Altered microRNA expression in bovine subcutaneous and visceral adipose tissues from cattle under different diet

Inulin-induced differences on serum extracellular vesicles derived miRNAs in dairy cows suffering from subclinical mastitis

MicroRNA (miRNA) profiles vary with the nutritional and pathological conditions of cattle. In this study, we aimed to investigate the effects of inulin supplement on miRNA profiles derived from serum extracellular vesicles (EVs). Our goal was to determine the differences in miRNA expressions and analyse the pathways in which they are involved. Based on the results of California mastitis test and milk somatic cell counts, ten lactating cows with subclinical mastitis were randomly divided into two groups: an inulin group and a control group (n = 5 in each group). The inulin group received a daily supplement of 300 g of inulin while the control group did not receive any supplementation. After a 5-week treatment period, serum-derived EV-miRNAs from each cow were isolated. High-throughput sequencing was conducted to identify differentially expressed miRNAs. GO and KEGG bioinformatics analysis was performed to examine the target genes of these differentially expressed miRNAs. The EV-RNA concentration and small RNA content were not affected by the inulin treatment. A total of 162 known miRNAs and 180 novel miRNAs were identified from 10 samples in the two groups. Among the known miRNAs, 23 miRNAs were found to be differentially expressed between the two groups, with 18 upregulated and five downregulated in the inulin group compared to the control group. Pathway analysis revealed the involvement of these differentially expressed miRNAs in the regulation of cell structure and function, lipid oxidation and metabolism, immunity and inflammation, as well as digestion and absorption of nutrients. Overall, our study provides a molecular-level explanation for the reported beneficial health effects of inulin supplementation in cows with subclinical mastitis.

Bovine rumen epithelial miRNA-mRNA dynamics reveals post-transcriptional regulation of gene expression upon transition to high-grain feeding and phytogenic supplementation

The rumen epithelium has a pivotal role in nutrient uptake and host health. This study aimed to explore the role of microRNAs (miRNAs) in the epithelial transcriptome during diet transition from forage to high-grain feeding and the modulation through supplementation with a phytogenic feed additive. Rumen biopsies were collected from 9 ruminally-cannulated non-lactating Holstein cows fed a baseline forage diet (FD) and then transitioned to high-grain feeding (HG; 65% concentrate on a dry matter basis). Cows were randomly allocated into a control group (CON, n = 5) and a group supplemented with a phytogenic feed additive (PHY, n = 4). MiRNA and mRNA sequencing was performed in parallel and transcripts were analyzed for differential expression, pathway enrichment analysis, and miRNA-mRNA interaction networks. We identified 527 miRNAs shared by all samples of the rumen epithelium, from which, bta-miR-21-5p, bta-miR-143 and bta-miR-24-3p were the most expressed. Six miRNAs were differentially expressed between CON and PHY and 8 miRNAs between FD and HG feeding, which were mainly associated with fat metabolism. Transcriptome analysis identified 9481 differentially expressed genes (DEGs) between FD and HG, whereas PHY supplementation resulted in 5 DEGs. DEGs were mainly involved in epithelium development and morphogenesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways associated with tricarboxylic acid and short chain fatty acid (SCFA) metabolism were enriched in DEGs between diets. MiRNA target prediction and anti-correlation analysis was used to construct networks and identify DEGs targeted by DE miRNAs responsive to diet or PHY. This study allowed the identification of potential miRNA regulation mechanisms of gene expression during transition from FD to HG feeding and phytogenic supplementation, evidencing a direct role of miRNAs in host responses to nutrition.

Identification of microRNA Transcriptome Involved in Bovine Intramuscular Fat Deposition

Background

Intramuscular fat deposition in beef is a major determinant of carcass quality and value in the USA. The objective of this study was to examine changes in microRNA (miRNA) transcriptome that are involved with intramuscular fat deposition with time-on-concentrates (TOC). Yearling steers were individually fed a high concentrate diet and changes in intramuscular fat deposition were monitored by real-time ultrasound at 28 to 33 d intervals. Longissimus muscle biopsies collected on d 0, 92 and 124 TOC to examine changes in miRNA transcriptome that are involved in intramuscular fat deposition.

Results

Steer body weight increased (P < 0.0001) at each weigh day during TOC. Fat thickness increased (P < 0.005) from d 28 to 124. Ribeye area was larger (P < 0.001) on d 124 than d 61, which was larger than d 0 and 28. Ultrasound intramuscular fat content was greater (P < 0.001) on d 92 and 124 compared to d 0, 28 or 61. Sequencing of the muscle biopsy samples identified one miRNA, bta-miR-122, that was up-regulated (P < 0.005) at d 92 and 124 compared to d 0. At d 92 TOC, mRNA expression levels of fatty acid binding protein 4 (FABP4) and elongase 6 (ELOVL6) were up-regulated (P < 0.01) compared to d 0; whereas at d 124, lipogenic genes involved in de novo fatty acid synthesis, fatty acid transport, elongation and desaturation were highly up-regulated compared to d0.

Conclusions

Small RNA sequencing identified bta-miR-122 as a potential miRNA of interest that may be involved in intramuscular fat deposition with increasing TOC. Increased intramuscular fat content, as measured by real-time ultrasound, combined with differential gene expression suggests that preadipocyte differentiation may be stimulated first, which is followed by a global up-regulation of lipogenic genes involved in de novo fatty acid synthesis that provide fatty acids for subsequent hypertrophy.

Emerging Roles of Non-Coding RNAs in the Feed Efficiency of Livestock Species

A global population of already more than seven billion people has led to an increased demand for food and water, and especially the demand for meat. Moreover, the cost of feed used in animal production has also increased dramatically, which requires animal breeders to find alternatives to reduce feed consumption. Understanding the biology underlying feed efficiency (FE) allows for a better selection of feed-efficient animals. Non-coding RNAs (ncRNAs), especially micro RNAs (miRNAs) and long non-coding RNAs (lncRNAs), play important roles in the regulation of bio-logical processes and disease development. The functions of ncRNAs in the biology of FE have emerged as they participate in the regulation of many genes and pathways related to the major FE indicators, such as residual feed intake and feed conversion ratio. This review provides the state of the art studies related to the ncRNAs associated with FE in livestock species. The contribution of ncRNAs to FE in the liver, muscle, and adipose tissues were summarized. The research gap of the function of ncRNAs in key processes for improved FE, such as the nutrition, heat stress, and gut–brain axis, was examined. Finally, the potential uses of ncRNAs for the improvement of FE were discussed.

