Long intergenic non-coding RNAs (lincRNAs) have been considered to play a key regulatory role in various biological processes. An increasing number of studies have utilized transcriptome analysis to obtain lincRNAs with functions related to cancer, but lincRNAs affecting growth rates in weaned piglets are rarely described. Although lincRNAs have been systematically identified in various mouse tissues and cell lines, studies of lincRNA in pigs remain rare. Therefore, identifying and characterizing novel lincRNAs affecting the growth performance of weaned piglets is of great importance. Here, we reconstructed 101,988 lincRNA transcripts and identified 1,078 lincRNAs in two groups of longissimus dorsi muscle (LDM) and subcutaneous fat (SF) based on published RNA-seq datasets. These lincRNAs exhibit typical characteristics, such as shorter lengths and lower expression relative to protein-encoding genes. Gene ontology analysis revealed that some lincRNAs could be involved in weaned piglet related processes, such as insulin resistance and the AMPK signaling pathway. We also compared the positional relationship between differentially expressed lincRNAs (DELs) and quantitative trait loci (QTL) and found that some of DELs may play an important role in piglet growth and development. Our work details part of the lincRNAs that may affect the growth performance of weaned piglets and promotes future studies of lincRNAs for molecular-assisted development in weaned piglets.

/pdf/transcriptome-analysis-suggests-the-roles-of-long-intergenic-3e4rivcgma.pdf

Transcriptome Analysis Suggests the Roles of Long Intergenic Non-coding RNAs in the Growth Performance of Weaned Piglets.

Polyadenylation, a critical step in the production of mature mRNA for translation in most eukaryotes, involves cleavage and poly(A) tail addition at the 3′ end of mRNAs at the polyadenylation site (PAS). Sometimes, one gene can have more than one PAS, which can produce the alternative polyadenylation (APA) phenomenon and affect the stability, localization and translation of the mRNA. In this study, we discovered 28,363 PASs using pig RNAseq data, with 13,033 located in 7,403 genes. Among the genes, 41% were identified to have more than one PAS. PAS distribution analysis indicated that the PAS position was highly variable in genes. Additionally, the analysis of RNAseq data from the liver and testis showed a difference in their PAS number and usage. RT-PCR and qRT-PCR were performed to confirm our findings by detecting the expression of 3′UTR isoforms for five candidate genes. The analysis of RNAseq data under a different androstenone level and salmonella inoculation indicated that the functional usage of PAS might participate in the immune response and may be related to the androstenone level in pigs. This study provides new insights into pig PAS and facilitates further functional research of PAS.

/pdf/genome-wide-analysis-and-functional-characterization-of-the-r7oj3y9lzo.pdf

Genome-Wide Analysis and Functional Characterization of the Polyadenylation Site in Pigs Using RNAseq Data.

The reprogramming of cellular memory in specific cell types, and in visceral adipocytes in particular, appears to be a fundamental aspect of obesity and its related negative health outcomes. We explored the hypothesis that adipose tissue contains epigenetically distinct subpopulations of adipocytes that are differentially potentiated to record cellular memories of their environment. Adipocytes are large, fragile, and technically difficult to efficiently isolate and fractionate. We developed fluorescence nuclear cytometry (FNC) and fluorescence activated nuclear sorting (FANS) of cellular nuclei from visceral adipose tissue (VAT) using the levels of the pan-adipocyte protein, peroxisome proliferator-activated receptor gamma-2 (PPARg2), to distinguish classes of PPARg2-Positive (PPARg2-Pos) adipocyte nuclei from PPARg2-Negative (PPARg2-Neg) leukocyte and endothelial cell nuclei. PPARg2-Pos nuclei were 10-fold enriched for most adipocyte marker transcripts relative to PPARg2-Neg nuclei. PPARg2-Pos nuclei showed 2- to 50-fold higher levels of transcripts encoding most of the chromatin-remodeling factors assayed, which regulate the methylation of histones and DNA cytosine (e.g., DNMT1, TET1, TET2, KDM4A, KMT2C, SETDB1, PAXIP1, ARID1A, JMJD6, CARM1, and PRMT5). PPARg2-Pos nuclei were large with decondensed chromatin. TAB-seq demonstrated 5-hydroxymethylcytosine (5hmC) levels were remarkably dynamic in gene bodies of various classes of VAT nuclei, dropping 3.8-fold from the highest quintile of expressed genes to the lowest. In short, VAT-derived adipocytes appear to be more actively remodeling their chromatin than non-adipocytes.

/pdf/subsets-of-visceral-adipose-tissue-nuclei-with-distinct-1l0wphclma.pdf

Subsets of Visceral Adipose Tissue Nuclei with Distinct Levels of 5-Hydroxymethylcytosine

Skeletal muscle satellite cells are a class of undifferentiated mononuclear myogenic stem cells distributed between the myofibroblast and membrane basement. Since their development determines the development of skeletal muscles, knowledge of their proliferation, differentiation, and fate is vital for understanding skeletal muscle development. Increasing evidence have shown that long noncoding RNA (lncRNA) plays an important role in regulating the development process of satellite cells. Based on the results of our previous studies, we screened lncRNA MSTRG.59589, which is highly expressed in skeletal muscle tissue. In the present study, knockdown of MSTRG.59589 significantly inhibited satellite cell differentiation at various time points, whereas overexpression of MSTRG.59589 demonstrated opposite effects. An MSTRG.59589 knockdown cell model was constructed for transcriptome sequencing, and RNA sequencing analysis screened out a large number of differentially expressed genes. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses of these differentially expressed genes revealed that they are mainly enriched in actin cytoskeleton, muscle contraction, and other pathways related to muscle development. Mechanistic analyses showed that MSTRG.59589 could promote the differentiation process of skeletal muscle satellite cells by positively regulating the expression level of the target gene PALLD. This experiment lays a theoretical foundation for deeper studies on the mechanism of MSTRG.59589 in the differentiation of porcine skeletal muscle satellite cells.

