Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Antibody crossreactivity with mRNA cap accounts for widespread appearance of m1A throughout the transcriptome

ABSTRACT: N1-methyladenosine (m1A) was recently identified as a new mRNA modification based on its mapping to the 5’UTRs of thousands of mRNAs with an m1A-binding antibody. More recent studies have questioned the prevalence of m1A. To address this discrepancy, we mapped m1A using ultra-deep RNA-Seq datasets based on m1A-induced misincorporations during reverse transcription. Using this approach, we find m1A only in the mitochondrial MT-ND5 transcript. In contrast, m1A mapping using an m1A-binding antibody showed binding to transcription start nucleotides in mRNA 5’UTRs. Biochemical measurements indicate that m1A is not present at these sites. Instead, we find that the m1A antibody exhibits m1A-independent binding to mRNA cap structures. Our data demonstrate that high-stoichiometry m1A sites are rare in the transcriptome and that previous mapping of m1A to mRNA 5’UTRs reflect an unintended binding to mRNA caps.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE97909 | GEO | 2019/06/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Antibody crossreactivity with mRNA cap accounts for widespread appearance of m1A throughout the transcriptome

Project description:Antibody crossreactivity with mRNA cap accounts for widespread appearance of m1A throughout the transcriptome

| PRJNA383349 | ENA

m1A marks translation initiation sites in human and mouse messenger RNA [Sequencing]

2016-02-10 | E-GEOD-70485 | biostudies-arrayexpress

m1A marks translation initiation sites in human and mouse messenger RNA [Sequencing]

2016-02-10 | GSE70485 | GEO

m1A marks translation initiation sites in human and mouse messenger RNA [microarray]

Project description:We developed a novel approach, m1A-seq, for high-resolution mapping of the transcriptome-wide m1A landscape, based on antibody-mediated capture followed by massively parallel sequencing. Using this method we performed immunodepletion of methylated transcipts to assess the average methylation level Immunodepletion of m1A modified transcripts in human compared to the input, allows for estimation of the fraction of methylated transcripts. We compared the expression levels of sup (immunodepleted) and input methylated transcripts to deduce the fraction of m1A methylation.

2016-02-12 | E-GEOD-76057 | biostudies-arrayexpress

m1A marks translation initiation sites in human and mouse messenger RNA [microarray]

2016-02-12 | GSE76057 | GEO

Reversible and Dynamic m1A Methylation in the Human Transcriptome

Project description:N1-methyladenosine (m1A) is an abundant post-transcriptional RNA modification, yet little is known about its prevalence, topology and dynamics in mRNA. Here, we show that m1A is abundant in human mRNA, with an m1A/A ratio of ~0.02%. We develop m1A-ID-Seq, based on m1A immunoprecipitation and the inherent property of m1A to stall reverse transcription, for the transcriptome-wide m1A analysis. m1A-ID-Seq identifies 901 m1A peaks (from 583 genes) in mRNA and ncRNA, and reveals a prominent feature of enrichment in the 5â-untranslated region of mRNA transcripts, distinct from that of N6-methyladenosine, the most abundant internal mammalian mRNA modification. m1A in mRNA is also reversible by ALKBH3, a known DNA/RNA demethylase. Lastly, m1A responds dynamically to stimuli and hundreds of stress-induced m1A sites are identified. Collectively, our approaches allow comprehensive analysis of m1A methylation and provide an important tool for functional studies of potential epigenetic regulation via the reversible and dynamic m1A methylation. Identification of m1A sites in human embryonic kidney cells. Comparisons of m1A profiles of wild type HEK293T with ALKBH3 knock out cell line reveals the ALKBH3 specific sites. Stress inducible m1A sites are also identified by comparing the profiles of untreated cells with stress treated cells.

