Identification of differentially expressed miRNAs between white and black hair follicles by RNA-sequencing in the goat (Capra hircus)

Abstract

MicroRNAs (miRNAs) play a key role in many biological processes by regulating gene expression at the post-transcriptional level. A number of miRNAs have been identified from livestock species. However, compared with other animals, such as pigs and cows, the number of miRNAs identified in goats is quite low, particularly in hair follicles. In this study, to investigate the functional roles of miRNAs in goat hair follicles of goats with different coat colors, we sequenced miRNAs from two hair follicles samples (white and black) using Solexa sequencing. A total of 35,604,016 reads were obtained, which included 30,878,637 clean reads (86.73%). MiRDeep2 software identified 214 miRNAs. Among them, 205 were conserved among species and nine were novel miRNAs. Furthermore, DESeq software identified six differentially expressed miRNAs. Quantitative PCR confirmed differential expression of two miRNAs, miR-10b and miR-211. KEGG pathways were analyzed using the DAVID website for the predicted target genes of the differentially expressed miRNAs. Several signaling pathways including Notch and MAPK pathways may affect the process of coat color formation. Our study showed that the identified miRNAs might play an essential role in black and white follicle formation in goats.

Figure 1

Predicted secondary structures of novel miRNAs. The red color indicates the mature sequence, the yellow color indicates the loop sequence, the blue color indicates the predicted star sequence, and the purple indicates the miRNA star sequences.

Figure 2

Plot of normalized mean versus log2-fold change for the miRNAs in black and white hair follicles. The red colour marks genes detected as differentially expressed. The red points and triangle below and above the red line indicate downregulation and upregulation, respectively in black hair follicles, and the reverse in white hair follicles. The symbols at the upper and lower plot border (the red and dark triangle) indicate genes with very large or infinite log fold change.

Figure 3

Top 20 pathways predicted to be targeted by differentially expressed miRNAs.

Figure 4

The possible regulatory pathway of melanogesis activation.

Figure 5

The expression of miR-211 and miR-10b in two tissues. MiR-211 is highly expressed in black hair follicle (BF) compared with the white hair follicle (WF). Results are the mean ± SD from triplicate determinations. p < 0.01(**). MiR-10b is highly expressed in black hair follicles (BF) in compared with the white hair follicles (WF). Results are the mean ± SD from triplicate determinations. p < 0.05(*).

Figure 6

The white and black hair follicles were collected from three 1-year old crossbred black and white goats.