CG-content log-ratio distributions of Caenorhabditis elegans and Drosophila melanogaster mirtrons

TL;DR

This study investigates CG-content ratios in mirtrons of C. elegans and D. melanogaster, revealing they generally have lower CG-content than surrounding regions, contrasting with typical pre-miRNAs, and highlighting differences across species.

Contribution

It introduces a simple log-ratio measure of CG-content and demonstrates its effectiveness in distinguishing mirtrons from pre-miRNAs across species.

Findings

C. elegans and D. melanogaster mirtrons have lower CG-content than their genomic neighborhoods.

Most pre-miRNAs have higher CG-content compared to their surrounding regions.

Mammalian and primate mirtrons show higher CG-content ratios, contrasting with invertebrate mirtrons.

Abstract

Mirtrons are a special type of pre-miRNA which originate from intronic regions and are spliced directly from the transcript instead of being processed by Drosha. The splicing mechanism is better understood for the processing of mRNA for which was established that there is a characteristic CG content around splice sites. Here we analyse the CG-content ratio of pre-miRNAs and mirtrons and compare them with their genomic neighbourhood in an attempt to establish key properties which are easy to evaluate and to understand their biogenesis. We propose a simple log-ratio of the CG-content comparing the precursor sequence and is flanking region. We discovered that Caenorhabditis elegans and Drosophila melanogaster mirtrons, so far without exception, have smaller CG-content than their genomic neighbourhood. This is markedly different from usual pre-miRNAs which mostly have larger CG-content when compared to their genomic neighbourhood. We also analysed some mammalian and primate mirtrons which, in contrast the invertebrate mirtrons, have higher CG-content ratio.