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/lp/springer_journal/tata-box-polymorphisms-in-genes-of-commercial-and-laboratory-animals-XSHaVdgvHc
- Publisher
- Springer Journals
- Copyright
- Copyright © 2010 by Pleiades Publishing, Ltd.
- Subject
- Biomedicine; Microbial Genetics and Genomics; Animal Genetics and Genomics; Human Genetics
- ISSN
- 1022-7954
- eISSN
- 1608-3369
- D.O.I.
- 10.1134/S1022795410040022
- Publisher site
- See Article on Publisher Site
Abstract
Most of more than 11 million experimentally established polymorphisms, accumulated in dbSNP, were identified in the intergenic spacers or coding DNA regions. This fact enables interpretation of the former polymorphisms as neutral, while the latter makes clear the biological sense of the associated mutant phenotypes, “the defect of certain proteins”. The association of polymorphisms in regulatory DNA regions with mutant phenotypes is poorly studied. Specifically, the defects in certain DNA/protein binding sites were identified in less than 500 cases. In TATA-containing genes of eukaryotes the TATA box, the TBP (TATA-binding protein) binding site, is located about 30 bp upstream from the transcription start site. Interaction between DNA and TBP triggers assemblage of the preinitiation complex. For 38 TATA box polymorphisms in the genes of commercial and laboratory animals and plants, the effect on TBP-binding activity was evaluated using the equilibrium equation for the four subsequent steps of TBP/TATA box binding (nonspecific binding ↔ sliding ↔ recognition ↔ stabilization). According to the GenBank data, these 38 polymorphisms were associated with the change in a number of selectively valuable traits. Statistically significant congruence of in silico analysis performed with mutant phenotypes (α < 0.05, binomial law) provides suggestion of the mechanism of phenotypic manifestation of these polymorphisms (changing of the TBP-binding activity), as well a validates the possibility of developing the universal test system for experimental-computer prediction of the effects of TATA box mutations in specified genes on selectively valuable traits of the species, varieties, and breeds.
Journal
Russian Journal of Genetics – Springer Journals
Published: Apr 25, 2010
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References
-
The Complete Genome of an Individual by Massively Parallel DNA SequencingWheeler, D.A.; Srinivasan, M.; Egholm, M.
-
The Diploid Genome Sequence of an Asian IndividualWang, J.; Wang, W.; Li, R.
-
Large-Scale Identification, Mapping, and Genotyping of Single-Nucleotide Polymorphisms in the Human GenomeWang, D.; Fan, J.; Siao, C.
-
Population Genomics: Genome-Wide Sampling of Insect PopulationsBlack, W.; Baer, C.; Antolin, M.
-
Genome-Wide Variation in the Human and Fruitfly: A ComparisonAquadro, C.; Bauer DuMont, V.; Reed, F.A.
-
SNP Frequency, Haplotype Structure and Linkage Disequilibrium in Elite Maize Inbred LinesChing, A.; Caldwell, K.; Jung, M.
-
Search for and Analysis of Single Nucleotide Polymorphisms (SNPs) in Rice (Oryza sativa, Oryza rufipogon) and Establishment of SNP MarkersNasu, S.; Suzuki, J.; Ohta, R.
-
Generation and Mapping of AFLP, SSRs and SNPs in Lycopersicon esculentumSuliman-Pollatschek, S.; Kashkush, K.; Shats, H.
-
Intraspecific DNA Variation in Nuclear Genes of the Mosquito Aedes aegyptiMorlais, I.; Severson, D.
-
Genome-Wide Single-Nucleotide Polymorphism Map for Candida albicansForche, A.; Magee, P.; Magee, B.; May, G.
-
Identification and Analysis of Single Nucleotide Polymorphisms (SNPs) in the Mosquito Anopheles funestus, Malaria VectorWondji, C.S.; Hemingway, J.; Ranson, H.
-
Detection of Genome-Wide Polymorphisms in the AT-Rich Plasmodium falciparum Genome Using a High-Density MicroarrayJiang, H.; Yi, M.; Mu, J.
-
Single Nucleotide Polymorphism Discovery in Barley Using AutoSNPdbDuran, C.; Appleby, N.; Vardy, M.
-
The Birth and Death of Human Single-Nucleotide Polymorphisms: New Experimental Evidence and Implications for Human History and MedicineMiller, R.; Kwok, P.
