Search

The brain as an important organ can be affected largely by aging, and the comprehensive transcriptional underpinnings of brain aging remain poorly understood. Here, we performed a high throughput RNA sequencing to evaluate the expression profiles of messenger RNA (mRNA), long non-coding RNAs (lncRNAs), micro RNAs (miRNAs), and circular RNAs (circRNAs) in porcine brain. We have identified 714 mRNAs, 38lncRNAs, 41miRNAs, and 148circRNAs were age-related genes in the porcine cerebral cortex. The lncRNAs, miRNAs and circRNAs have effect on the age of porcine brain due to the much changes of expression level as noncoding RNAs. The up-regulated genes were significantly enriched for stress response, reproductive regulatory process, immune response and metabolic process, and the down-regulated genes were related to neurologic function, stress response and signaling pathway. The synaptic transmission pathway may be the key role in aging of porcine brain that it was co-enriched for in both differentially expressed mRNAs and lncRNAs. Moreover, some lncRNAs and their target genes were also differentially expressed during brain aging. We further assessed the multi-group cooperative control relationships and constructed circRNA-miRNA co-expression networks during brain aging. We also selected 2 mRNAs, 2 lncRNAs, 2 miRNAs, and 1 circRNAs to perform the q-PCR, and the expression patterns were highly consistent between the two methods confirming the high reproducibility and reliability of the gene expression profiling in our study. In conclusion, our findings will contribute to understand the transcriptional underpinnings of brain aging and provide a foundation for future studies on the molecular mechanisms underlying brain aging.

Obesity due to excessive lipid accumulation is closely associated with metabolic diseases such as type 2 diabetes, insulin resistance and inflammation. Therefore, a detailed understanding of the molecular mechanisms that underlie adipogenesis is crucial to develop treatments for diseases related to obesity. Here, we found that the microRNA-204-5p (miR-204-5p) was expressed at low levels in fat tissues from obese mice fed long-term with a high-fat diet (HFD). Overexpression or inhibition of miR-204-5p in vitro in 3T3-L1 preadipocytes significantly inhibited or promoted 3T3-L1 proliferation, respectively, an effect mediated by regulating cell proliferation factors. miR-204-5p also induced preadipocyte apoptosis by directly targeting the 3' UTR region of Bcl-2, reducing the constitutive suppression of Bcl-2 on p53-dependent apoptosis. Interestingly, overexpression of miR-204-5p during adipocyte differentiation significantly increased the number of oil red O+ cells, triglyceride accumulation and the expression of markers associated with adipocyte differentiation. In contrast, inhibition of miR-204-5p had the opposite effect on 3T3-L1 adipocyte differentiation. Luciferase activity assays and qRT-PCR showed that miR-204-5p regulates adipocyte differentiation by negatively regulating KLF3, a negative regulator of lipogenesis. Taken together, our findings showed that miR-204-5p inhibits proliferation and induces apoptosis of preadipocytes by regulating Bcl-2, but also promotes adipocyte differentiation by targeting KLF3.

Efforts have been made to characterize the high-altitude adaption in Tibetan pigs and identified vast of genes or genomic regions undergone natural selection. Nonetheless, information concerning gene expression and DNA methylation changes response to low-altitude acclimation in Tibetan pigs is long overdue. To explore the exceptional mechanisms of gene expression and DNA methylation that are induced by low altitude environments in Tibetan pigs, we performed a comparative transcriptomic and DNA methylation analysis of skeletal muscle between indigenous Tibetan pigs that reside in high altitude regions (~4000m) and their counterparts that migrated to the geographically neighboring low-altitude regions (~500m) for nearly ten generations. Many genes that related to hypoxia response (EGLN3 and FLT1) and energy metabolism (TFB2M) were differentially expressed, but without significant DNA methylation changes. We also found genes embedded in differentially methylated regions were mainly involved in 'Starch and sucrose metabolism', 'glucuronosyltransferase activity' processes. Specifically, our results showed increased SIN3A mRNA expression, with hypomethylation status of its promoter, in longissimus dorsi muscle of low-altitude Tibetan pig. Another gene, CACNG6, showed decreasing expression level with an elevated methylation in its intron 3. These results indicated DNA-methylation-mediated expression alterations in low-altitude acclimation. We envision that this study will serve as a valuable resource for mammal acclimation research and agricultural food industry.

