Long noncoding RNA ZFP36L2-AS functions as a metabolic modulator to regulate muscle development

Identification of deleterious non-synonymous single nucleotide polymorphisms in the mRNA decay activator ZFP36L2

More than 4,000 single nucleotide polymorphisms (SNP) variants have been identified in the human ZFP36L2 gene, however only a few have been studied in the context of protein function. The tandem zinc finger domain of ZFP36L2, an RNA binding protein, is the functional domain that binds to its target mRNAs. This protein/RNA interaction triggers mRNA degradation, controlling gene expression. We identified 32 non-synonymous SNPs (nsSNPs) in the tandem zinc finger domain of ZFP36L2 that could have possible deleterious impacts in humans. Using different bioinformatic strategies, we prioritized five among these 32 nsSNPs, namely rs375096815, rs1183688047, rs1214015428, rs1215671792 and rs920398592 to be validated. When we experimentally tested the functionality of these protein variants using gel shift assays, all five (Y154H, R160W, R184C, G204D, and C206F) resulted in a dramatic reduction in RNA binding compared to the WT protein. To understand the mechanistic effect of these variants on the protein/RNA interaction, we employed DUET, DynaMut and PyMOL to investigate structural changes in the protein. Additionally, we conducted Molecular Docking and Molecular Dynamics Simulations to fine tune the active behaviour of this biomolecular system at an atomic level. Our results propose atomic explanations for the impact of each of these five genetic variants identified.

Functions and Therapeutic Potentials of Long Noncoding RNA in Skeletal Muscle Atrophy and Dystrophy

Skeletal muscle is the most abundant tissue in the human body and is responsible for movement, metabolism, energy production and longevity. Muscle atrophy is a frequent complication of several diseases and occurs when protein degradation exceeds protein synthesis. Genetics, ageing, nerve injury, weightlessness, cancer, chronic diseases, the accumulation of metabolic byproducts and other stimuli can lead to muscle atrophy. Muscular dystrophy is a neuromuscular disorder, part of which is caused by the deficiency of dystrophin protein and is mostly related to genetics. Muscle atrophy and muscular dystrophy are accompanied by dynamic changes in transcriptomic, translational and epigenetic regulation. Multiple signalling pathways, such as the transforming growth factor-β (TGF-β) signalling pathway, the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT)/mechanistic target of rapamycin (mTOR) pathway, inflammatory signalling pathways, neuromechanical signalling pathways, endoplasmic reticulum stress and glucocorticoids signalling pathways, regulate muscle atrophy. A large number of long noncoding RNAs (lncRNAs) have been found to be abnormally expressed in atrophic muscles and dystrophic muscles and regulate the balance of muscle protein synthesis and degradation or dystrophin protein expression. These lncRNAs may serve as potential targets for treating muscle atrophy and muscular dystrophy. In this review, we summarized the known lncRNAs related to muscular dystrophy and muscle atrophy induced by denervation, ageing, weightlessness, cachexia and abnormal myogenesis, along with their molecular mechanisms. Finally, we explored the potential of using these lncRNAs as therapeutic targets for muscle atrophy and muscular dystrophy, including the methods of discovery and clinical application prospects for functional lncRNAs.

Non-Coding RNAs in Regulating Fat Deposition in Farm Animals

Fat deposition represents a crucial feature in the expenditure of physical energy and affects the meat quality of farm animals. It is regulated by multiple genes and regulators. Of them, non-coding RNAs (ncRNAs) play a critical role in modulating the fat deposition process. As well as being an important protein source, farm animals can be used as medical models, so many researchers worldwide have explored their mechanism of fat deposition. This article summarizes the transcription factors, regulatory genes, and signaling pathways involved in the molecular regulation process of fat deposition; outlines the progress of researching the roles of microRNAs (miRNAs), long ncRNAs (lncRNAs), and circular RNAs (circRNAs) in fat deposition in common farm animals including pigs, cattle, sheep, ducks, and chickens; and identifies scientific problems in the field that must be further investigated. It has been demonstrated that ncRNAs play a critical role in regulating the fat deposition process and have great potential in improving meat quality traits.

