scholarly journals Comprehensive analysis of differentially expressed circRNAs and ceRNA regulatory network in porcine skeletal muscle

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Meng Li ◽  
Na Zhang ◽  
Wanfeng Zhang ◽  
Wei Hei ◽  
Chunbo Cai ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Regulatory Network ◽  
Growth Regulation ◽  
Muscle Development ◽  
Muscle Growth ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Large White ◽  
Skeletal Muscle Growth ◽  
Cerna Network

Abstract Background Circular RNA (circRNA), a novel class of non-coding RNA, has a closed-loop structure with important functions in skeletal muscle growth. The purpose of this study was to investigate the role of differentially expressed circRNAs (DEcircRNAs), as well as the DEcircRNA-miRNA-mRNA regulatory network, at different stages of porcine skeletal muscle development. Here, we present a panoramic view of circRNA expression in porcine skeletal muscle from Large White and Mashen pigs at 1, 90, and 180 days of age. Results We identified a total of 5819 circRNAs. DEcircRNA analysis at different stages showed 327 DEcircRNAs present in both breeds. DEcircRNA host genes were concentrated predominately in TGF-β, MAPK, FoxO, and other signaling pathways related to skeletal muscle growth and fat deposition. Further prediction showed that 128 DEcircRNAs could bind to 253 miRNAs, while miRNAs could target 945 mRNAs. The constructed ceRNA network plays a vital role in skeletal muscle growth and development, and fat deposition. Circ_0015885/miR-23b/SESN3 in the ceRNA network attracted our attention. miR-23b and SESN3 were found to participate in skeletal muscle growth regulation, also playing an important role in fat deposition. Using convergent and divergent primer amplification, RNase R digestion, and qRT-PCR, circ_0015885, an exonic circRNA derived from Homer Scaffold Protein 1 (HOMER1), was confirmed to be differentially expressed during skeletal muscle growth. In summary, circ_0015885 may further regulate SESN3 expression by interacting with miR-23b to function in skeletal muscle. Conclusions This study not only enriched the circRNA library in pigs, but also laid a solid foundation for the screening of key circRNAs during skeletal muscle growth and intramural fat deposition. In addition, circ_0015885/miR-23b/SESN3, a new network regulating skeletal muscle growth and fat deposition, was identified as important for increasing the growth rate of pigs and improving meat quality.

scholarly journals Comprehensive Analysis of Differentially Expressed CircRNAs and CeRNA Regulatory Network in Porcine Skeletal Muscle

2020 ◽  
Author(s):  
Meng Li ◽  
Na Zhang ◽  
Wanfeng Zhang ◽  
Wei Hei ◽  
Chunbo Cai ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Regulatory Network ◽  
Growth Regulation ◽  
Muscle Development ◽  
Muscle Growth ◽  
Fat Deposition ◽  
Differentially Expressed ◽  
Large White ◽  
Skeletal Muscle Growth ◽  
Cerna Network

Abstract Background: Circular RNA (circRNA), a novel class of non-coding RNA, has a closed-loop structure with important functions in skeletal muscle growth. The purpose of this study was to investigate the role of differentially expressed circRNAs (DEcircRNAs), as well as the DEcircRNA-miRNA-mRNA regulatory network, at different stages of porcine skeletal muscle development. Here, we present a panoramic view of circRNA expression in porcine skeletal muscle from Large White and Mashen pigs at 1, 90, and 180 days of age. Results: We identified a total of 5,819 circRNAs. DEcircRNA analysis at different stages showed 327 DEcircRNAs present in both breeds. DEcircRNA host genes were concentrated predominately in TGF-β, MAPK, FoxO, and other signaling pathways related to skeletal muscle growth and fat deposition. Further prediction showed that 128 DEcircRNAs could bind to 253 miRNAs, while miRNAs could target 945 mRNAs. The constructed ceRNA network plays a vital role in skeletal muscle growth and development, and fat deposition. Circ_0015885/miR-23b/SESN3 in the ceRNA network attracted our attention. miR-23b and SESN3 were found to participate in skeletal muscle growth regulation, also playing an important role in fat deposition. Using convergent and divergent primer amplification, RNase R digestion, and qRT-PCR, circ_0015885, an exonic circRNA derived from Homer Scaffold Protein 1 (HOMER1), was confirmed to be differentially expressed during skeletal muscle growth. In summary, circ_0015885 may further regulate SESN3 expression by interacting with miR-23b to function in skeletal muscle. Conclusions: This study not only enriched the circRNA library in pigs, but also laid a solid foundation for the screening of key circRNAs during skeletal muscle growth and intramural fat deposition. In addition, circ_0015885/miR-23b/SESN3, a new network regulating skeletal muscle growth and fat deposition, was identified as important for increasing the growth rate of pigs and improving meat quality.

