gga-mir-133a-3p Regulates Myoblasts Proliferation and Differentiation by Targeting PRRX1

Regulatory role of lncMD1 in goat skeletal muscle satellite cell differentiation via miR-133a-3p and miR-361-3p targeting

Skeletal muscle satellite cells (SMSCs) are pivotal in skeletal muscle development and are influenced by numerous regulatory factors. This study focuses on the regulatory and functional mechanism roles of lncMD1, a muscle-specific long non-coding RNA, in the proliferation and differentiation of goat SMSCs. Employing in vitro cultured goat SMSCs, this study demonstrated that lncMD1, functions as a decoy for miR-133a-3p and miR-361-3p. This interaction competitively binds these microRNAs to modulate the expression of dynactin subunit 2 (DCTN2) and dynactin subunit 1 (DCTN1), thereby affects SMSCs proliferation and differentiation. These findings enhance the understanding of non-coding RNAs in goat SMSCs growth cycles and offer a theoretical foundation for exploring the molecular processes of goat skeletal muscle myogenic development.

The first embryonic landscape of G-quadruplexes related to myogenesis

BACKGROUND

DNA G-quadruplexes (G4s) represent a distinctive class of non-canonical DNA secondary structures. Despite their recognition as potential therapeutic targets in some cancers, the developmental role of G4 structures remains enigmatic. Mammalian embryonic myogenesis studies are hindered by limitations, prompting the use of chicken embryo-derived myoblasts as a model to explore G4 dynamics. This study aims to reveal the embryonic G4s landscape and elucidate the underlying mechanisms for candidate G4s that influence embryonic myogenesis.

RESULTS

This investigation unveils a significant reduction in G4s abundance during myogenesis. G4s stabilizer pyridostatin impedes embryonic myogenesis, emphasizing the regulatory role of G4s in this process. G4 Cut&Tag sequencing and RNA-seq analyses identify potential G4s and DEGs influencing embryonic myogenesis. Integration of G4 and DEG candidates identifies 32 G4s located in promoter regions capable of modulating gene transcription. WGBS elucidates DNA methylation dynamics during embryonic myogenesis. Coordinating transcriptome data with DNA G4s and DNA methylation profiles constructs a G4-DMR-DEG network, revealing nine interaction pairs. Notably, the NFATC2 promoter region sequence is confirmed to form a G4 structure, reducing promoter mCpG content and upregulating NFATC2 transcriptional activity.

CONCLUSIONS

This comprehensive study unravels the first embryonic genomic G4s landscape, highlighting the regulatory role of NFATC2 G4 in orchestrating transcriptional activity through promoter DNA methylation during myogenesis.

Unraveling the molecular landscape of breast muscle development in domestic Yuzhong pigeons and European meat pigeon: Insights from Iso-seq and RNA-seq analysis

The mechanisms governing gene regulation in domestic Yuzhong pigeon breast muscle development remain largely elusive. Here, we conducted a comparative analysis using Iso-seq and RNA-seq data from domestic Yuzhong pigeons and European meat pigeons to uncover signaling pathways and genes involved in breast muscle development. The Iso-seq data from domestic Yuzhong pigeons yielded 131,377,075 subreads, resulting in 16,587 non-redundant high-quality full-length transcripts post-correction. Furthermore, utilizing pfam, CPC, PLEK, and CPAT, we predicted 5575, 4973, 2333, and 4336 lncRNAs, respectively. Notably, several genes potentially implicated in breast muscle development were identified, including tropomyosin beta chain, myosin regulatory light chain 2, and myosin binding protein C. KEGG enrichment analysis revealed critical signaling pathways in breast muscle development, spanning carbon metabolism, biosynthesis of amino acids, glycolysis/gluconeogenesis, estrogen signaling, PI3K-AKT signaling, protein processing in the endoplasmic reticulum, oxidative phosphorylation, pentose phosphate pathway, fructose and mannose metabolism, and tight junctions. These findings offer insights into the biological processes driving breast muscle development in domestic Yuzhong pigeon, contributing to our understanding of this complex phenomenon.

Transcriptome analysis of mRNA and miRNA in the development of LeiZhou goat muscles

The progression of muscle development is a pivotal aspect of animal ontogenesis, where miRNA and mRNA exert substantial influence as prominent players. It is important to understand the molecular mechanisms involved in skeletal muscle development to enhance the quality and yield of meat produced by Leizhou goats. We employed RNA sequencing (RNA-SEQ) technology to generate miRNA-mRNA profiles in Leizhou goats, capturing their developmental progression at 0, 3, and 6 months of age. A total of 977 mRNAs and 174 miRNAs were found to be differentially expressed based on our analysis. Metabolic pathways, calcium signaling pathways, and amino acid synthesis and metabolism were found to be significantly enriched among the differentially expressed mRNA in the enrichment analysis. Meanwhile, we found that among these differentially expressed mRNA, some may be related to muscle development, such as MYL10, RYR3, and CSRP3. Additionally,, we identified five muscle-specific miRNAs (miR-127-3p, miR-133a-3p, miR-193b-3p, miR-365-3p, and miR-381) that consistently exhibited high expression levels across all three stages. These miRNAs work with their target genes (FHL3, SESN1, PACSIN3, LMCD1) to regulate muscle development. Taken together, our findings suggest that several miRNAs and mRNAs are involved in regulating muscle development and cell growth in goats. By uncovering the molecular mechanisms involved in muscle growth and development, these findings contribute valuable knowledge that can inform breeding strategies aimed at enhancing meat yield and quality in Leizhou goats.