-
Mining for SNPs and SSRs Using SNPServer, dbSNP and SSR Taxonomy TreeBatley, J.; Edwards, D.
-
DNA and Protein Footprinting Analysis of the Modulation of DNA Binding by the N-Terminal Domain of the S. cerevisiae TATA Bindung ProteinGupta, S.; Cheng, H.; Mollah, A.
-
The Amino-Terminal Tails of the Core Histones and the Translational Position of the TATA Box Determine TBP/TFIIA Association with Nucleosomal DNAGodde, J.; Nakatani, Y.; Wolffe, A.
-
The Organization of the Histone Genes in Drosophila melanogaster: Functional and Evolutionary ImplicationsLifton, R.; Goldberg, M.; Karp, R.
-
EPD in Its Twentieth Year: Towards Complete Promoter Coverage of Selected Model OrganismsSchmid, C.D.; Perier, R.; Praz, V.
-
Weight Matrix Descriptions of Four Eukaryotic RNA Polymerase II Promoter Elements Derived from 502 Unrelated Promoter SequencesBucher, P.
-
Nearest-Neighbor Non-Additivity versus Long-Range Non-Additivity in TATA-Box Structure and Its Implication for TBP-Binding MechanismFaiger, H.; Ivanchenko, M.; Haran, T.
-
Yeast TATA-Binding Protein TFIID Binds to TATA Elements with Both Consensus and Nonconsensus DNA SequencesHahn, S.; Buratowski, S.; Sharp, P.; Guarente, L.
-
Evidence for Functional Binding and Stable Sliding of the TATA Binding Protein on Nonspecific DNAColeman, R.; Pugh, B.
-
Comparison of TATA-Binding Protein Recognition of a Variant and Consensus DNA PromotersPowell, R.; Parkhurst, K.; Parkhurst, L.
-
A High-Resolution Map of Active Promoters in the Human GenomeKim, T.; Barrera, L.; Zheng, M.
-
Interaction of Recombinant TATA-Binding Protein with TATA Boxes of Mammalian Gene PromotersSavinkova, L.K.; Drachkova, I.A.; Ponomarenko, M.P.
-
Interaction between Yeast TATA-Binding Protein and Short Promoter RegionsSokolenko, A.A.; Sandomirskii, I.I.; Savinkova, L.K.
-
Computer Modeling of TATA-Box Sequences of Eukaryotic PromotersPonomarenko, M.P.; Savinkova, L.K.; Kel’, A.E.
-
Identification of Sequence-Dependent Features Correlating to Activity of DNA Sites Interacting with ProteinsPonomarenko, M.; Ponomarenko, J.; Frolov, A.
-
A Step-by-Step Model of TBP/TATA Box Binding Allows Predicting Human Hereditary Diseases by Single Nucleotide PolymorphismPonomarenko, P.M.; Savinkova, L.K.; Drachkova, I.A.
-
TATA Box Polymorphisms in Human Gene Promoters and Associated Hereditary PathologiesSavinkova, L.K.; Ponomarenko, M.P.; Ponomarenko, P.M.
-
Prediction of the Affinity of the TATA-Binding Protein to TATA Boxes with Single Nucleotide PolymorphismsPonomarenko, P.M.; Ponomarenko, M.P.; Drachkova, I.A.
-
Gen-BankBenson, D.; Karsch-Mizrachi, I.; Lipman, D.
-
Patent Searches as a Complement to Literature Searches in the Life Sciences—a “How-To” TutorialSeeber, F.
-
The Porcine Gonadotropin-Releasing Hormone Receptor Gene (GNRHR): Genomic Organization, Polymorphisms, and Association with the Number of Corpora LuteaJiang, Z.; Gibson, J.; Archibald, A.
-
Digenic Mutations Account for Variable Phenotypes in Idiopathic Hypogonadotropic HypogonadismPitteloud, N.; Quinton, R.; Pearce, S.
-
Functional Promoter Variants of Highly Conserved Inducible hsp70 Genes Significantly Affect Stress ResponseSchwerin, M.; Maak, S.; Kalbe, C.
-
Decreased Expression of the Heat Shock Protein hsp70-2 Is Associated with the Pathogenesis of Male InfertilityFeng, H.; Sandlow, J.; Sparks, A.
