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ABSTRACT: N6-Adenosine (m6A) Methylation profiling in Arabidopsis thaliana wild-type and fio1-2 by nanopore DRS sequencing

PROVIDER: PRJNA749003 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15216003_1.fastq.gz	Fastqsanger.gz
	SRR15216004_1.fastq.gz	Fastqsanger.gz
	SRR15216005_1.fastq.gz	Fastqsanger.gz
	SRR15216006_1.fastq.gz	Fastqsanger.gz
	SRR15216007_1.fastq.gz	Fastqsanger.gz

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Project description:N6-Adenosine methylation (m6A) in Arabidopsis thaliana mitochondria

| PRJNA472433 | ENA

Identification and Characterization of the Mammalian Nuclear RNA N6-Adenosine Methyltransferase Core Complex

Project description:N6-methyladenosine (m6A) is the most prevalent internal modification found in mammalian messenger and non-coding RNAs. The discoveries of functionally significant demethylases that reverse this methylation as well as the recently revealed m6A distributions in mammalian transcriptomes strongly indicate regulatory functions of this modification. Here we report the identification and characterization of the mammalian nuclear RNA N6-adenosine methyltransferase core (RNMTC) complex. Besides METTL3, a methyltransferase which was the only known component of RNMTC in the past, we discovered that a previously uncharacterized methyltransferase, METTL14, exhibits a N6-adenosine methyltransferase activity higher than METTL3. Together with WTAP, the third component that dramatically affects the cellular m6A level, these three proteins form the core complex that orchestrates m6A deposition on mammalian nuclear RNA. Biochemistry assays, imaging experiments, as well as transcriptome-wide analyses of the binding sites and their effects on m6A methylation support methylation function and reveal new insights of RNMTC. PAR-CLIP and m6A-seq in HeLa cells

2013-11-29 | E-GEOD-46705 | biostudies-arrayexpress

mRNA ADENOSINE METHYLASE promotes drought tolerance through N6-methyladenosine-dependent and independent impacts on mRNA regulation in Arabidopsis

Project description:• Among many mRNA modifications, adenine methylation at the N6 position (N6-methyladenosine, m6A) is known to affect mRNA biology extensively. The influence of m6A has yet to be assessed under drought, one of the most impactful abiotic stresses. • We show that Arabidopsis thaliana (L.) Heynh. (Arabidopsis) plants lacking mRNA ADENOSINE METHYLASE (MTA) are drought sensitive. Subsequently, we comprehensively assess the impacts of MTA-dependent m6A changes during drought on mRNA abundance, stability, and translation in Arabidopsis. • During drought, there is a global trend towards hyper-methylation of many protein-coding transcripts that does not occur in mta. We also observe complex regulation of m6A at a transcript-specific level, possibly reflecting compensation by other m6A components. Importantly, a subset of transcripts that are hyper-methylated in an MTA-dependent manner exhibited reduced turnover and translation in mta, compared to wild-type plants, during drought. Additionally, MTA impacts transcript stability and translation independently of m6A. We also correlate drought-associated deposition of m6A with increased translation of modulators of drought response, such as RD29A, COR47, COR413, ALDH2B, ERD7, and ABF4 in WT, which is impaired in mta. • m6A is dynamic during drought and, alongside MTA, promotes tolerance by regulating drought-responsive changes in transcript turnover and translation.

2024-10-07 | GSE243365 | GEO

Arabidopsis thaliana

Project description:Profiling of N6-Adenosine (m6A) Methylation in Arabidopsis thaliana wild-type and fip37-4 LEC1:FIP37

| PRJNA304438 | ENA

Adenosine methylation is widespread throughout the transcriptome and prominent within 3' UTRs

Project description:Here, we use a novel technique for locating regions of N6-adenosine methylation (m6A) throughout the transcriptome and present a profile of m6A sites in the mouse brain. Our use of methylated RNA immunoprecipitation combined with RNA-seq (MeRIP-Seq) identifies thousands of RNAs which contain m6A sites. In addition, we find that regions of m6A formation are particularly enriched near stop codons, which might provide clues into the potential funciton of this highly prevalent RNA modificaiton. Examination of m6A sites in murine brain RNA.

2012-05-16 | E-GEOD-29714 | biostudies-arrayexpress

Arabidopsis thaliana

Project description:Profiling of mRNA N6-Adenosine Methylation (m6A) in Arabidopsis

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Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3' UTRs and Near Stop Codons (OLD)

2012-12-31 | E-GEOD-34734 | biostudies-arrayexpress

Arabidopsis Messenger RNA N6-methyladenosine Demethylation Regulates Plant Development

Project description:N6-methyladenosine (m6A) is the most abundant internal modification in the messenger RNA (mRNA) of all higher eukaryotes. This modification has been shown to be reversible in mammals; it is installed by a methyltransferase heterodimer complex of METTL3 and METTL14 bound with WTAP, and reversed by iron(II)- and Î±-ketoglutarate-dependent demethylases FTO and ALKBH5. This modification exhibits significant functional roles in various biological processes. The m6A modification as a RNA mark is recognized by reader proteins, such as YTH domain family proteins and HNRNPA2B1; m6A can also act as a structure switch to affect RNA-protein interactions for biological regulation. In Arabidopsis thaliana, the methyltransferase subunit MTA (the plant orthologue of human METTL3, encoded by At4g10760) was well characterized and FIP37 (the plant orthologue of human WTAP) was first identified as the interacting partner of MTA. Here we report the discovery and characterization of reversible m6A methylation mediated by AtALKBH10B (encoded by At4g02940) in A. thaliana, and noticeable roles of this RNA demethylase in affecting plant development and floral transition. Our findings reveal potential broad functions of reversible mRNA methylation in plants. m6A peaks were identified from wild type Columbia-0 and atalkbh10b-1 mutant in two biological replicates

2016-03-24 | E-GEOD-79523 | biostudies-arrayexpress

RNA-Seq and N6-Adenosine (m6A) Methylation profiling in Arabidopsis thaliana wild-type and fip37-4 LEC1:FIP37

Project description:RNA-Seq and N6-Adenosine (m6A) Methylation profiling in Arabidopsis thaliana wild-type and fip37-4 LEC1:FIP37

| PRJNA304436 | ENA

An epitranscriptomic mechanism regulating chlorophyll biosynthesis in Arabidopsis

Project description:Light modulates expression of nuclear-encoded chloroplast proteins to promote chlorophyll biosynthesis and photosynthesis in plants. Photoregulatory mechanisms regulating transcription and protein stability of nuclear-encoded chloroplast proteins have been extensively studied, but how photoresponsive mRNA metabolism affecting chloroplast proteins remains not well understood. We performed a systematic analysis of the photoresponsive transcriptomes, m6A epitranscriptomes, translatomes, and proteomes in Arabidopsis, leading to a hypothesis that the blue light receptor cryptochromes activate the RNA methyltransferase, FIONA 1 (FIO1), to increase RNA methylation, translation of the nuclear-encoded chlorophyll synthesis enzymes (CSEs), and chlorophyll synthesis. We further demonstrate that the photoresponsive CRY2-interacting protein, SPA1, acts as a chaperone to mediate co-condensation of the CRY2/FIO1 complex, activating the FIO1 methyltransferase activity. This finding demonstrates a previously unknown photoregulatory mechanism controlling chlorophyll biosynthesis in plants.

2024-01-26 | PXD040660 | Pride

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