Genome-wide association study and pathway analysis for fat deposition traits in nellore cattle raised in pasture-based systems

Genome-wide association study (GWAS) is a powerful tool to identify candidate genes and genomic regions underlying key biological mechanisms associated with economically important traits. In this context, the aim of this study was to identify genomic regions and metabolic pathways associated with backfat thickness (BFT) and rump fat thickness (RFT) in Nellore cattle, raised in pasture-based systems. Ultrasound-based measurements of BFT and RFT (adjusted to 18 months of age) were collected in 11,750 animals, with 39,903 animals in the pedigree file. Additionally, 1,440 animals were genotyped using the GGP-indicus 35K SNP chip, containing 33,623 SNPs after the quality control. The single-step GWAS analyses were performed using the BLUPF90 family programs. Candidate genes were identified through the Ensembl database incorporated in the BioMart tool, while PANTHER and REVIGO were used to identify the key metabolic pathways and gene networks. A total of 18 genomic regions located on 10 different chromosomes and harbouring 23 candidate genes were identified for BFT. For RFT, 22 genomic regions were found on 14 chromosomes, with a total of 29 candidate genes identified. The results of the pathway analyses showed important genes for BFT, including TBL1XR1, AHCYL2, SLC4A7, AADAT, VPS53, IDH2 and ETS1, which are involved in lipid metabolism, synthesis of cellular amino acids, transport of solutes, transport between Golgi Complex membranes, cell differentiation and cellular development. The main genes identified for RFT were GSK3β, LRP1B, EXT1, GRB2, SORCS1 and SLMAP, which are involved in metabolic pathways such as glycogen synthesis, lipid transport and homeostasis, polysaccharide and carbohydrate metabolism. Polymorphisms located in these candidate genes can be incorporated in commercial genotyping platforms to improve the accuracy of imputation and genomic evaluations for carcass fatness. In addition to uncovering biological mechanisms associated with carcass quality, the key gene pathways identified can also be incorporated in biology-driven genomic prediction methods.

Association of leptin genotype with growth performance, adipocyte cellularity, meat quality, and fatty acid profile in beef steers fed flaxseed or high-oleate sunflower seed diets with or without triticale dried distiller's grains

Leptin genotypes can be identified as homozygous normal (CC), homozygous mutant (TT), and heterozygous (CT) based on a single-nucleotide polymorphism in exon 2 of the leptin gene, which has been associated with feed intake and fat deposition in cattle. The experiment was designed as 2 × 2 × 2 factorial with three main factors: (1) genotype (CT or TT) and diets fed 2) with or without triticale dried distiller's grains with solubles (DDG), and 3) with either flaxseed (FS) or high-oleate sunflower seed (SS). Evaluations included growth performance, subcutaneous fat deposition, adipocyte cellularity, meat quality, and fatty acid (FA) profile of various depots. Beef steers (n = 40, 459 ± 31 kg) of either CT or TT genotypes were housed in individual pens with ad libitum access to one of the four diets: 75% steam-rolled barley + 10% barley silage with 10% FS or SS (non-DDG diets, NDG) and 46.5% barley + 10% barley silage + 30% DDG, with 8.5% FS or SS, all on a dry matter basis. Growth performance, ultrasound subcutaneous fat thickness, rib eye area (REA), and plasma FA were measured prior to and during the finishing period. At slaughter, samples of subcutaneous fat, perirenal fat, and Longissimus thoracis (LT) muscle were collected for FA analysis and carcass and meat quality were measured. Compared with CT cattle, TT tended to have less (P = 0.06) C18:2-c9,t11 (rumenic acid) in plasma and subcutaneous fat and a greater proportion (P < 0.05) of C18:0 in subcutaneous, perirenal, and LT fat. Cattle with TT genotype also tended (P < 0.1) to have more total saturated and less unsaturated (USFA) and monounsaturated fats (MUFA) and had less (P = 0.04) linoleic acid in LT. Ultrasound fat thickness, REA, and average diameter of adipocytes in subcutaneous fat at 12 wk were not affected (P > 0.39) by genotype. Generally, carcass and meat quality were similar (P > 0.1) among diets, although adding FS tended to increase (P = 0.06) total USFA of subcutaneous fat including omega-3 FA (P < 0.001). For the high-fat diets evaluated, CT cattle would have more potential to produce beef with enhanced health benefits than would TT cattle.

Maternal supplementation with fish oil modulates inflammation-related MicroRNAs and genes in suckling lambs

Dietary n-3 long-chain fatty acids (n-3 LCFA) have been shown to modify lipid metabolism and immune function. The objective of this study was to evaluate the effect of periparturient fish oil (FO) supplementation on the inflammation and metabolic health of ewes and their lambs at a molecular level. Prepartum ewes were fed control diet (CON, n = 12) or CON supplemented with 2% DM of calcium soap of FO (n = 12) from 28 days before until 21 days after parturition. The ewes were evaluated for plasma metabolites and milk composition. The experiment was followed by analyzing the relative transcript abundance of circulating microRNAs (miRNAs) in plasma and targeted miRNA/mRNA expression in peripheral blood mononuclear cells (PBMCs) in both ewes and lambs. FO treatment decreased prepartum feed intake (1812 ± 35 vs 1674 ± 33 g/day, P < 0.01), whereas the influence on plasma metabolites was negligible. Dietary FO supplementation decreased milk fat percentage (8.82 ± 0.49 vs 7.03 ± 0.45, P = 0.02) and reduced milk n-6/n-3 (P < 0.05). Also, it altered the expression of plasma-circulating miRNAs in both ewe and lamb (P < 0.05). Furthermore, maternal nutrition of FO downregulated the relative expression of miR-33a and miR-146b and transcript abundance of genes IL-1β (0.41-fold) and NF-κB (0.25-fold) in lambs' PBMC. In conclusion, results showed that FO supplementation starting antepartum affects milk composition and circulating miRNA in dams and the inflammatory markers in lambs delivered by the supplemented ewes. These may provide a strategy to maintain immune balance during gestation and develop the immune system in lambs.

Milagro F, Sánchez J, de la Garza AL, Castro H. miRNAs and Novel Food Compounds Related to the Browning Process

Obesity prevalence is rapidly increasing worldwide. With the discovery of brown adipose tissue (BAT) in adult humans, BAT activation has emerged as a potential strategy for increasing energy expenditure. Recently, the presence of a third type of fat, referred to as beige or brite (brown in white), has been recognized to be present in certain kinds of white adipose tissue (WAT) depots. It has been suggested that WAT can undergo the process of browning in response to stimuli that induce and enhance the expression of thermogenesis: a metabolic feature typically associated with BAT. MicroRNAs (miRNAs) are small transcriptional regulators that control gene expression in a variety of tissues, including WAT and BAT. Likewise, it was shown that several food compounds could influence miRNAs associated with browning, thus, potentially contributing to the management of excessive adipose tissue accumulation (obesity) through specific nutritional and dietetic approaches. Therefore, this has created significant excitement towards the development of a promising dietary strategy to promote browning/beiging in WAT to potentially contribute to combat the growing epidemic of obesity. For this reason, we summarize the current knowledge about miRNAs and food compounds that could be applied in promoting adipose browning, as well as the cellular mechanisms involved.

