A step-by-step model of TBP/TATA box binding allows predicting human hereditary diseases by single nucleotide polymorphism

Пономаренко, П. М.; Савинкова, Л. К.; Драчкова, И. А.; Лысова, М. В.; Arshinova, T. V.; Пономаренко, М. П.; Колчанов, Н. А.

doi:10.1134/s1607672908020117

Cited by 37 publications

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References 13 publications

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“…39 Table 6 shows the robustness of this correlations with respect to all rank, generalized and dichotic tests available within STATISTICA. Finally, in the bottom line of this table there is Fisher's F -test validating the signi¯cant impact of both TBP a±nity 34 to the promoters 35 and nucleosome score 36 on '-values of transcription changes, after auxin treatment in addition to AuxRE's impact, F ¼ 4:07, p < 0:025. This signi¯cant independence between both impacts of TBP/promotera±nity and nucleosomal DNA into the auxin response on the one hand and the impact of AuxRE on this response on another hand means that both TBP/promotera±nity and nucleosomal DNA impacts should be associated with Aux/IAA-dependent protein-protein speci¯city 5 of this response rather than with the AuxREdependent protein/DNA-sensitivity.…”

Section: Sequence-based Prediction Of Transcription Upregulation By Amentioning

confidence: 99%

“…According to earlier recommendations, 34 the four-step model of transcription upregulation by auxin in plants ( Fig. 1) was modeled by the following empirical equation:…”

Section: Sequence-based Prediction Of Transcription Up-regulation By mentioning

confidence: 99%

“…1(c) and 1(d)) we found negative and positive correlations respectively between genes' transcription increases in response to auxin and contextual features around AuxRE using Activity 33 tools described in our previous paper. 29 Taking all these¯ndings together we derived an empirical equation 34 of four-step auxin response (Fig. 1).…”

Section: Introductionmentioning

confidence: 99%

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Sequence-based prediction of transcription upregulation by auxin in plants

Пономаренко

2015

J. Bioinform. Comput. Biol.

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Auxin is one of the main regulators of growth and development in plants. Prediction of auxin response based on gene sequence is of high importance. We found the TGTCNC consensus of 111 known natural and artificially mutated auxin response elements (AuxREs) with measured auxin-caused relative increase in genes' transcription levels, so-called either "a response to auxin" or "an auxin response." This consensus was identical to the most cited AuxRE motif. Also, we found several DNA sequence features that correlate with auxin-caused increase in genes' transcription levels, namely: number of matches with TGTCNC, homology score based on nucleotide frequencies at the consensus positions, abundances of five trinucleotides and five B-helical DNA features around these known AuxREs. We combined these correlations using a four-step empirical model of auxin response based on a gene's sequence with four steps, namely: (1) search for AuxREs with no auxin; (2) stop at the found AuxRE; (3) repression of the basal transcription of the gene having this AuxRE; and (4) manifold increase of this gene's transcription in response to auxin. Independently measured increases in transcription levels in response to auxin for 70 Arabidopsis genes were found to significantly correlate with predictions of this equation (r = 0.44, p < 0.001) as well as with TATA-binding protein (TBP)'s affinity to promoters of these genes and with nucleosome packing of these promoters (both, p < 0.025). Finally, we improved our equation for prediction of a gene's transcription increase in response to auxin by taking into account TBP-binding and nucleosome packing (r = 0.53, p < 10(-6)). Fisher's F-test validated the significant impact of both TBP/promoter-affinity and promoter nucleosome on auxin response in addition to those of AuxRE, F = 4.07, p < 0.025. It means that both TATA-box and nucleosome should be taken into account to recognize transcription factor binding sites upon DNA sequences: in the case of the TATA-less nucleosome-rich promoters, recognition scores must be higher than in the case of the TATA-containing nucleosome-free promoters at the same transcription activity.

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Section: Sequence-based Prediction Of Transcription Upregulation By Amentioning

confidence: 99%

“…According to earlier recommendations, 34 the four-step model of transcription upregulation by auxin in plants ( Fig. 1) was modeled by the following empirical equation:…”

Section: Sequence-based Prediction Of Transcription Up-regulation By mentioning

confidence: 99%

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Sequence-based prediction of transcription upregulation by auxin in plants

Пономаренко

2015

J. Bioinform. Comput. Biol.

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“…Reference human genome (Colonna et al, 2014) Standard statistical software R Z-score: an estimate of the significance of a change of gene expression in a person with a minor allele of a particular SNP with reference to the norm as the ancestral allele (Ponomarenko et al, 2008) BioPerl Illustrative prediction of a candidate SNP marker for dominant and subordinate behavior in humans with the Webservice in the case of the known SNP marker rs3813929 for resistance to olanzapine (Landrum et al, 2014) determined by an excess of seroto nin receptor 2C (Ellingrod et al, 2005).…”

Section: Discussionmentioning

confidence: 99%

“…Мы фокусировали наши предыдущие исследования на районе [-70;-20] перед стартами белок-кодирующих транскриптов в геноме человека, куда проецируются из-вестные сайты связывания ТВР, самые изученные регуля-торные сигналы генома (Ponomarenko et al, 2013). Была создана вычислительная модель трехшагового связывания ТВР/ТАТА-бокс (Ponomarenko et al, 2008): скольжение ТВР вдоль ДНК → остановка ТВР на ТАТА-боксе → ста-билизация комплекса ТВР/ТАТА изгибом спирали ДНК, как это годом позже наблюдали в опыте R.F. Delgadillo с коллегами (2009).…”

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Candidate SNP markers of social dominance, which may affect the affinity of the TATAbinding protein for human gene promoters

Чадаева¹,

Рассказов²,

Шарыпова³

et al. 2016

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The Mechanism by which TATA-Box Polymorphisms Associated with Human Hereditary Diseases Influence Interactions with the TATA-Binding Protein

et al. 2014

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SNPs in ТАТА boxes are the cause of monogenic diseases, contribute to a large number of complex diseases, and have implications for human sensitivity to external and internal environmental signals. The aim of this work was to explore the kinetic characteristics of the formation of human ТВР complexes with ТАТА boxes, in which the SNPs are associated with β-thalassemias of diverse severity, immunosuppression, neurological disorders, and so on. It has for the first time been demonstrated, using an electrophoretic mobility shift assay, that TBP interacts with SNP-containing ТАТА boxes with a significant (8-36-fold) decrease in TBP/ТАТА association rate constant (ka ) as compared with that in healthy people, a smaller decrease in dissociation rate constant (kd ) and changes in the half-lives of TBP/ТАТА complexes. Carriers of the -24G allele (rs 1800202T>G) in the TATA box of the triosephosphate isomerase gene promoter, associated with neurological and muscular disorders, were observed to have a 36-fold decrease in TBP/TATA association rate constant that are consistent with TPI deficiency shown for patients who carry this defective allele. The kinetic characteristics of TBP/ТАТА complexes obtained suggest that, at a molecular level, hereditary diseases are largely caused by changes in TBP/ТАТА association rates and these changes have a bearing on disease severity.

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A step-by-step model of TBP/TATA box binding allows predicting human hereditary diseases by single nucleotide polymorphism

Cited by 37 publications

References 13 publications

Sequence-based prediction of transcription upregulation by auxin in plants

Sequence-based prediction of transcription upregulation by auxin in plants

Candidate SNP markers of social dominance, which may affect the affinity of the TATAbinding protein for human gene promoters

The Mechanism by which TATA-Box Polymorphisms Associated with Human Hereditary Diseases Influence Interactions with the TATA-Binding Protein

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