Regulatory SNPs and transcriptional factor binding sites in ADRBK1, AKT3, ATF3, DIO2, TBXA2R and VEGFA

Buroker, Norman E.

doi:10.4161/21541264.2014.964559

Cited by 26 publications

(20 citation statements)

References 84 publications

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“…Despite the differences between the specific functions of AKT isoforms, all 3 subtypes are potential candidate genes associated with phenotype variation in humans and animals. The single-nucleotide polymorphism of AKT3 (rs4590656) was found to be associated with three physiological parameters (hemoglobin, hematocrit, and red blood cell count) in people with chronic altitude sickness, indicating a strong association of this gene with angiogenesis [ 29 ]. A study by Gottlob et al [ 30 ] showed that the level of ATP in the fibroblasts cell line in mice significantly depends on the AKT family.…”

Section: Discussionmentioning

confidence: 99%

Assessing the Effect of SNPs on Litter Traits in Pigs

et al. 2020

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The reproductive ability of sows is the principle of continuous and efficient production, based on such traits as the number of piglets, the total number of parities, and the period of economic use. Currently, SNPs associated with the TNB and NBA are presented in the PigQTLdb. The aim of this work was the assessment of the SNP effects on the litter traits in Large White (LW, n = 502) and Landrace (LN, n = 432) sow breeds in a farm in Russia. 9 SNPs (SNP_1: rs80956812; SNP_2: rs81471381; SNP_3: rs80891106; SNP_4: rs81399474; SNP_5: rs81421148; SNP_6: rs81242222; SNP_7: rs81319839; SNP_8: rs81312912; SNP_9: rs80962240) were selected for the study. Associative analysis was performed using the GLM procedure in R version 3.5.1. The analysis of reproductive traits was carried out according to the results of the first parity, the second and subsequent parities, and totals for lifetime of sows. The significant effect on litter traits in LW was determined for SNP rs80956812, SNP rs81471381, SNP rs81421148, and SNP rs81399474. The significant effect on litter traits in LN was determined for SNP rs81421148 and SNP rs81319839. AKT3 gene was identified as perspective candidate gene, whose biological functions, as well as the results obtained in our work and in other studies, indicate its potential role in the reproductive process regulation in pigs. In general, the data obtained help to explain the genetic mechanisms of reproductive traits.

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Section: Discussionmentioning

confidence: 99%

Assessing the Effect of SNPs on Litter Traits in Pigs

et al. 2020

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“…Moreover, the importance of exploring genetic regulatory elements such as TFBS in the intronic regions is further highlighted when we consider that more than 90% of the identified single nucleotide polymorphisms (SNPs), located within regulatory or interoic regions, and not in coding regions of the genes. The functional regulatory SNPs (rSNPs) in TFBS may lead to multiple consequences such as variations in gene expression, phenotypes, and even susceptibility to environmental exposure (epigenetic trait) [ 31 ]. Accordingly, the complete non-coding regions of the hFVIII gene were surveyed in order to identify and describe the characteristics of its Cis-acting regulatory elements especially hFVIII-TFBs.…”

Section: Discussionmentioning

confidence: 99%

Intronic regions of the human coagulation factor VIII gene harboring transcription factor binding sites with a strong bias towards the short-interspersed elements

Haddad-Mashadrizeh

Hemmat

Aslamkhan

2020

Heliyon

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Increasing data show that intronic derived regulatory elements, such as transcription factor binding sites (TFBs), play key roles in gene regulation, and malfunction. Accordingly, characterizing the sequence context of the intronic regions of the human coagulation factor VIII ( hFVIII ) gene can be important. In this study, the intronic regions of the hFVIII gene were scrutinized based on in-silico methods. The results disclosed that these regions harbor a rich array of functional elements such as repetitive elements (REs), splicing sites, and transcription factor binding sites (TFBs). Among these elements, TFBs and REs showed a significant distribution and correlation to each other. This survey indicated that 31% of TFBs are localized in the intronic regions of the gene. Moreover, TFBs indicate a strong bias in the regions far from splice sites of introns with mapping to different REs. Accordingly, TFBs showed highly bias toward Short Interspersed Elements (SINEs), which in turn they covering about 12% of the total of REs. However, the distribution pattern of TFBs-REs showed different bias in the intronic regions, spatially into the Introns 13 and 25. The rich array of SINE-TFBs and CR1-TFBs were situated within 5′UTR of the gene that may be an important driving force for regulatory innovation of the hFVIII gene. Taken together, these data may lead to revealing intronic regions with the capacity to renewing gene regulatory networks of the hFVIII gene. On the other hand, these correlations might provide the novel idea for a new hypothesis of molecular evolution of the FVIII gene, and treatment of Hemophilia A which should be considered in future studies.

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“…Because a SNP in a TFBS could disrupt binding of the respective TF [75], we next investigated the impact of the local-eQTL variant on the binding activity of the four different TFs predicted to bind the sites overlapping ntc-linked local-eQTLs: Broad, Daughterless, Sage, and Relish. To do so and given the difficulty in performing line-specific ChIP on these TFs, we used our in-house MITOMI setup [73] to measure in vitro the binding affinity of the selected TFs to double-stranded 20-mers that encompassed the respective binding site and that represented either the reference or alternate alleles.…”

Section: Large-scale In Vivo Local-eqtl Characterization Via Allelespmentioning

confidence: 99%

cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel

et al. 2020

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Background: Resistance to enteric pathogens is a complex trait at the crossroads of multiple biological processes. We have previously shown in the Drosophila Genetic Reference Panel (DGRP) that resistance to infection is highly heritable, but our understanding of how the effects of genetic variants affect different molecular mechanisms to determine gut immunocompetence is still limited. Results: To address this, we perform a systems genetics analysis of the gut transcriptomes from 38 DGRP lines that were orally infected with Pseudomonas entomophila. We identify a large number of condition-specific, expression quantitative trait loci (local-eQTLs) with infection-specific ones located in regions enriched for FOX transcription factor motifs. By assessing the allelic imbalance in the transcriptomes of 19 F1 hybrid lines from a large round robin design, we independently attribute a robust cis-regulatory effect to only 10% of these detected local-eQTLs. However, additional analyses indicate that many local-eQTLs may act in trans instead. Comparison of the transcriptomes of DGRP lines that were either susceptible or resistant to Pseudomonas entomophila infection reveals nutcracker as the only differentially expressed gene. Interestingly, we find that nutcracker is linked to infection-specific eQTLs that correlate with its expression level and to enteric infection susceptibility. Further regulatory analysis reveals one particular eQTL that significantly decreases the binding affinity for the repressor Broad, driving differential allele-specific nutcracker expression. Conclusions: Our collective findings point to a large number of infection-specific cis-and transacting eQTLs in the DGRP, including one common non-coding variant that lowers enteric infection susceptibility.

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Regulatory SNPs and transcriptional factor binding sites in ADRBK1, AKT3, ATF3, DIO2, TBXA2R and VEGFA

Cited by 26 publications

References 84 publications

Assessing the Effect of SNPs on Litter Traits in Pigs

Assessing the Effect of SNPs on Litter Traits in Pigs

Intronic regions of the human coagulation factor VIII gene harboring transcription factor binding sites with a strong bias towards the short-interspersed elements

cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel

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