Porcine transient receptor potential channel 1 (TRPC1) regulates muscle growth via the Wnt/β-catenin and Wnt/Ca2+ pathways

Transient receptor potential canonical (TRPC) channels allow the intracellular entry of Ca2+ and play important roles in several physio-pathological processes. In this study, we constructed transgenic mice expressing porcine TRPC1 (Tg-pTRPC1) to verify the effects of TRPC1 on skeletal muscle growth and elucidate the underlying mechanism. Porcine TRPC1 increased the muscle mass, fiber cross-sectional area, and exercise endurance of mice and accelerated muscle repair and regeneration. TRPC1 overexpression enhanced β-catenin expression and promoted myogenesis, which was partly reversed by inhibitors of β-catenin. TRPC1 facilitated the accumulation of intracellular Ca2+ and nuclear translocation of the NFATC2/NFATC2IP complex involved in the Wnt/Ca2+ pathway, promoting muscle growth. Paired related homeobox 1 (Prrx1) promoted the expression of TRPC1, NFATC2, and NFATC2IP that participate in the regulation of muscle growth. Taken together, our findings indicate that porcine TRPC1 promoted by Prrx1 could regulate muscle development through activating the canonical Wnt/β-catenin and non-canonical Wnt/Ca2+ pathways.

MiR-424-5p targets HSP90AA1 to facilitate proliferation and restrain differentiation in skeletal muscle development

MiR-424-5p was found to be a potential regulator in the proliferation, migration, and invasion of various cancer cells. However, the effects and functional mechanism of miR-424-5p in the process of myogenesis are still unclear. Previously, using microRNA (miRNA) sequencing and expression analysis, we discovered that miR-424-5p was expressed differentially in the different skeletal muscle growth periods of Xuhuai goats. We hypothesized that miR-424-5p might play an important role in skeletal muscle myogenesis. Then, we found that the proliferation ability of the mouse myoblast cell (C2C12 myoblast cell line) was significantly augmented, whereas the C2C12 differentiation was repressed after increasing the expression of miR-424-5p. Mechanistically, HSP90AA1 presented a close interrelation with miR-424-5p, which was predicted as a target gene in the progression of skeletal muscle myogenesis, using transcriptome sequencing, dual luciferase reporter gene detection, and qRT-PCR. The silencing of HSP90AA1 obviously increased C2C12 proliferation and diminished differentiation, which is consistent with the ability of miR-424-5p in C2C12. Altogether, our findings indicated the role of miR-424-5p as a novel potential regulator via HSP90AA1 during muscle myogenesis progression.

Transcriptomic Analysis on Pectoral Muscle of European Meat Pigeons and Shiqi Pigeons during Embryonic Development

In avian muscle development, embryonic muscle development determines the number of myofibers after birth. Therefore, in this study, we investigated the phenotypic differences and the molecular mechanism of pectoral muscle development of the European meat pigeon Mimas strain (later called European meat pigeon) and Shiqi pigeon on embryonic day 6 (E6), day 10 (E10), day 14 (E14) and day 1 after birth (P1). The results showed that the myofiber density of the Shiqi pigeon was significantly higher than that of the European meat pigeon on E6, and myofibers with a diameter in the range of 50~100 μm of the Shiqi pigeon on P1 were significantly higher than those of European meat pigeon. A total of 204 differential expressed genes (DEGs) were obtained from RNA-seq analysis in comparison between pigeon breeds at the same stage. DEGs related to muscle development were found to significantly enrich the cellular amino acid catabolism, carboxylic acid catabolism, extracellular matrix receptor interaction, REDOX enzyme activity, calcium signaling pathway, ECM receptor interaction, PPAR signaling pathway and other pathways. Using Cytoscape software to create mutual mapping, we identified 33 candidate genes. RT-qPCR was performed to verify the 8 DEGs selected-DES, MYOD, MYF6, PTGS1, MYF5, MYH1, MSTN and PPARG-and the results were consistent with RNA-seq. This study provides basic data for revealing the distinct embryonic development mechanism of pectoral muscle between European meat pigeons and Shiqi pigeons.