microRNA (miRNA) is a small endogenous noncoding RNA molecule that plays multiple roles in regulating most biological processes. However, for China’s national treasure giant panda, a world-famous rare and protected species, reports of its miRNA have been found only in blood and breast milk. To explore the miRNA expression differences between different giant panda tissues, here, we generated the miRNA profiles of five tissues (heart, liver, spleen, lung, and kidney) from four giant pandas with Illumina Hiseq 2500 platform, and filtered the differentially expressed miRNAs (DEmiRs) in each tissue, predicted the target genes of miRNA from each tissue based on the DEmiRs. Then, the GO and KEGG enrichment analysis were conducted using the target genes predicted from DEmiRs in each tissue. The RNA-seq generated an average of 0.718 GB base per sample. A total of 1,256 known miRNAs and 12 novel miRNAs were identified, and there were 215, 131, 185, 83, and 126 tissue-specific DEmiRs filtered in the heart, liver, spleen, lung, and kidney, respectively, including miR-1b-5p, miR-122-5p, miR-143, miR-126-5p, and miR-10b-5p, respectively. The predicted target genes, including MYL2, LRP5, MIF, CFD, and PEBP1 in the heart, liver, spleen, lung, and kidney, respectively, were closely associated with tissue-specific biological functions. The enrichment analysis results of target genes showed tissue-specific characteristics, such as the significantly enriched GO terms extracellular matrix in the heart and insulin-like growth factor binding in the liver. The miRNA profiles of the heart, liver, spleen, lung, and kidney of giant panda have been reported in this study, it reveals the miRNA expression differences between different tissues of the giant panda, and provides valuable genetic resources for the further related molecular genetic research of the rare and protected species giant panda and other mammals.

MicroRNAs (miRNAs) are a class of endogenous non-coding RNAs involved in regulating various biological processes at the post-transcription level. Accumulating evidence suggests that hypoxia caused by acute myocardial infarction induces cardiomyocyte damage including apoptosis. Previous studies regarding the miRNAome in H9c2 cells under hypoxia have shown that hypoxia modulates miRNA expression in H9c2 cells, including miR-532-5p. We therefore investigated whether miR-532-5p has a potential function in the cardiomyocyte response to hypoxia. In the present study, we found that miR-532-5p, which was down-regulated in hypoxia-exposed H9c2 cells and the myocardium of acute myocardial infarction rats, alleviated hypoxia-induced H9c2 cell apoptosis. Additionally, we identified PDCD4 as the direct target of miR-532-5p, which partly elucidates the anti-apoptotic mechanism of miR-532-5p. In summary, this study revealed that miR-532-5p has cardioprotective effects against hypoxia-induced apoptosis in H9c2 cells.

MicroRNAs (miRNAs) are small, non-coding RNAs, which are involved in regulation of a variety of biological processes. Since previous studies regarding the role of miRNAs in the regulation of adipogenic differentiation have shown that miRNA-27a, one member of miRNA-23a∼27a∼24 cluster, could suppress adipogenesis. We now investigated whether miRNA-23a regulates adipogenic differentiation. In the present study, we showed that the expression of miRNA-23a is decreased during the process of adipogenic differentiation. Over-expression of miRNA-23a decreased lipid accumulation and triglyceride content in 3T3-L1 adipocytes. Our results also demonstrated that miRNA-23a decreases mRNA levels of adipocyte-specific genes involved in lipogenic transcription, fatty acid synthesis and fatty acid transport. These findings suggested miRNA-23a to be a new type of adipogenic depressor and to play an important role in regulating adipocyte differentiation.

