Systematic microRNAome profiling reveals the roles of microRNAs in milk protein metabolism and quality: insights on low-quality forage utilization

Abstract

In this study, we investigated the molecular regulatory mechanisms of milk protein production in dairy cows by studying the miRNAomes of five key metabolic tissues involved in protein synthesis and metabolism from dairy cows fed high-and low-quality diets. In total, 340, 338, 337, 330, and 328 miRNAs were expressed in the rumen, duodenum, jejunum, liver, and mammary gland tissues, respectively. Some miRNAs were highly correlated with feed and nitrogen efficiency, with target genes involved in transportation and phosphorylation of amino acid (AA). Additionally, low-quality forage diets (corn stover and rice straw) influenced the expression of feed and nitrogen efficiency-associated miRNAs such as miR-99b in rumen, miR-2336 in duodenum, miR-652 in jejunum, miR-1 in liver, and miR-181a in mammary gland. Ruminal miR-21-3p and liver miR-2285f were predicted to regulate AA transportation by targeting ATP1A2 and SLC7A8, respectively. Furthermore, bovine-specific miRNAs regulated the proliferation and morphology of rumen epithelium, as well as the metabolism of liver lipids and branched-chain AAs, revealing bovine-specific mechanisms. Our results suggest that miRNAs expressed in these five tissues play roles in regulating transportation of AA for downstream milk production, which is an important mechanism that may be associated with low milk protein under lowquality forage feed.Enhancing the protein content in milk is essential for improvement of milk quality in developing countries, especially under a lack of high-quality forage. Milk protein has been considered one of the best protein sources for humans 1 , especially whey protein, whose amino acids (AA) and associated compounds can provide nutrition and bioactive substrates for humans 2 . With the improvement of Chinese quality of life, total milk production has continuously increased, leading to the rapid development of the Chinese dairy industry, which has increased 12.8% annually on average since 2000 [3][4][5] . However, in China, milk production per cow is relatively low compared with that in the developed counties such as the USA 6 . The poor milk quality has been a huge concern due to its low nutrient content, especially protein 7 . Nitrogen (N) metabolism can directly impact milk protein yield and quality. N efficiency, the ratio of milk protein yield to crude protein intake, has been considered a key regulator for milk protein synthesis 8 . When N efficiency is low, a large proportion of N will be excreted through urine, reducing the N flow to the mammary gland for milk protein synthesis 9 . Therefore, N efficiency can also be estimated by measuring the content of milk urea N (MUN), with a lower MUN content representing higher N efficiency 10 . Feed efficiency, the ratio of milk production to dry matter intake, is also an important trait that indicates the efficiency of grocery nutrients transferred to the milk of dairy cows 11 . Therefore, lower feed and N efficiency can not only decrease the nutrients enriched in the milk but also increase the energy waste...

Complementary transcriptomic and proteomic analyses reveal regulatory mechanisms of milk protein production in dairy cows consuming different forages

“…Dairy cows fed AH-based diets had higher milk yield and milk protein content than cows fed corn stover (CS)-based diets6910 and RS-based diets611. In addition, low milk protein production on low-quality forages (CS and RS) was found to be associated with low feed- and nitrogen-use efficiency in mammary glands in a microRNA transcriptomic study7. However, further studies are still required to more completely define the differences in mammary gland responses to alternative dietary energy and protein profiles provided by rations with differing forage sources.…”

Genome-wide profiling of microRNAs and prediction of mRNA targets in 17 bovine tissues

“…Significant differentially expressed (after corrected for multiple testing P-value <0.01 and absolute fold change >2) mature miRNAs were observed in all tissues except in black skin (Table 2; Figure 3A). Known miRNAs with high tissue-specificity showed significant differential expression in our analysis, such as miR-375 in adrenal gland (Ludwig et al 2016; Gai et al 2017), miR-219 in brain caudal lobe and brain cerebellum (Ludwig et al 2016), and miR-122 in liver (Jopling 2012; Szabo and Bala 2013; Modepalli et al 2014; Wang et al 2016a). No novel miRNAs were found to be up-regulated in any tissues, but some novel miRNAs were down-regulated in adrenal gland, brain cerebellum, lung, ovary, spleen and thyroid.…”

“…Micro RNAs (miRNAs) are a class of single-stranded, short-length (typically 19-24nt), endogenous, non-coding RNAs (ncRNAs) that are involved in almost all biological processes, including development, differentiation, immunity, reproduction and longevity (Kloosterman and Plasterk 2006; Hasuwa et al 2013; Renthal et al 2013; Li and Belmonte 2015; Mehta and Baltimore 2016; Wang et al 2016a; Cowled et al 2017; loannidis and Donadeu 2017; Bartel 2018). Close to three decades of miRNA studies have revealed that miRNAs have broadly conserved biogenesis and conserved target sites at the three prime untranslated regions (3’UTRs) of the messenger RNAs (mRNAs) in eukaryotes (Bartel 2018).…”

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.…”

“…A change in diet that interferes with energy balance has been shown to change miRNA expression pattern in cow liver [103]. Wang et al [104] fed cows with high-and low-quality forage diets (corn stover and rice straw) and showed that miR-125b, miR-141, miR-181a, miR-221 and miR-15b changed their expression patterns across different tissues including MG. We have examined the expression pattern of miRNAs following MG adaptation to dietary supplementation with 5% linseed oil or 5% safflower oil using miRNA sequencing and identified seven differentially regulated miRNAs, including six upregulated (miR-199c, miR-199a-3p, miR-98, miR-378, miR-148b and miR-21-5p) and one downregulated (miR-200a) by both linseed and safflower oil. The target genes of these seven miRNAs have functions related to gene expression and general cellular metabolism and are enriched in four pathways of lipid metabolism (3-phosphoinositide biosynthesis, 3-phosphoinositide degradation, D-myo-inisitol-5-phosphate metabolism and the superpathway of inositol phosphate compounds) [51].…”