Identification and Characterization of Circular RNAs in Longissimus Dorsi Muscle Tissue from Two Goat Breeds using RNA-Seq

Abstract Background: Circular RNAs (circRNAs) are a class of non-coding RNA that play crucial roles in the development of skeletal muscle. However, little is known about the role of circRNAs in caprine skeletal muscle. In this study, the muscle fiber size and expression profiles of circRNAs were compared in Longissimus dorsi muscle of Liaoning cashmere (LC) goats and Ziwuling black (ZB) goats with significant phenotypic differences in meat production performance, using hematoxylin and eosin staining and RNA-Seq, respectively.Results: The muscle fiber size in LC goats were larger than those in ZB goats (P < 0.05). A total of 10,875 circRNAs were identified and 214 of these were differentially expressed between the two caprine breeds. The authentication and expression levels of 20 circRNAs were confirmed using reverse transcriptase-polymerase chain reaction (RT-PCR) and DNA sequencing. The parent genes of differentially expressed circRNAs were mainly enriched in connective tissue development, Rap1, cGMP-PKG, cAMP and Ras signaling pathway. Some miRNAs reportedly associated with skeletal muscle development and intramuscular fat deposition would be targeted by several differentially expressed circRNAs and the most highly expressed circRNA (circ_001086).Conclusion: These results provide an improved understanding of the functions of circRNAs in skeletal muscle development of goats.

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Identification of Differentially Expressed Genes in Different Types of Broiler Skeletal Muscle Fibers Using the RNA-seq Technique

BioMed Research International ◽

10.1155/2020/9478949 ◽

2020 ◽

Vol 2020 ◽

pp. 1-13

Author(s):

Han Wang ◽

Zhonghao Shen ◽

Xiaolong Zhou ◽

Songbai Yang ◽

Feifei Yan ◽

...

Keyword(s):

Skeletal Muscle ◽

Differentially Expressed Genes ◽

Muscle Fiber ◽

Muscle Development ◽

Skeletal Muscle Fiber ◽

Differentially Expressed ◽

Muscle Fiber Types ◽

Type I ◽

Fiber Types ◽

Rna Seq

The difference in muscle fiber types is very important to the muscle development and meat quality of broilers. At present, the molecular regulation mechanisms of skeletal muscle fiber-type transformation in broilers are still unclear. In this study, differentially expressed genes between breast and leg muscles in broilers were analyzed using RNA-seq. A total of 767 DEGs were identified. Compared with leg muscle, there were 429 upregulated genes and 338 downregulated genes in breast muscle. Gene Ontology (GO) enrichment indicated that these DEGs were mainly involved in cellular processes, single organism processes, cells, and cellular components, as well as binding and catalytic activity. KEGG analysis shows that a total of 230 DEGs were mapped to 126 KEGG pathways and significantly enriched in the four pathways of glycolysis/gluconeogenesis, starch and sucrose metabolism, insulin signalling pathways, and the biosynthesis of amino acids. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) was used to verify the differential expression of 7 selected DEGs, and the results were consistent with RNA-seq data. In addition, the expression profile of MyHC isoforms in chicken skeletal muscle cells showed that with the extension of differentiation time, the expression of fast fiber subunits (types IIA and IIB) gradually increased, while slow muscle fiber subunits (type I) showed a downward trend after 4 days of differentiation. The differential genes screened in this study will provide some new ideas for further understanding the molecular mechanism of skeletal muscle fiber transformation in broilers.

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Morphological changes and functional circRNAs screening of rabbit skeletal muscle development

BMC Genomics ◽

10.1186/s12864-021-07706-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Qi Zheng ◽

Cuiyun Zhu ◽

Jing Jing ◽

Yinghui Ling ◽

Shuaiqi Qin ◽

...

