تجزیه و تحلیل تلفیقی و مقایسه‌ای پروفایل‌ رونویسی و شبکه‌های تنظیمی RNA درون‌زای رقابتی به منظور شناسایی ژن‌های کلیدی مرتبط با تنش حرارتی در جوجه‌های گوشتی

REFERENCES

Amiri Roudbar, M., Mohammadabadi, M. R., Ayatollahi  Mehrgardi, A., Abdollahi-Arpanahi, R., Momen, M., Morota, G., Brito Lopes, F., Gianola, D., & Rosa, G. J. M. (2020). Integration of single nucleotide variants and whole-genome DNA methylation profiles for classification of rheumatoid arthritis cases from controls. Heredity, 124(5), 658–674.

Andrews, S., Krueger, F., Segonds-Pichon, A., Biggins, L., Krueger, C., & Wingett, S. (2010). FastQC: A quality control tool for high throughput sequence data. Available online: http://www.bioinformatics.babraham. ac.uk/projects/fastqc

Sadollahpour Nanaei, H., Kharrati-Koopaee, H., & Esmailizadeh, A. (2022). Genetic diversity and signatures of selection for heat tolerance and immune response in Iranian native chickens. BMC Genomics, 23(1), 224.

Baaklini, I., Wong, M. J., Hantouche, C., Patel, Y., Shrier, A., & Young, J. C. (2012). The DNAJA2 substrate release mechanism is essential for chaperone-mediated folding. Journal of Biological Chemistry, 287(50), 41939-41954.

Barazandeh, A., Mohammadabadi, M. R., Ghaderi-Zefrehei, M., & Nezamabadi-Pour, H. (2016). Genome-wide analysis of CpG islands in some livestock genomes and their relationship with genomic features. Czech Journal of Animal Science, 61(11), 487–495.

Barreto Sánchez, A. L., Wang, Q., Thiam, M., Wang, Z., Zhang, J., Zhang, Q., Zhang, N., Li, Q., Wen, J. & Zhao, G. (2022). Liver transcriptome response to heat stress in Beijing You chickens and Guang Ming broilers. Genes, 13(3), 416.

Bernardo, M. V., Yelo, E., Gimeno, L., Campillo, J. A., & Parrado, A. (2007). Identification of apoptosis-related PLZF target genes. Biochemical and Biophysical Research Communications, 359(2), 317-322.

Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114-2120.

Bordbar, F., Mohammadabadi, M., Jensen, J., Xu, L., Li, J., & Zhang, L. (2022). Identification of candidate genes regulating carcass depth and hind leg circumference in Simmental beef cattle using Illumina Bovine Beadchip and next-generation sequencing analyses. Animals (Basel), 12(9), 1103.

Cassuce, D. C., Tinôco, I. D. F., Baêta, F. C., Zolnier, S., Cecon, P. R., & Vieira, M. D. F. (2013). Thermal comfort temperature update for broiler chickens up to 21 days of age. Engenharia Agrícola, 33, 28-36.

Chen, B., Piel, W. H., Gui, L., Bruford, E., & Monteiro, A. (2005). The HSP90 family of genes in the human genome: insights into their divergence and evolution. Genomics, 86(6), 627-637.

Chen, B., Yang, B., Zhu, J., Wu, J., Sha, J., Sun, J., Bao, E. & Zhang, X. (2020). Hsp90 relieves heat stress-induced damage in mouse kidneys: Involvement of antiapoptotic PKM2-AKT and autophagic HIF-1α signaling. International Journal of Molecular Sciences, 21(5), 1646.

Cheng, S. Z., Guang-Xin, E., Liu, C. L., Basang, W. D., Zhu, Y. B., Na, R. S., Han, Y.G., Zeng, Y., Wang, X., Ni, W.W., Yang, B.G. & Huang, Y. F. (2020). SNP of AHSA2 gene in three cattle breeds using snapshot technology. Journal of Genetics, 99, 1-6.

Davis, S. & Meltzer, P.S. (2007). GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Bioinformatics, 23(14), 1846-1847.

Dehghanian Reyhan, V., Ghafouri, F., Sadeghi, M., Miraei-Ashtiani, S.R., Kastelic, J.P., Barkema, H.W. &  Shirali, M. (2023). Integrated comparative transcriptome and circRNA-lncRNA-miRNA-mRNA ceRNA regulatory network analyses identify molecular mechanisms associated with intramuscular fat content in beef cattle. Animals, 13(16), 2598.