Transcriptome profile of skeletal muscle at different developmental stages in Large White and Mashen pigs

2019 ◽  
Vol 99 (4) ◽  
pp. 867-880
Author(s):  
Xiaohong Guo ◽  
Wanfeng Zhang ◽  
Meng Li ◽  
Pengfei Gao ◽  
Wei Hei ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Candidate Genes ◽  
Growth And Development ◽  
Muscle Development ◽  
Developmental Stages ◽  
Muscle Growth ◽  
Individual Growth ◽  
Growth Stages ◽  
Large White ◽  
Skeletal Muscle Growth

From the perspectives of promoting individual growth and development, increasing pork yield, and improving feed utilization, it is desirable to screen candidate genes underlying pig muscle growth and regulation. In this study, we investigated transcriptome differences at 1, 90, and 180 d of age in Large White and Mashen pigs, characterized differentially expressed genes (DEGs), and screened candidate genes affecting skeletal muscle growth and development. RNA-seq was applied to analyze the transcriptome of the longissimus dorsi (LD) in the two breeds. In LD samples from the two breeds at three growth stages, 7215, 6332, 237, 3935, 3404, and 846 DEGs were obtained for L01 vs. L90, L01 vs. L180, L90 vs. L180, MS01 vs. MS90, MS01 vs. MS180, and MS90 vs. MS180, respectively. Significant tendencies in DEG expression could be grouped into eight profiles. Based on the functional analysis of DEGs, 16 candidate genes related to skeletal muscle growth and development were identified, including PCK2, GNAS, ADCY2, PRKAB1, PRKAB2, PRKAG1, PRKAG2, PHKA1, PHKA2, PHKG1, PHKG2, ITPR3, IGF1R, FGFR4, FGF1, and FGF18. The results of this study thus provide a theoretical basis for the mechanisms and candidate genes underlying skeletal muscle development in pigs.

scholarly journals Analysis of dynamic and widespread lncRNA and miRNA expression in fetal sheep skeletal muscle

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9957
Author(s):  
Chao Yuan ◽  
Ke Zhang ◽  
Yaojing Yue ◽  
Tingting Guo ◽  
Jianbin Liu ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Muscle Development ◽  
Expression Profiles ◽  
Muscle Growth ◽  
Skeletal Muscle Development ◽  
Fetal Sheep ◽  
Lncrna Gene ◽  
Skeletal Muscle Growth ◽  
Wide Range ◽  
Non Coding Rnas

The sheep is an economically important animal, and there is currently a major focus on improving its meat quality through breeding. There are variations in the growth regulation mechanisms of different sheep breeds, making fundamental research on skeletal muscle growth essential in understanding the regulation of (thus far) unknown genes. Skeletal muscle development is a complex biological process regulated by numerous genes and non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). In this study, we used deep sequencing data from sheep longissimus dorsi (LD) muscles sampled at day 60, 90, and 120 of gestation, as well as at day 0 and 360 following birth, to identify and examine the lncRNA and miRNA temporal expression profiles that regulate sheep skeletal myogenesis. We stained LD muscles using histological sections to analyse the area and circumference of muscle fibers from the embryonic to postnatal development stages. Our results showed that embryonic skeletal muscle growth can be characterized by time. We obtained a total of 694 different lncRNAs and compared the differential expression between the E60 vs. E90, E90 vs. E120, E120 vs. D0, and D0 vs. D360 lncRNA and gene samples. Of the total 701 known sheep miRNAs we detected, the following showed a wide range of expression during the embryonic stage: miR-2387, miR-105, miR-767, miR-432, and miR-433. We propose that the detected lncRNA expression was time-specific during the gestational and postnatal stages. GO and KEGG analyses of the genes targeted by different miRNAs and lncRNAs revealed that these significantly enriched processes and pathways were consistent with skeletal muscle development over time across all sampled stages. We found four visual lncRNA–gene regulatory networks that can be used to explore the function of lncRNAs in sheep and may be valuable in helping improve muscle growth. This study also describes the function of several lncRNAs that interact with miRNAs to regulate myogenic differentiation.

