Differential isoform expression and alternative splicing in sex determination in mice

Benjamín Planells,Patrick Lonergan,Eva Pericuesta,Alfonso Gutiérrez-Adán,Isabel Gómez-Redondo

doi:10.1186/s12864-019-5572-x

Abstract

BackgroundAlternative splicing (AS) may play an important role in gonadal sex determination (GSD) in mammals. The present study was designed to identify differentially expressed isoforms and AS modifications accompanying GSD in mice.ResultsUsing deep RNA-sequencing, we performed a transcriptional analysis of XX and XY gonads during sex determination on embryonic days 11 (E11) and 12 (E12). Analysis of differentially expressed genes (DEG) identified hundreds of genes related to GSD and early sex differentiation that may represent good candidates for sex reversal. Expression at time point E11 in males was significantly enriched in RNA splicing and mRNA processing Gene Ontology terms. Differentially expressed isoform analysis identified hundreds of specific isoforms related to GSD, many of which showed no differences in the DEG analysis. Hundreds of AS events were identified as modified at E11 and E12. Female E11 gonads featured sex-biased upregulation of intron retention (in genes related to regulation of transcription, protein phosphorylation, protein transport and mRNA splicing) and exon skipping (in genes related to chromatin repression) suggesting AS as a post-transcription mechanism that controls sex determination of the bipotential fetal gonad.ConclusionOur data suggests an important role of splicing regulatory mechanisms for sex determination in mice.

Highlights

Alternative splicing (AS) may play an important role in gonadal sex determination (GSD) in mammals
RNA-seq analysis and sex-dependent differential gene expression before and after the Sry expression peak in mouse gonads To identify the initial molecular changes associated with GSD, we first confirmed by qPCR that peak Sry expression in gonads occurs at time point embryonic days 11 (E11).5 (Fig. 1A)
We pooled three pairs of genital ridges from three different XX or XY individuals at the two time points to minimize the effect of biological variability and performed RNA-seq

Summary

Introduction

Alternative splicing (AS) may play an important role in gonadal sex determination (GSD) in mammals. The present study was designed to identify differentially expressed isoforms and AS modifications accompanying GSD in mice. The majority of eukaryote genes have multiple transcriptional isoforms. Originating from the same locus, mRNA isoforms are molecules of different exon composition and length, which may code for different forms of the corresponding protein. These isoforms may be produced from different transcriptional starting sites and terminated at different polyadenylation sites, or may be a consequence of alternative splicing (AS) [1]. AS may affect mRNA localization, stability, translation, or may change the reading frame, resulting in different protein isoforms with diverse functions and/or localizations [3]. Sequences of isoforms found on the basis of experimental evidence are deposited in public databases and are available through

Methods

Results

Discussion

Conclusion