Multi-Omics Insights into Regulatory Mechanisms Underlying Differential Deposition of Intramuscular and Abdominal Fat in Chickens

Excessive abdominal fat deposition in chickens disadvantages feed conversion, meat production, and reproductive performance. Intramuscular fat contributes to meat texture, tenderness, and flavor, serving as a vital indicator of overall meat quality. Therefore, a comprehensive analysis of the regulatory mechanisms governing differential deposition of abdominal versus intramuscular fat is essential in breeding higher-quality chickens with ideal fat distribution. This review systematically summarizes the regulatory mechanisms underlying intramuscular and abdominal fat traits at chromatin, genomic, transcriptional, post-transcriptional, translational, and epigenetic-modification scales. Additionally, we summarize the role of non-coding RNAs and protein-coding genes in governing intramuscular and abdominal fat deposition. These insights provide a valuable theoretical foundation for the genetic engineering of high-quality and high-yielding chicken breeds.

Plumbagin alleviates muscle atrophy in female mice through inhibiting the DANCR/NF-κB axis

BACKGROUND

Muscle atrophy is a condition of the skeletal muscular system closely related to inflammation and significantly affects a person's quality of life and physical activity. It is characterized primarily by the progressive loss of muscle mass, strength, and function. Plumbagin (PB), the main bioactive component of the traditional Chinese medicine Plumbago zeylanica L., has bFeen shown to treat various inflammatory diseases, such as osteoporosis, osteoarthritis, and sepsis. Furthermore, many biological processes, including inflammation, involve differentiation antagonistic nonprotein-coding RNA (DANCR). However, their role and clinical importance in myogenesis and amyotrophy are not well understood.

PURPOSE

This study aimed to explore the role of DANCR and the inflammatory response in the anti-muscle atrophy effects of PB.

METHODS

The expression of DANCR in muscle atrophic mice and during myogenic differentiation was examined using quantitative reverse transcription PCR (RT‒qPCR). The mechanism of DANCR in muscle atrophy was confirmed through gene knockdown, RNA sequencing (RNA-seq), RNA pull-down, RNA immunoprecipitation (RIP), immunofluorescence (IF), and luciferase reporter gene assays. Bioinformatics was utilized to investigate the mechanism by which PB treatment affects muscle atrophy. The relationship between PB and DANCR was verified by surface plasmon resonance (SPR) and RT‒qPCR. Additionally, the role of PB in muscle atrophy was explored through its control of DANCR-mediated regulation of the NF-κB pathway. Finally, the effect of PB on the myogenic differentiation of human skeletal muscle cells (HsKMCs) was investigated.

RESULTS

DANCR expression was upregulated in the muscle tissues of mice with muscle atrophy and downregulated during myogenic differentiation. Knockout of DANCR promoted myogenic differentiation and significantly alleviated the loss of muscle mass, strength, and function in mice with muscle atrophy. The primary mechanism involved DANCR directly binding to the p65 protein to regulate NF-κB pathway activity. Experiments revealed that PB could target the degradation of DANCR, reduce the nuclear entry of p65, and inhibit the activation of the NF-κB pathway. Consequently, PB significantly inhibited myotube atrophy and the inflammatory response in HsKMCs and promoted their myogenic differentiation by regulating the NF-κB pathway.

CONCLUSIONS

Our results suggest that PB regulates myogenesis and prevents amyotrophy by targeting the degradation of DANCR and inhibiting the activation of the NF-κB pathway. This study reveals the crucial role of DANCR in maintaining muscle physiology during muscle atrophy and identifies PB as an effective drug that can target DANCR degradation to alleviate muscle atrophy.

