Differential Regulation of Male-Hormones-Related Enhancers Revealed by Chromatin Accessibility and Transcriptional Profiles in Pig Liver

Surgical castration can effectively avoid boar taint and improve pork quality by removing the synthesis of androstenone in the testis, thereby reducing its deposition in adipose tissue. The expression of genes involved in testis-derived hormone metabolism was altered following surgical castration, but the upstream regulatory factors and underlying mechanism remain unclear. In this study, we systematically profiled chromatin accessibility and transcriptional dynamics in liver tissue of castrated and intact full-sibling Yorkshire pigs. First, we identified 897 differentially expressed genes and 6864 differential accessible regions (DARs) using RNA- and ATAC-seq. By integrating the RNA- and ATAC-seq results, 227 genes were identified, and a significant positive correlation was revealed between differential gene expression and the ATAC-seq signal. We constructed a transcription factor regulatory network after motif analysis of DARs and identified a candidate transcription factor (TF) SP1 that targeted the HSD3B1 gene, which was responsible for the metabolism of androstenone. Subsequently, we annotated DARs by incorporating H3K27ac ChIP-seq data, marking 2234 typical enhancers and 245 super enhancers involved in the regulation of all testis-derived hormones. Among these, four typical enhancers associated with HSD3B1 were identified. Furthermore, an in-depth investigation was conducted on the androstenone-related enhancers, and an androstenone-related mutation was identified in a newfound candidatetypical enhancer (andEN) with dual-luciferase assays. These findings provide further insights into how enhancers function as links between phenotypic and non-coding area variations. The discovery of upstream TF and enhancers of HSD3B1 contributes to understanding the regulatory networks of androstenone metabolism and provides an important foundation for improving pork quality.

Combining genome-wide association study based on low-coverage whole genome sequencing and transcriptome analysis to reveal the key candidate genes affecting meat color in pigs

Meat color is an attractive trait that influences consumers' purchase decisions at the point of sale. To decipher the genetic basis of meat color traits, we performed a genome-wide association study based on low-coverage whole-genome sequencing. In total, 669 (Pietrain × Duroc) × (Landrace × Yorkshire) pigs were genotyped using low-coverage whole-genome sequencing. Single nucleotide polymorphism (SNP) calling and genotype imputation were performed using the BaseVar + STITCH channel. Six individuals with an average depth of 12.05× whole-genome resequencing were randomly selected to assess the accuracy of imputation. Heritability evaluation and genome-wide association study for meat color traits were conducted. Functional enrichment analysis of the candidate genes from genome-wide association study and integration analysis with our previous transcriptome data were conducted. The imputation accuracy parameters, allele frequency R² , concordance rate, and dosage R² were 0.959, 0.952, and 0.933, respectively. The heritability values of a*_45 min , b*_45 min , L*_45 min , C*, and H⁰ were 0.19, 0.11, 0.06, 0.16, and 0.26, respectively. In total, 3884 significant SNPs and 15 QTL, corresponding to 382 genes, were associated with meat color traits. Functional enrichment analysis revealed that 10 genes were the potential candidates for regulating meat color. Moreover, integration analysis revealed that DMRT2, EFNA5, FGF10, and COL11A2 were the most promising candidates affecting meat color. In summary, this study provides new insights into the molecular basis of meat color traits, and provides a new theoretical basis for the molecular breeding of meat color traits in pigs.

A Combined Differential Proteome and Transcriptome Profiling of Fast- and Slow-Twitch Skeletal Muscle in Pigs

Skeletal muscle fiber types can contribute in part to affecting pork quality parameters. Biceps femoris (Bf) (fast muscle or white muscle) and Soleus (Sol) (slow muscle or red muscle) are two typical skeletal muscles characterized by obvious muscle fiber type differences in pigs. However, the critical proteins and potential regulatory mechanisms regulating porcine skeletal muscle fibers have yet to be clearly defined. In this study, the isobaric Tag for Relative and Absolute Quantification (iTRAQ)-based proteome was used to identify the key proteins affecting the skeletal muscle fiber types with Bf and Sol, by integrating the previous transcriptome data, while function enrichment analysis and a protein–protein interaction (PPI) network were utilized to explore the potential regulatory mechanisms of skeletal muscle fibers. A total of 126 differentially abundant proteins (DAPs) between the Bf and Sol were identified, and 12 genes were found to be overlapping between differentially expressed genes (DEGs) and DAPs, which are the critical proteins regulating the formation of skeletal muscle fibers. Functional enrichment and PPI analysis showed that the DAPs were mainly involved in the skeletal-muscle-associated structural proteins, mitochondria and energy metabolism, tricarboxylic acid cycle, fatty acid metabolism, and kinase activity, suggesting that PPI networks including DAPs are the main regulatory network affecting muscle fiber formation. Overall, these data provide valuable information for understanding the molecular mechanism underlying the formation and conversion of muscle fiber types, and provide potential markers for the evaluation of meat quality.

