Complete stranded RNA profiling during early mouse gonad development

Sexual dimorphism in mouse gonads becomes evident at around E12.5, followed by germ cell differentiation. While prior studies have concentrated on protein-coding genes, our research expands this by profiling the complete spectrum of stranded RNAs including long and short RNAs in one preparation. We identified 2 419 differentially expressed genes (DEGs) in the comparison between E12.5 and E11.5 mouse gonads, along with 333 and 770 DEGs in E13.5 vs. E12.5 and E14.5 vs. E13.5, respectively. A total of 22 RNA types were annotated, highlighting mRNA, tRNA, lncRNA, antisense RNA, snoRNA, and miRNA as the most significantly varied types. Serial chromosomal ideographs revealed active chromatin hubs encompassing Hox, tRNA, and stefin gene clusters. Chromosomes 11 and 13 exhibited a higher density of DEGs. Notably, some unassigned reads were mapped to the Sox9 TESCO enhancer, with qPCR results confirming elevated expression of TESCO enhancer RNA at E12.5. By integrating data from public databases, we propose potential regulatory networks involving transcription factors (TFs), miR6236, Snord33, lincRNA Neat1, Anks1b, and Lars2. Our study provides the first complete stranded RNA profiling during early gonad development and serves as a reference for future functional genetic and epigenetic research in reproductive biology.