Signaling pathways and regulatory networks in quail skeletal muscle development: insights from whole transcriptome sequencing

Quail, as an advantageous avian model organism due to its compact size and short reproductive cycle, holds substantial potential for enhancing our understanding of skeletal muscle development. The quantity of skeletal muscle represents a vital economic trait in poultry production. Unraveling the molecular mechanisms governing quail skeletal muscle development is of paramount importance for optimizing meat and egg yield through selective breeding programs. However, a comprehensive characterization of the regulatory dynamics and molecular control underpinning quail skeletal muscle development remains elusive. In this study, through the application of HE staining on quail leg muscle sections, coupled with preceding fluorescence quantification PCR of markers indicative of skeletal muscle differentiation, we have delineated embryonic day 9 (E9) and embryonic day 14 (E14) as the start and ending points, respectively, of quail skeletal muscle differentiation. Then, we employed whole transcriptome sequencing to investigate the temporal expression profiles of leg muscles in quail embryos at the initiation of differentiation (E9) and upon completion of differentiation (E14). Our analysis revealed the expression patterns of 12,012 genes, 625 lncRNAs, 14,457 circRNAs, and 969 miRNAs in quail skeletal muscle samples. Differential expression analysis between the E14 and E9 groups uncovered 3,479 differentially expressed mRNAs, 124 lncRNAs, 292 circRNAs, and 154 miRNAs. Furthermore, enrichment analysis highlighted the heightened activity of signaling pathways related to skeletal muscle metabolism and intermuscular fat formation, such as the ECM-receptor interaction, focal adhesion, and PPAR signaling pathway during E14 skeletal muscle development. Conversely, the E9 stage exhibited a prevalence of pathways associated with myoblast proliferation, exemplified by cell cycle processes. Additionally, we constructed regulatory networks encompassing lncRNA‒mRNA, miRNA‒mRNA, lncRNA‒miRNA-mRNA, and circRNA-miRNA‒mRNA interactions, thus shedding light on their putative roles within quail skeletal muscle. Collectively, our findings illuminate the gene and non-coding RNA expression characteristics during quail skeletal muscle development, serving as a foundation for future investigations into the regulatory mechanisms governing non-coding RNA and quail skeletal muscle development in poultry production.

Synthesis, Herbicidal Activity, and Molecular Mode of Action Evaluation of Novel Aryloxyphenoxypropionate/Amide Derivatives Containing a Quinazolinone Moiety

To develop aryloxyphenoxypropionate herbicides with a novel structure and improved activity, a total of 39 aryloxyphenoxypropionate/amide derivatives containing quinazolinone moiety were synthesized and further bioevaluated. The bioassay results in the greenhouse showed that most of the target compounds had good herbicidal activity under postemergence conditions, of which, QPP-I-6 displayed excellent herbicidal activity against Echinochloa crusgalli, Digitaria sanguinalis, Spartina alterniflora, Eleusine indica, and Pennisetum alopecuroides with inhibition rates >90% at a dosage of 187.5 g ha-1. More importantly, QPP-I-6 displayed higher crop safety to Gossypium hirsutum, Glycine max, and Arachis hypogaea than the commercial herbicide quizalofop-p-ethyl. Studying the molecular mode of action by phenotypic observation, membrane permeability evaluation, transcriptomic analysis, and in vivo ACCase activity evaluation reveals that QPP-I-6 is a novel ACCase inhibitor. The present work demonstrates that QPP-I-6 can serve as a lead compound for further developing novel ACCase-inhibiting herbicides.

