into EVs derived from KRAS mutant cell lines. We found that decreased levels of Mettl3, a writer of N6-methyladenosine (m6A) modification, altered extracellular transfer of miRNAs containing consensus sequences for m6A. Further, EVs prepared from cells expressing shRNAs against Mettl3 were incapable of conferring colony growth in 3D to wild type KRAS cells. Our data indicate that m6A modification plays an important role in miRNA export to EVs.

2021-08-25 | GSE182382 | GEO

Multi-omics analysis of hematopoietic progenitors in the fetal liver of Mettl3 deficient mice

Project description:N6-methyladenosine (m6A) is the most abundant RNA modification, but little is known about its role in mammalian hematopoietic development. Conditional deletion of the m6A writer METTL3 in murine fetal liver results in hematopoietic failure and perinatal lethality. Loss of METTL3 and m6A activates an aberrant innate immune response, mediated by the formation of endogenous double-stranded RNAs (dsRNAs). The aberrantly formed dsRNAs are long, highly m6A modified in their native state, characterized by low folding energies and predominantly protein-coding. We identified coinciding activation of innate immune pattern recognition receptor pathways normally tasked with the detection of foreign dsRNAs. Our results suggest that m6A modification protects against endogenous dsRNA formation and a deleterious innate immune response during mammalian hematopoietic development. Keywords: innate immune response, dsRNA, RNA modification, N6-methyladenosine, METTL3, hematopoietic development, RNA-seq, H3K4me3, CUT&RUN, J2-RIP, dropseq, single cell RNA-seq, scRNA-seq, LSK, fetal liver

2020-06-01 | GSE148882 | GEO

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