Identification of genes directly responding to DLK1 signaling in Callipyge sheep

Livestock species as emerging models for genomic imprinting

Genomic imprinting is an epigenetically-regulated process of central importance in mammalian development and evolution. It involves multiple levels of regulation, with spatio-temporal heterogeneity, leading to the context-dependent and parent-of-origin specific expression of a small fraction of the genome. Genomic imprinting studies have therefore been essential to increase basic knowledge in functional genomics, evolution biology and developmental biology, as well as with regard to potential clinical and agrigenomic perspectives. Here we offer an overview on the contribution of livestock research, which features attractive resources in several respects, for better understanding genomic imprinting and its functional impacts. Given the related broad implications and complexity, we promote the use of such resources for studying genomic imprinting in a holistic and integrative view. We hope this mini-review will draw attention to the relevance of livestock genomic imprinting studies and stimulate research in this area.

The Role of Protein Methyltransferases in Immunity

The immune system protects our body from bacteria, viruses, and toxins and removes malignant cells. Activation of immune cells requires the onset of a network of important signaling proteins. Methylation of these proteins affects their structure and biological function. Under stimulation, T cells, B cells, and other immune cells undergo activation, development, proliferation, differentiation, and manufacture of cytokines and antibodies. Methyltransferases alter the above processes and lead to diverse outcomes depending on the degree and type of methylation. In the previous two decades, methyltransferases have been reported to mediate a great variety of immune stages. Elucidating the roles of methylation in immunity not only contributes to understanding the immune mechanism but is helpful in the development of new immunotherapeutic strategies. Hence, we review herein the studies on methylation in immunity, aiming to provide ideas for new approaches.

Effects of porcine reproductive and respiratory syndrome virus (PRRSV) on thyroid hormone metabolism in the late gestation fetus

Porcine reproductive and respiratory syndrome virus (PRRSV) in late gestation causes a profound suppression of circulating maternal and fetal thyroid hormone during a critical window of development. To understand this relationship, we evaluated thyroid hormone metabolism at the maternal-fetal interface and within fetal tissues, along with hormone metabolite levels in serum. Fetuses were classified using an established model based on viral load in serum and thymus, and preservation status, including uninfected (UNIF), high-viral load viable (HV-VIA), and high-viral load meconium-stained (HV-MEC), with additional controls from sham-inoculated gilts (CON). Expression of three iodothyronine deiodinases, five sulfotransferases, sulfatase, and two solute carriers known to transport thyroid hormone were evaluated in maternal endometrium and fetal placenta, liver, and kidney. Serum thyroxin (T4), reverse triiodothyronine (rT3), and diiodothyronine (T2) were evaluated via liquid chromatography tandem mass spectrometry. Significant changes in gene expression were observed in all four tissues, with the liver being the most severely impacted. We observed local and fetal specific regulation of maternal tissues through significant upregulation of DIO2 and DIO3 expression in the endometrium corresponding to infected but viable fetuses relative to uninfected and control fetuses. Expression levels of DIO2 and DIO3 were significantly higher in the resilient (HV-VIA) fetuses relative to the susceptible (HV-MEC) fetuses. A substantial decrease in serum T4 was confirmed, with no corresponding increase in rT3 or T2. Collectively, these results show that thyroid hormone metabolism is altered at the maternal-fetal interface and within the PRRSV infected fetus and is associated with fetal viability.

Short-term exposure to a clinical dose of metformin increases skeletal muscle mitochondrial H2O2 emission and production in healthy, older adults: A randomized controlled trial

BACKGROUND AND AIMS

Metformin is the most commonly prescribed medication to treat diabetes. Emerging evidence suggests that metformin could have off target effects that might help promote healthy muscle aging, but these effects have not been thoroughly studied in glucose tolerant older individuals. The purpose of this study was to investigate the short-term effects of metformin consumption on skeletal muscle mitochondrial bioenergetics in healthy older adults.

METHODS

We obtained muscle biopsy samples from 16 healthy older adults previously naïve to metformin and treated with metformin (METF; 3F, 5M), or placebo (CON; 3F, 5M), for two weeks using a randomized and blinded study design. Samples were analyzed using high-resolution respirometry, immunofluorescence, and immunoblotting to assess muscle mitochondrial bioenergetics, satellite cell (SC) content, and associated protein markers.