Influence of Pasture on Stearoyl-CoA Desaturase and miRNA 103 Expression in Goat Milk: Preliminary Results

Simple Summary

An experiment to determine the effect of pasture on stearoyl-CoA desaturase (SCD) and micro-RNA (miRNA) 103 expression was carried out on dairy goats. SCD is involved in determining milk content of conjugated linoleic acids (CLAs) that are considered an important health factor in human nutrition. The alterations of the normal pathway of expression of miRNAs can have consequences on the normal cellular physiology and lead to different types of pathologies. The pasture significantly affected milk fat as well as fatty acid profile in goats, in particular CLAs showed higher levels in grazing animals with potential beneficial effects on human health. The pasture affected only the SCD trend, while that of miRNA 103 was influenced only by the stage of lactation. Due to the increasing interest of consumers for the healthy aspects of foods of animal origin, there is an important ongoing debate in the scientific community concerning those factors affecting milk quality in terms of human health. To our knowledge, this is the first observation of the effects of pasture on miRNA expression in milk from ruminant species.

Abstract

The effect of pasture on the stearoyl-CoA desaturase (SCD) and miRNA 103 expression was evaluated on dairy goats divided into two homogeneous groups (G, grazing, and S, stable). Group S was housed in a stall and received alfalfa hay as forage, while group G was led to pasture. The goats of both the groups received the same amount of concentrate. Milk yield did not differ statistically between the groups. Group G showed significantly higher fat (4.10% vs. 2.94%, p < 0.01) and protein percentage (3.43% vs. 3.25%; p < 0.05) than group S. Among milk fatty acids, group S showed significantly higher levels of saturated fatty acids (SFA) and lower values of mono-unsaturated fatty acid (MUFA). The percentages of polyunsaturated fatty acid (PUFA) were not different between groups even if pasture significantly affected the percentages of C18:3 and total omega 3. In group G, total CLAs were twice than in group S (0.646% vs. 0.311%; p < 0.01) mainly due to the differences in CLA cis9 trans 11 (0.623% vs. 0.304%; p < 0.01). Milk total CLA in grazing group was significantly (p < 0.01) higher in August according to the highest value of both linoleic and α-linolenic acids in the pasture. In grazing animals, SCD expression decreased from April to June, increased in July and decreased again in August, while it was almost unvaried along the trial in group S. By contrast, the expression of miRNA 103 showed a similar trend for both groups, decreasing from April to June, increasing in July and falling down in August. To our knowledge, this is the first observation of the effects of pasture on miRNA expression in milk from ruminant species.

Nutrient supply alters transcriptome regulation in adipose tissue of pre-weaning Holstein calves

Performance of dairy cows can be influenced by early life nutrient supply. Adipose tissue is diet sensitive and an important component in that process as it is involved in the regulation of energetic, reproductive and immunological functions. However, it is not clear how early life nutrition alters the molecular regulation of adipose tissue in calves and potentially adult individuals. This study aimed at determining how differences in pre-weaning nutrient supply alter gene expression profiles and physiology in omental adipose tissue. A total of 12 female Holstein calves were fed two levels of milk replacer supply: a restricted amount of 11.72 MJ of metabolizable energy (ME) intake per day (n = 6) or an enhanced amount of 1.26 MJ ME intake per kg of metabolic body weight (BW^0.75), resulting in supply from 17.58 to 35.17 MJ ME intake per day (n = 6). All calves had ad libitum access to a commercial calf starter and water. Analysis of the transcriptome profiles at 54 ± 2 days of age revealed that a total of 396 out of 19,968 genes were differentially expressed (DE) between groups (p < 0.001, FDR < 0.1). The directional expression of DE genes through Ingenuity Pathway Analysis showed that an enhanced nutrient supply alters adipose tissue physiology of pre-weaned calves. Several biological functions were increased (Z-score > +2), including Lipid Metabolism (Fatty Acid Metabolism), Cell Cycle (Entry into Interphase, Interphase, Mitosis and Cell Cycle Progression), Cellular Assembly and Organization (Cytoskeleton Formation and Cytoplasm Development) and Molecular Transport (Transport of Carboxylic Acid). These changes were potentially orchestrated by the activation/inhibition of 17 upstream regulators genes. Our findings indicate that adipose tissue of calves under an enhanced nutrient supply is physiologically distinct from restricted calves due to an increased development/expansion rate and also a higher metabolic activity through increased fatty acid metabolism.

Screening of exosomal miRNAs derived from subcutaneous and visceral adipose tissues: Determination of targets for the treatment of obesity and associated metabolic disorders

Exosomal micro (mi)RNAs have been suggested to have important roles in abdominal obesity, and to be associated with metabolic alterations via posttranscriptional regulation of target genes. However, exosomal miRNA profiles in subcutaneous adipose tissue (SAT) and visceral adipose tissue (VAT) have rarely been investigated. In the present study, microarray data were obtained from the Gene Expression Omnibus database with the following accession numbers: GSE68885 (exosomal miRNAs in SAT obtained from seven patients with obesity and five lean patients), GSE50574 (exosomal miRNAs in VAT obtained from seven patients with obesity and five lean patients) and GSE29718 [mRNAs in SAT (obtained from seven patients with obesity and eight lean patients) and VAT (obtained from three patients with obesity and two lean patients)]. Differentially expressed (DE)‑miRNAs and differentially expressed genes (DEGs) were identified using the Linear Models for Microarray Data method, and mRNA targets of DE‑miRNAs were predicted using the miRWalk2.0 database. Potential functions of DE‑miRNA target genes were determined using the Database for Annotation, Visualization and Integrated Discovery. As a result, 10 exosomal DE‑miRNAs were identified in SAT between patients with obesity and lean patients, while 58 DE‑miRNAs were identified in VAT between patients with obesity and lean patients. miRNA (miR)‑4517 was revealed to be a downregulated exosomal miRNA between SAT and VAT, while the other DE‑miRNAs were SAT‑(e.g. hsa‑miR‑3156‑5p and hsa‑miR‑4460) or VAT‑(e.g. hsa‑miR‑582‑5p, hsa‑miR‑566 and miR‑548) specific. Following overlapping with the target genes of DE‑miRNAs, only one DEG [cluster of differentiation 86 (CD86)] was identified in SAT samples, whereas 25 DEGs (e.g. fibroblast growth factor 2 (FGF2), FOS like 2, AP‑1 transcription factor subunit (FOSL2); and adenosine monophosphate deaminase 3 (AMPD3)] were identified in VAT samples. CD86 was revealed to be regulated by hsa‑miR‑3156‑5p; whereas FGF2, FOSL2 and AMPD3 were revealed to be regulated by hsa‑miR‑582‑5p, hsa‑miR‑566 and miR‑548, respectively. Functional enrichment analysis demonstrated that these target genes may be associated with inflammation. In conclusion, exosomal miRNAs may represent underlying therapeutic targets for the treatment of abdominal obesity and metabolic disorders via regulation of inflammatory genes.