Resveratrol promotes mammary cell proliferation and antioxidation capacity during pregnancy and lactation in mice

AIMS

Reproduction can induce maternal oxidative stress, and resveratrol is able to alleviate oxidative stress. This study aimed to investigate the protective effects of resveratrol supplementation in mice during pregnancy and lactation.

METHODS AND RESULTS

Pregnant mice were randomly divided into three groups: (i) Pure water (Con); (ii) Cellulose sodium dissolves with 20 mg kg^-1 resveratrol (R1) and (iii) Cellulose sodium dissolves with 40 mg kg^-1 resveratrol (R2). The experiment starts at pregnancy and ends at weaning. The results showed that resveratrol increased mammary cell proliferation and the mRNA expressions of UDP glucuronosyltransferase family 1 member A1 (UGT1A1) and cytochrome P450 proteins (CYP1A1), while decreased superoxide dismutase, extracellular (SOD3) in the mammary gland. Further study showed that resveratrol promoted the mRNA expressions of genes involved in mitophagy, such as transcription factor Eβ (Tfeβ), Bcl1lc3β, homosapiens microtubule-associated protein 1 light-chain 3 beta (Map1lc3β), Parkin, sequestosome1 (p62), autophagy-related protein (Atg5) and Beclin-1 (Becn1) in the mammary gland. Moreover, resveratrol increased the abundances of some intestinal microbial species. 40 mg kg^-1 resveratrol significantly increased the contents of Acidobacteri, unidentified acidbacteria, Bacilales, Staphylococcaceae and Staphylococcus at phylum, class, order, family and genus level respectively.

CONCLUSION

Our results indicate that resveratrol supplementation may promote mammary cell proliferation and antioxidant ability through mitophagy and regulating gut microbiota in pregnant mice.

SIGNIFICANCE AND IMPACT OF THE STUDY

Current study proved that resveratrol could affect mammary cell proliferation and antioxidation capacity during pregnancy and lactation in mice for the first time. The underlying mechanisms may be related to mitophagy and gut microbiota.

Dietary leucine supplementation improves intestinal health of mice through intestinal SIgA secretion

AIMS

Leucine supplementation promotes intestinal health, but the mechanism is largely unknown. This study aimed to elucidate the mechanisms underlying the beneficial effects of leucine on intestinal homeostasis.

METHODS AND RESULTS

Female ICR mice (6-week-old) were randomly assigned into three groups: (i) mice received a basal diet; (ii) mice received a dietary 0·5% crystalline l-leucine supplementation; and (iii) mice received a dietary 1·0% crystalline l-leucine supplementation. Our results showed that leucine supplementation stimulated the secretion of SIgA in mice ileum and expression of cytokines related to SIgA production. Moreover, leucine supplementation improved the expression of mTOR and p70S6K1 expression. Further study showed that leucine supplementation markedly decreased microbiota richness and induced a shift in the Firmicutes : Bacteroidetes ratio in favour of Firmicutes.

CONCLUSIONS

Therefore, our data suggested that leucine supplementation could enhance intestinal health through the regulation of mTOR pathway and promoting SIgA secretion in the mouse intestine, which might be associated with intestinal microbiota.

SIGNIFICANCE AND IMPACT OF THE STUDY

The present study found that dietary leucine supplementation of mice could improve intestinal health by enhancing intestinal SIgA secretion via a nonexclusive mechanism, which might include T cell-dependent pathway, T cell-independent pathway and gut microbiota.

[Pulsatility indexes of fetal middle cerebral artery and umbilical artery for predicting intrauterine fetal growth retardation]

OBJECTIVE

To evaluate the role of fetal cerebral and umbilical blood flow for predicting intrauterine fetal growth retardation (IUGR).

METHODS

Doppler ultrasonography was used to study pulsatility indexes (PI) of the fetal middle cerebral artery (MCA) and umbilical artery (UA) in 84 normal late pregnancies and 31 IUGR cases.

RESULTS

MCA PI were significantly lower in IUGR fetuses than that of normal fetuses (P < 0.01). UA PI and UA PI/MCA PI ratio were higher in IUGR group than that of normal group (P < 0.01). The sensitivities of MCA PI, UA PI and UA PI/MCA PI ratio for predicting IUGR were 80.64%, 70.96% and 87.09% respectively at the cut off level with 2 standard deviation (SD). The specificities were 94.05%, 88.90% and 97.61% respectively.

CONCLUSIONS

Doppler ultrasonography for predicting IUGR was a practical and sensitive method.