ACETYL-COA PRODUCTION BY OCTANOIC ACID ALLEVIATES ACUTE COMPARTMENT SYNDROME-INDUCED SKELETAL MUSCLE INJURY THROUGH REGULATING MITOPHAGY

ABSTRACT

Background: Treatment of acute compartment syndrome (ACS)-induced skeletal muscle injury remains a challenge. Previous studies have shown that octanoic acid is a promising treatment for ACS owing to its potential ability to regulate metabolic/epigenetic pathways in ischemic injury. The present study was designed to investigate the efficacy and underlying mechanism of octanoic acid in ACS-induced skeletal muscle injury. Methods: In this study, we established a saline infusion ACS rat model. Subsequently, we assessed the protective effects of sodium octanoate (NaO, sodium salt of octanoic acid) on ACS-induced skeletal muscle injury. Afterward, the level of acetyl-coenzyme A and histone acetylation in the skeletal muscle tissue were quantified. Moreover, we investigated the activation of the AMP-activated protein kinas pathway and the occurrence of mitophagy in the skeletal muscle tissue. Lastly, we scrutinized the expression of proteins associated with mitochondrial dynamics in the skeletal muscle tissue. Results: The administration of NaO attenuated muscle inflammation, alleviating oxidative stress and muscle edema. Moreover, NaO treatment enhanced muscle blood perfusion, leading to the inhibition of apoptosis-related skeletal muscle cell death after ACS. In addition, NaO demonstrated the ability to halt skeletal muscle fibrosis and enhance the functional recovery of muscle post-ACS. Further analysis indicates that NaO treatment increases the acetyl-CoA level in muscle and the process of histone acetylation by acetyl-CoA. Lastly, we found NaO treatment exerts a stimulatory impact on the activation of the AMPK pathway, thus promoting mitophagy and improving mitochondrial dynamics. Conclusion: Our findings indicate that octanoic acid may ameliorate skeletal muscle injury induced by ACS. Its protective effects may be attributed to the promotion of acetyl-CoA synthesis and histone acetylation within the muscular tissue, as well as its activation of the AMPK-related mitophagy pathway.

MYH1G-AS is a chromatin-associated lncRNA that regulates skeletal muscle development in chicken

BACKGROUND

Skeletal muscle development is pivotal for animal growth and health. Recently, long noncoding RNAs (lncRNAs) were found to interact with chromatin through diverse roles. However, little is known about how lncRNAs act as chromatin-associated RNAs to regulate skeletal muscle development. Here, we aim to investigate the regulation of chromatin-associated RNA (MYH1G-AS) during skeletal muscle development.

METHODS

We provided comprehensive insight into the RNA profile and chromatin accessibility of different myofibers, combining RNA sequencing (RNA-seq) with an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). The dual-luciferase reporter assay and chromatin immunoprecipitation (ChIP) assay were used to analyze the transcriptional regulation mechanism of MYH1G-AS. ALKBH5-mediated MYH1G-AS N6-methyladenosine (m6A) demethylation was assessed by a single-base elongation and ligation-based qPCR amplification method (SELECT) assay. Functions of MYH1G-AS were investigated through a primary myoblast and lentivirus/cholesterol-modified antisense oligonucleotide (ASO)-mediated animal model. To validate the interaction of MYH1G-AS with fibroblast growth factor 18 (FGF18) protein, RNA pull down and an RNA immunoprecipitation (RIP) assay were performed. Specifically, the interaction between FGF18 and SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 (SMARCA5) protein was analyzed by coimmunoprecipitation (Co-IP) and a yeast two-hybrid assay.

RESULTS

A total of 45 differentially expressed (DE) lncRNAs, with DE ATAC-seq peaks in their promoter region, were classified as open chromatin-associated lncRNAs. A skeletal muscle-specific lncRNA (MSTRG.15576.9; MYH1G-AS), which is one of the open chromatin-associated lncRNA, was identified. MYH1G-AS transcription is coordinately regulated by transcription factors (TF) SMAD3 and SP2. Moreover, SP2 represses ALKBH5 transcription to weaken ALKBH5-mediated m6A demethylation of MYH1G-AS, thus destroying MYH1G-AS RNA stability. MYH1G-AS accelerates myoblast proliferation but restrains myoblast differentiation. Moreover, MYH1G-AS drives a switch from slow-twitch to fast-twitch fibers and causes muscle atrophy. Mechanistically, MYH1G-AS inhibits FGF18 protein stabilization to reduce the interaction of FGF18 to SMARCA5, thus repressing chromatin accessibility of the SMAD4 promoter to activate the SMAD4-dependent pathway.

