Weighted gene co-expression network indicates that the DYNLL2 is an important regulator of chicken breast muscle development and is regulated by miR-148a-3p

Li, Yuanfang; Yuan, Pengtao; Fan, Shengxin; Zhai, Bin; Jin, Wenjiao; Li, Donghua; Li, Hong; Sun, Guirong; Han, Ruili; Liu, Xiaojun; Tian, Yadong; Li, Guoxi; Kang, Xiangtao

doi:10.1186/s12864-022-08522-8

Cited by 11 publications

(7 citation statements)

References 67 publications

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“…Among these miRNAs that can bind to circRNAs, miR-206 is an essential regulator of skeletal myoblast differentiation [ 43 , 44 ]. MiR-148a-3p contributes to myoblastic differentiation by targeting DYNLL2 and promoting myosin heavy chain (MYHC) protein expression [ 45 ]. MiR-499-5p can regulate the development of skeletal muscle by regulating muscle gene expression through the NFATc1/MEF2C pathway [ 46 ].…”

Section: Discussionmentioning

confidence: 99%

CircRNAs Related to Breast Muscle Development and Their Interaction Regulatory Network in Gushi Chicken

Yuan

Zhao

et al. 2022

Genes

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Circular RNAs (circRNAs) play a significant regulatory role during skeletal muscle development. To identify circRNAs during postnatal skeletal muscle development in chickens, we constructed 12 cDNA libraries from breast muscle tissues of Chinese Gushi chickens at 6, 14, 22, and 30 weeks and performed RNA sequencing. In total, 2112 circRNAs were identified, and among them 79.92% were derived from exons. CircRNAs are distributed on all chromosomes of chickens, especially chromosomes 1–9 and Z. Bioinformatics analysis showed that each circRNA had an average of 38 miRNA binding sites, 61.32% of which have internal ribosomal entry site (IRES) elements. Furthermore, in total 543 differentially expressed circRNAs (DE-circRNAs) were identified. Functional enrichment analysis revealed that DE-circRNAs source genes are engaged in biological processes and muscle development-related pathways; for example, cell differentiation, sarcomere, and myofibril formation, mTOR signaling pathway, and TGF-β signaling pathway, etc. We also established a competitive endogenous RNA (ceRNA) regulatory network associated with skeletal muscle development. The results in this report indicate that circRNAs can mediate the development of chicken skeletal muscle by means of a complex ceRNA network among circRNAs, miRNAs, genes, and pathways. The findings of this study might help increase the number of known circRNAs in skeletal muscle tissue and offer a worthwhile resource to further investigate the function of circRNAs in chicken skeletal muscle development.

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Section: Discussionmentioning

confidence: 99%

CircRNAs Related to Breast Muscle Development and Their Interaction Regulatory Network in Gushi Chicken

Yuan

Zhao

et al. 2022

Genes

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“…During the development of the Gushi chicken breast muscle, these genes may influence intramuscular fat content and fatty acid composition to varying degrees through their involvement in fatty acid oxidation. In addition, within the turquoise module, we identified the DYNLL2 gene, which had previously been established in our earlier research as playing a pivotal role in the proliferation and differentiation of myoblasts in breast muscles [ 43 ]. In this study, the turquoise module housing this gene is not correlated with the traits related to breast muscle fatty acid composition.…”

Section: Discussionmentioning

confidence: 99%

Weighted gene co-expression network analysis identified hub genes critical to fatty acid composition in Gushi chicken breast muscle

Zhai,

Zhao,

et al. 2023

BMC Genomics

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Background The composition and content of fatty acids in the breast muscle are important factors influencing meat quality. In this study, we investigated the fatty acid composition and content in the breast muscle of Gushi chickens at different developmental stages (14 weeks, 22 weeks, and 30 weeks). Additionally, we utilized transcriptomic data from the same tissue and employed WGCNA and module identification methods to identify key genes associated with the fatty acid composition in Gushi chicken breast muscle and elucidate their regulatory networks. Results Among them, six modules (blue, brown, green, light yellow, purple, and red modules) showed significant correlations with fatty acid content and metabolic characteristics. Enrichment analysis revealed that these modules were involved in multiple signaling pathways related to fatty acid metabolism, including fatty acid metabolism, PPAR signaling pathway, and fatty acid biosynthesis. Through analysis of key genes, we identified 136 genes significantly associated with fatty acid phenotypic traits. Protein–protein interaction network analysis revealed that nine of these genes were closely related to fatty acid metabolism. Additionally, through correlation analysis of transcriptome data, we identified 51 key ceRNA regulatory networks, including six central genes, 7 miRNAs, and 28 lncRNAs. Conclusion This study successfully identified key genes closely associated with the fatty acid composition in Gushi chicken breast muscle, as well as their post-transcriptional regulatory networks. These findings provide new insights into the molecular regulatory mechanisms underlying the flavor characteristics of chicken meat and the composition of fatty acids in the breast muscle.

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“…In calves, WGCNA identified bta-miR-145 and bta-miR-199a-3p as important hub miRNAs regulating rumen development, immune system, and protein digestion [ 23 ]. This technique also established that DYNLL2 and its target miR-148-3p are important regulators of chicken myogenesis [ 24 ]. In this study, the WGCNA technique revealed key modules and hub genes related to leg muscles of embryos at four different development stages.…”

Section: Discussionmentioning

confidence: 99%

MiRNA sequencing of Embryonic Myogenesis in Chengkou Mountain Chicken

Shi

Liu

et al. 2022

BMC Genomics

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Background Skeletal muscle tissue is among the largest organ systems in mammals, essential for survival and movement. Embryonic muscle development determines the quantity and quality of muscles after the birth of an individual. MicroRNAs (miRNAs) are a significant class of non-coding RNAs that bind to the 3’UTR region of mRNA to regulate gene function. Total RNA was extracted from the leg muscles of chicken embryos in different developmental stages of Chengkou Mountain Chicken and used to generate 171,407,341 clean small RNA reads. Target prediction, GO, and KEGG enrichment analyses determined the significantly enriched genes and pathways. Differential analysis determined the significantly different miRNAs between chicken embryo leg muscles at different developmental stages. Meanwhile, the weighted correlation network analysis (WGCNA) identified key modules in different developmental stages, and the hub miRNAs were screened following the KME value. Results The clean reads contained 2047 miRNAs, including 721 existing miRNAs, 1059 known miRNAs, and 267 novel miRNAs. Many genes and pathways related to muscle development were identified, including ERBB4, MEF2C, FZD4, the Wnt, Notch, and MAPK signaling pathways. The WGCNA established the greenyellow module and gga-miR-130b-5p for E12, magenta module and gga-miR-1643-5p for E16, purple module and gga-miR-12218-5p for E19, cyan module and gga-miR-132b-5p for E21. Conclusion These results lay a foundation for further research on the molecular regulatory mechanism of embryonic muscle development in Chengkou mountain chicken and provide a reference for other poultry and livestock muscle development studies.

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Weighted gene co-expression network indicates that the DYNLL2 is an important regulator of chicken breast muscle development and is regulated by miR-148a-3p

Cited by 11 publications

References 67 publications

CircRNAs Related to Breast Muscle Development and Their Interaction Regulatory Network in Gushi Chicken

CircRNAs Related to Breast Muscle Development and Their Interaction Regulatory Network in Gushi Chicken

Weighted gene co-expression network analysis identified hub genes critical to fatty acid composition in Gushi chicken breast muscle

MiRNA sequencing of Embryonic Myogenesis in Chengkou Mountain Chicken

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