Myonuclear accretion is a major determinant of avian skeletal muscle growth

1997 ◽  
Vol 272 (2) ◽  
pp. C565-C571 ◽  
Author(s):  
P. E. Mozdziak ◽  
E. Schultz ◽  
R. G. Cassens
Keyword(s):  
Skeletal Muscle ◽  
Mitotic Activity ◽  
Satellite Cell ◽  
Muscle Development ◽  
Muscle Growth ◽  
Growth Potential ◽  
Unit Size ◽  
Skeletal Muscle Growth ◽  
Age Related ◽  
Related Increase

The role of satellite cells and DNA unit size in determining skeletal muscle growth was studied after mitotic activity was inhibited in the left pectoralis thoracicus of 2-wk-old tom turkeys by means of a 25-Gy dose of irradiation. Toms were killed and muscle weights were obtained 1 (n = 5), 4 (n = 6), 7 (n = 6), and 15 (n = 4) wk after irradiation. Satellite cell mitotic activity and DNA unit size were determined using enzymatically isolated myofiber segments and image analysis. Irradiated and nonirradiated muscle weights increased (P < 0.01) between all ages examined, but irradiated muscle weights were significantly (P < 0.01) lower than nonirradiated muscle weights at 4, 7, and 15 wk after irradiation. Satellite cell mitotic activity was lower (P < 0.01) in irradiated than in nonirradiated muscles at 1 and 4 wk after irradiation and resulted in a significant reduction (P < 0.05) in the number of myofiber nuclei per millimeter at 4 and 7 wk after irradiation. Satellite cell mitotic activity was higher (P < 0.05) in irradiated than in nonirradiated muscles at 7 wk after irradiation, but at 15 wk after irradiation it had fallen to low levels in both muscles. There was no significant (P > 0.10) difference in DNA unit size between muscles at any time, but there was an age-related increase (P < 0.01) for both muscles. Irradiation reduced muscle growth through a transient reduction in myonuclear production at a critical time (3-6 wk of age) in posthatch skeletal muscle development. The age-related increase in DNA unit size was not accelerated to compensate for the reduction in myonuclear accretion. Thus it appears that muscle growth potential is governed mostly by myonuclear accretion and to a lesser extent by DNA unit size.

An integrated analysis of mRNA and miRNA in skeletal muscle from myostatin-edited Meishan pigs

Genome ◽  
2019 ◽  
Vol 62 (5) ◽  
pp. 305-315 ◽  
Author(s):  
Shanshan Xie ◽  
Xiang Li ◽  
Lili Qian ◽  
Chunbo Cai ◽  
Gaojun Xiao ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Growth And Development ◽  
Target Genes ◽  
Muscle Growth ◽  
Genetically Engineered ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Signal Pathways ◽  
Skeletal Muscle Growth ◽  
Differentially Expressed Mirnas

Myostatin (MSTN) is a key muscle factor that negatively regulates skeletal muscle growth and development. Our laboratory recently produced genetically engineered Meishan pigs containing a ZFN-edited MSTN loss-of-function mutation (MSTN−/−, MKO) that led to the hypertrophy of skeletal muscles. In this study, we performed transcriptome sequencing and miRNA sequencing in skeletal muscle samples from MKO and wildtype Meishan (MWT) pigs to investigate the effect of MSTN−/− on expression of mRNA and miRNA. Our results indicated that, compared to MWT pigs, there were 200 genes and 4 miRNAs being significantly up-regulated, and 238 genes and 5 miRNAs being significantly down-regulated in MKO pigs. Analysis by GO and KEGG pathways revealed that differentially expressed miRNAs and their target genes of those differentially expressed miRNAs were involved in the signal pathways of skeletal muscle growth and development such as AMPK, mTOR, and TGF-beta. An integrated analysis of the correlation between miRNA-mRNA and transcriptome predicated that XK and METTL8 were target genes for miR-499-5p, while LRP4 was a target gene for miR-490-3p. Our results provide important clues to help us further investigate MSTN′s regulatory mechanisms during skeletal muscle growth and development.

scholarly journals Age-Related Exosomal and Endogenous Expression Patterns of miR-1, miR-133a, miR-133b, and miR-206 in Skeletal Muscles

2021 ◽  
Vol 12 ◽  
Author(s):  
Chrystalla Mytidou ◽  
Andrie Koutsoulidou ◽  
Margarita Zachariou ◽  
Marianna Prokopi ◽  
Konstantinos Kapnisis ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Skeletal Muscles ◽  
Connexin 43 ◽  
Muscle Development ◽  
Serum Response Factor ◽  
Expression Patterns ◽  
Muscle Growth ◽  
Skeletal Muscle Growth ◽  
Endogenous Expression ◽  
Age Related

