scholarly journals Comprehensive Analysis of LncRNA Reveals the Temporal-Specific Module of Goat Skeletal Muscle Development

2019 ◽  
Vol 20 (16) ◽  
pp. 3950 ◽  
Author(s):  
Yinghui Ling ◽  
Qi Zheng ◽  
Menghua Sui ◽  
Lu Zhu ◽  
Lina Xu ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Signaling Pathway ◽  
Muscle Development ◽  
Developmental Stages ◽  
Mapk Signaling ◽  
Capra Hircus ◽  
Skeletal Muscle Development ◽  
Complex Processes ◽  
P53 Signaling ◽  
Functional Transition

A series of complex processes regulate muscle development, and lncRNAs play essential roles in the regulation of skeletal myogenesis. Using RNA sequencing, we profiled the lncRNA expression during goat (Capra hircus) skeletal muscle development, which included seven stages across fetal 45 (F45), 65 (F65), 90 (F90), 120 (F120), 135 (F135) days, born for 24 h (B1) and 90 (B90) days. A total of 15,079 lncRNAs were identified in the seven stages, and they were less conservative with other species (human, cow, and mouse). Among them, 547 were differentially expressed, and they divided the seven stages into three functional transition periods. Following weighted gene co-expression network analysis (WGCNA), five lncRNA modules specific for developmental stages were defined as three types: ‘Early modules’, ‘late modules’, and ‘individual-stage-specific modules’. The enrichment content showed that ‘early modules’ were related to muscle structure formation, ‘late modules’ participated in the ‘p53 signaling pathway’ and other pathways, the F90-highly related module was involved in the ‘MAPK signaling pathway’, and other pathways. Furthermore, we identified hub-lncRNA in three types of modules, and LNC_011371, LNC_ 007561, and LNC_001728 may play important roles in goat skeletal muscle. These data will facilitate further exploration of skeletal muscle lncRNA functions at different developmental stages in goats.

scholarly journals Inhibition of the JNK/MAPK signaling pathway by myogenesis-associated miRNAs is required for skeletal muscle development

2018 ◽  
Vol 25 (9) ◽  
pp. 1581-1597 ◽  
Author(s):  
Shu-Juan Xie ◽  
Jun-Hao Li ◽  
Hua-Feng Chen ◽  
Ye-Ya Tan ◽  
Shu-Rong Liu ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Signaling Pathway ◽  
Muscle Development ◽  
Mapk Signaling ◽  
Mapk Signaling Pathway ◽  
Skeletal Muscle Development

scholarly journals Mechanism and Functions of Identified miRNAs in Poultry Skeletal Muscle Development – A Review

2019 ◽  
Vol 19 (4) ◽  
pp. 887-904
Author(s):  
Asiamah Amponsah Collins ◽  
Kun Zou ◽  
Zhang Li ◽  
Su Ying
Keyword(s):  
Skeletal Muscle ◽  
Candidate Genes ◽  
Skeletal Muscles ◽  
Muscle Development ◽  
Muscle Growth ◽  
Skeletal Muscle Development ◽  
Single Nucleotide ◽  
Complex Processes ◽  
Muscle Formation ◽  
Gene Regulatory

AbstractDevelopment of the skeletal muscle goes through several complex processes regulated by numerous genetic factors. Although much efforts have been made to understand the mechanisms involved in increased muscle yield, little work is done about the miRNAs and candidate genes that are involved in the skeletal muscle development in poultry. Comprehensive research of candidate genes and single nucleotide related to poultry muscle growth is yet to be experimentally unraveled. However, over a few periods, studies in miRNA have disclosed that they actively participate in muscle formation, differentiation, and determination in poultry. Specifically, miR-1, miR-133, and miR-206 influence tissue development, and they are highly expressed in the skeletal muscles. Candidate genes such as CEBPB, MUSTN1, MSTN, IGF1, FOXO3, mTOR, and NFKB1, have also been identified to express in the poultry skeletal muscles development. However, further researches, analysis, and comprehensive studies should be made on the various miRNAs and gene regulatory factors that influence the skeletal muscle development in poultry. The objective of this review is to summarize recent knowledge in miRNAs and their mode of action as well as transcription and candidate genes identified to regulate poultry skeletal muscle development.