Domestication and subsequent selective pressures have produced a large variety of pig coat colors in different regions and breeds. The melanocortin 1 receptor (MC1R) gene plays a crucial role in determining coat color of mammals. Here, we investigated genetic diversity and selection at the coding region of the porcine melanocortin receptor 1 (MC1R) in Tibetan pigs and Landrace pigs. By contrast, genetic variability was much lower in Landrace pigs than in Tibetan pigs. Meanwhile, haplotype analysis showed that Tibetan pigs possessed shared haplotypes, suggesting a possibility of recent introgression event by way of crossbreeding with neighboring domestic pigs or shared ancestral polymorphism. Additionally, we detected positive selection at the MC1R in both Tibetan pigs and Landrace pigs through the dN/dS analysis. These findings suggested that novel phenotypic change (dark coat color) caused by novel mutations may help Tibetan pigs against intensive solar ultraviolet (UV) radiation and camouflage in wild environment, whereas white coat color in Landrace were intentionally selected by human after domestication. Furthermore, both the phylogenetic analysis and the network analysis provided clues that MC1R in Asian and European wild boars may have initially experienced different selective pressures, and MC1R alleles diversified in modern domesticated pigs.

Natural antisense transcripts (NATs) are widely present in mammalian genomes and act as pivotal regulator molecules to control gene expression. However, studies on the NATs of pigs are relatively rare. Here, we identified a novel antisense transcript, designated PLA2G16-AS, transcribed from the phospholipase A2 group XVI locus (PLA2G16) in the porcine genome, which is a well-known regulatory molecule of fat deposition. PLA2G16-AS and PLA2G16 were dominantly expressed in porcine adipose tissue, and were differentially expressed between Tibetan pigs and Rongchang pigs. In addition, PLA2G16-AS has a weak sequence conservation among different vertebrates. PLA2G16-AS was also shown to form an RNA-RNA duplex with PLA2G16, and to regulate PLA2G16 expression at the mRNA level. Moreover, the overexpression of PLA2G16-AS increased the stability of PLA2G16 mRNA in porcine cells. We envision that our findings of a NAT for a regulatory gene associated with lipolysis might further our understanding of the molecular regulation of fat deposition.

Adipose triglyceride lipase (ATGL), catalyzing the initial step of hydrolysis of triacylglycerol (TAG) in adipocytes, has been known to be inhibited by G0/G1 switch protein 2 (G0S2). In this study, we determined tissue expression pattern and polymorphism of G0S2 gene in porcine. The results showed that the G0S2 transcript levels were very high in the liver and, to a lesser degree, in adipose tissues of greater omentum and suet fat; and low G0S2 transcript levels were observed in other tissues. A comparative study on the transcript levels between ATGL and G0S2 genes showed that ATGL transcript levels were high in all six adipose tissues, but negligible in the liver. Higher transcript levels were obtained for sows in adipose tissues of the inner layer of subcutaneous fat and suet fat, but higher expression values were found for boars in the liver, spleen, and stomach. 19 single nucleotide polymorphisms (SNPs), including 4 nonsynonymous SNPs (g.-307A>T, g.-394C>G, g.-565G>A, and g.-566T>C), were found in porcine G0S2 genomic DNA. Association analyses showed that the g.-565G>A and g.-742T>A SNPs were associated with back fat thickness (BFT). In conclusion, G0S2 mRNAs are abundantly expressed in porcine liver and adipose tissues of greater omentum and suet fat, and sex affects porcine G0S2 tissue transcript levels; meanwhile, the genetic diversity of porcine G0S2 gene is abundant and 2 SNPs are a genetic factor affecting BFT.

