Skeletal Muscle Transcriptome Analysis of Hanzhong Ma Duck at Different Growth Stages Using RNA-Seq

As one of the most important poultry worldwide, ducks (Anas platyrhynchos) are raised mainly for meat and egg products, and muscle development in ducks is important for meat production. Therefore, an investigation of gene expression in duck skeletal muscle would significantly contribute to our understanding of muscle development. In this study, twenty-four cDNA libraries were constructed from breast and leg muscles of Hanzhong Ma ducks at day 17, 21, 27 of the embryo and postnatal at 6-month-old. High-throughput sequencing and bioinformatics were used to determine the abundances and characteristics of transcripts. A total of 632,172,628 (average 52,681,052) and 637,213,938 (average 53,101,162) reads were obtained from the sequencing data of breast and leg muscles, respectively. Over 71.63% and 77.36% of the reads could be mapped to the Anas platyrhynchos genome. In the skeletal muscle of Hanzhong duck, intron variant (INTRON), synonymous variant (SYNONYMOUS_CODING), and prime 3′ UTR variant (UTR_3_PRIME) were the main single nucleotide polymorphisms (SNP) annotation information, and “INTRON”, “UTR_3_PRIME”, and downstream-gene variant (DOWNSTREAM) were the main insertion-deletion (InDel) annotation information. The predicted number of alternative splicing (AS) in all samples were mainly alternative 5′ first exon (transcription start site)-the first exon splicing (TSS) and alternative 3′ last exon (transcription terminal site)-the last exon splicing (TTS). Besides, there were 292 to 2801 annotated differentially expressed genes (DEGs) in breast muscle and 304 to 1950 annotated DEGs in leg muscle from different databases. It is worth noting that 75 DEGs in breast muscle and 49 DEGs in leg muscle were co-expressed at all developmental points of comparison, respectively. The RNA-Seq data were confirmed to be reliable by qPCR. The identified DEGs, such as CREBL2, RHEB, GDF6, SHISA2, MYLK2, ACTN3, RYR3, and STMN1, were specially highlighted, indicating their strong associations with muscle development in the Hanzhong Ma duck. KEGG pathway analysis suggested that regulation of actin cytoskeleton, oxidative phosphorylation, and focal adhesion were involved in the development of skeletal muscle. The findings from this study can contribute to future investigations of the growth and development mechanism in duck skeletal muscle.

Download Full-text

Characterization and Comparative Transcriptomic Analysis of Skeletal Muscle in Pekin Duck at Different Growth Stages Using RNA-seq

Animals ◽

10.3390/ani11030834 ◽

2021 ◽

Vol 11 (3) ◽

pp. 834

Author(s):

Zhigang Hu ◽

Junting Cao ◽

Liyan Ge ◽

Jianqin Zhang ◽

Huilin Zhang ◽

...

Keyword(s):

Skeletal Muscle ◽

Cell Differentiation ◽

Muscle Cell ◽

Growth And Development ◽

Muscle Development ◽

Pekin Duck ◽

Functional Study ◽

Growth Stages ◽

Exon Splicing ◽

Different Growth Stages

Skeletal muscle, accounting for approximately 50% of body weight, is the largest and most important tissue. In this study, the gene expression profiles and pathways in skeletal muscle of Pekin duck were investigated and compared at embryonic day 17, 21, and 27 and postnatally at 6 months of age. An average of 49,555,936 reads in each sample was obtained from the transcriptome libraries. Over 70.0% of alternative splicing (AS) in each sample was mainly alternative 5’ first exon (transcription start site)-the first exon splicing (TSS) and alternative 3’ last exon (transcription terminal site)-the last exon splicing (TTS), indicating that TSS and TTS were the most common AS event in Pekin ducks, and these AS events were closely related to the regulation of muscle development at different growth stages. The results provided a valuable genomic resource for selective breeding and functional studies of genes. A total of 299 novel genes with ≥2 exons were obtained. There were 294 to 2806 differentially expressed genes (DEGs) in each pairwise comparison of Pekin duck. Notably, 90 DEGs in breast muscle and 9 DEGs in leg muscle were co-expressed at all developmental points. DEGs were validated by qPCR analysis, which confirmed the tendency of the expression. DEGs related to muscle development were involved in biological processes such as “endodermal cell differentiation”, “muscle cell cellular homeostasis”, “skeletal muscle tissue growth” and “skeletal muscle cell differentiation”, and were involved in pathways such as oxidative phosphorylation, ECM-receptor (extracellular matrix receptor) interaction, focal adhesion, carbon metabolism, and biosynthesis of amino acids. Some DEGs, including MYL4, IGF2BP1, CSRP3, SPP1 and KLHL31, as well as LAMB2, LAMA2, ITGB1 and OPN, played crucial roles in muscle growth and development. This study provides valuable information about the expression profile of mRNAs and pathways from duck skeletal muscle at different growth stages, and further functional study of these mRNAs and pathways could provide new ideas for studying the molecular networks of growth and development in duck skeletal muscle.