Keyword(s):

Skeletal Muscle ◽

Muscle Development ◽

Expression Profiles ◽

Paraffin Section ◽

Rabbit Skeletal Muscle ◽

Differentially Expressed ◽

Adult Rabbit ◽

Rna Seq ◽

Skeletal Muscle Development ◽

Host Genes

Abstract Background The temporal expression pattern of circular RNAs (circRNAs) across developmental stages is essential for skeletal muscle growth and functional analysis. However, there are few analyses on the potential functions of circRNAs in rabbit skeletal muscle development. Results Initially, the paraffin sections showed extremely significant differences in the diameter, number, area and density of skeletal muscle fibers of the fetus, child, adult rabbit hind legs (P < 0.01). Then, RNA-seq libraries of these three stages were constructed. A total of 481 differentially expressed circRNAs (DE-circRNAs) and 5,658 differentially expressed genes (DEGs) were identified. Subsequently, DE-circRNAs, whose host genes were DEGs or non-DEGs, were analyzed by GO respectively. In the fetus vs. child group, up-regulated DE-circRNAs (whose host genes were DEGs) were related to muscle fiber structure, and down-regulated ones were related to mitosis. The up-regulated DE-circRNAs (whose host genes were non-DEGs) were involved in enzyme activity, methylation and glycosylation, and the down-regulated ones were involved in mitosis and catabolism. In the fetus vs. adult group, the up-regulated DE-circRNAs (whose host genes were DEGs) were related to skeletal muscle basic structure, and the down-regulated ones were also associated with cell proliferation. But the up-regulated DE-circRNAs (whose host genes were non-DEGs) were connected with regulation of histone ubiquitination, chromatin and organelles. The down-regulated DE-circRNAs were connected with the catabolism processes. In addition, novel_circ_0022663 and novel_circ_0005489, which might have coding potential, and novel_circ_0004210 and novel_circ_0001669, which might have miRNA sponge capability, were screened out. Conclusions In this study, hind leg muscles of fetus, child and adult rabbits were collected for paraffin section and RNA-seq to observe the structural changes of skeletal muscle and obtain circRNA expression profiles at different stages. These data provided a catalog of circRNAs related to muscle development in New Zealand rabbits, allowing us to better understand the functional transitions in mammalian muscle development.

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Genome-Wide Expression Profiling of mRNAs, lncRNAs and circRNAs in Skeletal Muscle of Two Different Pig Breeds

Animals ◽

10.3390/ani11113169 ◽

2021 ◽

Vol 11 (11) ◽

pp. 3169

Author(s):

Xinhua Hou ◽

Ligang Wang ◽

Fuping Zhao ◽

Xin Liu ◽

Hongmei Gao ◽

...

Keyword(s):

Skeletal Muscle ◽

Fatty Acid ◽

Fatty Acid Metabolism ◽

Muscle Development ◽

Target Genes ◽

Acid Metabolism ◽

Differentially Expressed ◽

Rna Seq ◽

Skeletal Muscle Development ◽

Pig Breeds

RNA-Seq technology is widely used to analyze global changes in the transcriptome and investigate the influence on relevant phenotypic traits. Beijing Black pigs show differences in growth rate and meat quality compared to western pig breeds. However, the molecular mechanisms responsible for such phenotypic differences remain unknown. In this study, longissimus dorsi muscles from Beijing Black and Yorkshire pigs were used to construct RNA libraries and perform RNA-seq. Significantly different expressions were observed in 1051 mRNAs, 322 lncRNAs, and 82 circRNAs. GO and KEGG pathway annotation showed that differentially expressed mRNAs participated in skeletal muscle development and fatty acid metabolism, which determined the muscle-related traits. To explore the regulatory role of lncRNAs, the cis and trans-target genes were predicted and these lncRNAswere involved in the biological processes related to skeletal muscle development and fatty acid metabolismvia their target genes. CircRNAs play a ceRNA role by binding to miRNAs. Therefore, the potential miRNAs of differentially expressed circRNAs were predicted and interaction networks among circRNAs, miRNAs, and key regulatory mRNAs were constructed to illustrate the function of circRNAs underlying skeletal muscle development and fatty acid metabolism. This study provides new clues for elucidating muscle phenotypic variation in pigs.

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

Animals ◽

10.3390/ani10081417 ◽

2020 ◽

Vol 10 (8) ◽

pp. 1417

Author(s):

Chuan Li ◽

Ting Xiong ◽

Mingfang Zhou ◽

Lei Wan ◽

Suwang Xi ◽

...

Keyword(s):

Skeletal Muscle ◽

Muscle Development ◽

Target Genes ◽

Mapk Signaling ◽

Differentially Expressed ◽

Mitogen Activated Protein Kinase ◽

Luciferase Reporter ◽

Meat Production ◽

Skeletal Muscle Development ◽

Differentially Expressed Mirnas

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.

