Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Apr 12:11:e15093.
doi: 10.7717/peerj.15093. eCollection 2023.

Identification of key genes in bovine muscle development by co-expression analysis

Junxing Zhang #  1 , Hui Sheng #  1 , Cuili Pan  1 , Shuzhe Wang  1 , Mengli Yang  1 , Chunli Hu  1 , Dawei Wei  1 , Yachun Wang  2 , Yun Ma  1
Affiliations

Identification of key genes in bovine muscle development by co-expression analysis

Junxing Zhang et al. PeerJ. .

Abstract

Background: Skeletal muscle is not only an important tissue involved in exercise and metabolism, but also an important part of livestock and poultry meat products. Its growth and development determines the output and quality of meat to a certain extent, and has an important impact on the economic benefits of animal husbandry. Skeletal muscle development is a complex regulatory network process, and its molecular mechanism needs to be further studied.

Method: We used a weighted co-expression network (WGCNA) and single gene set enrichment analysis (GSEA) to study the RNA-seq data set of bovine tissue differential expression analysis, and the core genes and functional enrichment pathways closely related to muscle tissue development were screened. Finally, the accuracy of the analysis results was verified by tissue expression profile detection and bovine skeletal muscle satellite cell differentiation model in vitro (BSMSCs).

Results: In this study, Atp2a1, Tmod4, Lmod3, Ryr1 and Mybpc2 were identified as marker genes in muscle tissue, which are mainly involved in glycolysis/gluconeogenesis, AMPK pathway and insulin pathway. The assay results showed that these five genes were highly expressed in muscle tissue and positively correlated with the differentiation of bovine BSMSCs.

Conclusions: In this study, several muscle tissue characteristic genes were excavated, which may play an important role in muscle development and provide new insights for bovine molecular genetic breeding.

Keywords: BSMSCs; Breeding; GSEA; Muscle; WGCNA.

PubMed Disclaimer

Conflict of interest statement

The authors declare there are no competing interests.

Figures

Figure 1
Figure 1. Sample dendrogram of GSE137943 dataset.
Figure 2
Figure 2. Gene co expression network was constructed by GSE137943 dataset.
Analysis of the scale-free fit index for soft-thresholding powers (left) and the mean connectivity for various soft-thresholding powers (right); (B) Gene expression clustering tree and recognition module in co-expression network; (C) network heatmap plot in the co-expression modules.
Figure 3
Figure 3. Module-trait correlations analysis in muscle tissue (GSE137943).
(A) Heat map of correlation between GSE137943 data set module and muscle tissue; (B) Significance of genes related to muscle tissue in the magenta module (each dot represents a gene in the magenta module); (C) Module eigengene (y-axis) across samples (x-axis) from the magenta module (associated to muscle tissue).
Figure 4
Figure 4. GO and KEGG analysis.
The visualization results of (A) partial GO biological function analysis and (B) partial KEGG analysis of magenta module gene. The first 10 important enrichment pathways are shown.
Figure 5
Figure 5. Identification of Hub gene.
(A) Correlation of the top 20 genes with high MM and GS in the magenta module; (B) the top 20 genes with the highest connection degree in magenta module were identified by Cytoscape software; (C) identify the common genes in the co-expression network and PPI network.
Figure 6
Figure 6. The gene set enrichment analysis results of hub gene.
Pathway enrichment analysis of genes positively associated with (A) Atp2a1, (B) Tmod4, (C) Lmod3, (D) Mybpc2 and (E) Ryr1 in the GSE137943 dataset.
Figure 7
Figure 7. Expression of hub genes in dataset GSE137943.
(A–E) Expression levels of (A) Atp2a1, (B) Tmod4, (C) Lmod3, (D) Mybpc2, and (E) Ryr1 were significantly increased in muscle tissue.
Figure 8
Figure 8. Expression of hub genes in dataset GSE116775.
(A–E) Expression levels of (A) Atp2a1, (B) Tmod4, (C) Lmod3, (D) Mybpc2, and (E) Ryr1 were significantly increased in muscle tissue.
Figure 9
Figure 9. The expression level of hub gene in newborn calf tissue samples was detected.
(A–E) Compared with other tissues, the expression levels of (A) Atp2a1, (B) Tmod4, (C) Lmod3, (D) Mybpc2, and (E) Ryr1 in muscle tissue were significantly increased.
Figure 10
Figure 10. Expression levels of hub genes were examined in tissue samples from 2.5 year old cattle.
(A–E) Compared with other tissues, the expression levels of (A) Atp2a1, (B) Tmod4, (C) Lmod3, (D) Mybpc2, and (E) Ryr1 in muscle tissue were significantly increased.
Figure 11
Figure 11. To induce myogenic differentiation of bovine skeletal muscle satellite cells.
(A) Cell state map of bovine BSMSCs in different culture periods; GM: Proliferative phase, DM1-5: Cell differentiation day 1 to day 5; (B–C) The mRNA expression levels of MyOG and MyHC in different culture periods were detected; (D) The bovine BSMSCs differentiated for 0 (D0), 3 (D3) and 5 days (D5) were analyzed by immunofluorescence staining (x200). Compared with the control, two asterisks (**) means extremely significant difference (P < 0.01).
Figure 12
Figure 12. Expression levels of hub genes in bovine skeletal muscle satellite cells at different culture periods.
(A–E) Compared with that before differentiation, the expression levels of (A) Atp2a1, (B) Tmod4, (C) Lmod3, (D) Mybpc2, and (E) Ryr1 were significantly increased after induction.
Figure 13
Figure 13. Circos plot to indicate the relationship between hub genes and KEGG pathways.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Bennett PM, Furst DO, Gautel M. The C-protein (myosin binding protein C) family: regulators of contraction and sarcomere formation? Reviews of Physiology Biochemistry and Pharmacology. 1999;138:203–234. doi: 10.1007/BFb0119628. - DOI - PubMed
    1. Botia JA, Vandrovcova J, Forabosco P, Guelfi S, D’Sa K, The United Kingdom Brain Expression Consortium. Hardy J, Lewis CM, Ryten M, Weale ME. An additional k-means clustering step improves the biological features of WGCNA gene co-expression networks. BMC Systems Biology. 2017;11(1):47. doi: 10.1186/s12918-017-0420-6. - DOI - PMC - PubMed
    1. Brillantes AM, Bezprozvannaya S, Marks AR. Developmental and tissue-specific regulation of rabbit skeletal and cardiac muscle calcium channels involved in excitation-contraction coupling. Circulation Research. 1994;75(3):503–510. doi: 10.1161/01.res.75.3.503. - DOI - PubMed
    1. Calabrese G, Bennett BJ, Orozco L, Kang HM, Eskin E, Dombret C, De Backer O, Lusis AJ, Farber CR. Systems genetic analysis of osteoblast-lineage cells. PLOS Genetics. 2012;8(12):e1003150. doi: 10.1371/journal.pgen.1003150. - DOI - PMC - PubMed
    1. Chang MW, Yang JH, Tsitsipatis D, Yang X, Martindale JL, Munk R, Pandey PR, Banskota N, Romero B, Batish M, Piao Y, Mazan-Mamczarz K, De S, Abdelmohsen K, Wilson GM, Gorospe M. Enhanced myogenesis through lncFAM-mediated recruitment of HNRNPL to the MYBPC2 promoter. Nucleic Acids Research. 2022;50(22):13026–13044. doi: 10.1093/nar/gkac1174. - DOI - PMC - PubMed

Publication types

LinkOut - more resources