Complete stranded RNA profiling during early mouse gonad development

Sexual dimorphism in mouse gonads becomes evident at around embryonic day (E)12.5, 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 2419 differentially expressed genes (DEGs) in the comparison between E12.5 and E11.5 mouse gonads, along with 333 and 770 DEGs in E13.5 versus E12.5 and in E14.5 versus E13.5, respectively. A total of 22 RNA types were annotated, highlighting mRNA, tRNA, long non-coding RNA, antisense RNA, small nucleolar RNA, and microRNA 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 <i>Sox9</i> TESCO (testis-specific enhancer core sequence enhancer), with quantitative PCR 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, miR6236, Snord33, long intergenic non-coding RNA <i>Neat1</i>, <i>Anks1b</i>, and <i>Lars2</i>. 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.