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Chromosome mapping of five differently expressed miRNAs in porcine skeletal muscle development (Brief Report)

Archives Animal Breeding ◽

10.5194/aab-53-734-2010 ◽

2010 ◽

Vol 53 (6) ◽

pp. 734-736

Author(s):

H. B. He ◽

S. H. Zhao ◽

X. Y. Li

Keyword(s):

Skeletal Muscle ◽

Muscle Development ◽

Expression Profiles ◽

Chromosome Mapping ◽

Differentially Expressed ◽

Skeletal Muscle Development ◽

Regulate Gene Expression ◽

Mirna Expression Profiles ◽

Differentially Expressed Mirnas ◽

Regulatory Rnas

Abstract. MicroRNAs (miRNAs) are a class of short, non-coding regulatory RNAs, which are approximately 22 nucleotides in length. Typically, miRNAs negatively regulate gene expression by binding with the 3' untranslated region (UTR) of its regulatory target mRNAs. MicroRNAs are known to play diverse roles in fundamental biological processes, such as proliferation, differentiation and apoptosis (Bartel 2004, 2009). It has been reported that miR-1, miR-133, miR-181 and miR-206 play important roles in skeletal muscle proliferation and hypertrophy (Callis et al. 2007, McCarthy -Esser 2007). We have detected porcine miRNA expression profiles during different stage of skeletal muscle development and a total of 140 miRNAs were differentially expressed (HUANG et al. 2008). In this study, we mapped five differentially expressed miRNAs (mir-29c, mir-103-1, mir-127, mir-193b and mir-218-1) using the radiation hybrid (IMpRH) panel (YERLE et al. 1998).

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Comprehensive Analysis of mRNA, lncRNA, circRNA, and miRNA Expression Profiles and Their ceRNA Networks in the Longissimus Dorsi Muscle of Cattle-Yak and Yak

Frontiers in Genetics ◽

10.3389/fgene.2021.772557 ◽

2021 ◽

Vol 12 ◽

Author(s):

Chun Huang ◽

Fei Ge ◽

Xiaoming Ma ◽

Rongfeng Dai ◽

Renqing Dingkao ◽

...

Keyword(s):

Signaling Pathway ◽

Molecular Basis ◽

Muscle Development ◽

Expression Profiles ◽

Economic Benefits ◽

Production Performance ◽

Differentially Expressed ◽

Myoblast Differentiation ◽

Longissimus Dorsi ◽

Non Coding Rnas

Cattle-yak, as the hybrid offspring of cattle (Bos taurus) and yak (Bos grunniens), demonstrates obvious heterosis in production performance. Male hybrid sterility has been focused on for a long time; however, the mRNAs and non-coding RNAs related to muscle development as well as their regulatory networks remain unclear. The phenotypic data showed that the production performance (i.e., body weight, withers height, body length, and chest girth) of cattle-yak was significantly better than that of the yak, and the economic benefits of the cattle-yak were higher under the same feeding conditions. Then, we detected the expression profiles of the longissimus dorsi muscle of cattle-yak and yak to systematically reveal the molecular basis using the high-throughput sequencing technology. Here, 7,126 mRNAs, 791 lncRNAs, and 1,057 circRNAs were identified to be differentially expressed between cattle-yaks and yaks in the longissimus dorsi muscle. These mRNAs, lncRNA targeted genes, and circRNA host genes were significantly enriched in myoblast differentiation and some signaling pathways related to muscle development (such as HIF-1 signaling pathway and PI3K-Akt signaling pathway). We constructed a competing endogenous RNA (ceRNA) network and found that some non-coding RNAs differentially expressed may be involved in the regulation of muscle traits. Taken together, this study may be used as a reference tool to provide the molecular basis for studying muscle development.

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The Landscape of Chromatin Accessibility in Skeletal Muscle During Embryonic Development in Pigs

10.21203/rs.3.rs-95713/v1 ◽

2020 ◽

Author(s):

Jingwei Yue ◽

Xinhua Hou ◽

Xin Liu ◽

Ligang Wang ◽

Hongmei Gao ◽

...

