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Related Concept Videos

RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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Related Experiment Video

Updated: Jun 20, 2026

Methylated RNA Immunoprecipitation Assay to Study m5C Modification in Arabidopsis
08:50

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Published on: May 14, 2020

Comprehensive Epitranscriptome Analysis from MeRIP-seq Data with exomePeak2.

Jingxian Zhou1,2,3, Zhen Wei4,5, Di Zhen4,6

  • 1Sino-French Hoffmann Institute, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou 511436, China.

Genomics, Proteomics & Bioinformatics
|March 4, 2026
PubMed
Summary
This summary is machine-generated.

We developed exomePeak2, a novel computational tool for analyzing N6-methyladenosine (m6A) epitranscriptome data. It offers state-of-the-art performance for m6A site detection and differential analysis, improving epitranscriptome insights.

Keywords:
N 6-methyladenosineDifferential methylationGC bias correctionMeRIP-seqPeak calling

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Last Updated: Jun 20, 2026

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • N6-methyladenosine (m6A) is the most abundant internal RNA modification, regulating crucial biological processes.
  • Methylated RNA Immunoprecipitation Sequencing (MeRIP-seq) is widely used for transcriptome-wide m6A profiling.

Purpose of the Study:

  • To develop a novel computational tool, exomePeak2, for comprehensive m6A epitranscriptome analysis.
  • To improve the accuracy and reliability of m6A site detection and differential methylation analysis.

Main Methods:

  • Developed exomePeak2 with a novel statistical model to address GC content bias and variable immunoprecipitation (IP) efficiency in MeRIP-seq data.
  • Implemented functions for absolute methylation dynamics, strand-specific library analysis, and peak calling with or without a reference transcriptome.

Main Results:

  • exomePeak2 achieves state-of-the-art performance in m6A site detection (peak calling) and differential methylation analysis.
  • The tool enables near base-resolution motif-based methylation level quantification.
  • exomePeak2 is applicable to other RNA modification analyses like hm5C and ac4C.

Conclusions:

  • exomePeak2 provides a more reliable and comprehensive approach to epitranscriptome analysis using MeRIP-seq data.
  • The tool enhances the understanding of RNA methylation dynamics and its biological impact.