ExcludonFinder: mapping transcriptional overlaps between neighboring genes

Area of Science:

• Bacterial genetics and gene regulation
• Computational biology and bioinformatics
• Molecular microbiology

Background:

• Bacteria regulate gene expression through mechanisms like overlapping transcription in untranslated regions (UTRs), forming structures known as excludons.
• Excludons lead to transcriptional interference and mRNA degradation, resulting in mutually exclusive gene expression patterns.
• A comprehensive genomic map of bacterial excludons has been lacking.

Purpose of the Study:

• To construct the first comprehensive excludon maps for Escherichia coli and Staphylococcus aureus genomes.
• To develop and utilize a novel computational tool, ExcludonFinder, for identifying excludons.
• To validate the identified excludons using multiple independent experimental datasets.

Main Methods:

• Utilized publicly available RNA-sequencing data from E. coli and S. aureus.
• Developed and applied the ExcludonFinder computational tool to identify excludons.
• Validated findings using datasets for double-stranded RNA capture, RNase III activity, transcriptional terminators, and single-cell expression analysis.

Main Results:

• Identified 16 divergent and 165 convergent excludons in E. coli.
• Identified 10 divergent and 28 convergent excludons in S. aureus.
• Demonstrated that the relBE-ydfV excludon in E. coli shows opposing expression under antibiotic stress, validating excludon function.

Conclusions:

• Excludons are a widespread regulatory mechanism in bacterial genomes.
• The constructed excludon maps provide a foundation for understanding bacterial gene regulation.
• Excludons play a significant role in bacterial responses to environmental stimuli, such as antibiotic stress.