Keyword(s):

Skeletal Muscle ◽

Transcription Factors ◽

Embryonic Development ◽

Muscle Development ◽

Chromatin Accessibility ◽

Regulatory Role ◽

Rna Seq ◽

Skeletal Muscle Development ◽

Embryonic Muscle ◽

Embryonic Muscle Development

Abstract Background: The development of skeletal muscle during the embryonic stage in pigs is precisely regulated by transcriptional regulation, which depends on chromatin accessibility. However, how chromatin accessibility plays a regulatory role during embryonic skeletal muscle development in pigs has not been reported. To gain insight into the landscape of chromatin accessibility and the associated genome-wide transcriptome during embryonic muscle development, we performed ATAC-seq and RNA-seq on skeletal muscle of pig embryos at 45, 70 and 100 days post coitus (dpc). Results: In total, 21638, 35447 and 60181 unique regions (or peaks) were found across 45 dpc (LW45), 70 dpc (LW70) and 100 dpc (LW100) embryos, respectively. More than 91% of peaks were annotated within -1 kb to 100 bp of transcription start sites (TSSs). First, widespread increases in specific accessible chromatin regions (ACRs) from 45 to 100 dpc embryos suggested that the regulatory mechanisms became increasingly complicated during embryonic development. Second, the findings of integrated ATAC-seq and RNA-seq analyses showed that not only the numbers but also the peak intensities of ACRs could control the expression of associated genes. Finally, motif screening of stage-specific ACRs revealed some transcription factors that regulated muscle development-related genes, such as MyoD, Mef2c, Mef2d and Pax7. Several potential transcriptional repressors, including E2F6, GRHL2, OTX2 and CTCF, were identified among those genes that exhibited different change trends between the ATAC-seq and RNA-seq data. Conclusions: This work indicates that chromatin accessibility plays an important regulatory role in the embryonic muscle development of pigs and regulates the temporal and spatial expression patterns of key genes in muscle development by influencing the binding of transcription factors. Our results contribute to a better understanding of the regulatory dynamics of genes involved in pig embryonic skeletal muscle development.

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Integrated analysis of miRNA-mediated ceRNA networks in ovine skeletal muscle development

10.21203/rs.3.rs-18319/v1 ◽

2020 ◽

Author(s):

Tianpei Shi ◽

Xinyue WANG ◽

Zhida ZHAO ◽

Wenping HU ◽

Li ZHANG

Keyword(s):

Skeletal Muscle ◽

Transcription Factors ◽

Muscle Development ◽

Muscle Growth ◽

Growth Potential ◽

Regulatory Role ◽

Integrated Analysis ◽

Interaction Patterns ◽

Rna Seq ◽

Skeletal Muscle Development

Abstract Background: The embryo stage is a key period for sheep skeletal muscle growth and development. Proliferation, differentiation, and hypertrophy of fibers affect muscle growth potential directly. Analyzing transcriptome data is of great significance for revealing important time nodes of fetus muscle development and screening related regulation factors. Muscle development is a complex biological process, including a intricate network of multiple factor interactions. Among them, non-coding RNA, especially miRNA-mediated regulation, plays a fine regulatory role. The purpose of this study was to investigate the important genes and transcripts involved in the genetic mechanism of embryos skeletal muscle development in late pregnancy. Results: Herein we did a small RNA sequencing(RNA-Seq) of embryo at 85 days (D85N), 105 days (D105N) and 135 days(D135N), then performed bioinformatic analysis in order to identify the miRNA-mediated co-expression networks. Our findings identified 505 DE-miRNAs. Integrating the current miRNA data and the previously obtained lncRNA data, multiple networks were constructed, including miRNA-mRNA, miRNA-target gene(TG)-pathway, lncRNA-miRNA-mRNA, and miRNA-TG-transcription factor (TF) network. The results showed that the miRNA-mRNA network and lncRNA-miRNA-mRNA network identified three important lncRNAs (MSTRG.3533, MSTRG.4324, and MSTRG.1470) and three miRNAs(miR-493-3p, miR-3959-3p and miR-410-5p). The four genes ( TEAD1 , ZBTB34 , GSK3B, and POGLUT1 ) and three transcription factors (C / EBPbeta, TFIID, and PR B) play a key regulatory role in the miRNA-TG-TF network. Notably, a similar trend of gene expression was reported by RT-qPCR for RNA-seq data. Conclusions: This study identified three miRNAs, three lncRNAs, four genes, and three transcription factors, and revealed their crucial role in fetal fibrogenesis and lipid metabolism. It also shows that D105N is a pivotal turning point from myotube differentiation to fiber hypertrophy. These findings provide valuable references for network interaction patterns, which helps to evaluate the biological significance of skeletal muscle in the late development stage.

