Epigenetic regulation of H3K27me3 in laying hens with fatty liver hemorrhagic syndrome induced by high-energy and low-protein diets.

BACKGROUND: Fatty liver hemorrhagic syndrome (FLHS) in the modern poultry industry is primarily caused by nutrition. Despite encouraging progress on FLHS, the mechanism through which nutrition influences susceptibility to FLHS is still lacking in terms of epigenetics. RESULTS: In this study, we analyzed the genome-wide patterns of trimethylated lysine residue 27 of histone H3 (H3K27me3) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq), and examined its association with transcriptomes in healthy and FLHS hens. The study results indicated that H3K27me3 levels were increased in the FLHS hens on a genome-wide scale. Additionally, H3K27me3 was found to occupy the entire gene and the distant intergenic region, which may function as silencer-like regulatory elements. The analysis of transcription factor (TF) motifs in hypermethylated peaks has demonstrated that 23 TFs are involved in the regulation of liver metabolism and development. Transcriptomic analysis indicated that differentially expressed genes (DEGs) were enriched in fatty acid metabolism, amino acid, and carbohydrate metabolism. The hub gene identified from PPI network is fatty acid synthase (FASN). Combined ChIP-seq and transcriptome analysis revealed that the increased H3K27me3 and down-regulated genes have significant enrichment in the ECM-receptor interaction, tight junction, cell adhesion molecules, adherens junction, and TGF-beta signaling pathways. CONCLUSIONS: Overall, the trimethylation modification of H3K27 has been shown to have significant regulatory function in FLHS, mediating the expression of crucial genes associated with the ECM-receptor interaction pathway. This highlights the epigenetic mechanisms of H3K27me3 and provides insights into exploring core regulatory targets and nutritional regulation strategies in FLHS.

Advances in the discovery of genetic elements underlying longissimus dorsi muscle growth and development in the pig.

As a major source of protein in human diets, pig meat plays a crucial role in ensuring global food security. Key determinants of meat production refer to the chemical and physical compositions or characteristics of muscle fibers, such as the number, hypertrophy potential, fiber-type conversion and intramuscular fat deposition. However, the growth and formation of muscle fibers comprises a complex process under spatio-temporal regulation, that is, the intermingled and concomitant proliferation, differentiation, migration and fusion of myoblasts. Recently, with the fast and continuous development of next-generation sequencing technology, the integration of quantitative trait loci mapping with genome-wide association studies (GWAS) has greatly helped animal geneticists to discover and explore thousands of functional or causal genetic elements underlying muscle growth and development. However, owing to the underlying complex molecular mechanisms, challenges to in-depth understanding and utilization remain, and the cost of large-scale sequencing, which requires integrated analyses of high-throughput omics data, is high. In this review, we mainly elaborate on research advances in integrative analyses (e.g. GWAS, omics) for identifying functional genes or genomic elements for longissimus dorsi muscle growth and development for different pig breeds, describing several successful transcriptome analyses and functional genomics cases, in an attempt to provide some perspective on the future functional annotation of genetic elements for muscle growth and development in pigs.

Using phenotypic and genotypic big data to investigate the effect of muscle fiber characteristics on meat quality and eating quality traits in pigs.

Determining genetic correlations (GCs) between phenotypes that can be replicated across breeds or generations is important for animal breeding. A comprehensive and objective evaluation of this is dependent on enough variations in the studied phenotypes. To this end, we constructed a worldwide distributed eight-breeds crossbreed mosaic pig population and estimated the genetic and phenotypic correlations of muscle fiber characteristics (MFCs) with meat quality and eating quality traits using F6 and F7 generations (∼590 samples/generation) of this population. The GCs of the density of type IIA fibers and type IIB fibers with the loin-eye area, a*, color score, firmness score, and those of the proportions of the two fiber types with pH24h and b* were moderate to high (|rg| ≥ 0.3) in both populations. We also obtained moderate to high GCs of mean fiber density with five sensory quality traits. Our results provide an important reference for improving meat quality through the genetic regulation of MFCs.

Whole-genome sequence-based association analyses on an eight-breed crossed heterogeneous stock of pigs reveal the genetic basis of skeletal muscle fiber characteristics.

