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Open Access Highly Accessed Research article

Discovery of cashmere goat (Capra hircus) microRNAs in skin and hair follicles by Solexa sequencing

Chao Yuan1, Xiaolong Wang1, Rongqing Geng12, Xiaolin He1, Lei Qu3 and Yulin Chen1*

Author Affiliations

1 College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, People’s Republic of China

2 College of Life Science and Technology, Yancheng Teachers University, Yancheng, People’s Republic of China

3 College of Life Science, Yulin University, Yulin, People’s Republic of China

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BMC Genomics 2013, 14:511  doi:10.1186/1471-2164-14-511

Published: 28 July 2013

Abstract

Background

MicroRNAs (miRNAs) are a large family of endogenous, non-coding RNAs, about 22 nucleotides long, which regulate gene expression through sequence-specific base pairing with target mRNAs. Extensive studies have shown that miRNA expression in the skin changes remarkably during distinct stages of the hair cycle in humans, mice, goats and sheep.

Results

In this study, the skin tissues were harvested from the three stages of hair follicle cycling (anagen, catagen and telogen) in a fibre-producing goat breed. In total, 63,109,004 raw reads were obtained by Solexa sequencing and 61,125,752 clean reads remained for the small RNA digitalisation analysis. This resulted in the identification of 399 conserved miRNAs; among these, 326 miRNAs were expressed in all three follicular cycling stages, whereas 3, 12 and 11 miRNAs were specifically expressed in anagen, catagen, and telogen, respectively. We also identified 172 potential novel miRNAs by Mireap, 36 miRNAs were expressed in all three cycling stages, whereas 23, 29 and 44 miRNAs were specifically expressed in anagen, catagen, and telogen, respectively. The expression level of five arbitrarily selected miRNAs was analyzed by quantitative PCR, and the results indicated that the expression patterns were consistent with the Solexa sequencing results. Gene Ontology and KEGG pathway analyses indicated that five major biological pathways (Metabolic pathways, Pathways in cancer, MAPK signalling pathway, Endocytosis and Focal adhesion) accounted for 23.08% of target genes among 278 biological functions, indicating that these pathways are likely to play significant roles during hair cycling.

Conclusions

During all hair cycle stages of cashmere goats, a large number of conserved and novel miRNAs were identified through a high-throughput sequencing approach. This study enriches the Capra hircus miRNA databases and provides a comprehensive miRNA transcriptome profile in the skin of goats during the hair follicle cycle.

Keywords:
Cashmere goat; MicroRNAs; Hair cycle; Hair follicle; Skin; Solexa sequencing