Astragalus polysaccharide promotes sheep satellite cell differentiation by regulating miR-133a through the MAPK/ERK signaling pathway

Astragalus polysaccharide (APS) possesses extensive biological activities, pharmacological effects, and anti-fatigue function. MiR-133a is a specifically expressed miRNA in skeletal muscle that participates in the regulation of myoblast proliferation and differentiation. However, little is known about the role of APS in the development of sheep skeletal muscle. In this study, we aimed to investigate the underlying mechanism of APS and miR-133a on the differentiation of sheep skeletal muscle satellite cells (SMSCs) and the regulatory relationship between APS and miR-133a. The results suggested that APS plays a positive regulatory role in the proliferation and differentiation of sheep SMSCs. Moreover, miR-133a significantly promotes SMSC differentiation and the activity of the MAPK/ERK signaling pathway. Importantly, we found that APS function requires the mediation of miR-133a in the differentiation of sheep SMSCs. Taken together, our results indicate that APS accelerates SMSC differentiation by regulating miR-133a via the MAPK/ERK signaling pathway in sheep.

Isolation, characterization, proteome, miRNAome, and the embryotrophic effects of chicken egg yolk nanovesicles (vitellovesicles)

Egg yolk constitutes about a third of the structure of the chicken egg however, the molecular structure and physiological effects of egg yolk-derived lipid membranous vesicles are not clearly understood. In this study, for the first record, the egg yolk nanovesicles (vitellovesicles, VVs) were isolated, characterized, and used as a supplement for porcine embryo culture. Yolks of ten freshly oviposited eggs were filtered and ultracentrifuged at 100,000 × g for 3 h to obtain a pellet. Cryogenic transmission electron microscopy and nanoparticle tracking analysis of the pellet revealed bilipid membranous vesicles. Protein contents of the pellet were analyzed using tandem mass spectrometry and the miRNA content was also profiled through BGISEQ-500 sequencer. VVs were supplemented with the in vitro culture medium of day-7 hatched parthenogenetic blastocysts. After 2 days of blastocyst culture, the embryonic cell count was increased in VVs supplemented embryos in comparison to the non-supplemented embryos. TUNEL assay showed that apoptotic cells were increased in control groups when compared with the VVs supplemented group. Reduced glutathione was increased by 2.5 folds in the VVs supplemented group while reactive oxygen species were increased by 5.3 folds in control groups. Quantitative PCR analysis showed that VVs significantly increased the expression of lipid metabolism-associated genes (monoglyceride lipase and lipase E), anti-apoptotic gene (BCL2), and superoxide dismutase, while significantly reducing apoptotic gene (BAX). Culturing embryos on Matrigel basement membrane matrix indicated that VVs significantly enhanced embryo attachment and embryonic stem cell outgrowths compared to the non-supplemented group. This considers the first report to characterize the molecular bioactive cargo contents of egg yolk nanovesicles to show their embryotrophic effect on mammalian embryos. This effect might be attributed to the protein and miRNA cargo contents of VVs. VVs can be used for the formulation of in vitro culture medium for mammalian embryos including humans.

MiR-133a-3p/Sirt1 epigenetic programming mediates hypercholesterolemia susceptibility in female offspring induced by prenatal dexamethasone exposure

Mounting evidence indicates that adverse intrauterine conditions increase offspring's hypercholesterolemia susceptibility in adulthood. This study aimed to confirm prenatal dexamethasone exposure (PDE)-induced hypercholesterolemia susceptibility in female adult offspring rats, and elucidate its intrauterine programming mechanism. Pregnant Wistar rats were injected with dexamethasone subcutaneously (0, 0.1 and 0.2 mg/kg·d) from gestational day (GD) 9 to 20. Serum and liver of the female offspring were collected at GD21 and postnatal week (PW) 12 and 28. PDE offspring showed elevated serum total cholesterol (TCH) levels and a cholesterol phenotype of high cardiovascular disease risk at PW12 and PW28. The histone acetylation levels of 3-hydroxy-3-methylglutaryl-coenzyme A reductase (Hmgcr) and its expression were consistently increased in the PDE offspring both in utero and after birth. Moreover, PDE promoted glucocorticoid receptor (GR) nuclear translocation and miR-133a-3p expression and inhibited sirtuin-1 (Sirt1) expression in the fetal liver. In vitro, dexamethasone increased intracellular and supernatant TCH levels and miR-133a-3p expression, decreased SIRT1 expression, and promoted HMGCR histone acetylation and expression in bone marrow mesenchymal stem cells (BMSCs) hepatoid differentiated cells and HepG2 cell line. GR siRNA, miR-133a-3p inhibitor or SIRT1 overexpression reversed dexamethasone-induced downstream molecular and phenotypic changes. Furthermore, elevated TCH levels in umbilical cord blood and increased HMGCR expression in peripheral blood mononuclear cells (PBMCs) were observed in human female neonates who had received dexamethasone treatment during pregnancy. In conclusion, PDE can cause persistent enhancement of hepatic cholesterol synthesis function before and after birth through GR/miR-133a-3p/Sirt1 pathway, eventually leading to increased hypercholesterolemia susceptibility in female offspring rats.