Sunflower oil supplementation affects the expression of miR-20a-5p and miR-142-5p in the lactating bovine mammary gland

Oil supplementation in dairy cattle diets is used to modulate milk fat composition, as well as the expression of mammary lipogenic genes, whose regulation remains unclear. MiRNAs are small non-coding RNA considered as crucial regulators of gene expression, offering clues to explain the mechanism underlying gene nutriregulation. The present study was designed to identify miRNAs whose expression in the cow mammary gland is modulated by sunflower oil supplementation. MiRNomes were obtained using RNAseq technology from the mammary gland of lactating cows receiving a low forage diet, supplemented or not with 4% sunflower oil. Among the 272 miRNAs characterized, eight were selected for RT-qPCR validations, showing the significant down-regulation of miR-142-5p and miR-20a-5p by sunflower supplementation. These two miRNAs are predicted to target genes whose expression was reported as differentially expressed by sunflower supplementation. Among their putative targets, ELOVL6 gene involved in lipid metabolism has been studied. However, a first analysis did not show its significant down-regulation, in response to the over-expression of miR-142-5p, of miR-20a-5p, or both, in a bovine mammary epithelial cell line. However, a clearer understanding of the miRNA expression by lipid supplementation would help to decipher the regulation of lactating cow mammary gland in response to nutrition.

High fat diet and associated changes in the expression of micro-RNAs in tissue: Lessons learned from animal studies

Environment and genetic factors play an important role in the development of obesity, and diet is one of the main contributing factors to this disease. High fat intake is associated with body weight gain, leading to obesity and other metabolic diseases. MicroRNAs (miRNAs) are a group of small, noncoding RNAs that are important regulators of gene expression at posttranscriptional level. Studies have shown that high fat intake, independent of body weight status, can significantly impact both negatively and positively the expression of miRNAs and thus the biological function of tissues such as adipose, skeletal, and cardiac muscle, liver, neuronal, and endothelial. This review will summarize the effects of high calorie diet in the form of high fat intake on miRNA expression in various tissues of animal models and of high fat fed offspring. We will also briefly review the impact of different dietary lipids on miRNA expression. Given changes in miRNA expression have been associated with the development of many diseases including obesity, understanding their biological role could have important clinical implications and offer tangible therapeutic targets for the prevention, management, and/or treatment of obesity and other lifestyle-related disorders.

Differences in Circulating microRNAs between Grazing and Grain-Fed Wagyu Cattle Are Associated with Altered Expression of Intramuscular microRNA, the Potential Target PTEN, and Lipogenic Genes

We aimed to understand the roles of miRNAs in the muscle tissue maturation and those of circulating microRNAs (c-miRNAs) in beef production of Japanese Black (JB) cattle (Wagyu), a breed with genetically background of superior intermuscular fat depot, by comparing different feeding conditions (indoor grain-feeding vs. grazing on pasture). The cattle at 18 months old were assigned to pasture feeding or conventional indoor grain feeding conditions for 5 months. Microarray analysis of c-miRNAs from the plasma extracellular vesicles led to the detection of a total of 202 bovine miRNAs in the plasma, including 15 miRNAs that differed between the feeding conditions. Validation of the microarray results by qPCR showed that the circulating miR-10b level in the grazing cattle was upregulated compared to that of the grain-fed cattle. In contrast, the levels of miR-17-5p, miR-19b, miR-29b, miR-30b-5p, miR-98, miR-142-5p, miR-301a, miR-374b, miR-425-5p, and miR-652 were lower in the grazing cattle than in the grain-fed cattle. Bioinformatic analysis indicated that the predicted target genes of those c-miRNAs were enriched in gene ontology terms associated with blood vessel morphogenesis, plasma membrane, focal adhesion, endocytosis, collagen, ECM-receptor interaction, and phosphorylation. In the grazing cattle, the elevation of miR-10b expression in the plasma was coincident with its elevation in the longissimus lumborum (LL) muscle. Expression of bovine-specific miR-2478, the most plasma-enriched miRNA, tended to be also upregulated in the muscle but not in the plasma. Furthermore, grazing caused the downregulated mRNA expression of predicted miR-10b and/or miR-2478 target genes, such as DNAJB2, PTEN, and SCD1. Thus, the feeding system used for JB cattle affected the c-miRNAs that could be indicators of grain feeding. Among these, miR-10b expression was especially associated with feeding-induced changes and with the expression of the potential target genes responsible for glucose homeostasis and intramuscular fat depot in the LL muscle of JB cattle.

Heterogeneity of white adipose tissue: molecular basis and clinical implications

Adipose tissue is a highly heterogeneous endocrine organ. The heterogeneity among different anatomical depots stems from their intrinsic differences in cellular and physiological properties, including developmental origin, adipogenic and proliferative capacity, glucose and lipid metabolism, insulin sensitivity, hormonal control, thermogenic ability and vascularization. Additional factors that influence adipose tissue heterogeneity are genetic predisposition, environment, gender and age. Under obese condition, these depot-specific differences translate into specific fat distribution patterns, which are closely associated with differential cardiometabolic risks. For instance, individuals with central obesity are more susceptible to developing diabetes and cardiovascular complications, whereas those with peripheral obesity are more metabolically healthy. This review summarizes the clinical and mechanistic evidence for the depot-specific differences that give rise to different metabolic consequences, and provides therapeutic insights for targeted treatment of obesity.

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

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 low-quality forage feed.

Characterization and Profiling of Liver microRNAs by RNA-sequencing in Cattle Divergently Selected for Residual Feed Intake

MicroRNAs (miRNAs) are short non-coding RNAs that post-transcriptionally regulate expression of mRNAs in many biological pathways. Liver plays an important role in the feed efficiency of animals and high and low efficient cattle demonstrated different gene expression profiles by microarray. Here we report comprehensive miRNAs profiles by next-gen deep sequencing in Angus cattle divergently selected for residual feed intake (RFI) and identify miRNAs related to feed efficiency in beef cattle. Two microRNA libraries were constructed from pooled RNA extracted from livers of low and high RFI cattle, and sequenced by Illumina genome analyser. In total, 23,628,103 high quality short sequence reads were obtained and more than half of these reads were matched to the bovine genome (UMD 3.1). We identified 305 known bovine miRNAs. Bta-miR-143, bta-miR-30, bta-miR-122, bta-miR-378, and bta-let-7 were the top five most abundant miRNAs families expressed in liver, representing more than 63% of expressed miRNAs. We also identified 52 homologous miRNAs and 10 novel putative bovine-specific miRNAs, based on precursor sequence and the secondary structure and utilizing the miRBase (v. 21). We compared the miRNAs profile between high and low RFI animals and ranked the most differentially expressed bovine known miRNAs. Bovine miR-143 was the most abundant miRNA in the bovine liver and comprised 20% of total expressed mapped miRNAs. The most highly expressed miRNA in liver of mice and humans, miR-122, was the third most abundant in our cattle liver samples. We also identified 10 putative novel bovine-specific miRNA candidates. Differentially expressed miRNAs between high and low RFI cattle were identified with 18 miRNAs being up-regulated and 7 other miRNAs down-regulated in low RFI cattle. Our study has identified comprehensive miRNAs expressed in bovine liver. Some of the expressed miRNAs are novel in cattle. The differentially expressed miRNAs between high and low RFI give some insights into liver miRNAs regulating physiological pathways underlying variation in this measure of feed efficiency in bovines.

