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M1A marks translation initiation sites in human and mouse messenger RNA [microarray]

ABSTRACT: 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

ORGANISM(S): Homo sapiens

PROVIDER: GSE76057 | GEO | 2016/02/12

SECONDARY ACCESSION(S): PRJNA306098

REPOSITORIES: GEO

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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 [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

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-02-12 | E-GEOD-76058 | biostudies-arrayexpress

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

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

| PRJNA288805 | ENA

m1A marks translation initiation sites in human and mouse messenger RNA

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-02-12 | GSE76058 | 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

The METTL5-TRMT112 N6-methyladenosine methyltransferase complex regulates metabolism and development via translation (Identification of m1A mRNA methyltransferase in nucleus by TMT11-LC-MS/MS)

Project description:m1A has long been known to be important in tRNA and rRNA, but we recently mapped many m1A sites in mRNA as well. m1A is found on the 5’ ends of genes, usually around the first splice site, but we have yet to understand how it effects transcript fate. Identifying the methyltransferase would be a major first step towards understanding m1A function.

2021-11-30 | PXD028832 | Pride

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

Chemical manipulation of m1A mediates its detection in human tRNA

Project description:N1-methyl adenosine (m1A) is a wide-spread RNA modification present in tRNA, rRNA and mRNA. m1A modification sites in tRNAs are evolutionary conserved and its formation on tRNA is catalyzed by methyltransferase TRMT61A and TRMT6 complex. m1A promotes translation initiation and elongation. Due to its positive charge under physiological conditions, m1A can notably modulate RNA structure. It also blocks Watson-Crick base pairing and causes mutation and truncation during reverse transcription. Several misincorporation-based high throughput sequencing methods have been developed to sequence m1A. In this study, we introduce a reduction-based m1A sequencing (red-m1A-seq). We report that NaBH4 reduction of m1A can improve the mutation and readthrough rates using commercially available RT enzymes to give better positive signature, while alkaline-catalyzed Dimroth rearrangement can efficiently convert m1A to m6A to provide good controls, allowing the detection of m1A with higher sensitivity and accuracy. We applied red‑m1A-seq to sequence human small RNA and we not only detected all the previously reported tRNA m1A sites, but also new m1A sites in mt-tRNAAsn-ATT and 5.8S rRNA.

2024-04-24 | GSE253657 | GEO

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