Identification of miRNA-mRNA Networks Associated with Pigeon Skeletal Muscle Development and Growth

The growth and development of skeletal muscle determine the productivity of pigeon meat production, and miRNA plays an important role in the growth and development of this type of muscle. However, there are few reports regarding miRNA regulating the growth and development of skeletal muscle in pigeons. To explore the function of miRNA in regulating the growth and development of pigeon skeletal muscle, we used RNA sequencing technology to study the transcriptome of pigeons at two embryonic stages (E8 and E13) and two growth stages (D1 and D10). A total of 32,527 mRNAs were identified in pigeon skeletal muscles, including 14,378 novel mRNAs and 18,149 known mRNAs. A total of 2362 miRNAs were identified, including 1758 known miRNAs and 624 novel miRNAs. In total, 839 differentially expressed miRNAs (DEmiRNAs) and 11,311 differentially expressed mRNAs (DEGs) were identified. STEM clustering analysis assigned DEmiRNAs to 20 profiles, of which 7 were significantly enriched (p-value < 0.05). These seven significantly enriched profiles can be classified into two categories. The first category represents DEmiRNAs continuously downregulated from the developmental stage to the growth stage of pigeon skeletal muscle, and the second category represents DEmiRNAs with low expression at the development and early growth stage, and significant upregulation at the high growth stage. We then constructed an miRNA−mRNA network based on target relationships between DEmiRNAs and DEGs belonging to the seven significantly enriched profiles. Based on the connectivity degree, 20 hub miRNAs responsible for pigeon skeletal muscle development and growth were identified, including cli-miR-20b-5p, miR-130-y, cli-miR-106-5p, cli-miR-181b-5p, miR-1-z, cli-miR-1a-3p, miR-23-y, cli-miR-30d-5p, miR-1-y, etc. The hub miRNAs involved in the miRNA−mRNA regulatory networks and their expression patterns during the development and growth of pigeon skeletal muscle were visualized. GO and KEGG enrichment analysis found potential biological processes and pathways related to muscle growth and development. Our findings expand the knowledge of miRNA expression in pigeons and provide a database for further investigation of the miRNA−mRNA regulatory mechanism underlying pigeon skeletal muscle development and growth.

A missense mutation in ISPD contributes to maintain muscle fiber stability

Background

Results

Conclusion

LncR-133a Suppresses Myoblast Differentiation by Sponging miR-133a-3p to Activate the FGFR1/ERK1/2 Signaling Pathway in Goats

Long noncoding RNAs (lncRNAs) are involved in a variety of biological processes and illnesses. While a considerable number of lncRNAs have been discovered in skeletal muscle to far, their role and underlying processes during myogenesis remain mostly unclear. In this study, we described a new functional lncRNA named lncR-133a. Gene overexpression and interference studies in goat skeletal muscle satellite cells (MuSCs) were used to establish its function. The molecular mechanism by which lncR-133a governs muscle differentiation was elucidated primarily using quantitative real-time PCR (qRT-PCR), Western blotting, dual-luciferase activity assays, RNA immunoprecipitation, biotin-labeled probe, and RNA fluorescence in situ hybridization analyses. LncR-133a was found to be substantially expressed in longissimus thoracis et lumborum muscle, and its expression levels changed during MuSC differentiation in goats. We validated that lncR-133a suppresses MuSC differentiation in vitro. Dual-luciferase reporter screening, Argonaute 2 (AGO2) RNA immunoprecipitation assays, biotin-labeled lncR-133a capture, and fluorescence in situ hybridization showed that lncR-133a interacted with miR-133a-3p. Additionally, miR-133a-3p facilitated MuSC differentiation, but lncR-133a reversed this effect. The luciferase reporter assay and functional analyses established that miR-133a-3p directly targets fibroblast growth factor receptor 1 (FGFR1). Moreover, lncR-133a directly reduced miR-133a-3p’s capacity to suppress FGFR1 expression, and positively regulated the phosphorylation of extracellular signal-regulated kinase 1/2 (ERK1/2). In summary, our results suggested that lncR-133a suppresses goat muscle differentiation by targeting miR-133a-3p and activating FGFR1/ERK1/2 signaling pathway.