Body condition score and plane of nutrition prepartum affect adipose tissue transcriptome regulators of metabolism and inflammation in grazing dairy cows during the transition period

Recent studies demonstrating a higher incidence of metabolic disorders after calving have challenged the management practice of increasing dietary energy density during the last ~3 wk prepartum. Despite our knowledge at the whole-animal level, the tissue-level mechanisms that are altered in response to feeding management prepartum remain unclear. Our hypothesis was that prepartum body condition score (BCS), in combination with feeding management, plays a central role in the peripartum changes associated with energy balance and inflammatory state. Twenty-eight mid-lactation grazing dairy cows of mixed age and breed were randomly allocated to 1 of 4 treatment groups in a 2 × 2 factorial arrangement: 2 prepartum BCS categories (4.0 and 5.0, based on a 10-point scale; BCS4, BCS5) obtained via differential feeding management during late-lactation, and 2 levels of energy intake during the 3 wk preceding calving (75 and 125% of estimated requirements). Subcutaneous adipose tissue was harvested via biopsy at -1, 1, and 4 wk relative to parturition. Quantitative polymerase chain reaction was used to measure mRNA and microRNA (miRNA) expression of targets related to fatty acid metabolism (lipogenesis, lipolysis), adipokine synthesis, and inflammation. Both prepartum BCS and feeding management had a significant effect on mRNA and miRNA expression throughout the peripartum period. Overfed BCS5 cows had the greatest prepartum expression of fatty acid synthase (FASN) and an overall greater expression of leptin (LEP); BCS5 was also associated with greater overall adiponectin (ADIPOQ) and peroxisome proliferator-activated receptor gamma (PPARG), whereas overfeeding upregulated expression of proadipogenic miRNA. Higher postpartum expression of chemokine ligand 5 (CCL5) and the cytokines interleukin 6 (IL6) and tumor necrosis factor (TNF) was detected in overfed BCS5 cows. Feed-restricted BCS4 cows had the highest overall interleukin 1 (IL1B) expression. Prepartum feed restriction resulted in greater chemokine ligand 2 (CCL2) expression. Overall, changes in mRNA expression were consistent with the expression pattern of inflammation-related miRNA. These data shed light on molecular mechanisms underlying the effect of prepartum BCS and feeding management on metabolic and inflammatory status of adipose tissue during the peripartum period. Data support the use of a controlled feed restriction prepartum in optimally conditioned cows, as well as the use of a higher level of dietary energy in under-conditioned cows.

Deep sequencing shows microRNA involvement in bovine mammary gland adaptation to diets supplemented with linseed oil or safflower oil

BACKGROUND

Bovine milk fat composition is responsive to dietary manipulation providing an avenue to modify the content of fatty acids and especially some specific unsaturated fatty acid (USFA) isomers of benefit to human health. MicroRNAs (miRNAs) regulate gene expression but their specific roles in bovine mammary gland lipogenesis are unclear. The objective of this study was to determine the expression pattern of miRNAs following mammary gland adaptation to dietary supplementation with 5 % linseed or safflower oil using next generation RNA-sequencing.

METHODS

Twenty-four Canadian Holstein dairy cows (twelve per treatment) in mid lactation were fed a control diet (total mixed ration of corn:grass silages) for 28 days followed by a treatment period (control diet supplemented with 5 % linseed or safflower oil) of 28 days. Milk samples were collected weekly for fat and individual fatty acid determination. RNA from mammary gland biopsies harvested on day-14 (control period) and on days +7 and +28 (treatment period) from six randomly selected cows per treatment was subjected to small RNA sequencing.

RESULTS

Milk fat percentage decreased significantly (P < 0.001) during treatment with the two diets as compared to the control period. The individual saturated fatty acids C4:0, C6:0, C8:0, C14:0 and C16:0 decreased significantly (P < 0.05) while five USFAs (C14:1, C18:1n11t, C20:3n3, C20:5n3 and CLA:t10c12) increased remarkably (P < 0.05) in response to both treatments. Analysis of 361 million sequence reads generated 321 known bovine miRNAs and 176 novel miRNAs. The expression of fourteen and twenty-two miRNAs was affected (P < 0.05) by linseed and safflower oil treatments, respectively. Seven miRNAs including six up-regulated (bta-miR-199c, miR-199a-3p, miR-98, miR-378, miR-148b and miR-21-5p) and one down-regulated (bta-miR-200a) were found to be regulated (P < 0.05) by both treatments, and thus considered core differentially expressed (DE) miRNAs. The gene targets of core DE miRNAs have functions related to gene expression and general cellular metabolism (P < 0.05) 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).

CONCLUSION

Our results suggest that DE miRNAs in this study might be important regulators of bovine mammary lipogenesis and metabolism. The novel miRNAs identified in this study will further enrich the bovine miRNome repertoire and contribute to understanding mammary gland biology.

Epigenetic marks: regulators of livestock phenotypes and conceivable sources of missing variation in livestock improvement programs

Improvement in animal productivity has been achieved over the years through careful breeding and selection programs. Today, variations in the genome are gaining increasing importance in livestock improvement strategies. Genomic information alone, however, explains only a part of the phenotypic variance in traits. It is likely that a portion of the unaccounted variance is embedded in the epigenome. The epigenome encompasses epigenetic marks such as DNA methylation, histone tail modifications, chromatin remodeling, and other molecules that can transmit epigenetic information such as non-coding RNA species. Epigenetic factors respond to external or internal environmental cues such as nutrition, pathogens, and climate, and have the ability to change gene expression leading to emergence of specific phenotypes. Accumulating evidence shows that epigenetic marks influence gene expression and phenotypic outcome in livestock species. This review examines available evidence of the influence of epigenetic marks on livestock (cattle, sheep, goat, and pig) traits and discusses the potential for consideration of epigenetic markers in livestock improvement programs. However, epigenetic research activities on farm animal species are currently limited partly due to lack of recognition, funding and a global network of researchers. Therefore, considerable less attention has been given to epigenetic research in livestock species in comparison to extensive work in humans and model organisms. Elucidating therefore the epigenetic determinants of animal diseases and complex traits may represent one of the principal challenges to use epigenetic markers for further improvement of animal productivity.