Dou, T., Zhao, S., Rong, H., Gu, D., Li, Q., Huang, Y., Xu, Z., Chu, X., Tao, L., Liu, L. and Ge, C. & Jia, J. (2017). Biological mechanisms discriminating growth rate and adult body weight phenotypes in two Chinese indigenous chicken breeds. BMC Genomics, 18, 1-12.

Du, P., Kibbe, W.A. & Lin, S.M. (2008). Lumi: a pipeline for processing Illumina microarray. Bioinformatics, 24(13), 1547-1548.

Ekhtiyari, M.S., Javanmard, A., Ghafouri, F., Sadr, A.S., Miraei-Ashtiani, S.R. & Shirali, M. (2023). Bioinformatics analysis of differentially gene expression profiles related to heat stress in brain, liver, and leg muscle of broiler chickens based on microarray technique. Iranian Journal of Animal Science, 54(3), 203-223 .(in Persian) .

Etches, R. J., John, T. M., & Gibbins, A. V. (2008). Behavioural, physiological, neuroendocrine and molecular responses to heat stress. Poultry Production in Hot Climates (pp. 48-79). Wallingford UK: CABI.

FAO (2022). Data from: Crops and livestock products dataset. License: CC BY-NC-SA 3.0 igo. Available at: http://www.fao.org/faostat/en/#data/QC (Accessed April 01, 2022).

Gautier, L., Cope, L., Bolstad, B.M. & Irizarry, R.A. (2004). Affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics, 20(3), 307-315.

Gerges, N. Z., Tran, I. C., Backos, D. S., Harrell, J. M., Chinkers, M., Pratt, W. B., & Esteban, J. A. (2004). Independent functions of hsp90 in neurotransmitter release and in the continuous synaptic cycling of AMPA receptors. Journal of Neuroscience, 24(20), 4758-4766.

Ghafouri, F., Bahrami, A., Sadeghi, M., Miraei-Ashtiani, S.R., Bakherad, M., Barkema, H.W. & Larose, S. (2021). Omics multi-layers networks provide novel mechanistic and functional insights into fat storage and lipid metabolism in poultry. Frontiers in Genetics, 12, 646297.

Ghafouri, F., Dehghanian Reyhan, V., Sadeghi, M., Miraei-Ashtiani, S.R., Kastelic, J.P., Barkema, H.W. & Shirali, M. (2024a). Integrated analysis of transcriptome profiles and lncRNA–miRNA–mRNA competing endogenous RNA regulatory network to identify biological functional effects of genes and pathways associated with Johne’s disease in dairy cattle. Non-coding RNA, 10(4), 38.

Ghafouri, F., Dehghanian Reyhan, V., Sadeghi, M., Miraei-Ashtiani, S.R., Kastelic, J.P., Barkema, H.W. & Shirali, M., (2024b). Competing endogenous RNAs (ceRNAs) and application of their regulatory networks in complex traits and diseases of ruminants. Ruminants, 4(2), 165-181.

Ghafouri, F., Sadeghi, M., Bahrami, A., Naserkheil, M., Dehghanian Reyhan, V., Javanmard, A., Miraei-Ashtiani, S.R., Ghahremani, S., Barkema, H.W., Abdollahi-Arpanahi, R. & Kastelic, J.P. (2023). Construction of a circRNA–lincRNA–lncRNA–miRNA–mRNA ceRNA regulatory network identifies genes and pathways linked to goat fertility. Frontiers in Genetics, 14, 1195480.

Guerreiro, E. N., Giachetto, P. F., Givisiez, P. E. N., Ferro, J. A., Ferro, M. I. T., Gabriel, J. E., Furlan, R.L. & Macari, M. (2004). Brain and hepatic Hsp70 protein levels in heat-acclimated broiler chickens during heat stress. Brazilian Journal of Poultry Science, 6, 201-206.

He, X., Lu, Z., Ma, B., Zhang, L., Li, J., Jiang, Y., Zhou, G. & Gao, F. (2018). Effects of chronic heat exposure on growth performance, intestinal epithelial histology, appetite and related hormones and genes expression in broilers. Journal of the Science of Food and Agriculture, 98(12), 4471-4478.