2016-02-05 | E-GEOD-73941 | biostudies-arrayexpress

Abundant mRNA m1A modification in dinoflagellates: a new layer of gene regulation [m1A-seq-TGIRT]

Project description:Dinoflagellates, a class of unicellular eukaryotic phytoplankton, exhibit minimal transcriptional regulation, representing a unique model for exploring gene expression. The biosynthesis, distribution, regulation, and function of mRNA N1-methyladenosine (m1A) remain controversial due to its limited presence in typical eukaryotic mRNA. This study found that m1A, rather than N6-methyladenosine (m6A), is the most prevalent internal mRNA modification in various dinoflagellate species, with an asymmetrically distribution along mature transcripts. In Amphidinium carterae, we identified 6549 m1A sites characterized by a non-tRNA T-loop-like sequence motif within the transcripts of 3196 genes, many involved in regulating carbon and nitrogen metabolism. With enrichment within 3'UTR, dinoflagellate mRNA m1A exhibits negative correlation with translation efficiency. Notably, nitrogen depletion led to a significant decrease in mRNA m1A. Furthermore, our analysis revealed that distinctive patterns of m1A modification influence the expression of metabolism-related genes through translation control. Thus, this study provides a comprehensive map of m1A in dinoflagellate mRNA, highlighting its crucial role as a post-transcriptional regulatory layer and enhancing the understanding of mRNA m1A modification.

2024-07-30 | GSE271240 | GEO

Amplicons of a ND5 mRNA segment to detect m1A1374 levels in HEK APPwt and Ctl cells

Project description:This experiment was set up to quantify m1A methylation levels at position 1374 of the mitochondrial encoded ND5 mRNA. To investigate the relevance of this methylation in Alzheimer's disease two cell lines were compared. HEK APPwt cells, transfected with a plasmid encoding the wild-type Amyloid-Precursor-protein and untransfected control cells were used. In the first step a RT was performed with SuperScript-IV (SS-IV) and a ND5 specific RT primer. Afterwards a PCR was conducted to amplify the sequence around the m1A position. The amplicon is about 100 bp length and was sequenced in an Illumina Sequencing was performed in a MiSeq 2x75 PE run. For both cell lines the m1A analysis method was conducted with 4 biological replicates of total RNA and 2 biological replicates of RNA isolated from mitochondrial extracts.

2023-07-21 | E-MTAB-12033 | biostudies-arrayexpress

RNA m1A methylation regulates glycolysis of cancer cells through modulating ATP5D

Project description:Studies on biological functions of RNA modifications such as N6-methyladenosine (m6A) in mRNA have sprung up in recent years, while the roles of N1-methyladenosine (m1A) in cancer progression remain largely unknown. We find m1A demethylase ALKBH3 can regulate the glycolysis of cancer cells via a demethylation activity dependent manner. Specifically, sequencing and functional studies confirm that ATP5D, one of the most important subunit of ATP synthase, is involved in m1A demethylase ALKBH3-regulated glycolysis of cancer cells. The m1A modified A71 at the Exon 1 of ATP5D negatively regulates its translation elongation via increasing the binding with YTHDF1/eRF1 complex, which facilitates the release of mRNA from ribosome complex. m1A also regulates mRNA stability of E2F1, which directly binds with ATP5D promoter to initiate its transcription. Targeted specific demethylation of ATP5D m1A by dm1ACRISPR system can significantly increase the expression of ATP5D and glycolysis of cancer cells. In vivo data confirm the roles of m1A/ATP5D in tumor growth and cancer progression. Our study for the first time reveals a crosstalk of mRNA m1A modification and cell metabolism, which expands the understanding of such interplays that are essential for cancer therapeutic application.

2022-02-02 | GSE195637 | GEO

Amplicons of a ND5 mRNA segment to detect m1A1374 levels in HEK pTRMT10C cells and control cells

Project description:This experiment was set up to assess the effect of TRMT10C overexpression on m1A methylation levels at position 1374 of the mitochondrial encoded ND5 mRNA. To investigate if TRMT10C is the writer enzyme for this m1A site, a cell system providing tetracycline-inducible TRMT10C expression was used (termed pTRMT10C cells). To control the effect of tetracycline itself, a corresponding control cell line without the tetracycline-inducible TRMT10C plasmid was used (termed Ctl cells). Method description: pTRMT10C and Ctl cells were incubated with three different concentrations of tetracycline (0 µg/mL, 0.1 µg/mL and 1 µg/mL) for 24 hours. The RNA was isolated using a Trizol-based protocol. Afterwards a Reverse transcription was performed with the RT SuperScript-IV (SS-IV) and a ND5 specific RT primer. Next, PCR was conducted to amplify the sequence around the m1A position. The amplicon is about 100 bp of length and was sequenced in an Illumina Sequencing MiSeq 2x75 PE run. For both cell lines the m1A analysis method was conducted with 4 biological replicates for each of the three tetracycline concenctraion.

2023-07-24 | E-MTAB-12038 | biostudies-arrayexpress

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