Preadipocyte and adipose tissue differentiation in meat animals: influence of species and anatomical location

Early in porcine adipose tissue development, the stromal-vascular (SV) elements control and dictate the extent of adipogenesis in a depot-dependent manner. The vasculature and collagen matrix differentiate before overt adipocyte differentiation. In the fetal pig, subcutaneous (SQ) layer development is predictive of adipocyte development, as the outer, middle, and inner layers of dorsal SQ adipose tissue develop and maintain layered morphology throughout postnatal growth of SQ adipose tissue. Bovine and ovine fetuses contain brown adipose tissue but SQ white adipose tissue is poorly developed structurally. Fetal adipose tissue differentiation is associated with the precocious expression of several genes encoding secreted factors and key transcription factors like peroxisome proliferator activated receptor (PPAR)γ and CCAAT/-enhancer-binding protein. Identification of adipocyte-associated genes differentially expressed by age, depot, and species in vivo and in vitro has been achieved using single-gene analysis, microarrays, suppressive subtraction hybridization, and next-generation sequencing applications. Gene polymorphisms in PPARγ, cathepsins, and uncoupling protein 3 have been associated with back fat accumulation. Genome scans have mapped several quantitative trait loci (QTL) predictive of adipose tissue-deposition phenotypes in cattle and pigs.

In silico identification of conserved microRNAs and their targets in bovine fat tissue

MicroRNAs (miRNAs) represent a newly identified class of non-protein-coding ~22 nt small RNA which plays important roles in multiple biological processes by degrading targeted mRNA or repressing mRNA translation. Here we present EST (expressed sequence tags)-based and GSS (Genomic Survey Sequences)-based combined approach for the detection of conserved miRNAs of cattle. A total of 20 conserved miRNAs that belong to 18 miRNA families were detected following a range of filtering criteria; their functions were further predicted and analyzed. To confirm our prediction, a miRNA-detecting microarray was designed with probes complementary to previously known mature miRNA sequences from 131 organisms. After hybridizing with small RNAs extracted from beef cattle subcutaneous fat tissue, 219 (32.30%) miRNAs were detected in the 679 known Bos taurus miRNAs and all the miRNAs predicted above were also detected. Conformation of 22 most abundant miRNA expression by qRT-PCR indicated that they were highly accumulated not only in subcutaneous fat tissue but also in intramuscular fat tissue. Bioinformatics of KEGG pathway analysis suggested that 4 differential expression miRNAs (miR-143, miR-145, miR-2325c and miR-2361) involved in different pathways and target genes may regulate the fat deposition differently. Taken together, our results expand the number of known bovine miRNAs and provide a thorough account of the miRNA transcriptome in bovine adipose tissue.

Intermuscular and intramuscular adipose tissues: Bad vs. good adipose tissues

Human studies of the influence of aging and other factors on intermuscular fat (INTMF) were reviewed. Intermuscular fat increased with weight loss, weight gain, or with no weight change with age in humans. An increase in INTMF represents a similar threat to type 2 diabetes and insulin resistance as does visceral adipose tissue (VAT). Studies of INTMF in animals covered topics such as quantitative deposition and genetic relationships with other fat depots. The relationship between leanness and higher proportions of INTMF fat in pigs was not observed in human studies and was not corroborated by other pig studies. In humans, changes in muscle mass, strength and quality are associated with INTMF accretion with aging. Gene expression profiling and intrinsic methylation differences in pigs demonstrated that INTMF and VAT are primarily associated with inflammatory and immune processes. It seems that in the pig and humans, INTMF and VAT share a similar pattern of distribution and a similar association of components dictating insulin sensitivity. Studies on intramuscular (IM) adipocyte development in meat animals were reviewed. Gene expression analysis and genetic analysis have identified candidate genes involved in IM adipocyte development. Intramuscular (IM) adipocyte development in human muscle is only seen during aging and some pathological circumstance. Several genetic links between human and meat animal adipogenesis have been identified. In pigs, the Lipin1 and Lipin 2 gene have strong genetic effects on IM accumulation. Lipin1 deficiency results in immature adipocyte development in human lipodystrophy. In humans, overexpression of Perilipin 2 (PLIN2) facilitates intramyocellular lipid accretion whereas in pigs PLIN2 gene expression is associated with IM deposition. Lipins and perilipins may influence intramuscular lipid regardless of species.

Adipose depots differ in cellularity, adipokines produced, gene expression, and cell systems

The race to manage the health concerns related to excess fat deposition has spawned a proliferation of clinical and basic research efforts to understand variables including dietary uptake, metabolism, and lipid deposition by adipocytes. A full appreciation of these variables must also include a depot-specific understanding of content and location in order to elucidate mechanisms governing cellular development and regulation of fat deposition. Because adipose tissue depots contain various cell types, differences in the cellularity among and within adipose depots are presently being documented to ascertain functional differences. This has led to the possibility of there being, within any one adipose depot, cellular distinctions that essentially result in adipose depots within depots. The papers comprising this issue will underscore numerous differences in cellularity (development, histogenesis, growth, metabolic function, regulation) of different adipose depots. Such information is useful in deciphering adipose depot involvement both in normal physiology and in pathology. Obesity, diabetes, metabolic syndrome, carcass composition of meat animals, performance of elite athletes, physiology/pathophysiology of aging, and numerous other diseases might be altered with a greater understanding of adipose depots and the cells that comprise them-including stem cells-during initial development and subsequent periods of normal/abnormal growth into senescence. Once thought to be dormant and innocuous, the adipocyte is emerging as a dynamic and influential cell and research will continue to identify complex physiologic regulation of processes involved in adipose depot physiology.

miRNome of Italian Large White pig subcutaneous fat tissue: new miRNAs, isomiRs and moRNAs

Small RNAs, such as micro-RNAs (miRNAs), are decisive regulators of gene expression, and they could determine adipose tissue traits. A better knowledge of porcine fat genomics is relevant given that the pig is a biomedical model for metabolic and cardiovascular human pathologies. Adipose tissue is particularly important for the meat industry. We explored the miRNome of two adult Italian Large White pig backfat samples by Illumina RNA-Seq. Using custom bioinformatic methods, the expressed miRNAs were identified and quantified and the nucleotide sequence variability of miRNA isoforms were analysed. We detected 222 known miRNAs, 68 new miRNAs and 17 miRNA-offset RNAs (moRNAs) expressed from known hairpins, and 312 new miRNAs expressed from 253 new hairpins. Porcine transcripts targeted by the most expressed miRNAs were predicted, showing that these miRNAs may have an impact on Wnt, insulin signalling and axon guidance pathways. The expression of five small RNAs, including moRNA ssc-5'-moR-21 and a miRNA from a new hairpin, was validated by a qRT-PCR assay, thus confirming the robustness of our results. The depicted miRNome complexity suggests that quantitative and qualitative features of miRNAs and non-canonical products of their precursors are worthy of further investigation to clarify their roles in the adipose tissue biology.