RESULTS

We found that metformin treatment did not alter maximal mitochondrial respiration rates in muscle compared to CON. In contrast, mitochondrial H2O2 emission and production were elevated in muscle samples from METF versus CON (METF emission: 2.59 ± 0.72 SE Fold, P = 0.04; METF production: 2.29 ± 0.53 SE Fold, P = 0.02). Furthermore, the change in H2O2 emission was positively correlated with the change in type 1 myofiber SC content and this was biased in METF participants (Pooled: R2 = 0.5816, P = 0.0006; METF: R2 = 0.674, P = 0.0125).

CONCLUSIONS

These findings suggest that acute exposure to metformin does not impact mitochondrial respiration in aged, glucose-tolerant muscle, but rather, influences mitochondrial-free radical and SC dynamics.

CLINICAL TRIAL REGISTRATION

NCT03107884, clinicaltrials.gov.

Functional Identification of Porcine DLK1 during Muscle Development

Simple Summary

Skeletal muscle is the largest tissue and serves as a protein reservoir and energy reservoir in the human and animal body. It also serves as the main metabolic activity site. The formation of skeletal muscle mainly depends on the differentiation and fusion of myocytes and other complex ordered processes; each step is regulated by various factors. In this study, we investigated the expression profiles, functional identification, and regulatory pathways of Delta-like 1 homolog (DLK1) in pigs and myocytes. We found that DLK1 was highly expressed in the muscle tissues of pigs. DLK1 promoted myocyte proliferation, migration, differentiation, fusion, and muscular hypertrophy, but suppressed muscle degradation. DLK1 also inhibited the Notch signaling pathway by regulating the expression of key factors in the pathway, thereby producing a phenotype in which DLK1 promotes muscle development. These findings provide valuable information to improve our understanding of the functional mechanisms of DLK1 that underly myogenesis to accelerate the process of animal genetic improvement.

Abstract

DLK1 is paternally expressed and is involved in metabolism switching, stem cell maintenance, cell proliferation, and differentiation. Porcine DLK1 was identified in our previous study as a candidate gene that regulates muscle development. In the present study, we characterized DLK1 expression in pigs, and the results showed that DLK1 was highly expressed in the muscles of pigs. In-vitro cellular tests showed that DLK1 promoted myoblast proliferation, migration, and muscular hypertrophy, and at the same time inhibited muscle degradation. The expression of myogenic and fusion markers and the formation of multinucleated myotubes were both upregulated in myoblasts with DLK1 overexpression. DLK1 levels in cultured myocytes were negatively correlated with the expression of key factors in the Notch pathway, suggesting that the suppression of Notch signaling pathways may mediate these processes. Collectively, our results suggest a biological function of DLK1 as an enhancer of muscle development by the inhibition of Notch pathways.

Preliminary Results about Lamb Meat Tenderness Based on the Study of Novel Isoforms and Alternative Splicing Regulation Pathways Using Iso-seq, RNA-seq and CTCF ChIP-seq Data

Tenderness is an important indicator of meat quality. Novel isoforms associated with meat tenderness and the role of the CCCTC-binding factor (CTCF) in regulating alternative splicing to produce isoforms in sheep are largely unknown. The current project studied six sheep from two crossbred populations (Dorper × Hu × Hu, DHH and Dorper × Dorper × Hu, DDH) with divergent meat tenderness. Pooled Iso-seq data were used to annotate the sheep genomes. Then, the updated genome annotation and six RNA-seq data were combined to identify differentially expressed isoforms (DEIs) in muscles between DHH and DDH. These data were also combined with peaks detected from CTCF ChIP-seq data to investigate the regulatory role of CTCF for the alternative splicing. As a result, a total of 624 DEIs were identified between DDH and DHH. For example, isoform 7.524.18 transcribed from CAPN3 may be associated with meat tenderness. In addition, a total of 86 genes were overlapped between genes with transcribed DEIs and genes in differential peaks identified by CTCF ChIP-seq. Among these overlapped genes, ANKRD23 produces different isoforms which may be regulated by CTCF via methylation. As preliminary research, our results identified novel isoforms associated with meat tenderness and revealed the possible regulating mechanisms of alternative splicing to produce isoforms.

