Dynamic changes of miRNAs in skeletal muscle development at New Zealand rabbits

Jing, Jing; Jiang, Xichun; Zhu, Cuiyun; Zheng, Qi; Ji, Qianyun; Yin, Huiqun; Huang, Jingtong; Zhu, Yixiao; Wang, Jiao; Qin, Shuaiqi; Ling, Yinghui

doi:10.1186/s12864-021-07896-5

Cited by 3 publications

(5 citation statements)

References 53 publications

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“…To better understand the RNA regulatory networks during skeletal muscle development in rabbits, we retrieved differentially expressed miRNAs during skeletal muscle development in rabbits in one previous study [ 30 ] and identified putative DEC-DEmiRNA interactions using miRanda software. We obtained 1594 DEC–DEmiRNA interaction pairs from D0 to D35 ( Figure 6 A and Table S5 ).…”

Section: Resultsmentioning

confidence: 99%

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Genome-Wide Identification and Characterization of Circular RNAs during Skeletal Muscle Development in Meat Rabbits

Zhao

et al. 2022

Animals

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Skeletal muscle development plays a vital role in muscle quality and yield in meat rabbits. Circular RNAs (circRNAs) are a new type of single-stranded endogenous non-coding RNAs involved in different biological processes. However, our knowledge of circRNAs regulating skeletal muscle development remains largely unknown in meat rabbits. In this study, we collected the leg muscle tissues of ZIKA rabbits at three key growth stages. By performing whole-transcriptome sequencing, we found the sequential expression of day 0- (D0-), D35-, and D70-selective mRNAs mainly functioned in muscle development, nervous development, and immune response during skeletal muscle development, respectively. Then, a combination of circRNA assembly from a circRNA-seq library and the whole-transcriptome sequencing data identified 6845 credible circRNAs in our samples. Most circRNAs were transcribed from exons of known genes, contained few exons, and showed short length, and these circRNAs were more conserved between rabbits and humans than between rabbits and mice. The upregulated circRNAs, which were synchronously changed with host genes, primarily played roles in MAPK signaling pathways and fatty acid biosynthesis. The prediction of circRNA–microRNA–mRNAs networks revealed that circRNAs might be the regulators that mainly functioned in rabbits’ muscle neuron development and metabolic processes. Our work provides a catalog of circRNAs regulating skeletal muscle development at key growth stages in rabbits and might give a new insight into rabbit breeding.

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Section: Resultsmentioning

confidence: 99%

“…The differentially expressed miRNAs during the skeletal muscle development of rabbits were retrieved from a previous study conducted by Jing and colleagues [ 30 ]. The sequences of mature miRNA were retrieved from miRbase [ 31 ].…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Identification and Characterization of Circular RNAs during Skeletal Muscle Development in Meat Rabbits

Zhao

et al. 2022

Animals

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“…The KEGG analysis identified several enriched pathways might be associated with the development process, e.g., AMPK signaling, MAPK signaling, RNA degradation, and tight junction pathways. The MAPK signaling pathway has also been associated with miRNA-target regulation in animal development ( Kaitetzidou et al, 2015 ; Wang et al, 2017 ; Jing et al, 2021 ). Moreover, several sex hormone-related pathways were enriched for DEMs’ target transcripts in the earliest pairwise comparison (DS2 vs DS1), including aldosterone synthesis and secretion, GnRH signaling, and ovarian steroidogenesis pathways.…”

Section: Discussionmentioning

confidence: 99%

“…Several studies have characterized miRNAs’ functional importance in diverse biological processes, such as growth ( Yi et al, 2014 ), tissue regeneration ( Rajaram et al, 2014 ), environmental stress ( Sun et al, 2020 ), and immune responses ( Qiao et al, 2021 ). To date, several studies have focused on the miRNAs’ roles of gene regulation during animal development ( Alberti and Cochella, 2017 ; Chen et al, 2020 ; Wu et al, 2020 ; Jing et al, 2021 ; Kusama et al, 2021 ). In teleosts, the dynamics of gene expression and its regulation in early development have been described in model fishes, such as zebrafish ( Danio rerio ) ( Nepal et al, 2016 ; Kasper et al, 2017 ; Shi et al, 2020 ) and medaka ( Oryzias latipes ) ( Tani et al, 2010 ), and important aquaculture species ( Rasal et al, 2016 ; Herkenhoff et al, 2018 ), such as rainbow trout ( Oncorhynchus mykiss ) ( Ramachandra et al, 2008 ), turbot ( Scophthalmus maximus ) ( Robledo et al, 2017 ), Nile tilapia ( Oreochromis niloticus ) ( Pinhal et al, 2018 ), European sea bass ( Dicentrarchus labrax ) ( Sarropoulou et al, 2019 ), and the common carp ( Cyprinus carpio ) ( Wang et al, 2017 ; Wang et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Dynamic Expression and Gene Regulation of MicroRNAs During Bighead Carp (Hypophthalmichthys nobilis) Early Development

Zhu

Wang

et al. 2022

Front. Genet.