Effect of diet on microRNA expression in ovine subcutaneous and visceral adipose tissues

Knowledge of the molecular mechanisms that regulate ovine adipogenesis is very limited. MicroRNAs (miRNA) have been reported as one of the regulatory mechanisms of adipogenesis. This study aimed to compare the expression of miRNA related to ovine adipogenesis in different adipose depots and to investigate whether their expression is affected by dietary fatty acid composition. We also investigated the role of miRNA in adipogenic gene regulation. Subcutaneous and visceral adipose tissue samples were collected at slaughter from 12 Canadian Arcott lambs fed a barley-based finishing diet where an algae meal (DHA-Gold; Schizochytrium spp.) replaced flax oil and barley grain at 0 or 3% DM (n = 6). Total RNA from each tissue was subjected to quantitative real time (qRT-) PCR analysis to determine the expression of 15 selected miRNA including 11 identified from bovine adipose tissues and 4 conserved between bovine and ovine species. MicroRNAs were differentially expressed according to diet in each tissue depot (miR-142-5p and miR-376d) in visceral and miR-142-5p, miR-92a, and miR-378 in subcutaneous adipose tissue; P ≤ 0.05) and in each tissue depot depending on diet (miR-101, miR-106, miR-136, miR-16b, miR-196a-1, miR-2368*, miR-2454, miR-296, miR-376d, miR-378, and miR-92a in both control and DHA-G diets and miR-478 in control; P ≤ 0.05). Six miRNA were subjected to functional analysis and 3 genes of interest (ACSL1, PPARα, and C/EBPα) were validated by qRT-PCR. Both diet and tissue depot affected expression levels of all 3 genes (P < 0.05). miR-101, miR-106, and miR-136 were negatively correlated with their respective predicted gene targets C/EBPα, PPARα, and ACSL1 in subcutaneous adipose tissue of lambs fed DHA-G. Yet miR-142-5p and miR-101 showed no correlation with ACSL1 or C/EBPα. The variability in expression patterns of miRNA across adipose depots reflects the tissue specific nature of adipogenic regulation. Although the examined miRNA appear to be conserved across ruminant species, our results indicate the presence of ovine specific regulatory mechanisms that can be influenced by diet.

MicroRNAs in bovine adipogenesis: genomic context, expression and function

Background

MicroRNAs (miRNAs) are small non-coding RNAs found to regulate several biological processes including adipogenesis. Understanding adipose tissue regulation is critical for beef cattle as fat is an important determinant of beef quality and nutrient value. This study analyzed the association between genomic context characteristics of miRNAs with their expression and function in bovine adipose tissue. Twenty-four subcutaneous adipose tissue biopsies were obtained from eight British-continental crossbred steers at 3 different time points. Total RNA was extracted and miRNAs were profiled using a miRNA microarray with expression further validated by qRT-PCR.

Results

A total of 224 miRNAs were detected of which 155 were expressed in all steers (n = 8), and defined as the core miRNAs of bovine subcutaneous adipose tissue. Core adipose miRNAs varied in terms of genomic location (59.5% intergenic, 38.7% intronic, 1.2% exonic, and 0.6% mirtron), organization (55.5% non-clustered and 44.5% clustered), and conservation (49% highly conserved, 14% conserved and 37% poorly conserved). Clustered miRNAs and highly conserved miRNAs were more highly expressed (p < 0.05) and had more predicted targets than non-clustered or less conserved miRNAs (p < 0.001). A total of 34 miRNAs were coordinately expressed, being part of six identified relevant networks. Two intronic miRNAs (miR-33a and miR-1281) were confirmed to have coordinated expression with their host genes, transcriptional factor SREBF2 and EP300 (a transcriptional co-activator of transcriptional factor C/EBPα), respectively which are involved in lipid metabolism, suggesting these miRNAs may also play a role in regulation of bovine lipid metabolism/adipogenesis. Furthermore, a total of 17 bovine specific miRNAs were predicted to be involved in the regulation of energy balance in adipose tissue.

Conclusions

These findings improve our understanding on the behavior of miRNAs in the regulation of bovine adipogenesis and fat metabolism as it reveals that miRNA expression patterns and functions are associated with miRNA genomic location, organization and conservation.

Alterations in hepatic miRNA expression during negative energy balance in postpartum dairy cattle

BACKGROUND

Negative energy balance (NEB), an altered metabolic state, occurs in early postpartum dairy cattle when energy demands to support lactation exceed energy intake. During NEB the liver undergoes oxidative stress and increased breakdown of fatty acids accompanied by changes in gene expression. It is now known that micro RNAs (miRNA) can have a role in mediating such alterations in gene expression through repression or degradation of target mRNAs. miRNA expression is known to be altered by metabolism and environmental factors and miRNAs are implicated in expression modulation of metabolism related genes.

RESULTS

miRNA expression was profiled in the liver of moderate yielding dairy cattle under severe NEB (SNEB) and mild NEB (MNEB) using the Affymetrix Gene Chip miRNA_2.0 array with 679 probe sets for Bos-taurus miRNAs. Ten miRNAs were found to be differentially expressed using the 'samr' statistical package (delta = 0.6) at a q-value FDR of < 12%. Five miRNAs including miR-17-5p, miR-31, miR-140, miR-1281 and miR-2885 were validated using RT-qPCR, to be up-regulated under SNEB. Liver diseases associated with these miRNAs include non-alcoholic fatty liver (NAFLD) and hepatocellular carcinoma (HCC). miR-140 and miR-17-5p are known to show differential expression under oxidative stress. A total of 32 down-regulated putative target genes were also identified among 418 differentially expressed hepatic genes previously reported for the same animal model. Among these, GPR37 (G protein-coupled receptor 37), HEYL (hairy/enhancer-of-split related with YRPW motif-like), DNJA1, CD14 (Cluster of differentiation 14) and GNS (glucosamine (N-acetyl)-6-sulfatase) are known to be associated with hepatic metabolic disorders. In addition miR-140 and miR-2885 have binding sites on the most down-regulated of these genes, FADS2 (Fatty acid desaturase 2) which encodes an enzyme critical in lipid biosynthesis. Furthermore, HNF3-gamma (Hepatocyte nuclear factor 3-gamma), a hepatic transcription factor (TF) that is involved in IGF-1 expression regulation and maintenance of glucose homeostasis is a putative target of miR-31.

CONCLUSIONS

This study shows that SNEB affects liver miRNA expression and these miRNAs have putative targets in hepatic genes down-regulated under this condition. This study highlights the potential role of miRNAs in transcription regulation of hepatic gene expression during SNEB in dairy cattle.

