MEditome: Computational Detection of RNA Edit Sites Using de Novo Assembly in Microbiomes

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• RNA editing, a post-transcriptional modification, diversifies transcriptomes and affects gene expression.
• While known in eukaryotes and some microbes, RNA editing in whole microbiomes is largely unexplored.
• Previous methods like MetaEdit relied on reference genomes, limiting discovery to known strains.

Purpose of the Study:

• To develop a computational pipeline for unbiased RNA editing site detection across all microbial organisms in a microbiome.
• To overcome limitations of reference-based approaches by employing de novo assembly.
• To investigate the role of RNA editing in microbial adaptation and host-microbe interactions.

Main Methods:

• Introduction of MEditome, a de novo assembly-based computational pipeline for microbiome RNA editing site detection.
• Application of MEditome to sequencing data from the Integrative Human Microbiome Project.
• Comparison of MEditome-identified sites with previously reported edits for validation.

Main Results:

• MEditome identified 2,295 unique RNA editing sites across diverse bacterial taxa.
• Identified edits in the hok/gef gene family and arginine-associated genes validated previous findings.
• Observed taxon-specific editing patterns and differential editing associated with inflammatory bowel disease.

Conclusions:

• MEditome enables comprehensive RNA editing discovery in microbiomes, including novel strains.
• RNA editing plays a role in bacterial adaptation, pathogenicity, and host-microbe interactions.
• Differential RNA editing patterns are linked to inflammatory bowel disease, suggesting a regulatory role.