Integrated Analysis Reveals a lncRNA-miRNA-mRNA Network Associated with Pigeon Skeletal Muscle Development

Growing evidence has demonstrated the emerging role of long non-coding RNA as competitive endogenous RNA (ceRNA) in regulating skeletal muscle development. However, the mechanism of ceRNA regulated by lncRNA in pigeon skeletal muscle development remains unclear. To reveal the function and regulatory mechanisms of lncRNA, we first analyzed the expression profiles of lncRNA, microRNA (miRNA), and mRNA during the development of pigeon skeletal muscle using high-throughput sequencing. We then constructed a lncRNA-miRNA-mRNA ceRNA network based on differentially expressed (DE) lncRNAs, miRNAs, and mRNAs according to the ceRNA hypothesis. Functional enrichment and short time-series expression miner (STEM) analysis were performed to explore the function of the ceRNA network. Hub lncRNA-miRNA-mRNA interactions were identified by connectivity degree and validated using dual-luciferase activity assay. The results showed that a total of 1625 DE lncRNAs, 11,311 DE mRNAs, and 573 DE miRNAs were identified. A ceRNA network containing 9120 lncRNA-miRNA-mRNA interactions was constructed. STEM analysis indicated that the function of the lncRNA-associated ceRNA network might be developmental specific. Functional enrichment analysis identified potential pathways regulating pigeon skeletal muscle development, such as cell cycle and MAPK signaling. Based on the connectivity degree, lncRNAs TCONS_00066712, TCONS_00026594, TCONS_00001557, TCONS_00001553, and TCONS_00003307 were identified as hub genes in the ceRNA network. lncRNA TCONS_00026594 might regulate the FSHD region gene 1 (FRG1)/ SRC proto-oncogene, non-receptor tyrosine kinase (SRC) by sponge adsorption of cli-miR-1a-3p to affect the development of pigeon skeletal muscle. Our findings provide a data basis for in-depth elucidation of the lncRNA-associated ceRNA mechanism underlying pigeon skeletal muscle development.

The Identification of Alternative Polyadenylation in Stomach Adenocarcinomas Using the Genotype-Tissue Expression Project and the Cancer Genome Atlas- Stomach Adenocarcinoma Profiles

Objective

Alternative polyadenylation (APA) is a common mechanism that is present in most human genes and determines the length of the messenger ribonucleic acid (mRNA) three prime untranslated region (3ʹ-UTR), which can give rise to changes in mRNA stability and localization. However, little is known about the specific changes related to APA in stomach adenocarcinomas (STADs).

Methods

We integrated RNA sequencing data from The Cancer Genome Atlas and Genotype-Tissue Expression project to comprehensively analyze APA events in 289 cases of STAD.

Results

Our results showed that APA events were widespread in patients with STAD and were rich in genes related to known STAD pathways. The APA events result in the loss of tumor-suppressing micro-ribonucleic acid (miRNA) binding sites and increased heterogeneity in the length of the 3ʹ-UTR altered genes. Survival analysis revealed that specific subsets of 3ʹ-UTR-altered genes independently characterized a poor prognostic cohort among patients with STAD, thereby indicating the potential of APA as a new prognostic biomarker.

Conclusion

Our single-cancer analysis showed that by losing miRNA regulation, APA can become a driving factor for regulating the expression of oncogenic genes in STAD and promote its development. Our research revealed that APA events regulated STAD genes that were functionally related, thereby providing a new approach for gaining a better understanding of the progress of STADs and a means for identifying new drug targets as avenues of treatment.

Identification of IGF2BP1-related lncRNA-miRNA-mRNA network in goat skeletal muscle satellite cells

Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) plays essential roles in the proliferation of skeletal muscle satellite cells (MuSCs). Increasing evidence has shown that IGF2BP1 regulates the expression of noncoding RNAs and mRNAs. However, the related molecular network remains to be fully understood. Therefore, we performed RNA sequencing and analyzed the microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and mRNAs differentially expressed in goat MuSCs treated with IGF2BP1 overexpressing and empty vectors. A total of 36 miRNAs, 59 lncRNAs, and 44 mRNAs were differentially expressed caused by IGF2BP1. Expectedly, they were enriched in muscle development-related Rap1, PI3K-AKT, and FoxO signaling pathways. Finally, we constructed a lncRNA-miRNA-mRNA interaction network containing 30 lncRNAs, 15 miRNAs, and 34 mRNAs, in which several miRNAs, including miR-133a-3p, miR-204-5p, miR-125a-3p, miR-145-3p, and miR-423-5p, relate with cell growth and participate in muscle development. Overall, we constructed an IGF2BP1-related network, which provides new insight into the myogenic proliferation of goat.