TdIF1-LSD1 Axis Regulates Epithelial-Mesenchymal Transition and Metastasis via Histone Demethylation of E-Cadherin Promoter in Lung Cancer

We have previously found that TdT-interacting factor 1 (TdIF1) is a potential oncogene expressed in non-small cell lung cancer (NSCLC) and is associated with poor prognosis. However, its exact mechanism is still unclear. The lysine-specific demethylase 1 (LSD1) is a crucial mediator of the epithelial-mesenchymal transition (EMT), an important process triggered during cancer metastasis. Here, we confirm that TdIF1 is highly expressed in NSCLC and related to lymph node metastasis through The Cancer Genome Atlas (TCGA) analysis of clinical samples. Silencing TdIF1 can regulate the expression of EMT-related factors and impair the migration and invasion ability of cancer cells in vitro. An analysis of tumor xenografts in nude mice confirmed that silencing TdIF1 inhibits tumor growth. Furthermore, we determined the interaction between TdIF1 and LSD1 using immunoprecipitation. Chromatin immunoprecipitation (ChIP) revealed that TdIF1 was enriched in the E-cadherin promoter region. The knockdown of TdIF1 repressed the enrichment of LSD1 at the E-cadherin promoter region, thereby regulating the level of promoter histone methylation and modulating E-cadherin transcription activity, ultimately leading to changes in EMT factors and cancer cell migration and invasion ability. The LSD1 inhibitor and TdIF1 knockdown combination showed a synergistic effect in inhibiting the growth, migration, and invasion of NSCLC cells. Taken together, this is the first demonstration that TdIF1 regulates E-cadherin transcription by recruiting LSD1 to the promoter region, thereby promoting EMT and tumor metastasis and highlighting the potential of TdIF1 as a therapeutic target for NSCLC.

Fennel (Foeniculum vulgare) seed powder increases Delta-Like Non-Canonical Notch Ligand 1 gene expression in testis, liver, and humeral muscle tissues of growing lambs

Delta-Like Non-Canonical Notch Ligand 1 (DLK1) is one of the key genes involved in the development of muscle, liver, pancreas, and lung cells; adipocytes production; and the improvement of digestion, growth performance, and meat quality. It has been documented that fennel is effective on increasing the DLK1 gene (DLK1) expression in the testis, liver, and muscle tissues, which may consequently have important implications for sheep production. Hence, the aim of the current investigation was to evaluate the fennel seed powder's effect on DLK1 expression in testis, liver, and humeral muscle tissues in growing lambs. For the purpose of this study, 30 male Kermani sheep were fed with three different group of diets (number of animals in each group was 10), including control (without any fennel seed powder), treatment 1 (with 10 g/kg of dry matter (DM) fennel seed powder), and treatment 2 (with 20 g/kg of DM fennel seed powder) during a 3-month period. Thereafter, total RNA was extracted, cDNA was synthesized, and Real-Time PCR was performed. The addition of fennel seed powder (in the treatment 1 and treatment 2 groups) in the growing lambs diets consequently resulted in greater expression of DLK1 in both the liver and humeral muscle tissues compared to the testis tissue (P < 0.05). Furthermore, the increased DLK1 expression was higher in the tissue of humeral muscle (P < 0.05) in comparison to the other two tissues. As well, the concentration of blood testosterone was greater (P < 0.05) for the animals fed with fennel powder compared to growing lambs fed with the control diet. However, the concentrations of blood liver enzymes, including serum glutamic oxaloacetic transaminase (SGOT) and serum glutamic pyruvic transaminase (SGPT), decreased by the addition of 10 g/kg DM fennel to diets of lambs compared to the control diet (no fennel). Therefore, it can be concluded that using fennel seed powder in the diet of growing lamb by affecting the expression of DLK1, can improve the concentrations of blood testosterone, SGOT, SGPT, and muscle structure (increased mass of muscle and size of muscle fiber).

Molecular Mechanisms of Skeletal Muscle Hypertrophy

Skeletal muscle hypertrophy can be induced by hormones and growth factors acting directly as positive regulators of muscle growth or indirectly by neutralizing negative regulators, and by mechanical signals mediating the effect of resistance exercise. Muscle growth during hypertrophy is controlled at the translational level, through the stimulation of protein synthesis, and at the transcriptional level, through the activation of ribosomal RNAs and muscle-specific genes. mTORC1 has a central role in the regulation of both protein synthesis and ribosomal biogenesis. Several transcription factors and co-activators, including MEF2, SRF, PGC-1α4, and YAP promote the growth of the myofibers. Satellite cell proliferation and fusion is involved in some but not all muscle hypertrophy models.

