Epididymal Region-Specific miRNA Expression and DNA Methylation and Their Roles in Controlling Gene Expression in Rats

Abstract

Region-specific gene expression is an intriguing feature of the mammalian epididymis. This unique property is essential for sperm maturation and storage, and it also implicates stringent and multi-level regulations of gene expression. Over the past decade, the androgen-driven activation of epididymal gene transcription has been extensively studied. However, it still remains largely unexplored whether and how other regulatory mechanisms, such as miRNAs and DNA methylation, are involved in controlling regional gene expression in the epididymis. Using microarray-based approaches, we studied the regional miRNA expression and DNA methylation profiles in 4 distinct epididymal regions (initial segment, caput, corpus and cauda) of rats. We found that the miR-200 family members were more expressed in caput, compared with cauda. By GSEA analysis, the differential expression of miR-200 family between caput and cauda was shown to be negatively correlated with their predicted target genes, among which 4 bona fide targets were verified by luciferase reporter assay. Predicted target genes of miR-200 family have enriched functions in anti-apoptosis, cell transportation and development, implying the regional diversity in epididymal functions. On the other hand, we revealed epididymal DNA methylation of 2002 CpG islands and 2771 gene promoters (-3.88-0.97kb), among which 1350 (67.43%) CpG islands and 2095 (75.60%) promoters contained region-specific DNA methylation. We observed significant and distinct functional enrichment in genes with specifically methylated promoters in each epididymal regions, but these DNA methylations did not show significant correlation with repressed gene transcription in the mature epididymis. Conclusively, we investigated the regional miRNA expression and DNA methylation in the rat epididymis and revealed a potential role of miR-200 family in gene expression regulation between caput and cauda. This may contribute to the distinct physiological function in sperm maturation / storage of caput / cauda epididymis.

Changes in Expression of Connexin Isoforms in the Caudal Epididymis of Adult Sprague-Dawley Rats exposed to Estradiol Benzoate or Flutamide at the Neonatal Age

“…Indeed, expression of forkhead box A2 ( Faxa2 ), which is one of androgen receptor coregulatory and involves in suppression of activation of lipocalin 5 by androgen, is higher in the corpus and caudal epididymis than the caput epididymis (Yu et al, 2006). Moreover, differential expression of various miRNAs among the epididymal segments has been extensively examined by other researches (Chu et al, 2015; Nixon et al, 2015). Taken together, different expressional patterns of Cx 26 gene at different epididymal regions by treatment of same exogenous materials would be reasonable to be considered.…”

miR-143 inhibits proliferation and induces apoptosis of mammary epithelial cells in dairy goat

“…MicroRNAs (miRNAs) are a subset of non-coding, endogenously initiated, approximately 22 nucleotides (nt) in length, short RNA molecules that post-transcriptionally control gene expression (Bartel 2004;Chu et al 2015). MiRNA genes are transcribed by RNA pol II or RNA pol III as mono-or polycistronic primary miRNA (pri-miRNA) transcripts, pri-miRNAs are processed in the nucleus by the Drosha-DGCR8 complex to produce ∼70 nt-long precursor miRNAs (pre-miRNAs), which are then transported to the cytoplasm by exportin-5 and Ran-GTP where they are processed by another RNAase IIIlike endonuclease, Dicer, into short (18-25 nt) doublestranded RNA (dsRNA) duplexes: miRNA/miRNA* (Denli et al 2004).…”

Segment-specific regulation of epididymal gene expression

“…Rhox5 promoter was not found to be methylated in that study (Chu et al 2015). Thus, further studies are required to obtain a better understanding of the species differences and the overall role of segment-specific DNA methylation in the epididymis.…”

“…Comparison of epididymal miRNA profiles between humans (Belleannee et al 2012a,b), mice (Nixon et al 2015a,b), and rats (Chu et al 2015) revealed a surprisingly low conservation of miRNAs across species (Fig. 4).…”

“…Note that all the conserved miRNAs showing segment specificity in the mouse epididymis are uniformly expressed in all the epididymal regions of rat and human epididymis. For the full data sets, readers are referred to the following original articles: mice, Nixon et al (2015a,b); rats, Chu et al (2015); humans, Belleannee et al (2012a,b).…”