Identification and characterization of microRNA in the dairy goat (Capra hircus) mammary gland by Solexa deep-sequencing technology

Abstract

microRNAs (miRNAs) perform critical roles in various biological and metabolic processes by regulating gene expression at the post-transcriptional level. To investigate the functional roles of miRNAs in the lactating mammary gland of Capra hircus, a library was constructed from the lactating mammary glands of Laoshan dairy goats (C. hircus) during early lactation. The miRNA expression profiles were systematically screened, and miRNAs were identified and characterized using Solexa deep-sequencing technology and bioinformatics. As a result, a total of 18,031,615 clean reads were obtained representing 305,711 unique sRNAs. A total of 12,086,616 sRNAs representing 3,701 unique sRNAs matched the known Bos taurus miRNA precursors in miRBase 17.0, and 300 known miRNAs and 15 miRNA were discovered. In addition, 131 novel miRNAs sequences were also obtained, and 147,703 putative targets were predicted. GO and KEGG pathway analysis showed that the majority of targets were involved in cellular processes and metabolic pathways. The 290 known miRNAs, 14 miRNA and 38 novel miRNAs were validated by sequencing a second library that was constructed from the same tissues as the first library. Our study provided the first large-scale identification and characterization of miRNAs in the mammary gland tissue of the dairy goat. The results indicate that the regulation of miRNA-mediated gene expression occurs during early lactation in dairy goats. This study significantly enriches the C. hircus miRNA repertoire and provides a reference for the elucidation of complex miRNA-mediated regulatory networks for gene expression in the physiology and developmental progression of the lactating mammary gland.

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.…”

Characterization of microRNAs from goat (Capra hircus) by Solexa deep-sequencing technology

“…The SOAP software was used to analyze sRNA expression and distribution on the genome. Gene ontology analysis was performed on the predicted target gene candidates of the novel miRNAs using 3 ontologies: molecular function, cellular components, and biological process (Ji et al, 2012). All of the predicted target genes were classified according to KEGG functional annotations, to identify the pathways actively regulated by miRNAs in goat (Kanehisa et al, 2008).…”

“…With the development of sequencing technology and bioinformatics, more and more miRNAs have been identified in animals (Ji et al, 2012). The number of miRNAs found and deposited in miRBase has risen almost exponentially.…”

“…In contrast, the Solexa deep-sequence technology (also known as high-throughput technology) is a large massively parallel sequencing technology that utilizes sequencing by synthesis with a simply operated automatic platform. The technology has become a powerful tool for discovering miRNAs and in small RNA (sRNA) research, because of its small requirements for sample quantity and its high throughput, repeatability, and accuracy, which have led to a sharp rise in the rate of novel miRNA discoveries (Ji et al, 2012).…”