Heidarpour, F., Mohammadabadi, M. R., Zaidul, I. S. M., Maherani, B., Saari, N., Hamid, A. A., Abas, F., Manap, M. Y. A, Mozafari, M. R, (2011). Use of prebiotics in oral delivery of bioactive compounds: a nanotechnology perspective. Pharmazie. 66(5), 319-324.

Hightower, L. E., & Guidon Jr, P. T. (1989). Selective release from cultured mammalian cells of heat-shock (stress) proteins that resemble glia-axon transfer proteins. Journal of Cellular Physiology, 138(2), 257-266.

Hill, M., & Tran, N. (2021). miRNA interplay: mechanisms and consequences in cancer. Disease Models & Mechanisms, 14(4), dmm047662.

Holmes, J. L., Sharp, S. Y., Hobbs, S., & Workman, P. (2008). Silencing of HSP90 cochaperone AHA1 expression decreases client protein activation and increases cellular sensitivity to the HSP90 inhibitor 17-allylamino-17-demethoxygeldanamycin. Cancer Research, 68(4), 1188-1197.

Hori, O., Matsumoto, M., Kuwabara, K., Maeda, Y., Ueda, H., Ohtsuki, T., Kinoshita, T., Ogawa, S., Stern, D.M. & Kamada, T. (1996). Exposure of astrocytes to hypoxia/reoxygenation enhances expression of glucose‐regulated protein 78 facilitating astrocyte release of the neuroprotective cytokine interleukin 6. Journal of Neurochemistry, 66(3), 973-979.

Hosseinzadeh, S. & Hasanpur, K. (2024). Whole genome discovery of regulatory genes responsible for the response of chicken to heat stress. Scientific Reports, 14(1), 6544.

Hu, L., Fang, H., Abbas, Z., Luo, H., Brito, L. F., Wang, Y., & Xu, Q. (2024). The HSP90AA1 Gene Is Involved in heat stress responses and its functional genetic polymorphism are associated with heat tolerance in Holstein cows. Journal of Dairy Science.

Huber, W., Carey, V.J., Gentleman, R., Anders, S., Carlson, M., Carvalho, B.S., Bravo, H.C., Davis, S., Gatto, L., Girke, T. & Gottardo, R. (2015). Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods, 12(2), 115-121.

Khabiri, A., Toroghi, R., Mohammadabadi, M., & Tabatabaeizadeh, S. E. (2023). Introduction of a Newcastle disease virus challenge strain (sub-genotype VII.1.1) isolated in Iran. Veterinary Research Forum, 14(4), e221.

Kim, D., Langmead, B., & Salzberg, S. L. (2015). HISAT: a fast spliced aligner with low memory requirements. Nature Methods, 12(4), 357-360.

Kong, L. N., Zhang, D. X., Ji, C. L., Zhang, X. Q., & Luo, Q. B. (2015). Association analysis between SNPs in the 5’-flanking region of the chicken GRP78 gene, thermotolerance parameters, and tissue mRNA expression. Genet. Mol. Res, 14, 6110-6123.

Kubota, S., Pasri, P., Okrathok, S., Jantasaeng, O., Rakngam, S., Mermillod, P., & Khempaka, S. (2023). Transcriptome analysis of the uterovaginal junction containing sperm storage tubules in heat-stressed breeder hens. Poultry Science, 102(8), 102797.

Lee-Yoon, D., Easton, D., Murawski, M., Burd, R., & Subjeck, J. R. (1995). Identification of a major subfamily of large hsp70-like proteins through the cloning of the mammalian 110-kDa heat shock protein. Journal of Biological Chemistry, 270(26), 15725-15733.

Li, G., Zhao, H., Guo, H., Wang, Y., Cui, X., Li, H., Xu, B. & Guo, X. (2020). Analyses of the function of DnaJ family proteins reveal an underlying regulatory mechanism of heat tolerance in honeybee. Science of the Total Environment, 716, 137036.

Li, Z., & Li, Z. (2012). Glucose regulated protein 78: a critical link between tumor microenvironment and cancer hallmarks. Biochimica et Biophysica Acta (BBA)-Reviews on Cancer, 1826(1), 13-22.

Liao, Y., Smyth, G. K., & Shi, W. (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7), 923-930.

Lin, Y., Ji, Z., Li, C., Liang, Q., Shi, J., Su, Z., Yao, X. & Zhang, X. (2024). Proteomics analysis for key molecules in adrenal glands of Wenchang chickens for their resistance to heat stress. Poultry Science, 103(11), 104161.

