Dataset Information

Transcriptome-wide profiling of N ⁶-methyladenosine via a selective chemical labeling method.

ABSTRACT: Studies of chemical modifications on RNA have ushered in the field of epitranscriptomics. N ⁶-Methyladenosine (m⁶A) is the most typical RNA modification and is indispensable for basic biological processes. This study presents a chemical pulldown method (m⁶A-ORL-Seq) for transcriptome-wide profiling of m⁶A. Moreover, chemical labeling results in a specific reverse transcription (RT) truncation signature. This study has identified four thousand high-confidence m⁶A sites at single-base resolution in the human transcriptome. Unlike previously reported methods based on m⁶A-antibody or m⁶A-sensitive enzymes, the antibody/enzyme-free chemical method provides a new perspective for single-base m⁶A detection at the transcriptome level.

SUBMITTER: Xie Y

PROVIDER: S-EPMC9600483 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature

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Publications

Transcriptome-wide profiling of N 6-methyladenosine via a selective chemical labeling method.

Xie Yalun Y Han Shaoqing S Li Qiming Q Fang Zhentian Z Yang Wei W Wei Qi Q Wang Yafen Y Zhou Yu Y Weng Xiaocheng X Zhou Xiang X

Chemical science 20221005 41

Studies of chemical modifications on RNA have ushered in the field of epitranscriptomics. N 6-Methyladenosine (m6A) is the most typical RNA modification and is indispensable for basic biological processes. This study presents a chemical pulldown method (m6A-ORL-Seq) for transcriptome-wide profiling of m6A. Moreover, chemical labeling results in a specific reverse transcription (RT) truncation signature. This study has identified four thousand hi ...[more]

PMID: 36349098

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Project description:BackgroundCucumber green mottle mosaic virus (CGMMV) causes substantial global losses in cucurbit crops, especially watermelon. N6-methyladenosine (m6A) methylation in RNA is one of the most important post-transcriptional modification mechanisms in eukaryotes. It has been shown to have important regulatory functions in some model plants, but there has been no research regarding m6A modifications in watermelon.ResultsWe measured the global m6A level in resistant watermelon after CGMMV infection using a colorimetric method. And the results found that the global m6A level significantly decreased in resistant watermelon after CGMMV infection. Specifically, m6A libraries were constructed for the resistant watermelon leaves collected 48 h after CGMMV infection and the whole-genome m6A-seq were carried out. Numerous m6A modified peaks were identified from CGMMV-infected and control (uninfected) samples. The modification distributions and motifs of these m6A peaks were highly conserved in watermelon transcripts but the modification was more abundant than in other reported crop plants. In early response to CGMMV infection, 422 differentially methylated genes (DMGs) were identified, most of which were hypomethylated, and probably associated with the increased expression of watermelon m6A demethylase gene ClALKBH4B. Gene Ontology (GO) analysis indicated quite a few DMGs were involved in RNA biology and stress responsive pathways. Combined with RNA-seq analysis, there was generally a negative correlation between m6A RNA methylation and transcript level in the watermelon transcriptome. Both the m6A methylation and transcript levels of 59 modified genes significantly changed in response to CGMMV infection and some were involved in plant immunity.ConclusionsOur study represents the first comprehensive characterization of m6A patterns in the watermelon transcriptome and helps to clarify the roles and regulatory mechanisms of m6A modification in watermelon in early responses to CGMMV.

Dataset Information

Transcriptome-wide profiling of N ⁶-methyladenosine via a selective chemical labeling method.

Publications

Transcriptome-wide profiling of <i>N</i> <sup>6</sup>-methyladenosine <i>via</i> a selective chemical labeling method.

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