Identification and Functional Prediction of Circular RNAs Related to Growth Traits and Skeletal Muscle Development in Duroc pigs

Ma, Lixia; Chen, Wei; Li, Shiyin; Qin, Ming; Zeng, Yongqing

doi:10.3389/fgene.2022.858763

Cited by 5 publications

(4 citation statements)

References 41 publications

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“…ADG is considered a growth trait of pigs and an essential indicator in the process of pig production that directly affects the economic efficiency of farmers. Our laboratory previously reported the identification and functional prediction of circular RNAs, long noncoding RNAs, and mRNAs related to growth traits and skeletal muscle development in Duroc pigs with different ADGs [ 18 ]. In this study, we applied WGBS technology for methylation analysis of Duroc pigs at various growth rates to identify significant differential DMR-related genes.…”

Section: Discussionmentioning

confidence: 99%

Integrated analysis of the DNA methylome and RNA transcriptome during the development of skeletal muscle in Duroc pigs

Li,

Wang,

Chen

et al. 2024

BMC Genomics

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Background Skeletal muscle development plays a crucial role in yield and quality of pork; however, this process is influenced by various factors. In this study, we employed whole-genome bisulfite sequencing (WGBS) and transcriptome sequencing to comprehensively investigate the longissimus dorsi muscle (LDM), aiming to identify key genes that impact the growth and development of Duroc pigs with different average daily gains (ADGs). Results Eight pigs were selected and divided into two groups based on ADGs: H (774.89 g) group and L (658.77 g) group. Each pair of the H and L groups were half-siblings. The results of methylation sequencing revealed 2631 differentially methylated genes (DMGs) involved in metabolic processes, signalling, insulin secretion, and other biological activities. Furthermore, a joint analysis was conducted on these DMGs and the differentially expressed genes (DEGs) obtained from transcriptome sequencing of the same individual. This analysis identified 316 differentially methylated and differentially expressed genes (DMEGs), including 18 DMEGs in promoter regions and 294 DMEGs in gene body regions. Finally, LPAR1 and MEF2C were selected as candidate genes associated with muscle development. Bisulfite sequencing PCR (BSP) and quantitative real-time PCR (qRT–PCR) revealed that the promoter region of LPAR1 exhibited significantly lower methylation levels (P < 0.05) and greater expression levels (P < 0.05) in the H group than in the L group. Additionally, hypermethylation was observed in the gene body region of MEF2C, as was a low expression level, in the H group (P < 0.05). Conclusions These results suggest that the differences in the ADGs of Duroc pigs fed the same diet may be influenced by the methylation levels and expression levels of genes related to skeletal muscle development.

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Section: Discussionmentioning

confidence: 99%

Integrated analysis of the DNA methylome and RNA transcriptome during the development of skeletal muscle in Duroc pigs

Li,

Wang,

Chen

et al. 2024

BMC Genomics

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“…Traditional gene function research has illuminated the involvement of MRFs, Mstn, and various signaling pathways in the fundamental processes regulating skeletal muscle development. However, with the advancement of novel technologies and research methods, it has become evident that non-coding RNAs, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), also play pivotal roles in skeletal muscle development (74). The following section will categorizes and briefly introduces the relevant genes related to the regulation of skeletal muscle fiber types in poultry.…”

Section: Regulatory Mechanisms Involved In the Poultry Skeletal Muscl...mentioning

confidence: 99%

Molecular mechanisms underlying the impact of muscle fiber types on meat quality in livestock and poultry

Mo,

Zhang,

Wang

et al. 2023

Front. Vet. Sci.

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In the past, the primary emphasis of livestock and poultry breeding was mainly on improving the growth rate, meat production efficiency and disease resistance. However, the improvement of meat quality has become a major industrial focus due to the ongoing advancements in livestock and poultry breeding. Skeletal muscles consist of multinucleated myofibers formed through the processes of myoblast proliferation, differentiation and fusion. Muscle fibers can be broadly classified into two main types: slow-twitch (Type I) and fast-twitch (Type II). Fast-twitch fibers can be further categorized into Type IIa, Type IIx, and Type IIb. The proportion of Type I and Type IIa muscle fibers is positively associated with meat quality, while the presence of Type IIb muscle fibers in skeletal muscle tissue is inversely related to meat quality. Consequently, muscle fiber composition directly influences meat quality. The distribution of these fiber types within skeletal muscle is governed by a complex network, which encompasses numerous pivotal regulators and intricate signaling pathways. This article aims to succinctly outline the parameters utilized for assessing meat quality, elucidate the relationship between muscle fiber composition and meat quality as well as elaborate on the relevant genetic factors and their molecular mechanisms that regulate muscle fiber types in livestock and poultry. This summary will enrich our comprehension of how to improve meat quality in livestock and poultry, providing valuable insights for future improvements.

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“…Because it is highly conservative in pigs and mice, C2C12 was used to verify the specific mechanism of circCSDE1 regulating the proliferation and differentiation of myoblasts [32]. Ma identified and predicted circRNA in Duroc pigs with different daily weight gain [33]. Yan screened the highly conservative circFGFR2, and explained that circFGFR2 regulates myogenesis and skeletal muscle regeneration through feedback loop on C2C12 [34].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide analysis of circular RNA-mediated ceRNA regulation in porcine skeletal muscle development

et al. 2023

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Background As a diverse and abundant class of endogenous RNAs, circular RNAs (circRNAs) participate in various biological processes including cell proliferation and apoptosis. Nevertheless, few researchers have investigated the role of circRNAs in muscle development in cultivated pigs. Results In this study, we used RNA-seq to construct circRNA expression profiles in skeletal muscle of Jinfen White pigs at the age of 1, 90, and 180 days. Among the 16,990 identified circRNAs, 584 circRNAs were differentially expressed. Moreover, the enrichment analysis of DE circRNA host genes showed that they were mainly involved in muscle contraction, muscle organ development and muscle system processes, as well as AMPK and cAMP-related signal pathways. We also constructed a circRNA–miRNA–mRNA co-expression network to find key circRNAs which many involved in the regulation of porcine skeletal muscle development through the competitive endogenous RNA (ceRNA) mechanism. It is noteworthy that circ_0018595/miR-1343/PGM1 axis may play a regulatory role in the development of porcine skeletal muscle. Conclusions This study identified the circRNAs and present the circRNA expression profile in the development of pigs, revealed that DE circRNA host genes participate in different cell fates and enriched the porcine ceRNA network. Thus, this work will become a valuable resource for further in-depth study of the regulatory mechanism of circRNA in the development of porcine skeletal muscle.

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Identification and Functional Prediction of Circular RNAs Related to Growth Traits and Skeletal Muscle Development in Duroc pigs

Cited by 5 publications

References 41 publications

Integrated analysis of the DNA methylome and RNA transcriptome during the development of skeletal muscle in Duroc pigs

Integrated analysis of the DNA methylome and RNA transcriptome during the development of skeletal muscle in Duroc pigs

Molecular mechanisms underlying the impact of muscle fiber types on meat quality in livestock and poultry

Genome-wide analysis of circular RNA-mediated ceRNA regulation in porcine skeletal muscle development

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