Identification of Novel and Differentially Expressed MicroRNAs of Dairy Goat Mammary Gland Tissues Using Solexa Sequencing and Bioinformatics

Abstract

MicroRNAs are small, noncoding RNA molecules that regulate gene expression at the post-transcriptional level and play an important role in various biological processes. Although most microRNAs expression profiles studies have been performed in humans or rodents, relatively limited knowledge also exists in other mammalian species. The identification of the full repertoire of microRNAs expressed in the lactating mammary gland of Capra hircus would significantly increase our understanding of the physiology of lactating mammary glands. In this study, two libraries were constructed using the lactating mammary gland tissues of Laoshan dairy goats (Capra hircus) during peak and late lactation. Solexa high-throughput sequencing technique and bioinformatics were used to determine the abundance and differential expression of the microRNAs between peak and late lactation. As a result, 19,044,002 and 7,385,833 clean reads were obtained, respectively, and 1,113 conserved known microRNAs and 31 potential novel microRNA candidates were identified. A total of 697 conserved microRNAs were significantly differentially expressed with a P-value<0.01, 272 microRNAs were up-regulated and 425 microRNAs were down-regulated during peak lactation. The results were validated using real-time quantitative RT-PCR. 762,557 annotated mRNA transcripts were predicted as putative target gene candidates. The GO annotation and KEGG pathway analysis suggested that differentially expressed microRNAs were involved in mammary gland physiology, including signal transduction, and cell-cell and cell-extracellular communications. This study provided the first global of the microRNA in Capra hircus and expanded the repertoire of microRNAs. Our results have great significance and value for the elucidation of complex regulatory networks between microRNAs and mRNAs and for the study of mammary gland physiology and lactation.

MicroRNA function in domestic animal physiology and diseases: a promising diagnostic tool for veterinary use

“…A similar study has been presented by Ji et al (29). The authors identified novel and differentially expressed microRNAs of dairy goat mammary gland tissues.…”

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

“…The dysregulation of miR-143 is implicated in a wide range of malignancies, including various forms of lymphoma, carcinomas of the breast, lung and pancreas and cervical cancer (Tripathi et al 2009;Liu et al 2012;Kapoor 2014). Although miR-143 has been extensively investigated in a variety of pathological tissues, but its specific functions in mammary gland development, lactation and involution remain elusive, and according to our previous studies, miR-143 seemed to be an interesting candidate for involvement in mammary gland development, lactation and involution (Ji et al 2012a(Ji et al , 2012b. In this study, MTT and cell count were used to test the functions of miR-143 on proliferation and viability of dairy goat mammary epithelia cells.…”

“…The miR-143 sequence was predicted in our previous studies of the miRNA expression profiles of dairy goat mammary gland tissues based on Illumina/Solexa highthroughput sequencing technology deposited in miRBase (Ji et al 2012a(Ji et al , 2012b. Multiple studies have shown that miR-143 is linked to the regulation of a diverse set of processes in vertebrates.…”

The Application of Genomic Technologies to Investigate the Inheritance of Economically Important Traits in Goats

“…In another study, Geng et al [130] compared skin mRNA expression at different hair follicle developmental stages (i.e., anagen, catagen, and telogen), thus identifying hundreds of differentially expressed genes. There has also been a sudden burst of studies analysing the expression profiles of miRNAs in the mammary gland [132][133][134][135], testis [136], and skin and hair follicles [137]. Interestingly, overexpression of caprine miR-103 in cultured mammary epithelial cells has been shown to have broad effects on lipid metabolism [135], stimulating the expression of genes related with lipogenesis, unsaturated fatty acid synthesis, triglyceride synthesis, cholesterol transport, fatty acid uptake, and fat droplet formation and downregulating those involved in lipid catabolism (lipolysis and fatty acid -oxidation).…”

“…The large-scale measurement of mRNA expression has been greatly facilitated by the development of next generation sequencing techniques, and it should play a crucial role in understanding how genetic polymorphisms and environmental factors modulate gene expression through complex biological networks that evolve in time and space. In this regard, genome sequencing and RNA-seq experiments have allowed to establish an initial catalog of the miRNA genes residing in the goat genome [103,[132][133][134][135][136][137], and in the next years we can anticipate that this list will be expanded to new miRNAs as well as to a plethora of regulatory RNAs, such as small interfering RNAs, Piwi-associated RNAs, and long noncoding RNAs, with significant effects on gene expression.…”