Ali Javadmanesh; Mojtaba Tahmoorespour; Fahime Mohammadi
Abstract
The formation of muscle myofibrils as well as the growth and hypertrophy of the muscle are controlled by various genes. Also, bioinformatics tools could be used to integrate and analyze heterogeneous data sets. In this study, by integrating the data obtained by expression array and RNA-Seq, related to ...
Read More
The formation of muscle myofibrils as well as the growth and hypertrophy of the muscle are controlled by various genes. Also, bioinformatics tools could be used to integrate and analyze heterogeneous data sets. In this study, by integrating the data obtained by expression array and RNA-Seq, related to the muscle tissue transcriptome of Texel sheep respectively before and after birth, the DEGs, gene network, GO and biological pathways has been investigated. The microarray expression profile was extracted from the GEO database, and the RNA-Seq expression profile was extracted from ArrayExpress database. DEGs were identified with limma and sva software packages in R environment and a gene network was drawn with STRING, an application in Cytoscape software. The clustering and gene ontology were done with CytoCluster and ClueGO applications. The results showed a significant difference between the juvenile and 70-days embryonic stages the expression of 103 genes, between the adult and juvenile stages the expression of 28 genes and between adult and 70-days embryonic stages the expression of 62 genes. By constructing the gene network between these DEGs, a total of 37 selected genes were identified. The results revealed the function of these genes in cell proliferation, protein synthesis, formation and organization of myofibrils, muscle contraction and lipid metabolism. By integrating the expression data, this study provided a general view of the differences in transcriptomes in the muscle tissue of sheep. Also, the selected genes such as BUB1, RFC2, KIAA0101, RAD51, CKS2 and UQCRB were identified for the first time being reported as effective genes for myogenesis.
Saad Badday Betti; Mojtaba Tahmoorespur; Ali Javadmanesh
Abstract
Long non-coding RNAs (lncRNAs) compose a plentiful category of transcripts that have gained increasing importance because of their roles in different biological processes. Although the function of most lncRNAs remains unclear. They are implicated in epigenetic regulation of gene expression, including ...
Read More
Long non-coding RNAs (lncRNAs) compose a plentiful category of transcripts that have gained increasing importance because of their roles in different biological processes. Although the function of most lncRNAs remains unclear. They are implicated in epigenetic regulation of gene expression, including muscle development and differentiation. We aimed to identify the effect of novel lncRNAs (Alternatively spliced) and their target genes on two stages of sheep skeletal muscle growth and development. FastQC files have been used to examine the quality control and the Trimmomatic program for trimming low-quality reads from twelve longissimus dorsal muscle tissue samples (including six young and six old from Texel sheep). Hisat2, Cufflink, Cuffmerge, and Cuffdiff investigated the expression levels. Novel lncRNAs (Alternative spliced) were distinguished using NONCODE databases and Cuffcompare software. In addition, the lncRNA–mRNA interactions and regulatory network visualization were identified via RIsearch and Cytoscape software, respectively. Those 139 novel lncRNA (Alternative spliced) transcripts had been recognized, probably 65 lncRNAs interacted with their target genes and regulated sheep skeletal muscle growth and development. Three novel lncRNA transcripts (TCONS_00041386, TCONS_00050059, and TCONS_00056428) showed a strong association and five transcripts (TCONS_00055761, TCONS_00055762, TCONS_00055763, TCONS_00055764, and TCONS_00055770) had made complex network correlations with mRNAs. Our research provided more knowledge of the associated mechanisms with novel lncRNAs, which could play a role in regulating sheep skeletal muscle tissue development and growth.
Balal Sadeghi; Mohammadreza Nassiri; Ali Masoudi-Nejad; Mojtaba Tahmoorespour; Hesam Dehghani; Hamed Ahmadi
Abstract
MicroRNAs (miRNA) are a class of noncoding and regulatory RNA molecules about 22 nucleotides in
length. MicroRNAs regulate gene expression by an RNA interfering pathway through cleavage or inhibition of
the translation of target mRNA. Many miRNAs have been reported for their important roles in developmental
processes ...
Read More
MicroRNAs (miRNA) are a class of noncoding and regulatory RNA molecules about 22 nucleotides in
length. MicroRNAs regulate gene expression by an RNA interfering pathway through cleavage or inhibition of
the translation of target mRNA. Many miRNAs have been reported for their important roles in developmental
processes in various animals, but there is limited information about cattle and sheep miRNAs. The comparative
genomics approach due to their conserved nature is a good source for the miRNAs discovery. Cattle and sheep
are ideal model organisms for biological and comparative genomics studies. In our study, a computational
method based on expressed sequence tag (EST) analysis was used for detection of cattle and sheep miRNAs. In
cattle, 25 miRNA candidates found by homology searching frequently clustered at certain chromosomes and
28 miRNAs in sheep had been detected. Our results show that the cattle and sheep miRNA database can be
providing useful information for investigating biological functions of miRNAs in cattle and sheep.
Furthermore, the bioinformatics approach is a good manner for studying these functions.