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Overexpression of the Rybp Gene Inhibits Differentiation of Bovine Myoblasts into Myotubes

International Journal of Molecular Sciences ◽

10.3390/ijms19072082 ◽

2018 ◽

Vol 19 (7) ◽

pp. 2082

Author(s):

Xiaotong Su ◽

Yanfang Zhao ◽

Yaning Wang ◽

Le Zhang ◽

Linsen Zan ◽

...

Keyword(s):

Skeletal Muscle ◽

Muscle Development ◽

Molecular Breeding ◽

Theoretical Foundation ◽

Negative Control ◽

Myoblast Differentiation ◽

Rna Seq ◽

Skeletal Muscle Development ◽

Morphological Differences ◽

Bovine Skeletal Muscle

RING1 and YY1 binding protein (Rybp) genes inhibit myogenesis in mice, but there are no reports on the effects of these genes in cattle. The aim of this study is to investigate the roles of the Rybp gene on bovine skeletal muscle development and myoblast differentiation. In the present study, the Rybp gene was overexpressed in bovine myoblasts via adenovirus. RNA-seq was performed to screen differentially expressed genes (DEGs). The results showed that overexpressing the Rybp gene inhibits the formation of myotubes. The morphological differences in myoblasts began on the second day and were very significant 6 days after adenovirus induction. A total of 1311 (707 upregulated and 604 downregulated) DEGs were screened using RNA-seq between myoblasts with added negative control adenoviruses (AD-NC) and Rybp adenoviruses (AD-Rybp) after 6 days of induction. Gene ontology (GO) and KEGG analysis revealed that the downregulated DEGs were mainly involved in biological functions related to muscle, and, of the 32 pathways, those associated with muscle development were significantly enriched for the identified DEGs. This study can not only provide a theoretical basis for the regulation of skeletal muscle development in cattle by exploring the roles of the Rybp gene in myoblast differentiation, but it can also lay a theoretical foundation for molecular breeding of beef cattle.

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Profiling and Functional Analysis of Long Noncoding RNAs and mRNAs during Porcine Skeletal Muscle Development

International Journal of Molecular Sciences ◽

10.3390/ijms22020503 ◽

2021 ◽

Vol 22 (2) ◽

pp. 503

Author(s):

Ya Tan ◽

Mailin Gan ◽

Linyuan Shen ◽

Liang Li ◽

Yuan Fan ◽

...

Keyword(s):

Gene Expression ◽

Skeletal Muscle ◽

Inflection Point ◽

Muscle Development ◽

Noncoding Rnas ◽

Long Noncoding Rnas ◽

Functional Enrichment ◽

Differentially Expressed ◽

Luciferase Assay ◽

Skeletal Muscle Development

Gene transcripts or mRNAs and long noncoding RNAs (lncRNAs) are differentially expressed during porcine skeletal muscle development. However, only a few studies have been conducted on skeletal muscle transcriptome in pigs based on timepoints according to the growth curve for porcine. Here, we investigated gene expression in Qingyu pigs at three different growth stages: the inflection point with the maximum growth rate (MGI), the inflection point of the gradually increasing stage to the rapidly increasing stage (GRI), and the inflection point of the rapidly increasing stage to the slowly increasing stage (RSI). Subsequently, we explored gene expression profiles during muscle development at the MGI, GRI and RSI stages by Ribo-Zero RNA sequencing. Qingyu pigs reached the MGI, GRI and RSI stages at 156.40, 23.82 and 288.97 days of age with 51.73, 3.14 and 107.03 kg body weight, respectively. A total of 14,530 mRNAs and 11,970 lncRNAs were identified at the three stages, and 645, 323 differentially expressed genes (DEGs) and 696, 760 differentially expressed lncRNAs (DELs) were identified in the GRI vs. MGI, and RSI vs. MGI, comparisons. Functional enrichment analysis revealed that genes involved in immune system development and energy metabolism (mainly relate to amino acid, carbohydrate and lipid) were enriched at the GRI and MGI stages, respectively, whereas genes involved in lipid metabolism were enriched at the RSI stage. We further characterized G1430, an abundant lncRNA. The full-length sequence (316 nt) of lncRNA G1430 was determined by rapid amplification of cDNA ends (RACE). Subcellular distribution analysis by quantitative real-time PCR (qRT-PCR) revealed that G1430 is a cytoplasmic lncRNA. Binding site prediction and dual luciferase assay showed that lncRNA G1430 directly binds to microRNA 133a (miR-133a). Our findings provide the basis for further investigation of the regulatory mechanisms and molecular genetics of muscle development in pigs.

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