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Related Concept Videos

RNA-seq03:21

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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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RNA Editing02:23

RNA Editing

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RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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Ribosome Profiling02:24

Ribosome Profiling

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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
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Related Experiment Video

Updated: Nov 3, 2025

2D-HELS MS Seq: A General LC-MS-Based Method for Direct and de novo Sequencing of RNA Mixtures with Different Nucleotide Modifications
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An Informatics Pipeline for Profiling and Annotating RNA Modifications.

Qi Liu1,2, Xiaoqiang Lang3, Richard I Gregory4,5,6,7,8

  • 1Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA. qi.liu2@childrens.harvard.edu.

Methods in Molecular Biology (Clifton, N.J.)
|June 4, 2021
PubMed
Summary
This summary is machine-generated.

This study introduces RNAmod, an online platform for identifying and annotating RNA modifications. It aids in understanding the epitranscriptome and its role in gene expression and disease.

Keywords:
AnnotationEpitranscriptomeIdentificationMeRIP-seqRBPRNA modificationRNA-binding proteinSoftwareToolWeb server

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Over 150 RNA modifications exist, collectively termed the epitranscriptome.
  • The function of most RNA modifications is poorly understood.
  • Understanding RNA modifications is crucial for gene expression regulation and disease processes.

Purpose of the Study:

  • To present a protocol for identifying and annotating RNA modifications.
  • To introduce RNAmod, an online platform for epitranscriptomic analysis.
  • To facilitate the study of RNA modification functions in biological processes.

Main Methods:

  • Informatic analysis of methylated RNA immunoprecipitation and sequencing (MeRIP-seq) data.
  • Utilizing the RNAmod online platform for annotation, analysis, and visualization.
  • Developing a one-stop solution for mRNA modification studies.

Main Results:

  • Demonstration of a method to identify and annotate RNA modifications using MeRIP-seq data.
  • RNAmod provides a user-friendly interface for epitranscriptomic data analysis.
  • The platform enables comprehensive annotation and visualization of mRNA modifications.

Conclusions:

  • RNAmod is a valuable tool for researchers studying the epitranscriptome.
  • This protocol aids in elucidating the functional relevance of RNA modifications.
  • Accurate identification and annotation are key to understanding the epitranscriptome's role in health and disease.