-
Polymorphisms within the Lactoferrin Gene Promoter in Various Cattle BreedsDaly, M.; Ross, P.; Giblin, L.
-
Study on the Polymorphism of Bovine Lactoferrin Gene and Its Relationship with MastitisLi, G.; Zhang, Y.; Sun, D.; Li, N.
-
Izbrannye trudy v 5 tomakhVavilov, N.I.
-
Domestication of Cereal Crops in the Old World: In Search for a New Approach to Solving Old ProblemGoncharov, N.P.; Glushkov, S.A.; Shumny, V.K.
-
New DNA Markers for High Molecular Weight Glutenin Subunits in WheatLiu, S.; Chao, S.; Anderson, J.
-
Spelt-Specific Alleles in HMW Glutenin Genes from Modern and Historical European Spelt (Triticum spelta L.)Blatter, R.; Jacomet, S.; Schlumbaum, A.
-
Characteristics of Ancient Local Varieties of Common Winter Wheat Based on Electrophoresis Spectra of High-Molecular GluteninAlpat’eva, N.V.; Gubareva, N.K.
-
Coexistence of Tetraploid and Hexaploid Naked Wheat in a Neolithic Lake Dwelling of Central Europe: Evidence from Morphology and Ancient DNASchlumbaum, A.; Neuhaus, J.; Jacomet, S.
-
Positional Cloning of the Wheat Vernalization Gene VRN1Yan, L.; Loukoianov, A.; Tranquilli, G.
-
The TATA Box Promoter Region of Maize Adh1 Affects its Organ-Specific ExpressionKloeckener-Gruissem, V.; Vogel, J.; Freeling, M.
-
Organ-Specific Expression of Maize Adh1 Is Altered after a Mu Transposon InsertionChen, C.; Oishi, K.; Kloeckener-Gruissem, B.
-
Transformation in Drosophila: New Experimental Approach in GeneticsZhimulev, I.F.
-
Hsp28stl: A P-Element Insertion Mutation That Alters the Expression of a Heat Shock Gene in Drosophila melanogasterEissenberg, J.; Elgin, S.
-
Remarkable Site Specificity of Local Transposition into the Hsp70 Promoter of Drosophila melanogasterShilova, V.; Garbuz, D.; Myasyankina, E.
-
Isolation and Expression of scabrous, a Gene Regulating Neurogenesis in DrosophilaMlodzik, M.; Baker, N.; Rubin, G.
-
Drosophila Hormone Receptor 38 Functions in Metamorphosis: A Role in Adult Cuticle FormationKozlova, T.; Pokholkova, G.; Tzertzinis, G.
-
Recent Evolutionary History of the Metallothionein Gene Mtn in DrosophilaTheodore, L.; Ho, A.; Maroni, G.
-
Targeted Disruption of Metallothionein I and II Genes Increases Sensitivity to CadmiumMasters, B.; Kelly, E.; Quaife, C.
-
Evolutionary Relationships and Sequence Variation of Alpha-Amylase Variants Encoded by Duplicated Genes in the Amy Locus of Drosophila melanogasterInomata, N.; Shibata, H.; Okuyama, E.
-
Nucleotide Variation of the Duplicated Amylase Genes in Drosophila kikkawaiInomata, N.; Yamazaki, T.
-
Conservation and Change in the DNA Sequences Coding for Alcohol Dehydrogenase in Sibling Species of DrosophilaBodmer, M.; Ashburner, M.
-
Genomic Organization, Chromosomal Localization, and Promoter Analysis of the Mouse Mail GeneShiina, T.; Morimatsu, M.; Kitamura, H.
-
Aldolase Excess in Blood in Myopathic MiceSchapira, F.; Schapira, G.; Dreyfus, J. 1957.
-
Diffluence Factors of Coagulated Human EjaculateMiroshnikov, V.M.; Nikolaev, A.A.; Lutskii, D.L.
-
The Common Marmoset (Callithrix jacchus) Has Two Very Similar Semenogelin Genes as the Result of Gene ConversionValtonen-Andre, C.; Olsson, A.; Kullberg, M.
-
Native Human TATA-Binding Protein Simultaineously Binds and Bends Promoter DNA without Slow Isomerization Step or TFIIB RequirementMasters, K.; Parkhurst, K.; Daugherty, M.
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