Identification and profiling of conserved and novel microRNAs from Chinese Qinchuan bovine longissimus thoracis

Sun, Jiajie; Li, Mijie; Li, Zhuanjian; Xue, Jing; Lan, Xianyong; Zhang, Chunlei; Lei, Chuzhao; Chen, Hong

doi:10.1186/1471-2164-14-42

Cited by 58 publications

(90 citation statements)

References 47 publications

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“…Most of the sequences are 22nt in length, and majority of the small RNAs are 21–23nt in length, which is the typical size range of Dicer-derived products. The results are consistent with the small RNA distribution of Boer goat [53], sheep [54] and cattle [52], [55]. The most abundant miRNAs identified in our study were highly consisted with study on Boer goat, which reported that miR-133, miR-1, miR-378 and miR-206 families were the top 20 miRNAs in 6 month old Boer goat longissimus tissue [53], indicating the importance of these miRNAs on skeletal muscle development and growth.…”

Section: Discussionsupporting

confidence: 90%

Identification and Profiling of microRNAs and Their Target Genes from Developing Caprine Skeletal Muscle

et al. 2014

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Goat is an important agricultural animal for meat production. Functional studies have demonstrated that microRNAs (miRNAs) regulate gene expression at the post-transcriptional level and play an important role in various biological processes. Although studies on miRNAs expression profiles have been performed in various animals, relatively limited information about goat muscle miRNAs has been reported. To investigate the miRNAs involved in regulating different periods of skeletal muscle development, we herein performed a comprehensive research for expression profiles of caprine miRNAs during two developmental stages of skeletal muscles: fetal stage and six month-old stage. As a result, 15,627,457 and 15,593,721 clean reads were obtained from the fetal goat library (FC) and the six month old goat library (SMC), respectively. 464 known miRNAs and 83 novel miRNA candidates were identified. Furthermore, by comparing the miRNA profile, 336 differentially expressed miRNAs were identified and then the potential targets of the differentially expressed miRNAs were predicted. To understand the regulatory network of miRNAs during muscle development, the mRNA expression profiles for the two development stages were characterized and 7322 differentially expressed genes (DEGs) were identified. Then the potential targets of miRNAs were compared to the DEGs, the intersection of the two gene sets were screened out and called differentially expressed targets (DE-targets), which were involved in 231 pathways. Ten of the 231 pathways that have smallest P-value were shown as network figures. Based on the analysis of pathways and networks, we found that miR-424-5p and miR-29a might have important regulatory effect on muscle development, which needed to be further studied. This study provided the first global view of the miRNAs in caprine muscle tissues. Our results help elucidation of complex regulatory networks between miRNAs and mRNAs and for the study of muscle development.

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Section: Discussionsupporting

confidence: 90%

Identification and Profiling of microRNAs and Their Target Genes from Developing Caprine Skeletal Muscle

et al. 2014

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“…36 We verified that the expression levels of miR-378a-3p was markedly higher in skeletal muscle than the levels in other tissues. The results suggested that miR-378a-3p might be a muscle-related miRNA, similar to other muscle-specific miRNAs that were reported previously.…”

Section: Discussionsupporting

confidence: 59%

“…36 The expression profile assay showed that miR-378a-3p expression was significantly higher than other miRNAs in the longissimus muscle (Fig. 1a), suggesting a potential role in muscle.…”

Section: Mirnas Expression Profile In Different Tissuesmentioning

confidence: 96%

miR-378a-3p promotes differentiation and inhibits proliferation of myoblasts by targeting HDAC4 in skeletal muscle development

Wei

Zhang

et al. 2016

RNA Biology

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Muscle development, or myogenesis, is a highly regulated, complex process. A subset of microRNAs (miRNAs) have been identified as critical regulators of myogenesis. Recently, miR-378a was found to be involved in myogenesis, but the mechanism of how miR-378a regulates the proliferation and differentiation of myoblasts has not been determined. We found that miR-378a-3p expression in muscle was significantly higher than in other tissues, suggesting an important effect on muscle development. Overexpression of miR-378a-3p increased the expression of MyoD and MHC in C2C12 myoblasts both at the level of mRNA and protein, confirming that miR-378a-3p promoted muscle cell differentiation. The forced expression of miR-378a-3p promoted apoptosis of C2C12 cells as evidenced by CCK-8 assay and Annexin V-FITC/PI staining results. Through TargetScan, histone acetylation enzyme 4 (HDAC4) was identified as a potential target of miR-378a-3p. We confirmed targeting of HDAC4 by miR-378a-3p using a dual luciferase assay and western blotting. Our RNAi analysis results also showed that HDAC4 significantly promoted differentiation of C2C12 cells and inhibited cell survival through Bcl-2. Therefore, we conclude that miR-378a-3p regulates skeletal muscle growth and promotes the differentiation of myoblasts through the post-transcriptional down-regulation of HDAC4.

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“…Scatter plot and log2-ratio figures were used to show the expression of miRNAs. The procedures used were as follows: 1) to obtain the ex-pression of transcripts per million, the expression of each miRNA in Qira black sheep and Hetian sheep was normalized; 2) using formulas described by previous studies (Huang et al, 2011;Sun et al, 2013;Yuan et al, 2013;Zhang et al, 2013), the fold-change and P values were calculated from the normalized expression.…”

Section: Discussionmentioning

confidence: 99%

Characterization and expression analysis of microRNAs in Qira black sheep and Hetian sheep ovaries using Solexa sequencing

Shen¹,

Chen²,

Jia³

et al. 2015

Genet. Mol. Res.

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ABSTRACT. The role of microRNAs (miRNAs) in the regulation of mammalian reproduction has been demonstrated previously. However, only a few studies have assessed the role of miRNAs in the reproduction processes of sheep. The elucidation of miRNA expression profiles in the ovaries of different sheep breeds representing fecundity extremes will be useful in understanding the roles of miRNAs in sheep reproduction. In this study, two small RNA libraries were constructed from ovary tissue taken from Qira black sheep and Hetian sheep during the estrous period and then sequenced using the Solexa sequencing method. We obtained 9,565,212 and 9,563,426 high-quality reads from Qira black sheep and Hetian sheep, respectively. In total, 531 miRNAs, including 98 putative miRNAs, were identified. Among the conserved miRNAs, 125 known miRNAs were significantly differentially expressed in the Qira black sheep and Hetian sheep libraries, with 24 upregulated and 101 downregulated in the Hetian sheep compared to the Qira black sheep. Four differentially expressed miRNAs were analyzed using real-time 7357 miRNA expression analysis in sheep ovaries ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 14 (3): 7356-7367 (2015) quantitative PCR to validate the reliability of the Solexa sequencing results. These results provide a foundation for future research on the regulation of miRNAs in sheep fertility and enrich the sheep miRNA databases.

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Identification and profiling of conserved and novel microRNAs from Chinese Qinchuan bovine longissimus thoracis

Cited by 58 publications

References 47 publications

Identification and Profiling of microRNAs and Their Target Genes from Developing Caprine Skeletal Muscle

Identification and Profiling of microRNAs and Their Target Genes from Developing Caprine Skeletal Muscle

miR-378a-3p promotes differentiation and inhibits proliferation of myoblasts by targeting HDAC4 in skeletal muscle development

Characterization and expression analysis of microRNAs in Qira black sheep and Hetian sheep ovaries using Solexa sequencing

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