Download Full-text

Transcriptome Analysis of Differentially Expressed mRNA Related to Pigeon Muscle Development

Animals ◽

10.3390/ani11082311 ◽

2021 ◽

Vol 11 (8) ◽

pp. 2311

Author(s):

Hao Ding ◽

Yueyue Lin ◽

Tao Zhang ◽

Lan Chen ◽

Genxi Zhang ◽

...

Keyword(s):

Gene Expression ◽

Skeletal Muscle ◽

Differentially Expressed Genes ◽

Growth And Development ◽

Muscle Development ◽

Expression Patterns ◽

Differentially Expressed ◽

Pathway Enrichment Analysis ◽

Growth Stages ◽

Gene Expression And Regulation

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.

Download Full-text

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

10.21203/rs.3.rs-944970/v1 ◽

2021 ◽

Author(s):

Jiyuan Shen ◽

Huimin Zhen ◽

Lu Li ◽

Yuting Zhang ◽

Jiqing Wang ◽

...

Keyword(s):

Skeletal Muscle ◽

Muscle Fiber ◽

Muscle Development ◽

Production Performance ◽

Differentially Expressed ◽

Circular Rnas ◽

Longissimus Dorsi ◽

Rna Seq ◽

Skeletal Muscle Development ◽

Fiber Size

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.

Download Full-text

Chromatin Interaction Responds to Breast Muscle Development and Intramuscular Fat Deposition Between Chinese Indigenous Chicken and Fast-Growing Broiler

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.782268 ◽

2021 ◽

Vol 9 ◽

Author(s):

Weihua Tian ◽

Zhang Wang ◽

Dandan Wang ◽

Yihao Zhi ◽

Jiajia Dong ◽

...

Keyword(s):

Skeletal Muscle ◽

Muscle Development ◽

Intramuscular Fat ◽

Breast Muscle ◽

Chromatin Interaction ◽

Chicken Breast ◽

Meat Production ◽

Skeletal Muscle Development ◽

Significant Difference ◽

Imf Content

Skeletal muscle development and intramuscular fat (IMF) content, which positively contribute to meat production and quality, are regulated by precisely orchestrated processes. However, changes in three-dimensional chromatin structure and interaction, a newly emerged mediator of gene expression, during the skeletal muscle development and IMF deposition have remained unclear. In the present study, we analyzed the differences in muscle development and IMF content between one-day-old commercial Arbor Acres broiler (AA) and Chinese indigenous Lushi blue-shelled-egg chicken (LS) and performed Hi-C analysis on their breast muscles. Our results indicated that significantly higher IMF content, however remarkably lower muscle fiber diameter was detected in breast muscle of LS chicken compared to that of AA broiler. The chromatin intra-interaction was prior to inter-interaction in both AA and LS chicken, and chromatin inter-interaction was heavily focused on the small and gene-rich chromosomes. For genomic compartmentalization, no significant difference in the number of B type compartments was found, but AA had more A type compartments versus LS. The A/B compartment switching of AA versus LS showed more A to B switching than B to A switching. There were no significant differences in the average sizes and distributions of topologically associating domains (TAD). Additionally, approximately 50% of TAD boundaries were overlapping. The reforming and disappearing events of TAD boundaries were identified between AA and LS chicken breast muscles. Among these, the HMGCR gene was located in the TAD-boundary regions in AA broilers, but in TAD-interior regions in LS chickens, and the IGF2BP3 gene was located in the AA-unique TAD boundaries. Both HMGCR and IGF2BP3 genes exhibited increased mRNA expression in one-day-old AA broiler breast muscles. It was demonstrated that the IGF2BP3 and HMGCR genes regulated by TAD boundary sliding were potential biomarkers for chicken breast muscle development and IMF deposition. Our data not only provide a valuable understanding of higher-order chromatin dynamics during muscle development and lipid accumulation but also reveal new insights into the regulatory mechanisms of muscle development and IMF deposition in chicken.

