Bizhan Mahmoudi; Hedayatollah Roshanfekr; Mohsen Sari; Mohammad Reza Bakhtiarizadeh
Volume 22, Issue 3 , September 2020, , Pages 337-348
Abstract
The objective of this study was to identify known intergenic lncRNAs related to biological pathways of acidosis in Holstein calves using ruminaltissue. Two groups of healthy calves (N=3) and affected by acidosis (N=3) were compared. Paired-end sequencing method was performed using theHiseq2500 illumine ...
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The objective of this study was to identify known intergenic lncRNAs related to biological pathways of acidosis in Holstein calves using ruminaltissue. Two groups of healthy calves (N=3) and affected by acidosis (N=3) were compared. Paired-end sequencing method was performed using theHiseq2500 illumine platform. Hisat2 software was used to align reads to the bovine reference genome and StringTie software package was used toassemble read files into transcripts. Using next generation sequencing, 1636 genes belonging to known intergenic lncRNAs were identified, of which56 genes showed significant differential expression (P≤0.05). Neighbor genes of known intergenic lncRNAs were determined on bovine genome.Analysis of biological pathways and molecular function showed that five biological pathways were significantly (P≤0.05) enriched. These pathwayswere Apelin signaling pathway, Gap junction, Glucagon signaling pathway, Renin secretion, and AGE-RAGE signaling pathway. Moreover, twomolecular functions including gap junction channel activity, and phosphatidyl inositol phospholipase C activity were significantly (P≤0.05) enriched.Some lncRNAs have different expression in healthy and acidosis samples, and the decreased pH acts as a stimulus to activate some biologicalsignaling pathways. In conclusion, it was indicated that lncRNAs with differential expression between the control group and the group affected byacidosis are associated with pathways related to rumen energy metabolism and signaling. Identified differentially expressed lncRNAs could be used asprognostic in acidosis and biomarkers or promising candidates in animal breeding.
Seyed Nader Albooshoke; Mohammad Reza Bakhtiarizadeh
Volume 21, Issue 2 , July 2019, , Pages 165-180
Abstract
This experiment was carried out to identify lncRNAs associated with skeletal muscle of the Isfahan native chicken and the Ross 708 commercial broiler chicken. To do this, after extraction of RNA from the breast muscle samples at the age of 28 days, paired-end sequencing was performed using the Illume ...
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This experiment was carried out to identify lncRNAs associated with skeletal muscle of the Isfahan native chicken and the Ross 708 commercial broiler chicken. To do this, after extraction of RNA from the breast muscle samples at the age of 28 days, paired-end sequencing was performed using the Illume Hiseq 2000 platform. Hisat2 software was used to align the clean reads to the chicken reference genome and the Stringtie software was used to assemble the transcripts. A total of 1097 lncRNAs were identified as 925 of which were intergenic and 172 were intronic. Also, the number of novel LncRNAs in intergenic and intronic groups were 432 and 128, respectively. Differential gene expression analysis led to the identification of 19 genes and 20 transcripts differentially expressed lncRNAs between two groups. Syntenic analysis showed that differentially expressed lncRNAs are located near by 45 protein encoding genes. Of these, the expression of five gene coding proteins (SCD gene in commercial chickens and GALNT15, KLHDC4, USP7 and ASB1 genes in native chicken) - whose expression was consistent with the expression of their lncRNA - were significantly expressed between two breeds. Functional enrichment analysis of these genes showed that all of them are involved in the skeletal muscle growth. The results of this study showed that the identified lncRNAs probably have the potential to regulate the genes involved in skeletal muscle growth. In this regard, they possibly cause the differences in growth rates between the two chicken breeds.