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

Ling, Yinghui; Zheng, Qi; Sui, Menghua; Zhu, Lu; Xu, Lei; Zhang, Yunhai; Liu, Ya; Fang, Fugui; Chu, Mingxing; Ma, Yue; Zhang, Xiaorong

doi:10.3390/ijms20163950

Cited by 32 publications

(36 citation statements)

References 60 publications

(49 reference statements)

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“…According to the present study, lncRNAs and mRNAs are expressed in a stage-dependent manner, consistent with previous studies [34][35][36]. The results of both hierarchical clustering and PCA showed that the GRI and MGI stages were more distinct than MGI and RSI stages at the mRNA or lncRNA level (Fig.…”

Section: Discussionsupporting

confidence: 92%

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

Tan¹,

Gan

Shen

et al. 2020

Preprint

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BackgroundGene 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: of the inflection point with the maximum growth rate (MGI), inflection point of gradual increase stage to rapid increasing stage (GRI) and inflection point of rapid increasing stage to 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. ResultsQingyu 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, 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 energy and 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). ConclusionThese findings indicate lncRNAs and a certain lncRNA G1430 involved in the regulatory mechanism during pig muscle development. Our findings provide the basis for further investigation of the regulatory mechanisms and molecular genetics of muscle development in pigs.

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Section: Discussionsupporting

confidence: 92%

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

Tan¹,

Gan

Shen

et al. 2020

Preprint

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“…Downregulated expression of the HDAC9 gene has been observed in callipyge animals relative to non-callipyge sheep[66] (Vuocolo et al, 2007). Furthermore, EYA2 was reported to be associated with muscle hypertrophy in goats[64] (Ling et al, 2019). From the genes mentioned here, LIG1 and STK38L were associated with BW in the Afrino population, while XIRP2 was linked to BW and TWW in the Grootfontein Merino population.…”

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confidence: 73%

Identification of Genes Targeted in South African Merino and Afrino Sheep Populations Under Long-Term Selection for Reproduction and Body Weight

Snyman¹,

Süllwald

Olivier³

et al. 2020

Preprint

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Background: Reproductive performance and body weight are of the utmost economic importance in determining the efficiency of sheep production. Simultaneous selection for increased reproductive performance and early growth traits is a common strategy in many flocks, but ambiguous results regarding the relationship between reproduction and body weight have been reported. The objective of this study was to perform a genome-wide association study (GWAS) in two South African Merino flocks and an Afrino sheep flock that were selected for both reproduction and body weight over decades. The GWAS aimed to identify SNPs associated with genes affecting the traits number of lambs born (NLB), number of lambs weaned (NLW), total weight of lamb weaned (TWW) and body weight (BW) and thus to ascertain which genes were targeted through directional selection.Results: In the GWAS, 16 SNP markers associated with reproductive traits were identified among the three populations, while 15 SNPs were associated with body weight. These SNPs were linked respectively to 26 and 21 documented genes in the sheep genome. Most of these genes were previously associated in literature with reproduction related, as well as with growth related traits in various farm animal species. This study, supported by results from previous studies performed on sheep and cattle, identified the following genes that warrant further investigation as to their functions and processes relating to growth and reproduction in sheep: MAP7D1, TRAPPC3, THRAP3, TRMP8, SPP2, HDAC9, ZFHX3, SIX6, C14orf39, TAF4B, TRSP1 EYA2, RBMS3, STL38L, BSPH1, LIG1, CABP5 and ELSPBP1. Conclusions: Long-term selection in the flocks for both body weight and reproductive traits, and especially on the composite trait TWW, have favoured genes with pleiotropic effects influencing both groups of traits. SNPs associated with these pleiotropic genes were detected in the association analyses for the various traits.

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“…Considering the knockdown of DICER1, we realized that the KEGG pathways of the downregulated mRNAs include PI3K-AKT signaling pathway [62], Focal adhesion [66], and ECM receptor interaction [66], which are also recognized to be associated with muscle development. Moreover, FoxO signaling pathway [66], MAPK signaling pathway [70], Rap1 signaling pathway [68,69], and mTOR signaling pathway [77] were also known to be associated with the upregulated miRNAs. Moreover, all these pathways are related to muscle development.…”

Section: Discussionmentioning

confidence: 98%

“…Moreover, Rap 1 is a small GTPase that regulates different processes, including tightening of cell-cell junction [68], cell polarity, and cell adhesion [69]. MAPK signaling pathway is indicated to regulate the regeneration and proliferation of muscle stem cells [70]. In addition, the MAPK signaling pathway plays a signi cant role during myoblast differentiation [71,72].…”

Section: Discussionmentioning

confidence: 99%

CDR1as related miRNA-mRNA networks in differentiating goat skeletal muscle satellite cells

Kyei

Liu

et al. 2020

Preprint

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Background: Myogenesis is a complex process controlled by several coding and non-coding RNAs (ncRNAs) such as circular RNAs (circRNAs) that well-known function as endogenous microRNAs (miRNAs) sponges. Over the past few years, numerous circRNAs have been known and their roles in biological processes have begun to be understood. Cerebellar Degeneration-Related protein 1 antisense (CDR1as), the most spotlighted circRNA as miR-7 sponge that has been blooming circRNAs’ research for a decade, and can potentially sponge several miRNAs in disease and muscle physiology. Nevertheless, the linear-RNAs-differed character that the acute interventions for circRNAs do not affect miRNAs levels, and has retarded the transcriptome-wide discovery of miRNAs sponged by. Therefore, the purpose of this study was to provide the transcriptomic effect of CDR1as during muscle differentiation.Methods: siCDR1as and siDICER1 were transfected into goat skeletal muscle satellite cells (SMSCs). RNA-seq technology and bioinformatics tools were used to analyze genes that are deregulated by siCDR1as and siDICER1. quantitative PCR was used to verify the expression levels of the differentially expressed mRNAs and miRNAs. Results: Here, to systematically identify miRNAs targeting CDR1as, we employed the critical enzyme DICER1 that governs the biogenesis of miRNAs. The deficiency of either DICER1 or CDR1as inhibited myogenic differentiation of SMSCs, and knockdown of DICER1 decreased the expression of CDR1as. Moreover, we screened for the targeted messenger RNAs (mRNAs) and miRNAs in SMSCs transfected with siDICER1 or siCDR1as respectively and found out that some well-known muscle-related pathways such as phosphoinositide 3-kinase (PI3K)-AKT signaling pathway, Rap1 signaling pathway, and MAPK signaling pathway were enriched in all groups. Further, regarding the miRNAs identified in siDICER1 and siCDR1as together with the sequence complementary information, we identified 11 miRNAs including miR-1, miR-206, and miR-27a-5p which are more likely to be novel targets for CDR1as. Conclusion: In summary, our study provides a perspective on the potential functions and relationship between CDR1as and DICER1 during muscle development.

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

Cited by 32 publications

References 60 publications

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

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

Identification of Genes Targeted in South African Merino and Afrino Sheep Populations Under Long-Term Selection for Reproduction and Body Weight

CDR1as related miRNA-mRNA networks in differentiating goat skeletal muscle satellite cells

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