Accumulating evidence has indicated that microRNAs (miRNAs) and endoplasmic reticulum (ER) stress play critical roles in myoblast differentiation. However, the regulation roles of miRNAs and ER stress in myogenic differentiation have not been fully revealed and need to be further studied. Here, we discovered that the expression levels of miR-181a-5p were strongly upregulated during C2C12 cell differentiation. miR-181a-5p overexpression promoted ER stress and differentiation of C2C12 cells, which was accompanied by increasing expression levels of marker genes related to ER stress-mediated apoptosis and myogenic differentiation. Opposite results were observed after inhibition of the miR-181a-5p expression. The gain- and loss-of-function experiments on C2C12 cells showed that miR-181a-5p affected the development of muscle fiber type, but had no significant influence on C2C12 cell proliferation. In the ER-stressed C2C12 cells induced by thapsigargin (Tg), the expression levels of both miR-181a-5p and marker genes related to ER stress and myogenesis were upregulated. In the ER-stressed C2C12 cells and porcine muscle fibroblast (PMF) cells pretreated with Tg, we found that miR-181a-5p targeted glucose-regulated protein, 78kDa/binding immunoglobulin protein (GRP78/BIP), and influenced cell apoptosis. In conclusion, these results indicate that miR-181a-5p and ER stress have positive synergistic effects on myogenic differentiation by increasing the expression levels of myogenic differentiation key genes and activating the ER stress-mediated apoptosis signaling pathway.

Domestic goats are distributed in a wide range of habitats and have acclimated to their local environmental conditions. To investigate the gene expression changes of goats that are induced by high altitude stress, we performed RNA-seq on 27 samples from the three hypoxia-sensitive tissues (heart, lung, and skeletal muscle) in three indigenous populations from distinct altitudes (600 m, 2000 m, and 3000 m). We generated 129Gb of high-quality sequencing data (~4Gb per sample) and catalogued the expression profiles of 12,421 annotated hircine genes in each sample. The analysis showed global similarities and differences of high-altitude transcriptomes among populations and tissues as well as revealed that the heart underwent the most high-altitude induced expression changes. We identified numerous differentially expressed genes that exhibited distinct expression patterns, and nonsynonymous single nucleotide variant-containing genes that were highly differentiated between the high- and low-altitude populations. These genes have known or potential roles in hypoxia response and were enriched in functional gene categories potentially responsible for high-altitude stress. Therefore, they are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms related to high-altitude acclimation.

Lipoprotein lipase (LPL) is a key enzyme in lipid metabolism and is transported by glycosylphosphatidylinositol-anchored high-density lipoprotein-binding protein 1 (GPIHBP1) from the interstitial spaces to the capillary lumen. Here, we cloned a cDNA and the genomic locus of the porcine GPIHBP1 gene, and investigated its tissue expression pattern and its genetic effects on adipose traits. Porcine GPIHBP1 exhibits a four-exon/three-intron structure, including a 543 bp open reading frame that encodes 180 amino acids. The porcine GPIHBP1 protein shows 49%–65% homology and shares the major conserved structural domains of GPIHBP1 proteins in other mammals. Porcine GPIHBP1 mRNA levels were high in the adipose tissue, muscle and lung, and higher mRNA levels were observed in sows compared to boars in adipose tissues of the inner and outer layers of subcutaneous fat, abdominal fat, and suet fat. The mRNA expression pattern of porcine GPIHBP1 and LPL genes was similar in most tissues except for the lung. Thirty six single nucleotide polymorphisms (SNPs) were found in the porcine GPIHBP1 gene. Association analyses showed that the g.-255G>C and g.-626T>G SNPs are associated with intramuscular fat content, and that the g.-1557T>C and g.-1948G>A SNPs are associated with back fat thickness. In conclusion, porcine GPIHBP1 mRNA is abundantly expressed in the adipose tissue, muscle and lung, and gender affects GPIHBP1 mRNA expression levels; furthermore, four GPIHBP1 SNPs are genetic factors affecting adipose traits.