Liu, Z., Liu, Y., Xing, T., Li, J., Zhang, L., Zhao, L., Jiang, Y. & Gao, F. (2024). Unraveling the role of long non-coding RNAs in chronic heat stress-induced muscle injury in broilers. Journal of Animal Science and Biotechnology, 15(1), 135.

Livingston, M. L., Pokoo-Aikins, A., Frost, T., Laprade, L., Hoang, V., Nogal, B., Phillips, C. & Cowieson, A. J. (2022). Effect of heat stress, dietary electrolytes, and vitamins E and C on growth performance and blood biochemistry of the broiler chicken. Frontiers in Animal Science, 3, 807267.

Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 1-21.

Lu, T., Li, L., Li, Y., & Li, X. (2023). RNA-sequencing reveals differentially expressed genes of laying hens fed Baihu Decoction under heat shock. The Journal of Poultry Science, 60(2), 2023012.

Luo, Q. B., Song, X. Y., Ji, C. L., Zhang, X. Q., & Zhang, D. X. (2014). Exploring the molecular mechanism of acute heat stress exposure in broiler chickens using gene expression profiling. Gene, 546(2), 200-205.

Madkour, M., Salman, F.M., El-Wardany, I., Abdel-Fattah, S.A., Alagawany, M., Hashem, N.M., Abdelnour, S.A., El-Kholy, M.S. & Dhama, K. (2022). Mitigating the detrimental effects of heat stress in poultry through thermal conditioning and nutritional manipulation. Journal of Thermal Biology, 103, 103169.

Marangoni, F., Corsello, G., Cricelli, C., Ferrara, N., Ghiselli, A., Lucchin, L. & Poli, A. (2015). Role of poultry meat in a balanced diet aimed at maintaining health and wellbeing: an Italian consensus document. Food & Nutrition Research, 59(1), 27606.

McInnes, L., Healy, J. & Melville, J. (2018). Umap: Uniform manifold approximation and projection for dimension reduction. ArXiv Preprint ArXiv:1802.03426.

McKenna, L. B., Schug, J., Vourekas, A., McKenna, J. B., Bramswig, N. C., Friedman, J. R., & Kaestner, K. H. (2010). MicroRNAs control intestinal epithelial differentiation, architecture, and barrier function. Gastroenterology, 139(5), 1654-1664.

Mohamed, B. A., Barakat, A. Z., Zimmermann, W. H., Bittner, R. E., Mühlfeld, C., Hünlich, M., Engel, W., Maier, L.S. & Adham, I. M. (2012). Targeted disruption of Hspa4 gene leads to cardiac hypertrophy and fibrosis. Journal of Molecular and Cellular Cardiology, 53(4), 459-468.

Mohammadabadi, M., Babenko, I. O., Borshch, O., Kalashnyk, O., Ievstafiieva, Y., & Buchkovska, V. (2024). Measuring the relative expression pattern of the UCP2 gene in different tissues of the Raini Cashmere goat. Agricultural Biotechnology Journal, 16(3), 317-332.

Naserkheil, M., Ghafouri, F., Zakizadeh, S., Pirany, N., Manzari, Z., Ghorbani, S., Banabazi, M.H., Bakhtiarizadeh, M.R., Huq, M.A., Park, M.N. & Barkema, H.W. (2022). Multi-omics integration and network analysis reveal potential hub genes and genetic mechanisms regulating bovine mastitis. Current Issues in Molecular Biology, 44(1), 309-328.

Nepusz, T., Yu, H. & Paccanaro, A. (2012). Detecting overlapping protein complexes in protein-protein interaction networks. Nature Methods, 9(5), 471-472.

Pritchett, E. M., Van Goor, A., Schneider, B. K., Young, M., Lamont, S. J., & Schmidt, C. J. (2023). Chicken pituitary transcriptomic responses to acute heat stress. Molecular Biology Reports, 50(6), 5233-5246.

Rauch, J. N., Zuiderweg, E. R., & Gestwicki, J. E. (2016). Non-canonical interactions between heat shock cognate protein 70 (Hsc70) and Bcl2-associated anthanogene (BAG) co-chaperones are important for client release. Journal of Biological Chemistry, 291(38), 19848-19857.

