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RNA-seq

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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.
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Updated: Mar 5, 2026

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

Published on: February 24, 2015

Statistical Methods for Transcriptome-Wide Analysis of RNA Methylation by Bisulfite Sequencing.

Brian J Parker¹

¹Department of Biology, New York University, 100 Washington Sq East, New York, NY, 10003, USA. brian.parker@nyu.edu.

Methods in Molecular Biology (Clifton, N.J.)

|March 29, 2017

Summary

This summary is machine-generated.

This study introduces statistical methods and a computational pipeline for analyzing 5-methylcytosine (m⁵C) RNA modifications. The approach enables transcriptome-wide differential m⁵C methylation detection using bisulfite conversion assays.

Keywords:

5-methylcytosine Bisulfite conversion Differential methylation Epitranscriptomics High-throughput sequencing RNA methylation

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Last Updated: Mar 5, 2026

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

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Published on: February 24, 2015

Targeted DNA Methylation Analysis by Next-generation Sequencing

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

DNA Methylation: Bisulphite Modification and Analysis

DNA Methylation: Bisulphite Modification and Analysis

Published on: October 21, 2011

Area of Science:

Molecular Biology
Bioinformatics
Genomics

Background:

RNA modifications, such as 5-methylcytosine (m⁵C), play crucial roles in gene regulation.
Accurate detection and quantification of m⁵C are essential for understanding its functional impact.
Bisulfite conversion is a key experimental technique for studying RNA methylation.

Purpose of the Study:

To present statistical methods for transcriptome-wide differential m⁵C methylation analysis.
To introduce a computational pipeline specifically designed for bisulfite conversion RNA samples.
To facilitate the comparison of m⁵C methylation patterns between different RNA samples.

Main Methods:

Utilizing bisulfite conversion for RNA sample preparation.
Developing and applying statistical models for methylation analysis.
Implementing a computational pipeline for data processing and interpretation.

Main Results:

The chapter details a robust methodology for m⁵C detection and quantification.
The presented computational pipeline is optimized for differential methylation analysis.
The methods allow for accurate transcriptome-wide assessment of m⁵C modifications.

Conclusions:

The developed statistical and computational tools enable comprehensive analysis of differential m⁵C RNA methylation.
This approach aids in identifying regulatory roles of m⁵C modifications.
The study provides a valuable resource for researchers in RNA epigenetics.