/pdf/long-noncoding-ribonucleic-acid-mstrg-59589-promotes-porcine-30yvl8wqx2.pdf

Long Noncoding Ribonucleic Acid MSTRG.59589 Promotes Porcine Skeletal Muscle Satellite Cells Differentiation by Enhancing the Function of PALLD.

Piglets with light weaning weight commonly have a slow post-weaning growth rate due to impaired skeletal muscle development. Therefore, the present study aimed to investigate the impact of birth weight and nutrient intake on skeletal muscle development, myofiber maturation, and metabolic status of early-weaned piglets. Twelve pairs of normal birth weight and intrauterine growth-retarded (IUGR) piglets (seven days old) were randomly assigned to receive adequate nutrient intake or restricted nutrient intake for 21 days. Serum and muscle samples were collected for further analysis. The results indicated that muscle weight, cross-sectional areas, and muscular glycogen were lower (p < 0.05) in both IUGR and restricted fed piglets. Nutrient restriction decreased the contents of RNA, the RNA to DNA ratio, and the percentages of myosin heavy chain (MyHC) IIx (p < 0.05), whereas increased the activity of β-hydroxy-acyl-CoA-dehydrogenase (HAD), the ratio of HAD to citrate synthase, as well as the percentages of MyHC I (p < 0.05). In addition, nutrient restriction significantly decreased muscular glycogen, mRNA levels of fatty acid transport protein 1, cationic amino acid transporter 1, and glucose transporter 4 in IUGR piglets compared with the other groups (p < 0.05). The results of the present study showed that IUGR impaired skeletal muscle growth and disturbed the hormone and mRNA expression of genes related to energy metabolism, which led to a more severe energy deficit when receiving postnatal nutritional restriction. Postnatal nutritional restriction resulted in delayed myofiber maturation of the piglets, which may be associated with the transformation of MyHC isoform and the change of metabolic status.

https://www.mdpi.com/2076-2615/10/1/156/pdf

Effects of Birth Weight and Postnatal Nutritional Restriction on Skeletal Muscle Development, Myofiber Maturation, and Metabolic Status of Early-Weaned Piglets.

Although most pigs recover rapidly from stresses associated with the transition of weaning, a portion of the population lags behind their contemporaries in growth performance. The underlying biological and molecular mechanisms involved in postweaning differences in growth performance are poorly understood. The objective of this experiment was to use transcriptional profiling of skeletal muscle and adipose tissue to develop a better understanding of the metabolic basis for poor weaned-pig transition. A total of 1,054 pigs was reared in commercial conditions and weighed at birth, weaning, and 3 wk postweaning. Transition ADG (tADG) was calculated as the ADG for the 3-wk period postweaning. Nine pigs from both the lowest 10th percentile (low tADG) and the 60th to 70th percentile (high tADG) were harvested at 3 wk postweaning. Differential expression analysis was conducted in longissimus dorsi muscle (LM) and subcutaneous adipose tissue using RNA-Seq methodology. In LM, 768 transcripts were differentially expressed (DE), 327 with higher expression in low tADG and 441 with higher expression in high tADG pigs (q 1.3). The list of DE genes with higher expression in low tADG LM was enriched in genes with functions related to protein catabolism (enrichment score > 1.3). Analysis of known gene-gene interactions identified possible regulators of these differences in gene expression in LM of high and low tADG pigs; these include forkhead box O1 (FOXO1), growth hormone (GH1), and the glucocorticoid receptor (NR3C1). Differences in gene expression between poor transitioning pigs and their contemporaries indicate a shift to decreased protein synthesis, increased protein degradation, and reduced glucose metabolism in the LM of low tADG pigs.

https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=1337&context=ans_pubs

Transcript profiles in longissimus dorsi muscle and subcutaneous adipose tissue: a comparison of pigs with different postweaning growth rates.

Gene expression profiling of longissimus dorsi and adipose tissue in pigs with differing post-weaning growth rate

Results of this study are presented in Table 1 and Table 2. There were no significant interactions (P>0.10) between tylosin phosphate, DDGS or sampling period. Inclusion of DDGS reduced apparent ileal digestibility (65.3 vs. 71.9%; P 0.10); therefore, standardized ileal digestibility of amino acid values were calculated using means of the two nitrogen-free diets. The standardized ileal digestibility of Lys (79.6 vs. 84.1%; P<0.0001) and all other indispensible amino acids, except Leu, was lower in the DDGS diets. Inclusion of tylosin phosphate did not influence standardized ileal digestilbity of AA.

https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=1782&context=ans_air

Impact of Tylosin Phosphate and Distillers Dried Grains with Solubles on Amino Acid and Energy Digestibility of Diets Fed to Growing Pigs

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Transcript profiles in longissimus dorsi muscle and subcutaneous adipose tissue: a comparison of pigs with different postweaning growth rates.

Gene expression profiling of longissimus dorsi and adipose tissue in pigs with differing post-weaning growth rate

Impact of Tylosin Phosphate and Distillers Dried Grains with Solubles on Amino Acid and Energy Digestibility of Diets Fed to Growing Pigs