• Asian-Australasian Journal of Animal Sciences
• /
• v.30 no.12
• /
• pp.1679-1683
• /
• 2017

Objective: An experiment was conducted to study the association between the single nucleotide polymorphisms (SNPs) in 5'-untranslated regions (5'-UTR) of equine chorionic gonadotropin (eCG) genes and the serum eCG levels. Methods: SNPs in 5'-UTR of eCG genes were screened across 10 horse breeds, including 7 Chinese indigenous breeds and 3 imported breeds using iPLEX chemistry, and the association between the serum eCG levels of 174 pregnant Da'an mares and their serum eCG levels (determined with ELISA) was analyzed. Results: Four SNPs were identified in the 5'-UTR of the $eCG{\alpha}$ gene, and one of them was unique in the indigenous breeds. There were 2 SNPs detected at the 5' end of the $eCG{\beta}$ subunit gene, and one of them was only found in the Chinese breeds. The SNP g.39948246T>C at the 5'-UTR of $eCG{\alpha}$ was associated significantly with eCG levels of 75-day pregnant mare serum (p<0.05) in Da'an mares. Prediction analysis on binding sites of transcription factors showed that the g.39948246T>C mutation causes appearance of the specific binding site of hepatocyte nuclear factor 3 forkhead homolog 2 (HFH-2), which is a transcriptional repressor belonging to the forkhead protein family of transcription factors. Conclusion: The SNP g.39948246T>C at the 5'-UTR of $eCG{\alpha}$ is associated with eCG levels of 75-day pregnant mare serum (p<0.05).

• Genomics & Informatics
• /
• v.20 no.2
• /
• pp.19.1-19.15
• /
• 2022

Alfalfa (Medicago sativa) is an important food and feed crop which rich in mineral sources. The WUSCHEL-related homeobox (WOX) gene family plays important roles in plant development and identification of putative gene families, their structure, and potential functions is a primary step for not only understanding the genetic mechanisms behind various biological process but also for genetic improvement. A variety of computational tools, including MAFFT, HMMER, hidden Markov models, Pfam, SMART, MEGA, ProtTest, BLASTn, and BRAD, among others, were used. We identified 34 MsWOX genes based on a systematic analysis of the alfalfa plant genome spread in eight chromosomes. This is an expansion of the gene family which we attribute to observed chromosomal duplications. Sequence alignment analysis revealed 61 conserved proteins containing a homeodomain. Phylogenetic study sung reveal five evolutionary clades with 15 motif distributions. Gene structure analysis reveals various exon, intron, and untranslated structures which are consistent in genes from similar clades. Functional analysis prediction of promoter regions reveals various transcription binding sites containing key growth, development, and stress-responsive transcription factor families such as MYB, ERF, AP2, and NAC which are spread across the genes. Most of the genes are predicted to be in the nucleus. Also, there are duplication events in some genes which explain the expansion of the family. The present research provides a clue on the potential roles of MsWOX family genes that will be useful for further understanding their functional roles in alfalfa plants.

• Asian Pacific Journal of Cancer Prevention
• /
• v.17 no.8
• /
• pp.3971-3977
• /
• 2016

Background: Breast cancer, the commonest cancer among women in the world, ranks top in India with an incidence rate of 1,45,000 new cases and mortality rate of 70,000 women every year. Chemotherapy outcome for breast cancer is hampered due to poor response and irreversible dose-dependent cardiotoxicity which is determined by genetic variations in drug metabolizing enzymes and transporters. Pregnane X receptor (PXR), a member of the nuclear receptor superfamily, induces expression of drug metabolizing enzymes (DMEs) and transporters leading to regulation of xenobiotic metabolism. Materials and Methods: A genomic region spanning PXR 3' UTR was amplified and sequenced using genomic DNA isolated from 96 South Indian breast cancer patients. Genetic variants observed in our study subjects were queried in miRSNP to establish SNPs that alter miRNA binding sites in PXR 3' UTR. In addition, enrichment analysis was carried out to understand the network of miRNAs and PXR in drug metabolism using DIANA miRpath and miRwalk pathway prediction tools. Results: In this study, we identified SNPs rs3732359, rs3732360, rs1054190, rs1054191 and rs6438550 in the PXR 3; UTR region. The SNPs rs3732360, rs1054190 and rs1054191 were located in the binding site of miR-500a-3p, miR-532-3p and miR-374a-3p resulting in the altered PXR level due to the deregulation of post-transcriptional control and this leads to poor treatment response and toxicity. Conclusions: Genetic variants identified in PXR 3' UTR and their effects on PXR levels through post-transcriptional regulation provide a genetic basis for interindividual variability in treatment response and toxicity associated with chemotherapy.

• Asian-Australasian Journal of Animal Sciences
• /
• v.33 no.2
• /
• pp.219-229
• /
• 2020

Objective: Considering the physiological and clinical importance of leptin receptor (LEPR) in regulating obesity and the fact that porcine LEPR expression is not known to be controlled by lncRNAs and miRNAs, we aim to characterize this gene as a potential target of SSC-miR-323 and the lncRNA TCONS_00010987. Methods: Bioinformatics analyses revealed that lncRNA TCONS_00010987 and LEPR have SSC-miR-323-binding sites and that LEPR might be a target of lncRNA TCONS_00010987 based on cis prediction. Wild-type and mutant TCONS_00010987-target sequence fragments and wild-type and mutant LEPR 3'-UTR fragments were generated and cloned into pmiRRB-REPORT^TM-Control vectors to construct respective recombinant plasmids. HEK293T cells were co-transfected with the SSC-miR-323 mimics or a negative control with constructs harboring the corresponding binding sites and relative luciferase activities were determined. Tissue expression patterns of lncRNA TCONS_00010987, SSC-miR-323, and LEPR in Anqing six-end-white (AQ, the obese breed) and Large White (LW, the lean breed) pigs were detected by real-time quantitative polymerase chain reaction; backfat expression of LEPR protein was detected by western blotting. Results: Target gene fragments were successfully cloned, and the four recombinant vectors were constructed. Compared to the negative control, SSC-miR-323 mimics significantly inhibited luciferase activity from the wild-type TCONS_00010987-target sequence and wild-type LEPR-3'-UTR (p<0.01 for both) but not from the mutant TCONS_00010987-target sequence and mutant LEPR-3'-UTR (p>0.05 for both). Backfat expression levels of TCONS_00010987 and LEPR in AQ pigs were significantly higher than those in LW pigs (p<0.01), whereas levels of SSC-miR-323 in AQ pigs were significantly lower than those in LW pigs (p<0.05). LEPR protein levels in the backfat tissues of AQ pigs were markedly higher than those in LW pigs (p<0.01). Conclusion: LEPR is a potential target of SSC-miR-323, and TCONS_00010987 might act as a sponge for SSC-miR-323 to regulate LEPR expression.