Abstract
The Tibetan chicken (Gallus gallus) provides high quality protein and iron for humans, which shows many phenotypic adaptations to the low oxygen. Study of the genetic mechanisms of circular RNAs (circRNAs) in hypoxia adaptation has not been reported. Four embryonic heart tissue samples from Tibetan chickens and Daheng broilers were collected. Differentially expressed circRNAs (DEcircRNAs) were identified via high-throughput sequencing. Bioinformatic analysis was used to indicate the functions and pathways of the DEcircRNAs. A total of 29 DEcircRNAs were identified between 4 Tibetan chickens and 4 Daheng broilers, including 15 upregulated and 14 downregulated DEcircRNAs in Tibetan chickens. GO analysis revealed that the DEcircRNAs were mainly involved in lung development or oxygen metabolism, such as ubiqunegative regulation of mesenchymal cell proliferation involved in lung development, oxidoreductase activity, and peroxisome. Pathway analysis showed that DEcircRNAs were mainly enriched in oxidative phosphorylation, tight junction, VEGF/MAPK/PPAR/Ras/PI3K-Akt signaling pathway. We also constructed a circRNA-miRNA-mRNA-pathway network to visualize the regulatory relationship associated with hypoxia adaptation of the tight junction pathways. The circRNA expression profile was obtained to complement the current Tibetan chicken circRNA database and provides new information for future studies into biological adaptation to hypoxic stress in the Tibetan chicken.
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Data availability
The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. The RNA-seq data generated in this study is available in National Center for Biotechnology Information under accession number PRJNA686151.
Code availability
Not applicable.
Abbreviations
- CircRNAs:
-
circular RNAs
- DEcircRNAs:
-
differentially expressed circRNAs
- lncRNAs:
-
long noncoding RNAs
- GO:
-
Gene Ontology
- KEGG:
-
Kyoto Encyclopedia of Genes and Genomes
- BP:
-
biological processes
- MF:
-
molecular functions
- CC:
-
cell compositions
- PAK1:
-
p21 protein (Cdc42/Rac)-activated kinase 1
- VEGF:
-
vascular endothelial growth factor
- MAPK:
-
mitogen-activated protein kinase
- PLIN1:
-
perilipin 1
- PPAR:
-
peroxisome proliferators-activated receptor
- CLDN:
-
claudin
- MYH11:
-
myosin, heavy chain 11, smooth muscle
- MYH1A:
-
myosin, heavy chain 1 A, skeletal muscle
- PPP2R2C:
-
protein phosphatase 2, regulatory subunit B, gamma
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Funding
This work was supported by the Science Fund for Distinguished Young Scholars of Sichuan Province (No. 2019JDJQ0021); The National modern agricultural technology system construction of China (no. CARS-41-G04); The Science and Technology support planning project of Sichuan Province (No. 2019YFN0009, No. 2020YFN0146, No. 2020YFSY0048, No. 2020YFN0096, 2021YFYZ0031).
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Conceptualization and Funding acquisition, CW.Y., and XS.J.; Data curation and Methodology, ZR.Z. and MH.Q.; Formal analysis, HR.D., QY.L., W.G., X.X., CL.Y., H.P., B.X., XY.S., L.Y., CM.H., and JL.C.; Investigation and Writing-original draft, ZR.Z., MH.Q., HR.D., QY.L., W.G., X.X., CL.Y., H.P., B.X., XY.S., L.Y., CM.H., and JL.C.; Writing – review & editing, ZR.Z. and MH.Q.; All authors read and approved the final manuscript.
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All experimental procedures adhered to the Guidelines of International Standards for Animal Welfare. The animals used in this study were approved by the Animal Care and Use Committee of Sichuan Animal Science Academy. All efforts were made to minimize the suffering of the experimental chickens.
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Zhang, Z., Qiu, M., Du, H. et al. High-throughput sequencing revealed the expression profile and potential key molecules of the circular RNAs involved in the process of hypoxic adaptation in Tibetan chickens. Biologia 76, 3439–3447 (2021). https://doi.org/10.1007/s11756-021-00848-0
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DOI: https://doi.org/10.1007/s11756-021-00848-0