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Updated: Jul 9, 2025

Analysis of Termination of Transcription Using BrUTP-strand-specific Transcription Run-on TRO Approach

Analysis of Termination of Transcription Using BrUTP-strand-specific Transcription Run-on TRO Approach

Published on: March 12, 2017

TRS: a method for determining transcript termini from RNAtag-seq sequencing data.

Amir Bar¹, Liron Argaman¹, Michal Eldar¹

¹Department of Microbiology and Molecular Genetics IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112102, Israel.

Nature Communications

|November 29, 2023

Summary

This summary is machine-generated.

We developed TRS, a computational method to identify bacterial transcript 3' termini from RNA-seq data. This approach enhances the study of gene expression regulation across diverse bacteria and conditions.

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3' End Sequencing Library Preparation with A-seq2

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

Area of Science:

Microbiology
Molecular Biology
Bioinformatics

Background:

Transcript 3' end determination is crucial for bacterial gene expression regulation, impacting transcript stability and function.
Existing experimental methods for identifying transcript 3' termini are limited in scope, applicable to few bacterial species and growth conditions.
RNA-sequencing (RNA-seq) data offers a potential resource for studying transcription termination, but requires specific analytical approaches.

Purpose of the Study:

To present a straightforward computational approach for identifying bacterial transcript 3' termini using existing RNA-seq data.
To leverage the specific read distribution patterns generated by the RNAtag-seq protocol for accurate terminus identification.
To enable large-scale analysis of bacterial transcription termination across various species and experimental conditions.

Main Methods:

Development of TRS (Termini by Read Starts), a computational pipeline designed to analyze RNAtag-seq data.
Exploitation of the observed overabundance of reads mapping to transcript 3' termini in RNAtag-seq datasets.
Validation of the reliability of the identified 3' termini through computational analysis.

Main Results:

The TRS pipeline successfully identifies bacterial transcript 3' termini from RNAtag-seq data.
The identified 3' termini demonstrate high reliability, validated by the computational approach.
The method does not require additional experimental procedures beyond standard RNA-seq.

Conclusions:

TRS provides a robust and accessible computational tool for determining bacterial transcript 3' termini.
The widespread availability of RNAtag-seq data makes this approach suitable for broad-scale investigations.
This method significantly advances the study of bacterial transcription termination, offering unprecedented scope and detail.