Skeletal muscle growth and maintenance depend on two tightly regulated processes, myogenesis and muscle regeneration. Both processes involve a series of crucial regulatory molecules including muscle-specific microRNAs, known as myomiRs. We recently showed that four myomiRs, miR-1, miR-133a, miR-133b, and miR-206, are encapsulated within muscle-derived exosomes and participate in local skeletal muscle communication. Although these four myomiRs have been extensively studied for their function in muscles, no information exists regarding their endogenous and exosomal levels across age. Here we aimed to identify any age-related changes in the endogenous and muscle-derived exosomal myomiR levels during acute skeletal muscle growth. The four endogenous and muscle-derived myomiRs were investigated in five skeletal muscles (extensor digitorum longus, soleus, tibialis anterior, gastrocnemius, and quadriceps) of 2-week–1-year-old wild-type male mice. The expression of miR-1, miR-133a, and miR-133b was found to increase rapidly until adolescence in all skeletal muscles, whereas during adulthood it remained relatively stable. By contrast, endogenous miR-206 levels were observed to decrease with age in all muscles, except for soleus. Differential expression of the four myomiRs is also inversely reflected on the production of two protein targets; serum response factor and connexin 43. Muscle-derived exosomal miR-1, miR-133a, and miR-133b levels were found to increase until the early adolescence, before reaching a plateau phase. Soleus was found to be the only skeletal muscle to release exosomes enriched in miR-206. In this study, we showed for the first time an in-depth longitudinal analysis of the endogenous and exosomal levels of the four myomiRs during skeletal muscle development. We showed that the endogenous expression and extracellular secretion of the four myomiRs are associated to the function and size of skeletal muscles as the mice age. Overall, our findings provide new insights for the myomiRs’ significant role in the first year of life in mice.

Altered mRNA abundance of ASB15 and four other genes in skeletal muscle following administration of β-adrenergic receptor agonists

2004 ◽  
Vol 16 (2) ◽  
pp. 275-283 ◽  
Author(s):  
Tara G. McDaneld ◽  
Deana L. Hancock ◽  
Diane E. Moody
Keyword(s):  
Skeletal Muscle ◽  
Adrenergic Receptor ◽  
Muscle Growth ◽  
Differentially Expressed Gene ◽  
Differentially Expressed ◽  
Female Rats ◽  
Trenbolone Acetate ◽  
Receptor Agonists ◽  
Skeletal Muscle Growth ◽  
Downstream Signaling

β-Adrenergic receptor agonists (BA) stimulate skeletal muscle growth. However, downstream signaling pathways that facilitate this effect remain poorly defined. Objectives of this study were to identify genes differentially expressed after administration of a novel BA and to evaluate the expression of one of those genes in additional models of skeletal muscle growth. Differentially expressed gene fragments were identified through differential display of skeletal muscle biopsies from five steers 24 h after administration of the BA. Five gene fragments designated DD53, DD143, DD163, DD209, and DD214 were identified. Tissue distribution of these genes was evaluated by RT-PCR. While DD53, DD163, DD209, and DD214 were expressed across tissues, DD143 mRNA expression was most abundant in skeletal muscle. DD143, later identified as bovine ASB15, was evaluated in rats following administration of anabolic compounds. Thirteen 7-wk-old female rats were randomly assigned to each of four treatment groups including: control, clenbuterol, trenbolone acetate (TBA), and growth hormone (GH). Changes in rat Asb-15 mRNA were measured at 30 min, 12 h, and 24 h following intraperitoneal injections of each compound. Clenbuterol treatment decreased Asb-15 mRNA in skeletal muscle at 12 and 24 h ( P < 0.01) and also decreased mRNA in lung at 12 h ( P < 0.05). TBA and GH treatments did not alter Asb-15 mRNA in any of the tissues evaluated ( P > 0.10). These results are the first to associate an Asb gene family member with muscle growth or BA administration and suggest a potential role for ASB15 in β-agonist-induced skeletal muscle hypertrophy.

scholarly journals Key Genes Regulating Skeletal Muscle Development and Growth in Farm Animals

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 835
Author(s):  
Mohammadreza Mohammadabadi ◽  
Farhad Bordbar ◽  
Just Jensen ◽  
Min Du ◽  
Wei Guo
Keyword(s):  
Skeletal Muscle ◽  
Candidate Genes ◽  
Meat Quality ◽  
Muscle Development ◽  
Muscle Growth ◽  
Farm Animals ◽  
Meat Production ◽  
Skeletal Muscle Development ◽  
Extrinsic Factors ◽  
Myogenic Regulatory Factor

Farm-animal species play crucial roles in satisfying demands for meat on a global scale, and they are genetically being developed to enhance the efficiency of meat production. In particular, one of the important breeders’ aims is to increase skeletal muscle growth in farm animals. The enhancement of muscle development and growth is crucial to meet consumers’ demands regarding meat quality. Fetal skeletal muscle development involves myogenesis (with myoblast proliferation, differentiation, and fusion), fibrogenesis, and adipogenesis. Typically, myogenesis is regulated by a convoluted network of intrinsic and extrinsic factors monitored by myogenic regulatory factor genes in two or three phases, as well as genes that code for kinases. Marker-assisted selection relies on candidate genes related positively or negatively to muscle development and can be a strong supplement to classical selection strategies in farm animals. This comprehensive review covers important (candidate) genes that regulate muscle development and growth in farm animals (cattle, sheep, chicken, and pig). The identification of these genes is an important step toward the goal of increasing meat yields and improves meat quality.

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