Skeletal muscle fiber characteristics (MFCs) have been extensively studied due to their importance to human health and athletic ability, as well as to the quantity and quality of livestock meat production. Hence, we performed a genome-wide association study (GWAS) on nine muscle fiber traits by using whole genome sequence data in an eight-breed crossed heterogeneous stock pig population. This GWAS revealed 67 quantitative trait loci (QTLs) for these traits. The most significant GWAS signal was detected in the region of Sus scrofa chromosome 12 (SSC12) containing the MYH gene family. Notably, we identified a significant SNP rs322008693 (P = 7.52E-09) as the most likely causal mutation for the total number of muscle fibers (TNMF) QTL on SSC1. The results of EMSA and luciferase assays indicated that the rs322008693 SNP resided in a functional element. These findings provide valuable molecular markers for pig meat production selection as well as for deciphering the genetic mechanisms of the muscle fiber physiology.

Effect of JAK-STAT pathway in regulation of fatty liver hemorrhagic syndrome in chickens.

OBJECTIVE: To explore the molecular mechanisms of fatty liver hemorrhagic syndrome (FLHS) in laying hens, an experiment was conducted to reveal the differences in histopathological observation and gene expression between FLHS group and normal group. METHODS: We compared the histopathological difference using hematoxylin and eosin staining and proceeded with RNA sequencing of adipose tissue to search differentially expressed genes and enriched biological processes and pathways. Then we validated the mRNA expression levels by real-time polymerase chain reaction and quantified protein levels in the circulation by enzyme-linked immunosorbent assay. RESULTS: We identified 100 differentially expressed transcripts corresponding to 66 genes (DEGs) were identified between FLHS-affected group and normal group. Seven DEGs were significantly enriched in the immune response process and lipid metabolic process, including phospholipase A2 group V, WAP kunitz and netrin domain containing 2, delta 4-desaturase sphingolipid 2, perilipin 3, interleukin-6 (IL-6), ciliary neurotrophic factor (CNTF), and suppressor of cytokine signaling 3 (SOCS3). And these genes could be the targets of immune response and be involved in metabolic homeostasis during the process of FLHS in laying hens. Based on functional categories of the DEGs, we further proposed a model to explain the etiology and pathogenesis of FLHS. IL-6 and SOCS3 mediate inflammatory responses and the satiety hormone of leptin, induce dysfunction of Jak-STAT signaling pathway, leading to insulin resistance and lipid metabolic disorders. Conversely, CNTF may reduce tissue destruction during inflammatory attacks and confer protection from inflammation-induced insulin resistance in FLHS chickens. CONCLUSION: These findings highlight the therapeutic implications of targeting the JAK-STAT pathway. Inhibition of IL6 and SOCS3 and facilitation of CNTF could serve as a favorable strategy to enhance insulin action and improve glucose homoeostasis, which are of importance for treating obesity-related disorders for chickens.

The effect of purine content on sensory quality of pork.

Although high level of purine in foods is considered a risk factor for hyperuricemia and gout, purine-rich foods continue to be popular for their delicious taste. The main objective of this study was to investigate the effects of purine bases on the sensory quality of pork. A total of 406 longissimus thoracis et lumborum samples were collected from a heterogeneous F6 pig population to determine purine composition and its correlation to sensory quality of pork. The contents of total purine and two major uricogenic bases (adenine and hypoxanthine) were negatively correlated with tenderness, juiciness, oiliness and overall liking (r < -0.2, P < 0.05), but they were not significantly correlated with umami. In contrast, guanine content, which accounts for only about 10% of the total purine content, was positively correlated with umami (r = 0.15, P < 0.05), and had no significant relationships with other sensory indicators. These results imply that purine bases with different uricogenic effects also influence different sensory quality indices of pork.

Dysregulated H3K27 Acetylation Is Implicated in Fatty Liver Hemorrhagic Syndrome in Chickens.

Epigenetic regulation of gene expression has been reported in the pathogenesis of metabolic disorders such as diabetes and liver steatosis in humans. However, the molecular mechanisms of fatty liver hemorrhagic syndrome (FLHS) in chickens have been rarely studied. H3K27ac chromatin immunoprecipitation coupled with high-throughput sequencing and high-throughput RNA sequencing was performed to compare genome-wide H3K27ac profiles and transcriptomes of liver tissue between healthy and FLHS chickens. In total, 1,321 differential H3K27ac regions and 443 differentially expressed genes were identified (| log2Fold change| ≥ 1 and P-value ≤ 0.05) between the two groups. Binding motifs for transcription factors involved in immune processes and metabolic homeostasis were enriched among those differential H3K27ac regions. Differential H3K27ac peaks were associated with multiple known FLHS risk genes, involved in lipid and energy metabolism (PCK1, APOA1, ANGPTL4, and FABP1) and the immune system (FGF7, PDGFRA, and KIT). Previous studies and our current results suggested that the high-energy, low-protein (HELP) diet might have an impact on histone modification and chromatin structure, leading to the dysregulation of candidate genes and the peroxisome proliferator-activated receptor (PPAR) signaling pathway, which causes excessive accumulation of fat in the liver tissue and induces the development of FLHS. These findings highlight that epigenetic modifications contribute to the regulation of gene expression and play a central regulatory role in FLHS. The PPAR signaling pathway and other genes implicated in FLHS are of great importance for the development of novel and specific therapies for FLHS-susceptible commercial laying hens.