Male-Biased gga-miR-2954 Regulates Myoblast Proliferation and Differentiation of Chicken Embryos by Targeting YY1

Previous studies have shown that gga-miR-2954 was highly expressed in the gonads and other tissues of male chickens, including muscle tissue. Yin Yang1 (YY1), which has functions in mammalian skeletal muscle development, was predicted to be a target gene of gga-miR-2954. The purpose of this study was to investigate whether gga-miR-2954 plays a role in skeletal muscle development by targeting YY1, and evaluate its function in the sexual dimorphism development of chicken muscle. Here, all the temporal and spatial expression profiles in chicken embryonic muscles showed that gga-miR-2954 is highly expressed in males and mainly localized in cytoplasm. Gga-miR-2954 exhibited upregulated expression of in vitro myoblast differentiation stages. Next, through the overexpression and loss-of-function experiments performed in chicken primary myoblasts, we found that gga-miR-2954 inhibited myoblast proliferation but promoted differentiation. During myogenesis, gga-miR-2954 could suppress the expression of YY1, which promoted myoblast proliferation and inhibited the process of myoblast cell differentiation into multinucleated myotubes. Overall, these findings reveal a novel role of gga-miR-2954 in skeletal muscle development through its function of the myoblast proliferation and differentiation by suppressing the expression of YY1. Moreover, gga-miR-2954 may contribute to the sex difference in chicken muscle development.

miR-7 regulates the apoptosis of chicken primary myoblasts through the KLF4 gene

1. MicroRNAs (miRNAs) play a vital role in the proliferation, differentiation, and apoptosis of myoblasts. However, the effect of miR-7 on the apoptosis of chicken primary myoblasts (CPMs) and its mechanism is still unclear.2. In this study, the expression of apoptosis marker genes (RAF1, Caspase3, Caspase9, Cytc, Fas) in CPMs was significantly increased after transfection of miR-7 mimic. The expression of the apoptosis marker genes in CPMs was significantly reduced after transfection with miR-7 inhibitor. Flow cytometry showed that the late apoptosis rate of the mimic group was significantly higher than the negative control (NC). The viable cells of the mimic group were significantly lower than the NC. In contrast, inhibition of miR-7 had the opposite effect.3. The dual-luciferase assay showed that the KLF4 was a target gene of miR-7. The rescue experiment showed that the KLF4 gene could attenuate the effect of miR-7 on the expression of apoptosis marker genes in CPMs.4. Determination of the function the KLF4 gene showed that the expression of the apoptosis marker genes in CPMs decreased significantly compared with the NC after its overexpression. Inhibition of KLF4 gene had the opposite effect. Flow cytometry showed that overexpression of the KLF4 gene inhibited early apoptosis of myoblasts (P ≤ 0.01), while interference with the KLF4 gene could promote early apoptosis of myoblasts (P ≤ 0.001).5. The results demonstrated, for the first time, that miR-7 promotes apoptosis in chicken primary myoblasts by regulating the expression of the KLF4 gene.

Transcriptome Analysis of Differentially Expressed mRNA Related to Pigeon Muscle Development

The mechanisms behind the gene expression and regulation that modulate the development and growth of pigeon skeletal muscle remain largely unknown. In this study, we performed gene expression analysis on skeletal muscle samples at different developmental and growth stages using RNA sequencing (RNA-Seq). The differentially expressed genes (DEGs) were identified using edgeR software. Weighted gene co-expression network analysis (WGCNA) was used to identify the gene modules related to the growth and development of pigeon skeletal muscle based on DEGs. A total of 11,311 DEGs were identified. WGCNA aggregated 11,311 DEGs into 12 modules. Black and brown modules were significantly correlated with the 1st and 10th day of skeletal muscle growth, while turquoise and cyan modules were significantly correlated with the 8th and 13th days of skeletal muscle embryonic development. Four mRNA-mRNA regulatory networks corresponding to the four significant modules were constructed and visualised using Cytoscape software. Twenty candidate mRNAs were identified based on their connectivity degrees in the networks, including Abca8b, TCONS-00004461, VWF, OGDH, TGIF1, DKK3, Gfpt1 and RFC5, etc. A KEGG pathway enrichment analysis showed that many pathways were related to the growth and development of pigeon skeletal muscle, including PI3K/AKT/mTOR, AMPK, FAK, and thyroid hormone pathways. Five differentially expressed genes (LAST2, MYPN, DKK3, B4GALT6 and OGDH) in the network were selected, and their expression patterns were quantified by qRT-PCR. The results were consistent with our sequencing results. These findings could enhance our understanding of the gene expression and regulation in the development and growth of pigeon muscle.

Identification and expression pattern analysis of miRNAs in pectoral muscle during pigeon (Columba livia) development

MicroRNAs (miRNAs) are a group of crucial regulators in the process of animal growth and development. However, little is known about the expression and function of miRNAs in pigeon muscles. To identify the miRNAs participating in the rapid development of pigeon pectoral muscles and quantitate their expression levels of pectoral muscles in different age stages, we performed miRNA transcriptome analysis in pigeon pectoral muscles by sequencing small RNAs over three different age stages (1-day old, 28 days old, and 2 years old). Dual-luciferase reporter assay was applied to validate the interaction between miRNA and its target gene. We identified 304 known miRNAs, 201 conserved miRNAs, and 86 novel miRNAs in pigeon pectoral muscles. 189 differentially expressed (DE) miRNAs were screened out during pigeon development. A short time-series expression miner (STEM) analysis indicated 89 DE miRNAs were significantly clustered in a progressively decreasing expression profile, and mainly enriched in biosynthesis-related GO categories and signaling pathways for MAPK and TGF-β. Dual-luciferase reporter assay indicated that a progressively down-regulated miRNA (miR-20b-5p) could directly target Krüppel-like factor 3 (KLF3) gene. To sum-up, our data expand the repertoire of pigeon miRNAs and enhance understanding of the mechanisms underlying rapid development in squabs.