CONCLUSIONS

Our results reveal a new pattern of the regulation of lncRNA expression at diverse levels and help expound the regulation of m6A methylation on chromatin status.

Combined analysis of lncRNA and mRNA emphasizes the potential role of tryptophan-mediated regulation of muscle development in weaned piglets by lncRNA

Pork is an important high-value protein source that fulfills the nutritional requirements for normal growth development, repair, and metabolism. Tryptophan (Trp), a crucial amino acid for piglet growth performance and muscle development, has an essential yet unclear regulatory mechanism. To investigate the biological basis of Trp regulation of piglet muscle development and identify the related regulatory pathways, we studied 20 weaned piglets. The piglets were divided into control (CON, 0.14% Trp) and high Trp (HT, 0.35% Trp) groups. They were fed with different Trp concentrations for 28 d, after which we collected the longissimus dorsi (LD) muscle for histomorphometric analysis and RNA extraction. Our results showed that the HT diet significantly increased the average daily weight gain, myocyte number, and muscle fiber density in weaned piglets. We then analyzed the differentially expressed (DE) genes in the LD muscle through RNA sequencing (RNA-seq). We identified 253 lncRNAs and 1,055 mRNAs mainly involved in myoblast proliferation and myofiber formation, particularly through the FoxO and AMPK signaling pathways and metabolism. Further analysis of the DE lncRNA targeting relationship and construction of a protein-protein interaction network resulted in the discovery of a novel lncRNA, XLOC_021675, or FRPMD, and elucidated its role in regulating piglet muscle development. Finally, we confirmed the RNA-seq results by reverse transcription polymerase chain reaction (RT-PCR). This study provides valuable insights into the regulatory mechanism of lncRNA-mediated Trp regulation of muscle development in weaned piglets offering a theoretical basis for optimizing piglet dietary ratios and enhancing pork production.

CircRRAS2 promotes myogenic differentiation of bovine MuSCs and is a novel regulatory molecule of muscle development

The proliferation and myogenic differentiation of muscle stem cells (MuSCs) are important factors affecting muscle development and beef quality. There is increasing evidence that circRNAs can regulate myogenesis. We found a novel circRNA, named circRRAS2 that is significantly upregulated in the differentiation phase of bovine MuSCs. Here, we aimed to determine its roles in the proliferation and myogenic differentiation of these cells. The results showed that circRRAS2 was expressed in several bovine tissues. CircRRAS2 inhibited MuSCs proliferation and promoted myoblast differentiation. In addition, chromatin isolation by using RNA purification and mass spectrometry in differentiated muscle cells identified 52 RNA-binding proteins that could potentially bind to circRRAS2, in order to regulate their differentiation. The results suggest that circRRAS2 could be a specific regulator of myogenesis in bovine muscle.HighlightsCircRRAS2 expression is higher in DM cells than in GM cells.CircRRAS2 could significantly inhibit the proliferation and apoptosis of bovine MuSCs.CircRRAS2 promotes the differentiation of bovine MuSCs into myotubes.CircRRAS2 may exert regulatory effects through multiple RNA binding proteins.

Decoding the regulatory roles of non-coding RNAs in cellular metabolism and disease

Non-coding RNAs, including long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs), are being studied extensively in a variety of fields. Their roles in metabolism have received increasing attention in recent years but are not yet clear. The regulation of glucose, fatty acid, and amino acid metabolism is an imperative physiological process that occurs in living organisms and takes part in cancer and cardiovascular diseases. Here, we summarize the important roles played by non-coding RNAs in glucose metabolism, fatty acid metabolism, and amino acid metabolism, as well as the mechanisms involved. We also summarize the therapeutic advances for non-coding RNAs in diseases such as obesity, cardiovascular disease, and some metabolic diseases. Overall, non-coding RNAs are indispensable factors in metabolism and have a significant role in the three major metabolisms, which may be exploited as therapeutic targets in the future.