Renaudeau, D., Collin, A., Yahav, S., De Basilio, V., Gourdine, J. L., & Collier, R. J. (2012). Adaptation to hot climate and strategies to alleviate heat stress in livestock production. Animal, 6(5), 707-728.

Reyhan, V. D., Sadeghi, M., Miraei-Ashtiani, S. R., Ghafouri, F., Kastelic, J. P., & Barkema, H. W. (2022). Integrated transcriptome and regulatory network analyses identify candidate genes and pathways modulating ewe fertility. Gene Reports, 28, 101659.

Ritchie, M.E., Phipson, B., Wu, D.I., Hu, Y., Law, C.W., Shi, W. & Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research, 43(7), e47-e47.

Robichon, C., Varret, M., Le Liepvre, X., Lasnier, F., Hajduch, E., Ferré, P. & Dugail, I. (2006). DnaJA4 is a SREBP-regulated chaperone involved in the cholesterol biosynthesis pathway. Biochimica et Biophysica Acta (BBA)-Molecular and Cell Biology of Lipids, 1761(9), 1107-1113.

Rosenzweig, R., Nillegoda, N. B., Mayer, M. P., & Bukau, B. (2019). The Hsp70 chaperone network. Nature Reviews Molecular Cell Biology, 20(11), 665-680.

Safaei, S. M. H., Dadpasand, M., Mohammadabadi, M., Atashi, H., Stavetska, R., Klopenko, N., & Kalashnyk, O. (2022). An Origanum majorana leaf diet influences Myogenin gene expression, performance, and carcass characteristics in lambs. Animals (Basel), 13(1), 14.

Safdar, M., & Özaslan, M. (2023). MicroRNAs as potential biomarkers for heat stress in livestock. Zeugma Biological Science, 4(2), 6-12.

Searchinger, T., Waite, R., Hanson, C., Ranganathan, J., Dumas, P., Matthews, E., & Klirs, C. (2019). Creating a sustainable food future: A menu of solutions to feed nearly 10 billion people by 2050. Final Report.

Smith, M. H., Ploegh, H. L., & Weissman, J. S. (2011). Road to ruin: targeting proteins for degradation in the endoplasmic reticulum. Science, 334(6059), 1086-1090.

Song, X.Y., Luo, Q.B. & Zhang, X.Q. (2012). Gene expression profiling of three tissues in chicken with heat stress by Affymetrix microarray. Available online at: https://www.ncbi.nlm.nih.gov/geo/query/ acc.cgi?acc=GSE23592

Subjeck, J. R., Sciandra, J. J., Chao, C. F., & Johnson, R. J. (1982). Heat shock proteins and biological response to hyperthermia. The British Journal of Cancer. Supplement, 5, 127.

Sun, L., Prince, T., Manjarrez, J. R., Scroggins, B. T., & Matts, R. L. (2012). Characterization of the interaction of Aha1 with components of the Hsp90 chaperone machine and client proteins. Biochimica et Biophysica Acta (BBA)-Molecular Cell Research, 1823(6), 1092-1101.

Szklarczyk, D., Gable, A.L., Lyon, D., Junge, A., Wyder, S., Huerta-Cepas, J., Simonovic, M., Doncheva, N.T., Morris, J.H., Bork, P. & Jensen, L.J. (2019). STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Research, 47(D1), 607-613.

Tona, G. O. (2018). Current and future improvements in livestock nutrition and feed resources. Animal Husbandry and Nutrition, 18, 73088.

Triantafilou, M., Fradelizi, D., & Triantafilou, K. (2001). Major histocompatibility class one molecule associates with glucose regulated protein (GRP) 78 on the cell surface. Human Immunology, 62(8), 764-770.

Wu, X., Du, X., Pian, H. & Yu, D. (2024). Effect of curcumin on hepatic mRNA and lncRNA Co-expression in heat-stressed laying hens. International Journal of Molecular Sciences, 25(10), 5393.

Yao, X., Zhu, J., Li, L., Yang, B., Chen, B., Bao, E., & Zhang, X. (2023). Hsp90 protected chicken primary myocardial cells from heat-stress injury by inhibiting oxidative stress and calcium overload in mitochondria. Biochemical Pharmacology, 209, 115434.

Zhao, Y., Wong, L. & Goh, W.W.B. (2020). How to do quantile normalization correctly for gene expression data analyses. Scientific Reports, 10(1), 1-11.