Haplotype Purging After Relaxation of Selection in Lines of Chickens that Had Undergone Long-Term Selection for High and Low Body Weight

Bi-directional selection for increased and decreased 56-day body weights (BW56) has been applied to two lines of White Plymouth Rock chickens—the Virginia high (HWS) and low (LWS) body weight lines. Correlated responses have been observed, including negative effects on traits related to fitness. Here, we use high and low body weight as proxies for fitness. On a genome-wide level, relaxed lines (HWR, LWR) bred from HWS and LWS purged some genetic variants in the selected lines. Whole-genome re-sequencing was here used to identify individual loci where alleles that accumulated during directional selection were purged when selection was relaxed. In total, 11 loci with significant purging signals were identified, five in the low (LW) and six in the high (HW) body weight lineages. Associations between purged haplotypes in these loci and BW56 were tested in an advanced intercross line (AIL). Two loci with purging signals and haplotype associations to BW56 are particularly interesting for further functional characterization, one locus on chromosome 6 in the LW covering the sour-taste receptor gene PKD2L1, a functional candidate gene for the decreased appetite observed in the LWS and a locus on chromosome 20 in the HW containing a skeletal muscle hypertrophy gene, DNTTIP1.

Analysis of DNA methylation profiles during sheep skeletal muscle development using whole-genome bisulfite sequencing

BACKGROUND

DNA methylation is an epigenetic regulatory form that plays an important role in regulating the gene expression and the tissues development.. However, DNA methylation regulators involved in sheep muscle development remain unclear. To explore the functional importance of genome-scale DNA methylation during sheep muscle growth, this study systematically investigated the genome-wide DNA methylation profiles at key stages of Hu sheep developmental (fetus and adult) using deep whole-genome bisulfite sequencing (WGBS).

RESULTS

Our study found that the expression levels of DNA methyltransferase (DNMT)-related genes were lower in fetal muscle than in the muscle of adults. The methylation levels in the CG context were higher than those in the CHG and CHH contexts, and methylation levels were highest in introns, followed by exons and downstream regions. Subsequently, we identified 48,491, 17, and 135 differentially methylated regions (DMRs) in the CG, CHG, and CHH sequence contexts and 11,522 differentially methylated genes (DMGs). The results of bisulfite sequencing PCR (BSP) correlated well with the WGBS-Seq data. Moreover, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation analysis revealed that some DMGs were involved in regulating skeletal muscle development and fatty acid metabolism. By combining the WGBS-Seq and previous RNA-Seq data, a total of 159 overlap genes were obtained between differentially expressed genes (DEGs) and DMGs (FPKM > 10 and fold change > 4). Finally, we found that 9 DMGs were likely to be involved in muscle growth and metabolism of Hu sheep.

CONCLUSIONS

We systemically studied the global DNA methylation patterns of fetal and adult muscle development in Hu sheep, which provided new insights into a better understanding of the epigenetic regulation of sheep muscle development.

Growth performance and meat characteristics of the first filial Awassi-Rambouillet callipyge ram lambs

Aim:

This study was designed to introduce the callipyge (CLPG) and 50% of Rambouillet sheep genes to improve meat quality and quantity of Awassi (AW) sheep.

Materials and Methods:

The CLPG mutation was introduced into the AW sheep through frozen semen of homozygous Rambouillet rams for the CLPG mutation. Four ram lambs from the first-generation Rambouillet callipyge Awassi (F1-RCA) and five from pure AW were recruited for a fattening trial conducted in individual pens using standard ration, following which ram lambs were slaughtered for carcass and meat evaluation.

Results:

Final body weight, dry matter intake, average daily gain, and feed conversion ratio were significantly higher in F1-RCA than AW. Hot and cold carcass weights and the other carcass cuts’ weights, except for the fat tail, were heavier in F1-RCA than AW. There was no difference in dressing percentage between the two genetic groups (p>0.05). All non-carcass components’ weights, except spleen, kidney, and testis, were higher in F1-RCA. Total lean, total bone, and intermuscular fat weight were greater in F1-RCA, but bone-to-lean ratio was lower in F1-RCA when compared with AW (p<0.01). No differences (p>0.05) were observed in all meat quality parameters for muscle longissimus with the exception of pH, redness color, and tenderness that were lower (p<0.05) in F1-RCA than AW. F1-RCA lambs had larger longissimus muscle area (30.9 vs. 16.9 cm²) and less leg fat depth (11.1 vs. 17.4 mm).

Conclusion:

The implications of this research show the potential of 50% of Rambouillet genes and the CLPG mutation to improve growth and meat characteristics in AW-Rambouillet crosses and can be used further to develop a meat-type AW with improved productivity and muscle mass.