Expression profiles of microRNAs from lactating and non-lactating bovine mammary glands and identification of miRNA related to lactation

Abstract

BackgroundMicroRNAs (miRNAs) have been implicated in the regulation of milk protein synthesis and development of the mammary gland (MG). However, the specific functions of miRNAs in these regulations are not clear. Therefore, the elucidation of miRNA expression profiles in the MG is an important step towards understanding the mechanisms of lactogenesis.ResultsTwo miRNA libraries were constructed from MG tissues taken from a lactating and a non-lactating Holstein dairy cow, respectively, and the short RNA sequences (18–30 nt) in these libraries were sequenced by Solexa sequencing method. The libraries included 885 pre-miRNAs encoding for 921 miRNAs, of which 884 miRNAs were unique sequences and 544 (61.5%) were expressed in both periods. A custom-designed microarray assay was then performed to compare miRNA expression patterns in the MG of lactating and non-lactating dairy cows. A total of 56 miRNAs in the lactating MG showed significant differences in expression compared to non-lactating MG (P<0.05). Integrative miRNA target prediction and network analysis approaches were employed to construct an interaction network of lactation-related miRNAs and their putative targets. Using a cell-based model, six miRNAs (miR-125b, miR-141, miR-181a, miR-199b, miR-484 and miR-500) were studied to reveal their possible biological significance.ConclusionOur study provides a broad view of the bovine MG miRNA expression profile characteristics. Eight hundred and eighty-four miRNAs were identified in bovine MG. Differences in types and expression levels of miRNAs were observed between lactating and non-lactating bovine MG. Systematic predictions aided in the identification of lactation-related miRNAs, providing insight into the types of miRNAs and their possible mechanisms in regulating lactation.

Non-Coding RNA Roles in Ruminant Mammary Gland Development and Lactation

“…The profiles of miRNAs in bovine MG tissue or milk have been investigated using different approaches, such as microarray [48,49], genome sequencing [4] and RNA sequencing [50][51][52][53][54][55][56][57]. A total of 496 miRNA genes were identified following sequencing of the cattle genome of which 135 were novel [4].The expression profiles of miRNAs in MG tissues and cells facilitate discovery of novel miRNAs and also identification of candidate miRNAs for different cell types, lactation stages, periods, disease response and so on.…”

“…Using microarray, Izumi et al [59] identified 100 and 53 known miRNAs in colostrum and mature milk, respectively. Using Solexa sequencing method, Li et al [60] reported 884 unique miRNAs sequences in the bovine MG (283 known, 505 novel and 96 conserved miRNAs). Le Guillou et al [61] identify 167 novel miRNAs in the bovine MG, many of which were also detected in mouse MG. Analysing three milk fractions (fat, whey and cells) and mammary gland tissues, we reported 210, 200 and 249 known and 33, 31 and 36 novel miRNAs in milk fat, whey and cells, respectively, and 321 known and 176 novel miRNAs in mammary gland tissues [62].…”

“…Li et al [50] in the dry period (30 days prepartum) compared to early lactation period (7 days postpartum) and one upregulated miRNA (miR-31) in early lactation compared to the dry period. Previously, we examined miRNA expression pattern during a lactation cycle to explore it regulatory mechanisms during lactation using milk fat as input tissue for sampling [63].…”

Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity

“…Regarding livestock species, the choice of methods for miRNA discovery and novel miRNA annotation vary among studies and species. For example, De Vliegher et al [85] used miRbase [86] and UNAFold [87] for miRNA annotation and discovery in bovine mammary gland tissues while Peng et al [88] used miRbase [86] and RNAfold [89] for these purposes in porcine mammary glands. In our own studies, miRbase [86] and mirDeep2 [74] were used to identify miRNAs in various tissues including bovine mammary gland tissues [90], milk fat [90][91][92], milk whey and cells [90].…”

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

“…MiRNA profile changes in mastitis-affected cows may be important information and, as the authors suggest, may play a crucial role in the treatment of mastitis in Holstein cattle. Bovine miRNA has also been analyzed in studies by Li et al (36). The authors described the expression profile of microRNAs from lactating and non-lactating bovine mammary glands (MG) and the identification of miRNAs related to lactation.…”