The cecal ecosystem is a great contributor to intramuscular fat deposition in broilers

Intramuscular fat (IMF) content is a meat quality trait of major economic importance in animal production. Emerging evidence has demonstrated that meat quality can be improved by regulating the gut microbiota. However, the organization and ecological properties of the gut microbiota and its relationship with the IMF content remain unclear in chickens. Here, we investigated the microbial communities of 206 cecal samples from broilers with excellent meat quality. We noted that the cecal microbial ecosystem obtained from hosts reared under the same management and dietary conditions showed clear compositional stratification. Two enterotypes, in which the ecological properties, including diversity and interaction strengths, were significantly different, described the microbial composition pattern. Compared with enterotype 2, enterotype 1, distinguished by the Clostridia_vadinBB60_group, had a higher fat deposition, although no discrepancy was found in growth performance and meat yield. A moderate correlation was observed in the IMF content between 2 muscle tissues, despite the IMF content of thigh muscle was 42.76% greater than that of breast muscle. Additionally, the lower abundance of cecal vadinBE97 was related to higher IMF levels in both muscle tissues. Although vadinBE97 accounted for 0.40% of the total abundance of genera in the cecum, it exhibited significant and positive correlations with other genera (accounting for 25.3% of the tested genera). Our results highlight important insights into the cecal microbial ecosystem and its association with meat quality. Microbial interactions should be carefully considered when developing approaches to improve the IMF content by regulating the gut microbiota in broilers.

Role of lncRNA Has2os in Skeletal Muscle Differentiation and Regeneration

Long non-coding RNAs (lncRNAs) regulate a series of physiological processes and play an important role in development, metabolism and disease. Our previous studies showed that lncRNAs involved in skeletal muscle differentiation. Here, we demonstrated that lncRNA Has2os is highly expressed in skeletal muscle and significantly elevated during skeletal cell differentiation. The knockdown of Has2os inhibited myocyte fusion and impeded the expression of the myogenic factors MyHC and Mef2C. Mechanically, Has2os regulates skeletal muscle differentiation by inhibiting the JNK/MAPK signaling pathway. Furthermore, we also revealed that Has2os is involved in the early stage of regeneration after muscle injury, and the JNK/MAPK signaling pathway is activated at both protein and mRNA levels during early repair. Our results demonstrate the new function of lncRNA Has2os, which plays crucial roles during skeletal muscle differentiation and muscle regeneration, providing a basis for the therapy of lncRNA-related muscle diseases.

The Functional Role of Long Non-Coding RNA in Myogenesis and Skeletal Muscle Atrophy

Skeletal muscle is a pivotal organ in humans that maintains locomotion and homeostasis. Muscle atrophy caused by sarcopenia and cachexia, which results in reduced muscle mass and impaired skeletal muscle function, is a serious health condition that decreases life longevity in humans. Recent studies have revealed the molecular mechanisms by which long non-coding RNAs (lncRNAs) regulate skeletal muscle mass and function through transcriptional regulation, fiber-type switching, and skeletal muscle cell proliferation. In addition, lncRNAs function as natural inhibitors of microRNAs and induce muscle hypertrophy or atrophy. Intriguingly, muscle atrophy modifies the expression of thousands of lncRNAs. Therefore, although their exact functions have not yet been fully elucidated, various novel lncRNAs associated with muscle atrophy have been identified. Here, we comprehensively review recent knowledge on the regulatory roles of lncRNAs in skeletal muscle atrophy. In addition, we discuss the issues and possibilities of targeting lncRNAs as a treatment for skeletal muscle atrophy and muscle wasting disorders in humans.