MicroRNA-33b downregulates the differentiation and development of porcine preadipocytes

Sterol regulatory element binding transcription factor (SREBF) is a key transcription regulator for lipid homeostasis. MicroRNA-33b (miR-33b) is embedded in intron 16 of porcine SREBF1 and is conserved among most mammals. Here, we investigated the effect of miR-33b on adipocyte differentiation and development in porcine subcutaneous pre-adipocytes (PSPA). PSPA were transiently transfected with miR-33b, and adipose differentiation was then induced. Delayed adipose differentiation and decreased lipid accumulation were observed in miR-33b-transfected PSPA. Computational predictions suggested that miR-33b may target early B cell factor 1 (EBF1), an adipocyte activator of lipogenesis regulators such as CCAAT-enhancer binding protein alpha (C/EBPα) and peroxisome proliferator-activated receptor gamma (PPARγ). Both gene and protein expression of EBF1 were downregulated in miR-33b-transfected PSPA, followed by considerable decreases in the expression of C/EBPα and PPARγ and their downstream lipogenic genes. However, miR-33b transfection did not markedly affect mRNA and protein expression of SREBF1. We also investigated differences in the expression of miR-33b and lipogenic genes in subcutaneous fat tissues between 5-month-old crossbred gilts derived from Landrace (lean-type) and Meishan (fatty-type) boars. Landrace-derived crossbred gilts expressed more miR-33b and less lipogenic genes than did gilts derived from Meishan. Our results suggest that miR-33b affected the differentiation and development of PSPA by attenuating the lipogenic gene expression cascade through EBF1 to C/EBPα and PPARγ. The differential expression of miR-33b observed in crossbred gilts may in part account for differences in lipogenic gene expression and the fat:lean ratio between pig breeds.

Recent developments in lipid metabolism in ruminants – the role of fat in maintaining animal health and performance

Optimising farm animal performance has long been the key focus of worldwide livestock production research. Advances in the understanding of metabolism/phenotype associations have outlined the central role of the lipid metabolism of farm animals for economically relevant phenotypic traits, such as animal health (immune status, fertility/reproductive capacity, adaptability/metabolic flexibility, robustness, well being) and performance aspects (meat/milk quality and quantity) and have led to an extensive exploitation of lipid metabolism manipulation strategies (e.g. tailored nutritional regimes, alimentary/intravenous fat supplementation, rumen-protected fat feeding, hormone application). This contribution gives an overview of established concepts to tailor animals’ lipid metabolism and highlights novel strategies to expand these application-oriented approaches via improved analysis tools, omics-approaches, cell model systems and systems biology methods.

Elucidation of molecular mechanisms of physiological variations between bovine subcutaneous and visceral fat depots under different nutritional regimes

Adipose tissue plays a critical role in energy homeostasis and metabolism. There is sparse understanding of the molecular regulation at the protein level of bovine adipose tissues, especially within different fat depots under different nutritional regimes. The objective of this study was to analyze the differences in protein expression between bovine subcutaneous and visceral fat depots in steers fed different diets and to identify the potential regulatory molecular mechanisms of protein expression. Subcutaneous and visceral fat tissues were collected from 16 British-continental steers (15.5 month old) fed a high-fat diet (7.1% fat, n=8) or a control diet (2.7% fat, n=8). Protein expression was profiled using label free quantification LC-MS/MS and expression of selected transcripts was evaluated using qRT-PCR. A total of 682 proteins were characterized and quantified with fat depot having more impact on protein expression, altering the level of 51.0% of the detected proteins, whereas diet affected only 5.3%. Functional analysis revealed that energy production and lipid metabolism were among the main functions associated with differentially expressed proteins between fat depots, with visceral fat being more metabolically active than subcutaneous fat as proteins associated with lipid and energy metabolism were upregulated. The expression of several proteins was significantly correlated to subcutaneous fat thickness and adipocyte size, indicating their potential as adiposity markers. A poor correlation (r=0.245) was observed between mRNA and protein levels for 9 genes, indicating that many proteins may be subjected to post-transcriptional regulation. A total of 8 miRNAs were predicted to regulate more than 20% of lipid metabolism proteins differentially expressed between fat depots, suggesting that miRNAs play a role in adipose tissue regulation. Our results show that proteomic changes support the distinct metabolic and physiological characteristics observed between subcutaneous and visceral adipose tissue depots in cattle.

MicroRNAs in domestic livestock

microRNAs (miRNAs) are a class of small noncoding RNA that bind to complementary sequences in the untranslated regions of multiple target mRNAs resulting in posttranscriptional regulation of gene expression. The recent discovery and expression-profiling studies of miRNAs in domestic livestock have revealed both their tissue-specific and temporal expression pattern. In addition, breed-dependent expression patterns as well as single nucleotide polymorphisms in either the miRNA or in the target mRNA binding site have revealed associations with traits of economic importance and highlight the potential use of miRNAs in future genomic selection programs.

Short communication: a mutation in the 3' untranslated region diminishes microRNA binding and alters expression of the OLR1 gene

The oxidized low-density lipoprotein (lectin-like) receptor 1 (OLR1) gene plays an important role in the degradation of the oxidized low-density lipoprotein, which causes damage to the arterial endothelium. Previous studies have shown that a single nucleotide polymorphism (SNP) in the 3' untranslated region (UTR) of OLR1 was associated with milk production and health traits in dairy cattle and with loin eye area and marbling depth in Qinchuan beef cattle. However, the mechanisms by which this SNP affects these traits are not well understood. MicroRNA (miRNA or mir) are small noncoding RNA that regulate gene expression by binding to target mRNA at their UTR to degrade or to repress translation of the target transcript. We hypothesized that miRNA bind to the 3' UTR of OLR1 to cause expression changes of the gene. To test this hypothesis, the Bos taurus autosome (bta)-mir-370miRNA was selected for this study based on bioinformatics prediction analysis. Two vectors that included A or C nucleotides of the 3' UTR SNP and 1 control vector were co-transfected with the vector of bta-miR-370 into human embryonic kidney 293 (HEK293) cells. Results of the dual-luciferase reporter assay showed that the activity of luciferase was significantly lower in cells transfected with the A nucleotide vector than that of the C nucleotide and control vectors. The assay also indicated that activity of miRNA bta-mir-370 was associated with a differential allelic regulation of OLR1 expression. These results imply that the 3' UTR SNP of the OLR1 gene is a strong candidate marker for selection in cattle breeding programs.

MicroRNAs in farm animals

MicroRNAs (miRNAs) are a class of ~22 nucleotide-long small noncoding RNAs that target mRNAs for translational repression or degradation. miRNAs target mRNAs by base-pairing with the 3'-untranslated regions (3'-UTRs) of mRNAs. miRNAs are present in various species, from animals to plants. In this review, we summarize the identification, expression, and function of miRNAs in four important farm animal species: cattle, chicken, pig and sheep. In each of these species, hundreds of miRNAs have been identified through homology search, small RNA cloning and next generation sequencing. Real-time RT-PCR and microarray experiments reveal that many miRNAs are expressed in a tissue-specific or spatiotemporal-specific manner in farm animals. Limited functional studies suggest that miRNAs have important roles in muscle development and hypertrophy, adipose tissue growth, oocyte maturation and early embryonic development in farm animals. Increasing evidence suggests that single-nucleotide polymorphisms in miRNA target sites or miRNA gene promoters may contribute to variation in production or health traits in farm animals.