Effects of a high energy and low protein diet on hepatic and plasma characteristics and Cidea and Cidec mRNA expression in liver and adipose tissue of laying hens with fatty liver hemorrhagic syndrome.

Cidea and Cidec are two members of Cell death-inducing DNA fragmentation factor-alpha-like effector family proteins, which could be involved in lipid or fat metabolism. To better understand the roles of Cidea and Cidec in fatty liver hemorrhagic syndrome (FLHS), 150 healthy 155-day-old Hyline Brown laying hens were randomly divided into control group (fed with basic diet) and experimental group (fed with high-energy low-protein [HELP] diet). Analysis of the liver by tissue sectioning and hematoxylin and eosin staining showed that the HELP diet induced micro-vesicular steatosis in laying hens. Subsequently, based on the liver color scores and the range of lipid accumulation observed in histological examination, we classified livers with <50% vacuolization as mild FLHS and >50% as severe FLHS. The results showed that the levels of Cidea and Cidec mRNA expression were markedly elevated in the liver and adipose tissues with FLHS and the levels of Cidea and Cidec mRNA expression in the liver with severe FLHS were significantly higher than that in the liver with mild FLHS. Thus, the present study revealed that the Cidea and Cidec genes may be involved in pathways of FLHS formation.

Single Infrared Image-Based Stripe Nonuniformity Correction via a Two-Stage Filtering Method.

The presence of stripe nonuniformity severely degrades the image quality and affects the performance in many infrared (IR) sensing applications. Prior works correct the nonuniformity by using similar spatial representations, which inevitably damage some detailed structures of the image. In this paper, we instead take advantage of spectral prior of stripe noise to solve its correction problem in single IR image. We first analyse the significant spectral difference between stripes and image structures and utilize this knowledge to characterize stripe nonuniformity. Then a two-stage filtering strategy is adopted combining spectral and spatial filtering. The proposed method enables stripe nonuniformity to be eliminated from coarse to fine, thus preserving image details well. Extensive experiments on simulated images and raw IR images demonstrate that the proposed method achieves superior correction performance over the recent state-of-the-art methods.

A whole-genome sequence based association study on pork eating quality traits and cooking loss in a specially designed heterogeneous F6 pig population.

To determine the genetic basis of pork eating quality traits and cooking loss, we herein performed a genome-wide association study (GWAS) for tenderness, juiciness, oiliness, umami, overall liking and cooking loss by using whole genome sequences of heterogeneous stock F6 pigs which were generated by crossing 4 typical western pig breeds (Duroc, Landrace, Large White and Pietrain) and 4 typical Asian pig breeds (Erhualian, Laiwu, Bamaxiang and Tibetan). We identified 50 associated loci (QTLs) and most of them are novel. Seven loci also showed pleiotropic associations with different traits. In addition, we identified multiple promising candidate genes for these traits, including PAK1 and AQP11 for cooking loss, EP300 for tenderness, SDK1 for juiciness, FITM2 and 5-linked MYH genes for oiliness, and TNNI2 and TNNT3 for overall liking. Our results provide not only a better understanding of the genetic basis for meat quality, but also a potential application in future breeding for these complex traits.

A Multi-hole Cryovial Eliminates Freezing Artifacts when Muscle Tissues are Directly Immersed in Liquid Nitrogen.

Studies on skeletal muscle physiology face the technical challenge of appropriately processing the specimens to obtain sections with clearly visible cytoplasmic compartments. Another hurdle is the tight apposition of myofibers to the surrounding tissues. Because the process of tissue fixation and paraffin embedding leads to the shrinkage of muscle fibers, freezing is an optimal means of hardening muscle tissue for sectioning. However, a commonly encountered issue, the formation of ice crystals, occurs during the preparation of frozen sections because of the high water content of muscle. The protocol presented here first describes a simple and efficient method for properly freezing muscle tissues by immersing them in liquid nitrogen. The problem with using liquid nitrogen alone is that it causes the formation of a nitrogen gas barrier next to the tissue, which acts as an insulator and inhibits the cooling of the tissues. To avoid this "vapor blanket" effect, a new cryovial was designed to increase the speed of liquid flow around the tissue surface. This was achieved by punching a total of 14 inlet holes in the wall of the vial. According to bubble dynamics, a higher rate of liquid flow results in smaller bubbles and fewer chances to form a gas barrier. When liquid nitrogen flows into the cryovial through the inlet holes, the flow velocity around the tissue is fast enough to eliminate the gas barrier. Compared to the method of freezing muscle tissues using pre-chilled isopentane, this protocol is simpler and more efficient and can be used to freeze muscle in a throughput manner. Furthermore, this method is optimal for institutions that do not have access to isopentane, which is extremely flammable at room temperature.

