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M6A-seq and RNA-seq in Arabidopsis dcl1 mutant

ABSTRACT: m6A-seq and RNA-seq in Arabidopsis dcl1 mutant

PROVIDER: PRJNA922955 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23050175_1.fastq.gz	Fastqsanger.gz
	SRR23050175_2.fastq.gz	Fastqsanger.gz
	SRR23050176_1.fastq.gz	Fastqsanger.gz
	SRR23050176_2.fastq.gz	Fastqsanger.gz
	SRR23050177_1.fastq.gz	Fastqsanger.gz

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m6A-seq and RNA-seq in Arabidopsis dcl1 mutant

Project description:N6-methyladenosine (m6A) modification is essential for plant growth and development. Recently, a possible involvement of miRNAs in m6A modification is reported in animal. To understand a potential involvement of miRNAs in sequence-specific deposition of m6A marks in plants, in this study, we performed m6A-seq and RNA-seq for a mutant of dicer-like 1 (dcl1), a key component in miRNA biogenesis in Arabidopsis. And the difference of m6A modification was compared between Col-0 mutant and dcl1 mutant.

2023-06-11 | GSE222644 | GEO

Transcriptome-wide high-throughput deep m6A-seq reveals unique m6A methylation differential patterns among three organs in Arabidopsis

Project description:m6A is a ubiquitous RNA modification in eukaryotes. Transcriptome-wide m6A patterns in Arabidopsis have been assayed recently. However, m6A differential patterns among organs have not been well characterized. The goal of the study is to comprehensively analyze m6A patterns of numerous types of RNAs, the relationship between transcript level and m6A methylation extent, and m6A differential patterns among organs in Arabidopsis. In total, 18 libraries were sequneced. For the 3 organs: leaf, flower and root, each organ has mRNA-Seq, m6A-Seq and Input sequenced. And each sequence has 2 replicats.

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

Project description:m6A profiling in two accessions of Arabidopsis thaliana (Can-0 and Hen-16) using the m6A-targeted antibody coupled with high-throughput sequencing m6A-seq in two accessions of Arabidopsis, two replicates for each sample

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Comparative sRNA-Seq analysis of TCV-infected wildtype and dcl1-9 mutant Arabidopsis thaliana

Project description:Belonging to the Carmovirus family, Turnip crinkle virus (TCV) is a positive-strand RNA virus that can infect Arabidopsis. Most Arabidopsis ecotypes are highly susceptible to TCV, except for the TCV resistant line Di-17 derived from ecotype Dijon. Previous studies showed that many of the stress related genes have changed significantly after TCV infection. Besides the virus-triggered genes, small RNAs also play critical roles in plant defense by triggering either transcriptional and/or post-transcriptional gene silencing. In this study, TCV-infected wildtype Arabidopsis thaliana and dcl1-9 mutant plants were subjected to transcriptome and small RNA analysis to investigate the role of DCL1 in virus defense network.

2017-01-11 | GSE85069 | GEO

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

Project description:This SuperSeries is composed of the following subset Series: GSE36958: Gene expression profiles of WT and ime4-/- mutant yeast cells, under vegetative and meiosis-inducing conditions GSE37001: METTL3 KD in HepG2 cells GSE37002: m6A mapping in human RNA (with treatments) GSE37003: m6A mapping in human RNA (untreated) GSE37004: m6A mapping in mouse RNA (mouse liver and human brain) Refer to individual Series

2012-04-24 | E-GEOD-37005 | biostudies-arrayexpress

Serrate modulates N6-Methyladenosine (m6A) RNA modification in Arabidopsis

Project description:N6-methyladenosine (m6A) is the most common prevalent internal modifications found in many of the eukaryotic mRNA and plays an important role in RNA metabolism including pre-mRNA processing, mRNA stability, RNA splicing, RNA export and nuclear retention. Serrate is a component of the Dicer complex, plays as a key factor in RNA metabolism. We here reported SERRATE acts as a key regulator of mRNA m6A modification in Arabidopsis. Loss function of SE results in significant global m6A level reduction in the se-1 mutant comparing to the Col-0. SE positively regulates the transcription of MTA and MTB. In addition, SE physically interacts and functionally works with the m6A writer complex MTA and MTB which affects the binding of m6A methylase to mRNA. Taking together, our data provides a molecular framework that SE modulates m6A mRNA modification in Arabidopsis.

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Comparative transcriptome analysis of TCV-infected wildtype and dcl1-9 mutant Arabidopsis thaliana

2017-01-11 | GSE85067 | GEO

m6A level and isoform characterization sequencing (m6A-LAIC-seq) reveal the census and complexity of the m6A epitranscriptome

Project description:N6-methyladenosine (m6A) is a widespread reversible chemical modification of RNAs, implicated in many aspects of RNA metabolism. Little quantitative information exists as to either how many transcript copies of particular genes are m6A modified (âm6A levelsâ), or the relationship of m6A modification(s) to alternative RNA isoforms. To deconvolute the m6A epitranscriptome, we developed m6A level and isoform-characterization sequencing (m6A-LAIC-seq). We found that cells exhibit a broad range of non-stoichiometric m6A levels with cell type specificity. At the level of isoform characterization, we discovered widespread differences in use of tandem alternative polyadenylation (APA) sites by methylated and nonmethylated transcript isoforms of individual genes. Strikingly, there is a strong bias for methylated transcripts to be coupled with proximal APA sites, resulting in shortened 3â untranslated regions (3â-UTRs), while nonmethylated transcript isoforms tend to use distal APA sites. m6A-LAIC-seq yields a new perspective on transcriptome complexity and links APA usage to m6A modifications. m6A-LAIC-seq of H1-ESC and GM12878 cell lines, each cell line has two replicates

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

Project description:N6-methyladenosine (m6A) represents the most prevalent internal modification on messenger RNA, and requires a multicomponent m6A methyltransferase complex in mammals. How their plant counterparts determine the global m6A modification landscape and its molecular link to plant development remain elusive. Here we show that FKBP12 INTERACTING PROTEIN 37 KD (FIP37) is a core component of the m6A methyltransferase complex, which underlies control of shoot stem cell fate in Arabidopsis. The mutants lacking FIP37 exhibit massive overproliferation of shoot meristems and a transcriptome-wide loss of m6A RNA modifications. We further demonstrate that FIP37 mediates m6A RNA modification on key shoot meristem genes inversely correlated with their mRNA stability, thus confining their transcript levels to prevent shoot meristem overproliferation. Our results suggest an indispensable role of FIP37 in mediating m6A mRNA modification, which is required for maintaining the shoot meristem as a renewable source for continuously producing all aerial organs in plants. m6A-seq in Arabidopsis thaliana (Col-0) wild-type and fip37-4 LEC1:FIP37, two replicates for each sample

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SAC-seq for transcriptome-wide quantitative sequencing of mRNA m6A at base resolution in Arabidopsis

Project description:Here, we reported transcriptome-wide m6A modification maps within single-base resolution using m6A-SAC-seq in rice and Arabidopsis. Our analysis uncovered a total of 205,691 m6A sites distributed across 22,574 genes in rice, and 188,282 m6A sites across 19,984 genes in Arabidopsis.

2024-04-19 | GSE245738 | GEO

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