Predicting the effect of non synonymous SNPs in bovine TLR4 gene

Mishra, Chinmoy; Kumar, Subodh; Yathish, H.M.

doi:10.1016/j.genrep.2016.11.005

Cited by 5 publications

(6 citation statements)

References 52 publications

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“…The sites where DNA sequences are with transcription factors are called binding sites. Alterations in transcription factor binding sites could cause a significant impact on transcription factor binding to gene regulatory areas and gene expression products [ 27 ]. We examined the region and discovered SNPs that could change transcription factor binding sites.…”

Section: Resultsmentioning

confidence: 99%

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Genomic and Computational Analysis of Novel SNPs in TNP1 Gene Promoter Region of Bos indicus Breeding Bulls

et al. 2022

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Transition nuclear proteins (TNPs), the principal proteins identified in the condensing spermatids chromatin, have been found to play a key role in histone displacement and chromatin condensation during mammalian spermatogenesis. One such gene belonging to the TNP family called TNP1 gene is abundantly expressed in the regulation of spermatogenesis, and its sequence is remarkably well conserved among mammals. Genomic analysis, by sequencing and computational approach, was used to identify the novel polymorphisms and to evaluate the molecular regulation of TNP1 gene expression in Sahiwal cattle breeding bulls. DNA samples were sequenced to identify novel single nucleotide polymorphisms (SNPs) in the TNP1 gene. Modern computational tools were used to predict putative transcription factor binding in the TNP1 promoter and CpG islands in the TNP1 promoter region. In the TNP1 gene, four SNPs, three TATA boxes, and one CAAT box were identified. One CAAT box was discovered at 89 bp upstream of start site ATG. The computational analyses indicated that the polymorphisms inside the promoter sequence results in an added HNF-1 transcription factor binding site. In contrast, the other variations may remove the naturally occurring SRF transcription factor binding site. The CpG islands in the TNP1 promoter region were predicted to be absent by the MethPrimer program before and after SNP site mutations. These findings pave the way for more research into the TNP1 gene’s promoter activity and the links between these SNPs and reproductive attributes in the Sahiwal breeding bulls.

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Section: Resultsmentioning

confidence: 99%

“…All allelic and genotypic frequencies for newly found SNPs were quantified and tested in the current investigation using the earlier developed method [ 27 ].…”

Section: Methodsmentioning

confidence: 99%

Genomic and Computational Analysis of Novel SNPs in TNP1 Gene Promoter Region of Bos indicus Breeding Bulls

et al. 2022

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“…Previous studies of the bovine TLR4 have identified over 800 SNPs, 160 of which are located within the coding sequence. 19/110 non-synonymous SNPs have been identified as damaging using multiple predictive software programs (Mishra et al, 2017). The higher number of non-synonymous SNPs identified in bovines compared to dogs and cats may reflect the higher number of individuals investigated or greater overall genetic diversity in this species.…”

Section: Discussionmentioning

confidence: 99%

Breed-specific variations in the coding region of toll-like receptor 4 in the domestic cat

Whitney

Haase

Beatty

et al. 2019

Veterinary Immunology and Immunopathology

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cluding sepsis, aspergillosis and inflammatory bowel disease. Some of these TLR4 polymorphisms are racially specific. We hypothesised that feline TLR4 polymorphisms might underlie an observed increased risk to infectious and inflammatory diseases in some cat breeds. The aim of this study was to identify breed-specific variations in the coding region of feline TLR4 and to model the effect of mutations on protein structure and function in silico. The entire coding region of TLR4 was sequenced in 8 groups (7 pure-bred, 1 crossbred) of domestic cats (Felis catus) comprising 158 individuals. Twenty-two single nucleotide polymorphisms (SNPs) were identified in TLR4, with 16 located in the coding region (11 non-synonymous) and four in the 3′UTR. Comparison of breed specific allelic frequencies indicated that Burmese and British shorthairs most commonly differed from other breeds. In silico analyses to predict the impact of the 11 non-synonymous variants indicated a deleterious effect on protein structure for one SNP (c.869 G > A), which was not associated with a specific breed. Overall, findings from this study do not support a role of TLR4 dysfunction in breed-predispositions to infectious diseases in domestic cats in Australia.

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“…They also found that the frequency of GG genotype at TLR4 (rs8193046) polymorphic site was higher in the cases than in the control ones, suggesting an association with disease susceptibility; whereas the AA genotype was more common in control ones than in the cases, suggesting a protective association with Colibacillosis. Mishra et al [15] and Seabury et al [16] reported that genotype AA was associated with resistance to Colibacillosis, while genotype GG was associated with the risk of developing the disease. Fig.…”

Section: A L V E S T L R 4 G E N E P O L Y M O R P H I S M a N D Comentioning

confidence: 99%

Molecular Study of Colibacillosis Susceptibility in Calves and Lambs

Judi¹,

Judi²,

Saqban³

2020

Nano BioMed ENG

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Single nucleotide polymorphism (SNP) is hereditary change in a DNA sequence that occurs when a single nucleotide in a genome is modified; SNPs are usually considered to be point mutations that have been evolutionarily successful enough to recur in a significant proportion of the population of a species. The ability of certain individuals to respond appropriately to Toll-like receptor (TLR) ligands may be impaired by single-nucleotide polymorphisms (SNPs) within TLR genes, terminating in a modified susceptibility to infectious or inflammatory disease that might contribute to the pathogenesis of complex diseases. Out of the 400 clinical samples of blood collected from calves and lambs suffering from diarrhea, the samples originated from Babylon Veterinary Teaching Hospital and Veterinary Clinics during the period from October 2018 to January 2019, 200 samples were suffering from diarrhea (100 samples of calves and 100 samples of lambs), and 200 samples were the control groups. Genotyping of TLR4 polymorphisms was carried out by using amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) technique. For calves' TLR4 (rs8193046) gene polymorphisms, the results showed there were significant differences in genotypes and alleles frequencies between the diarrheic cases and control groups (p < 0.05). GG homozygous genotype was overrepresented among diarrheic calves. The frequencies of G allele was higher in diarrheic calves compared to control groups. The calves' GG homozygous genotype was significantly associated with increased susceptibility to Colibacillosis in calves. For lamb-TLR4 (rs160202325) gene polymorphism, AG heterozygous genotype was overrepresented among the cases as of 20 (52.63%), whereas AA was obviously more presented among control individuals as of 6 (60%). There were no difference between diarrheic cases and control groups for allele frequencies.

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Predicting the effect of non synonymous SNPs in bovine TLR4 gene

Cited by 5 publications

References 52 publications

Genomic and Computational Analysis of Novel SNPs in TNP1 Gene Promoter Region of Bos indicus Breeding Bulls

Genomic and Computational Analysis of Novel SNPs in TNP1 Gene Promoter Region of Bos indicus Breeding Bulls

Breed-specific variations in the coding region of toll-like receptor 4 in the domestic cat

Molecular Study of Colibacillosis Susceptibility in Calves and Lambs

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