Differential gene expression pattern in hypothalamus of chickens during fasting-induced metabolic reprogramming: functions of glucose and lipid metabolism in the feed intake of chickens.

Fasting-induced hypothalamic metabolic reprogramming is involved in regulating energy homeostasis and appetite in mammals, but this phenomenon remains unclear in poultry. In this study, the expression patterns of a panel of genes related to neuropeptides, glucose, and lipid metabolism enzymes in the hypothalamus of chickens during fasting and refeeding were characterized by microarray analysis and quantitative PCR. Results showed that 48 h of fasting upregulated (P < 0.05) the mRNA expressions of orexigenic neuropeptide Y and agouti-related protein but downregulated (P < 0.05) that of anorexigenic neuropeptide pro-opiomelanocortin; growth hormone-releasing hormone; islet amyloid polypeptide; thyroid-stimulating hormone, ß; and glycoprotein hormones, α polypeptide. After 48 h of fasting, the mRNA expression of fatty acid ß-oxidation [peroxisome proliferator-activated receptor α (PPARα), carnitine palmitoyltransferase 1A, and forkhead box O1], energy sensor protein [sirtuin 1 (SIRT1) and forkhead box O1], and glycolysis inhibitor (pyruvate dehydrogenase kinase, isozyme 4) were enhanced, but that of fatty acid synthesis and transport associated genes (acetyl-CoA carboxylase α, fatty acid synthase, apolipoprotein A-I, endothelial lipase, and fatty acid binding protein 7) were suppressed. Liver and muscle also demonstrated similar expression patterns of genes related to glucose and lipid metabolism with hypothalamus, except for that of acetyl-CoA carboxylase α, acyl-CoA synthetase long-chain family member 4, and apolipoprotein A-I. The results of intracerebroventricular (ICV) injection experiments confirmed that α-lipoic acid (ALA, pyruvate dehydrogenase kinase, isozyme 4 inhibitor, 0.10 µmol) and NADH (SIRT1 inhibitor, 0.80 µmol) significantly suppressed the appetite of chickens, whereas 2-deoxy-d-glucose (glycolytic inhibitor, 0.12 to 1.20 µmol) and NAD(+) (SIRT1 activator, 0.08 to 0.80 µmol) increased feed intake in chickens. The orexigenic effect of NAD(+) was also blocked by cotreatment with NADH. However, ICV injection of either GW7647 (PPARα agonist) or GW6471 (PPARα antagonist) showed no effects on feed intake. Results suggested that hypothalamic glycolysis (inhibited by ALA and promoted by 2-deoxy-d-glucose) and SIRT1 (inhibited by NADH and promoted by NAD(+)), not PPARα, were probably involved in feed intake regulation in chickens.

The anorexigenic effect of serotonin is mediated by the generation of NADPH oxidase-dependent ROS.

Serotonin (5-HT) is a central inhibitor of food intake in mammals. Thus far, the intracellular mechanisms for the effect of serotonin on appetite regulation remain unclear. It has been recently demonstrated that reactive oxygen species (ROS) in the hypothalamus are a crucial integrative target for the regulation of food intake. To investigate the role of ROS in the serotonin-induced anorexigenic effects, conscious mice were treated with 5-HT alone or combination with Trolox (a ROS scavenger) or Apocynin (an NADPH oxidase inhibitor) by acute intracerebroventricular injection. Both Trolox and Apocynin reversed the anorexigenic action of 5-HT and the 5-HT-induced hypothalamic ROS elevation. The mRNA and protein expression levels of pro-opiomelanocortin (POMC) were dramatically increased after ICV injection with 5-HT. The anorexigenic action of 5-HT was accompanied by markedly elevated hypothalamic MDA levels and GSH-Px activity, while the SOD activity was decreased. Moreover, 5-HT significantly increased the mRNA expression of UCP-2 but reduced the levels of UCP-3. Both Trolox and Apocynin could block the 5-HT-induced changes in UCP-2 and UCP-3 gene expression. Our study demonstrates for the first time that the anorexigenic effect of 5-HT is mediated by the generation of ROS in the hypothalamus through an NADPH oxidase-dependent pathway.