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The early development of fish is regulated through dynamic and complex mechanisms involving the regulation of various genes. Many genes are subjected to post-transcriptional regulation by microRNAs (miRNAs). In the Chinese aquaculture industry, the native species bighead carp (Hypophthalmichthys nobilis) is important. However, the genetic regulation related to the early development of bighead carp is unknown. Here, we generated developmental profiles by miRNA sequencing to study the dynamic regulation of miRNAs during bighead carp early development. This study identified 1 046 miRNAs, comprising 312 known miRNAs and 734 uncharacterized miRNAs. Changes in miRNA expression were identified in the six early development stages. An obviously increased expression trend was detected during the development process, with the main burst of activity occurring after the earliest stage (early blastula, DS1). Investigations revealed that several miRNAs were dominantly expressed during the development process, especially in the later stages (e.g., miR-10b-5p, miR-21, miR-92a-3p, miR-206-3p, and miR-430a-3p), suggesting that these miRNAs exerted important functions during embryonic development. The differentially expressed miRNAs (DEMs) and time-serial analysis (profiles) of DEMs were analyzed. A total of 372 miRNAs were identified as DEMs (fold-change >2, and false discovery rate <0.05), and three expression profiles of the DEMs were detected to have co-expression patterns (r > 0.7, and p < 0.05). The broad negative regulation of target genes by miRNAs was speculated, and many development-related biological processes and pathways were enriched for the targets of the DEMs, which might be associated with maternal genome degradation and embryogenesis processes. In conclusion, we revealed the repertoire of miRNAs that are active during early development of bighead carp. These findings will increase our understanding of the regulatory mechanisms of early development of fish.

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“…In the process of skeletal muscle development, some muscle-specific miRNAs or muscle-rich expressions of miRNAs involved in myogenesis were reported. For example, miR-185-3p and miR-370-3p are highly and specifically expressed in leg muscles of New Zealand rabbit fetuses, children, and adults, affecting muscle development [ 11 ], and miR-22 can inhibit the proliferation of C2C12 cells and promote their differentiation [ 12 ]. More and more studies indicate that multiple muscle-enriched miRNAs play an extremely important and essential role in muscle development.…”

Section: Introductionmentioning

confidence: 99%

MicroRNA-542-3p targets Pten to inhibit the myoblasts proliferation but suppresses myogenic differentiation independent of targeted Pten

Li,

Yue,

Feng

et al. 2024

BMC Genomics

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Background Non-coding RNA is a key epigenetic regulation factor during skeletal muscle development and postnatal growth, and miR-542-3p was reported to be conserved and highly expressed in the skeletal muscle among different species. However, its exact functions in the proliferation of muscle stem cells and myogenesis remain to be determined. Methods Transfection of proliferative and differentiated C2C12 cells used miR-542-3p mimic and inhibitor. RT-qPCR, EdU staining, immunofluorescence staining, cell counting kit 8 (CCK-8), and Western blot were used to evaluate the proliferation and myogenic differentiation caused by miR-542-3p. The dual luciferase reporter analysis and rescued experiment of the target gene were used to reveal the molecular mechanism. Results The data shows overexpression of miR-542-3p downregulation of mRNA and protein levels of proliferation marker genes, reduction of EdU+ cells, and cellular vitality. Additionally, knocking it down promoted the aforementioned phenotypes. For differentiation, the miR-542-3p gain-of-function reduced both mRNA and protein levels of myogenic genes, including MYOG, MYOD1, et al. Furthermore, immunofluorescence staining immunized by MYHC antibody showed that the myotube number, fluorescence intensity, differentiation index, and myotube fusion index all decreased in the miR-542-3p mimic group, compared with the control group. Conversely, these phenotypes exhibited an increased trend in the miR-542-3p inhibitor group. Mechanistically, phosphatase and tensin homolog (Pten) was identified as the bona fide target gene of miR-542-3p by dual luciferase reporter gene assay, si-Pten combined with miR-542-3p inhibitor treatments totally rescued the promotion of proliferation by loss-function of miR-542-3p. Conclusions This study indicates that miR-542-3p inhibits the proliferation and differentiation of myoblast and Pten is a dependent target gene of miR-542-3p in myoblast proliferation, but not in differentiation.

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Dynamic changes of miRNAs in skeletal muscle development at New Zealand rabbits

Cited by 3 publications

References 53 publications

Genome-Wide Identification and Characterization of Circular RNAs during Skeletal Muscle Development in Meat Rabbits

Genome-Wide Identification and Characterization of Circular RNAs during Skeletal Muscle Development in Meat Rabbits

Dynamic Expression and Gene Regulation of MicroRNAs During Bighead Carp (Hypophthalmichthys nobilis) Early Development

MicroRNA-542-3p targets Pten to inhibit the myoblasts proliferation but suppresses myogenic differentiation independent of targeted Pten

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