Analysis of the Regulatory Effects of lncRNAs on Kidney Tissue in Ascites Susceptible Broiler

Document Type : Research Articles

Authors

• Kasra Ahmadian ¹
• Mohammadreza Nassiry ²
• Karim Hasanpur ³
• Ali Javadmanesh ⁴

¹ Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran.

² Department Animal Science, Faculty of agriculture, Ferdowsi University of Mashhad, Mashhad, Iran

³ Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran

⁴ Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Iran.

10.22067/ijasr.2023.83528.1162

Abstract

Introduction :Ascites syndrome, as a metabolic disorder, is one of the most non-infectious causes of death in the old age of breeding in the poultry industry, which causes annual losses of over one hundred million dollars and is an important economic concern. The growth rate of broiler and their high need for oxygen causes an increase in pumping, followed by heart failure, and heart failure is often associated with other diseases. Due to the relationship between the heart and the kidney, chronic heart failure leads to a decrease in filtered blood volume and a decrease in kidney function, which over time causes permanent damage to the kidneys. lncRNAs play important roles in a variety of different mechanisms related to cellular homeostasis and in a wide range of pathophysiological processes and pathogenesis of many diseases, including cardiovascular disorders, respiratory and kidney diseases, preliminary studies in human samples show shows that lncRNAs are strongly involved in the development and disease of the kidney. For this reason, the lncRNAs obtained from the RNA-seq data of the kidney tissue were investigated in the occurrence of ascites.
Materials and Methods :700 one-day-old chicks from one of the paternal lines of a commercial strain were kept under standard conditions until 21 days old. On the 21st day of the breeding period, cold stress (24 degrees Celsius) began and continued until the age of 48 days. After applying cold stress, the birds with ascites symptoms were grouped in the Ascites group and the rest in the Healthy group. On the 39th day of the breeding period, 70 slaughtered birds and kidney tissue samples from each bird were immediately transferred to the liquid nitrogen tank after separation. 16 ascites birds and 16 healthy birds were used for RNA extraction. Total RNA extraction was done individually using trizol (YTzol) solution, and then an equal amount of RNA from four tissue samples was combined and then cDNA was prepared from 4 ascites tissue samples and 4 healthy tissue samples. All small RNAs, such as rRNAs, tRNAs, etc., were removed by dt oligo beads, and finally, all mRNAs were used to prepare the library. Novagen company was used for sequencing using Illumine hiseq 2500 technology and paired-end reads. Several software such as hisat2, cufflinks, stringtie, cuffmerge and cuffdiff were used for mapping, aligning and analysis of gene expression differences. In order to extract coding and non-coding genes, FEELnc software was used with default settings. Potential target genes of lncRNAs were investigated by searching for protein coding genes located within 100 kb upstream and downstream of each lncRNA. In the following, a positive and negative correlation of 90% was obtained between two groups of coding and non-coding genes based on the degree of expression change. In order to investigate the metabolic, structural and functional pathways of significant genes, the Enrichr database, which is connected with other databases such as KEGG, was used.
Results and Discussion:In the current research, a total of eight samples produced 187640642 million paired reads with a size of 150 nucleotides and after quality control, 185258819 uncontaminated reads were obtained. The number of 1421 lncRNA transcripts related to 921 gene loci and 154 related target genes were identified in the comparison between ascites and healthy birds. Then, this number of genes were identified (154 genes) in order to check their functional characteristics using the Enrichr database, five functional pathways Glycine, serine and threonine metabolism, Rap1 signaling pathway, Sphingolipid metabolism, Phosphatidylinositolsignaling system, Mucin type O-glycan biosynthesis and related genes were significant. Out of 13 significant lncRNAs in these biological pathways, 12 are located on the antisense direction and one is located on the sense direction. In addition, 9 lncRNAs are exonic, 3 intronic and 1 in downstream position. These pathways are activated as damage modifiers in hypoxic conditions caused by ascites and provide the required energy and maintain kidney homeostasis in response to oxygen tension caused by ascites. On the other hand, they act as cell survival, increase proliferation and anti-apoptosis, which on the one hand reduce kidney damage and on the other hand make it function better, and in this way, reduce complications caused by ascites kidney damage.
Conclusion: Therefore, by targeting the important pathways of biology obtained and the genes affecting them for the prevention and treatment of ascites disease, it will provide a new insight for breeding.

Keywords

• Ascites
• Broiler
• Kidney
• lncRNA
• RNA-seq

Main Subjects

• Genetics & breeding

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©2023 The author(s). This is an open access article distributed under Creative Commons Attribution 4.0 International License (CC BY 4.0), which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source

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