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

Animals ◽  
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.

scholarly journals Integrated Analysis Reveals a lncRNA–miRNA–mRNA Network Associated with Pigeon Skeletal Muscle Development

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1787
Author(s):  
Tao Zhang ◽  
Can Chen ◽  
Shushu Han ◽  
Lan Chen ◽  
Hao Ding ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Muscle Development ◽  
Expression Profiles ◽  
Mapk Signaling ◽  
Functional Enrichment ◽  
Integrated Analysis ◽  
Skeletal Muscle Development ◽  
Stem Analysis ◽  
Cerna Network ◽  
Connectivity Degree

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

scholarly journals Analysis of long intergenic non-coding RNAs transcriptomic profiling in skeletal muscle growth during porcine embryonic development

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Wenjuan Zhao ◽  
Zijing Li ◽  
Quan Liu ◽  
Su Xie ◽  
Mengxun Li ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Signaling Pathway ◽  
Muscle Development ◽  
Target Genes ◽  
Muscle Growth ◽  
Skeletal Muscle Development ◽  
Protein Coding ◽  
Development Stages ◽  
Non Coding Rnas ◽  
Embryonic Muscle

AbstractSkeletal muscle growth plays a critical role during porcine muscle development stages. Genome-wide transcriptome analysis reveals that long intergenic non-coding RNAs (lincRNAs) are implicated as crucial regulator involving in epigenetic regulation. However, comprehensive analysis of lincRNAs in embryonic muscle development stages remain still elusive. Here, we investigated the transcriptome profiles of Duroc embryonic muscle tissues from days 33, 65, and 90 of gestation using RNA-seq, and 228 putative lincRNAs were identified. Moreover, these lincRNAs exhibit the characteristics of shorter transcripts length, longer exons, less exon numbers and lower expression level compared with protein-coding transcripts. Expression profile analysis showed that a total of 120 lincRNAs and 2638 mRNAs were differentially expressed. In addition, we also performed quantitative trait locus (QTL) mapping analysis for differentially expressed lincRNAs (DE lincRNAs), 113 of 120 DE lincRNAs were localized on 2200 QTLs, we observed many QTLs involved in growth and meat quality traits. Furthermore, we predicted potential target genes of DE lincRNAs in cis or trans regulation. Gene ontology and pathway analysis reveals that potential targets of DE lincRNAs mostly were enriched in the processes and pathways related to tissue development, MAPK signaling pathway, Wnt signaling pathway, TGF-beta signaling pathway and insulin signaling pathway, which involved in skeletal muscle physiological functions. Based on cluster analysis, co-expression network analysis of DE lincRNAs and their potential target genes indicated that DE lincRNAs highly regulated protein-coding genes associated with skeletal muscle development. In this study, many of the DE lincRNAs may play essential roles in pig muscle growth and muscle mass. Our study provides crucial information for further exploring the molecular mechanisms of lincRNAs during skeletal muscle development.

scholarly journals Analysis of Long Intergenic Non-Coding RNAs Transcriptomic Profiling in Skeletal Muscle Growth During Porcine Embryonic Development

2021 ◽  
Author(s):  
Wenjuan Zhao ◽  
Zijing Li ◽  
Quan Liu ◽  
Su Xie ◽  
Mengxun Li ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Signaling Pathway ◽  
Muscle Development ◽  
Target Genes ◽  
Muscle Growth ◽  
Skeletal Muscle Development ◽  
Protein Coding ◽  
Development Stages ◽  
Non Coding Rnas ◽  
Embryonic Muscle

Abstract Skeletal muscle growth plays a critical role during porcine muscle development stages. Genome-wide transcriptome analysis reveals that thousands of long intergenic non-coding RNAs (lincRNAs) have been identified in various species and implicated as crucial regulator involving in epigenetic regulation. However, comprehensive analysis of lincRNAs in embryonic muscle development stages remain still elusive. Here, we investigated the transcriptome profiles of duroc embryonic muscle tissues from days 33, 65, and 90 of gestation using RNA-seq, there were 228 putative lincRNAs identified. Moreover, these lincRNAs exhibit the characteristics of shorter transcripts length, longer exons, less exon numbers and lower expression level compared with protein-coding transcripts. Differential expression analysis showed that a total of 91 lincRNAs and 2638 mRNAs were differentially expressed. In addition, we also performed quantitative trait locus (QTL) mapping analysis for DE lincRNAs, 113 of 120 DE lincRNAs were localized on 2200 QTLs, we observed many QTLs involved in growth and meat quality traits. Furthermore, we predicted potential target genes of DE lincRNAs in cis or trans regulation. Gene ontology and pathway analysis reveals that potential targets of DE lincRNAs mostly were enriched in the processes and pathways related to tissue development, MAPK signaling pathway, Wnt signaling pathway, TGF-beta signaling pathway and insulin signaling pathway, which involved in skeletal muscle physiological functions. Based on cluster analysis, a co-expression network analysis of DE lincRNAs and their potential target genes indicated that DE lincRNAs highly regulated protein-coding genes associated with skeletal muscle development. In this study, many of the DE lincRNAs identified may play essential roles in pig muscle growth and muscle mass. Our study provides crucial information for exploring further the molecular mechanisms of lincRNAs during skeletal muscle development.

Systematic analyses reveal RNA editing events involved in skeletal muscle development of goat (Capra hircus)

2020 ◽  
Vol 20 (5) ◽  
pp. 633-643
Author(s):  
Liu Yang ◽  
Li Li ◽  
Bismark Kyei ◽  
Jiazhong Guo ◽  
Siyuan Zhan ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Rna Editing ◽  
Muscle Development ◽  
Capra Hircus ◽  
Skeletal Muscle Development
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