A pig BodyMap transcriptome reveals diverse tissue physiologies and evolutionary dynamics of transcription

A comprehensive transcriptomic survey of pigs can provide a mechanistic understanding of tissue specialization processes underlying economically valuable traits and accelerate their use as a biomedical model. Here we characterize four transcript types (lncRNAs, TUCPs, miRNAs, and circRNAs) and protein-coding genes in 31 adult pig tissues and two cell lines. We uncover the transcriptomic variability among 47 skeletal muscles, and six adipose depots linked to their different origins, metabolism, cell composition, physical activity, and mitochondrial pathways. We perform comparative analysis of the transcriptomes of seven tissues from pigs and nine other vertebrates to reveal that evolutionary divergence in transcription potentially contributes to lineage-specific biology. Long-range promoter–enhancer interaction analysis in subcutaneous adipose tissues across species suggests evolutionarily stable transcription patterns likely attributable to redundant enhancers buffering gene expression patterns against perturbations, thereby conferring robustness during speciation. This study can facilitate adoption of the pig as a biomedical model for human biology and disease and uncovers the molecular bases of valuable traits.

A comprehensive transcriptomic survey of the pig could enable mechanistic understanding of tissue specialization and accelerate its use as a biomedical model. Here the authors characterize four distinct transcript types in 31 adult pig tissues to dissect their distinct structural and transcriptional features and uncover transcriptomic variability related to tissue physiology.

A Variant Noncoding Region Regulates Prrx1 and Predisposes to Atrial Arrhythmias

[Figure: see text].

Characterization of microRNAs during Embryonic Skeletal Muscle Development in the Shan Ma Duck

Simple Summary

It is of great commercial interest to elucidate the genetic mechanisms associated with skeletal muscle development in the duck. In this study, we performed high throughput microRNA (miRNA) sequencing to identify the candidate miRNAs during two developmental stages of duck embryonic breast muscle. We detected 1091 miRNAs and 109 of them were differentially expressed between embryonic day 13 (E13) and E19. We also predicted the target genes of the differentially expressed miRNAs and subsequently analyzed the enriched gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathways, and finally constructed a protein–protein interaction (PPI) network with the target genes. Luciferase reporter assay showed that the growth-related genes, Fibroblast growth factor receptor like 1 (FGFRL1) and Insulin like growth factor 2 mRNA binding protein 1 (IGF2BP1), were target genes of miR-214-5p. These results can supplement the duck miRNA database and provide several candidate miRNAs for future studies on the regulation of embryonic skeletal muscle development.

Abstract

Poultry skeletal muscle provides high quality protein for humans. Study of the genetic mechanisms during duck skeletal muscle development contribute to future duck breeding and meat production. In the current study, three breast muscle samples from Shan Ma ducks at embryonic day 13 (E13) and E19 were collected, respectively. We detected microRNA (miRNA) expression using high throughput sequencing following bioinformatic analysis. qRT-PCR validated the reliability of sequencing results. We also identified target prediction results using the luciferase reporter assay. A total of 812 known miRNAs and 279 novel miRNAs were detected in six samples; as a result, 61 up-regulated and 48 down-regulated differentially expressed miRNAs were identified between E13 and E19 (|log2 fold change| ≥ 1 and p ≤ 0.05). Enrichment analysis showed that target genes of the differentially expressed miRNAs were enriched on many muscle development-related gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, especially mitogen-activated protein kinase (MAPK) signaling pathways. An interaction network was constructed using the target genes of the differentially expressed miRNAs. These results complement the current duck miRNA database and offer several miRNA candidates for future studies of skeletal muscle development in the duck.

Deletion of α-Synuclein in Prrx1-positive cells causes partial loss of function in the central nervous system (CNS) but does not affect ovariectomy induced bone loss