Download Full-text

Developmental atlas of the RNA editome in Sus scrofa skeletal muscle

DNA Research ◽

10.1093/dnares/dsz006 ◽

2019 ◽

Vol 26 (3) ◽

pp. 261-272 ◽

Cited By ~ 5

Author(s):

Yalan Yang ◽

Min Zhu ◽

Xinhao Fan ◽

Yilong Yao ◽

Junyu Yan ◽

...

Keyword(s):

Skeletal Muscle ◽

Rna Editing ◽

Sus Scrofa ◽

Muscle Development ◽

Rna Seq ◽

Sequencing Data ◽

Adenosine Deaminases ◽

Bisulphite Sequencing ◽

Highly Correlated ◽

Gain Loss

AbstractAdenosine-to-inosine (A-to-I) RNA editing meditated by adenosine deaminases acting on RNA (ADARs) enzymes is a widespread post-transcriptional event in mammals. However, A-to-I editing in skeletal muscle remains poorly understood. By integrating strand-specific RNA-seq, whole genome bisulphite sequencing, and genome sequencing data, we comprehensively profiled the A-to-I editome in developing skeletal muscles across 27 prenatal and postnatal stages in pig, an important farm animal and biomedical model. We detected 198,892 A-to-I editing sites and found that they occurred more frequently at prenatal stages and showed low conservation among pig, human, and mouse. Both the editing level and frequency decreased during development and were positively correlated with ADAR enzymes expression. The hyper-edited genes were functionally related to the cell cycle and cell division. A co-editing module associated with myogenesis was identified. The developmentally differential editing sites were functionally enriched in genes associated with muscle development, their editing levels were highly correlated with expression of their host mRNAs, and they potentially influenced the gain/loss of miRNA binding sites. Finally, we developed a database to visualize the Sus scrofa RNA editome. Our study presents the first profile of the dynamic A-to-I editome in developing animal skeletal muscle and provides evidences that RNA editing is a vital regulator of myogenesis.

Download Full-text

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.

Download Full-text

Integrative ATAC-seq and RNA-seq Analysis of the Longissimus Muscle of Luchuan and Duroc Pigs

Frontiers in Nutrition ◽

10.3389/fnut.2021.742672 ◽

2021 ◽

Vol 8 ◽

Author(s):

Weiwei Miao ◽

Zeqiang Ma ◽

Zhanyang Tang ◽

Lin Yu ◽

Siqi Liu ◽

...

Keyword(s):

Skeletal Muscle ◽

Transcription Factors ◽

Signaling Pathway ◽

Growth And Development ◽

Muscle Development ◽

Muscle Fibers ◽

Muscle Growth ◽

Rna Seq ◽

Accessible Chromatin

Luchuan pig is a typical obese pig breed in China, and the diameter and area of its longissimus dorsi muscle fibers are significantly smaller than those of Duroc (lean) pig. Skeletal muscle fiber characteristics are related to meat quality of livestock. There is a significant correlation between the quality of different breeds of pork and the characteristics of muscle fiber, which is an important factor affecting the quality of pork. The diameter and area of muscle fibers are related to muscle growth and development. Therefore, we used the assay for transposase-accessible chromatin using sequencing (ATAC-seq) and RNA sequencing (RNA-seq) analysis to investigate the potential mechanism underlying the difference in skeletal muscle growth and development between the two types of pigs. First, transposase-accessible chromatin was analyzed to map the landscape of open chromatin regions and transcription factor binding sites. We identified several transcription factors that potentially affected muscle growth and development, including TFAP4, MAX, NHLH1, FRX5, and TGIF1. We also found that transcription factors with basic helix-loop-helix structures had a preference for binding to genes involved in muscle development. Then, by integrating ATAC-seq and RNA-seq, we found that the Wnt signaling pathway, the mTOR signaling pathway, and other classical pathways regulate skeletal muscle development. In addition, some pathways that might regulate skeletal muscle growth, such as parathyroid hormone synthesis, secretion, and action, synthesis and degradation of ketone bodies, and the thyroid hormone signaling pathway, which were significantly enriched. After further study, we identified a number of candidate genes (ASNS, CARNS1, G0S2, PPP1R14C, and SH3BP5) that might be associated with muscle development. We also found that the differential regulation of chromatin openness at the level of some genes was contrary to the differential regulation at the level of transcription, suggesting that transcription factors and transcriptional repressors may be involved in the regulation of gene expression. Our study provided an in-depth understanding of the mechanism behind the differences in muscle fibers from two species of pig and provided an important foundation for further research on improving the quality of pork.

Download Full-text

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.

Download Full-text

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.

Download Full-text

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.

Download Full-text