batol asghari esfedan; Gholam Dashab; mohammadhossein banabazi; mohammad Rokouei
Volume 22, Issue 2 , June 2020, , Pages 187-198
Abstract
The aim of the present study was to investigate the codon usage pattern and their relationship with gene expression for genes with different expression between pure and crossbreed Sistani and Montbeliared breed. In this study, the results of differential gene expression analysis using RNA-Seq technology ...
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The aim of the present study was to investigate the codon usage pattern and their relationship with gene expression for genes with different expression between pure and crossbreed Sistani and Montbeliared breed. In this study, the results of differential gene expression analysis using RNA-Seq technology between pure and crossbreed Sistani and Montbeliared breed (two pure and two its crossbreed) were used. For this purpose, after determining the ORF regions for these genes, CodonW software was used to estimate codon usage pattern indices including CAI, ENC, GC and GC3s. Results showed that there was a significant correlation between total GC and GC3s (0.74). There was also a significant correlation between ENC and GC and GC3s (0.65, 0.77), indicating the role of mutation in codon formation. Based on the results of this study, the factors such as nucleotide composition (GC content), mutation, and gene expression level played important roles in codon formation in the genes studied in this study. This study is the first comparison between pure and crossbreed Sistani and Monti-billiard samples, which helps to better understand the evolutionary mechanisms of codon usage pattern formation and its association with gene expression.
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.
Zohreh Mozduri; Mohammad Reza Bakhtiarizadeh
Volume 18, Issue 1 , April 2016, , Pages 13-26
Abstract
This study was done to gain insights into transcriptional regulation of negative energy balance (NEB) assoctiated genes. Overexpressed genes in NEB were identified using microarray and RNA-seq data and promoter analysis of these overexpressed genes was applied to identify novel transcription factors. ...
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This study was done to gain insights into transcriptional regulation of negative energy balance (NEB) assoctiated genes. Overexpressed genes in NEB were identified using microarray and RNA-seq data and promoter analysis of these overexpressed genes was applied to identify novel transcription factors. Moreever, STRING database was used to construct a regulatory network of identified transcription factors. The results of the gene expression analysis revealed that eight genes in severe NEB are more frequent and significant (P<0.05) in comparison to the mild NEB. Promoter analysis showed that promoters of overexpressed genes are enriched in putative binding sites for 19 transcription factors. This group included known NEB-associated transcription factor (NF-κB), and a number of transcription factors (such as SP1, ZBP89, NFI, Zf9, MYC, ZBTB7A, FOXF2 and KLF6) that had not been previously reported to be associated with NEB. Based on the present results, 18 new effective candidate trsnacription factors introduced in this study can provide new information to gain a better understanding of the regulatory network involved in NEB.