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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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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.
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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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Using Nanocompore to Identify RNA Modifications from Direct RNA Nanopore Sequencing Data.

Logan Mulroney1,2,3, Ewan Birney2, Tommaso Leonardi1

  • 1Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milano, Italy.

Current Protocols
|February 25, 2023
PubMed
Summary

Nanopore sequencing enables transcriptome-wide RNA modification detection. The Nanocompore tool analyzes nanopore signals to identify RNA modifications without model training, offering high specificity.

Keywords:
NanocomporeRNARNA modificationsbioinformaticsdirect RNA nanopore sequencingnanopore sequencing

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • RNA modifications influence RNA function and are traditionally detected using low-throughput methods.
  • Nanopore sequencing offers direct RNA analysis for transcriptome-wide modification detection.

Purpose of the Study:

  • To introduce Nanocompore, a novel software tool for detecting RNA modifications using Nanopore sequencing data.
  • To provide protocols for implementing Nanocompore for RNA modification analysis.

Main Methods:

  • Direct RNA sequencing using Nanopore technology.
  • Signal analysis with Nanocompore to compare ionic current features between modified and unmodified RNA.
  • Basecalling, alignment, signal transformation, and statistical testing for modification site identification.

Main Results:

  • Nanocompore effectively detects RNA modifications by analyzing nanopore raw signal alterations.
  • The tool demonstrates high specificity and is not limited to specific modification types.
  • Two alternative protocols (f5c and Nextflow) are provided for Nanocompore implementation.

Conclusions:

  • Nanocompore provides a versatile and specific method for transcriptome-wide RNA modification detection.
  • This approach facilitates the functional investigation of RNA modifications in various biological contexts.