Integrative and comparative analysis of transcriptional profiles and competitive endogenous RNA regulatory networks to identify key genes associated with heat stress in broiler chickens

Document Type : Research Paper

Authors

Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Alborz, Iran.

Abstract

Broilers are particularly sensitive to high ambient temperatures, which may have a negative impact on their welfare and production efficiency. The aim of the study was to combine a literature review analysis of transcriptional profiling and a competitive endogenous regulatory network analysis (CERNA) to identify the key messenger and non-coding RNAs involved in the molecular regulation of the cells of the pituitary gland and the brain in heat stress broiler chickens. Overall, two long non-coding RNA, 11 microRNAs and 426 common mRNAs and genes were identified that showed significant differences in expression between the two tissues. From the analysis, 12 major genes (HSP90A1, HSPA5, HSP90B1, HSPA4, HUSY1, AHSA2, ALB, DNAJA1, DNAJA4, HSPA4L, and HSPH1) were found to be more extensively expressed in broiler chickens under heat stress than in control chickens. In addition, after reconstructing the competitive endogenous RNA regulatory network and the associated candidate modules, the main important metabolic signalling pathways identified were protein-folding chaperones, cellular component organisation, protein-binding to heat shock proteins, the endoplasmic reticulum chaperone complex, and protein-processing signalling pathways in the endoplasmic reticulum. Overall, considering the identified RNAs involved in the ceRNA regulatory network that underlie phenotypic differences in the severity of heat stress, this study may provide new insights into the molecular mechanisms underlying the control of heat stress severity and resistance in broiler chickens.

Keywords

Main Subjects

Extended Abstract

Introduction

Broilers are an important breed of livestock and play an important role in food security. In poultry farming, the higher production rate is largely dependent on nutrient intake, climate conditions and ambient humidity. In recent years, climate conditions have changed, leading to an increase in average global temperature, which is contributing to global warming. Broiler meat is an important and essential source of food for humans and accounts for about 34.3 per cent of global meat production. However, chickens are particularly sensitive to heat stress. Despite various efforts to mitigate the adverse effects of heat stress on broiler chickens, the molecular mechanisms and regulatory functions involved in their biological response are still not fully understood. The aim of this study was to combine the analysis of the transcriptional profiling with literature review and analysis of the competitive regulatory network of endogenous RNA (ceRNA). The aim of this approach was to identify the key messenger RNA (mRNA) and non-coding RNA (RNA) involved in the molecular regulation of the cells of the pituitary gland and the brain under heat stress in broiler chickens.

 

Materials and Methods

The study analysed transcription profiles from two types of brain tissue: pituitary gland and brain stem cells. We performed a comparative transcriptome analysis of the RNA-Seq and microarray data sets to detect the differences in gene expression between two groups of broiler chickens: the heat-treated group and the control group. Following this, we explored the ontology of the relevant genes as identified by data analysis and literature review. In addition, we reconstructed a competitive endogenous RNA regulatory network highlighting four candidate modules related to heat stress in broiler chickens.

 

Results and Discussion

Results from this study identified two long non-coding (ncRNA) RNAs, 11 microRNAs and 426 common mRNAs and genes that showed significant differences in expression between the two tissues. After analysing the interactions between the differentially expressed genes and building a network of protein interactions, we identified 12 major interaction genes (mRNAs): HSP90A1, HSPA5, HSP90B1, HSPA4, HSPA2, HSPA3, HSPA4L, HSPA2, ALB, DNAJA1, DNAJA4, and DNAJA4. These genes showed increased expression in broiler chickens under heat stress compared with control chickens. In addition, we reconstructed a competitive endogenous RNA regulatory network and identified four related candidate modules by means of clustering. An annotation analysis of the identified RNA has shown their association with 8, 7 and 27 relevant pathways for heat stress, respectively, in the categories of biological processes, molecular functions and cellular constituents. Notably, the major metabolic signalling pathways identified were those related to protein-folding chaperones, cellular component organisation, cellular processes, cellular biogenesis, thermal protein binding, endoplasmic reticulum chaperone complexes, and endoplasmic reticulum protein processing signalling.

 

Conclusion

The results suggest that combining transcriptomic profiles with literature reviews and analysis of the CERN in brain tissue samples, especially the pituitary and the cerebral cortex, under heat stress conditions, may help to identify key coding and non-coding RNA. This integrated approach provides valuable insights into the genetic and regulatory mechanisms involved in broiler chicken heat stress. In addition, it can help to address the problems of heat stress and improve their performance characteristics.

Author Contributions

Conceptualization: Faezeh Hesari, Mostafa Sadeghi, Seyed Reza Miraei-Ashtiani, and Farzad Ghafouri; methodology: Faezeh Hesari; formal analysis: Faezeh Hesari and Farzad Ghafouri; writing—original draft preparation, Faezeh Hesari; writing—review and editing: Mostafa Sadeghi, Seyed Reza Miraei-Ashtiani, and Farzad Ghafouri; supervision: Mostafa Sadeghi, Seyed Reza Miraei-Ashtiani, and Farzad Ghafouri. All authors have read and agreed to the published version of the manuscript.

Data Availability Statement

Datasets used in this study are publicly available and can be accessed from the National Center for Biotechnology Information (NCBI) with accession numbers GSE23592 and GSE89297. Further details on accessing the data are on the NCBI website at https://www.ncbi.nlm.nih.gov/geo/.

Acknowledgements

The authors express their thanks to the Gene Expression Omnibus (GEO) open repository database from National Center for Biotechnology Information (NCBI) for providing a platform to access molecular data.

Ethical considerations

The study did not involve human or animal subjects and therefore did not require ethical approval. The authors confirm that no data fabrication, falsification, plagiarism, or misconduct occurred.

Conflict of interest

The authors declare no conflicts of interest.

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Iranian Journal of animal Science
Volume 56, Issue 3
September 2025
Pages 665-688

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History

  • Receive Date: 25 February 2025
  • Revise Date: 27 March 2025
  • Accept Date: 06 April 2025

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