α-Synuclein is a small 140 amino acid polypeptide encoded by the Snca gene that is highly expressed in neural tissue, but it is also found in osteoblasts, erythroblasts, macrophages, and adipose tissue. Previously, using co-expression network analysis we found that Snca was a key regulator of skeletal homeostasis, and its deletion partially prevented bone loss after ovariectomy (OVX). Here we tested the hypothesis that Snca deletion in mesenchymal progenitors using the Prrx1Cre (Prrx1, Paired-related homeobox 1) limb enhancer would protect bone mass after OVX. Prrx1Cre;Snca^fl/fl and littermate controls (Snca^fl/fl) were sham operated or ovariectomized (OVX) at 8 weeks of age and sacrificed at 20 weeks. Independently, eight-week female and male Prrx1Cre;Snca^fl/fl mice and littermate controls were administered a high fat (60% fat) or low fat (10% fat) diet for 15 weeks. Bone loss was not prevented in either genotype after ovariectomy, but the Prrx1Cre;Snca^fl/fl. mice were partially protected from weight gain after OVX and high fat diet (HFD). Serum catecholamine levels were lower in the Prrx1Cre;Snca^fl/fl both on a low fat diet (LFD) and HFD versus fl/fl controls. Importantly, mutant mice exhibited a number of physical and behavioral phenotypes that were associated with conditional deletion of Snca in several brain regions. Cells labeled with Prrx1 were noted throughout the central nervous system (CNS). These data support earlier preliminary reports of Prrx1 expression in neural progenitors, and raise a cautionary note about the evaluation of skeletal and body composition phenotypes when using this Cre driver to study osteoprogenitor development.

MiR-148a-3p Regulates Skeletal Muscle Satellite Cell Differentiation and Apoptosis via the PI3K/AKT Signaling Pathway by Targeting Meox2

As bioinformatic approaches have been developed, it has been demonstrated that microRNAs (miRNAs) are involved in the formation of muscles and play important roles in regulation of muscle cell proliferation and differentiation. Previously, it has been demonstrated that miR-148a-3p is one of the most abundant miRNAs in chicken skeletal muscle. Here, we build on that work and demonstrate that miR-148a-3p is important in the control of differentiation of chicken skeletal muscle satellite cells (SMSCs). Elevated expression of miR-148a-3p significantly promoted differentiation and inhibited apoptosis of SMSCs but did not affect proliferation. Furthermore, it was observed that the mesenchyme homeobox 2 (Meox2) is a target gene of miR-148a-3p and that miR-148a-3p can down-regulate expression of Meox2, which promote differentiation of SMSCs and suppress apoptosis. Furthermore, miR-148a-3p overexpression encouraged activation of the PI3K/AKT signaling pathway, which could be recovered by overexpression of Meox2. Overall, these findings suggest that microRNA-148a-3p is a potent promoter of myogenesis via direct targeting of Meox2 and increase of the PI3K/AKT signaling pathway in chicken SMSCs.

Circular RNA circ-FoxO3 Inhibits Myoblast Cells Differentiation

CircRNA is a type of closed circular non-coding RNA formed by reverse splicing and plays an important role in regulating the growth and development of plants and animals. To investigate the function of circ-FoxO3 in mouse myoblast cells' (C2C12) differentiation and proliferation, we used RT-qPCR to detect the expression level of circ-FoxO3 in mouse myoblast cells at different densities and different differentiation stages, and the specific interference fragment was used to inhibit the expression level of circ-FoxO3 in myoblast cells to observe its effect on myoblast cells proliferation and differentiation. We found that the expression level of circ-FoxO3 in myoblast cells increased with the prolongation of myoblast cells differentiation time, and its expression level decreased with the proliferation of myoblast cells. At the same time, we found that the differentiation ability of the cells was significantly increased (p < 0.05), but the cell proliferation was unchanged (p > 0.05) after inhibiting the expression of circ-FoxO3 in myoblast cells. Combining the results of bioinformatics analysis and the dual luciferase reporter experiment, we found that circ-FoxO3 is a sponge of miR-138-5p, which regulates muscle differentiation. Our study shows that circ-FoxO3 can inhibit the differentiation of C2C12 myoblast cells and lay a scientific foundation for further study of skeletal muscle development at circRNA levels.

Circular RNA circHIPK3 Promotes the Proliferation and Differentiation of Chicken Myoblast Cells by Sponging miR-30a-3p

Circular RNAs and microRNAs widely exist in various species and play crucial roles in multiple biological processes. It is essential to study their roles in myogenesis. In our previous sequencing data, both miR-30a-3p and circular HIPK3 (circHIPK3) RNA, which are produced by the third exon of the HIPK3 gene, were differentially expressed among chicken skeletal muscles at 11 embryo age (E11), 16 embryo age (E16), and 1-day post-hatch (P1). Here, we investigated their potential roles in myogenesis. Proliferation experiment showed that miR-30a-3p could inhibit the proliferation of myoblast. Through dual-luciferase assay and Myosin heavy chain (MYHC) immunofluorescence, we found that miR-30a-3p could inhibit the differentiation of myoblast by binding to Myocyte Enhancer Factor 2 C (MEF2C), which could promote the differentiation of myoblast. Then, we found that circHIPK3 could act as a sponge of miR-30a-3p and exerted a counteractive effect of miR-30a-3p by promoting the proliferation and differentiation of myoblasts. Taking together, our data suggested that circHIPK3 could promote the chicken embryonic skeletal muscle development by sponging miR-30a-3p.