Human Genes Encoding Transcription Factors and Chromatin-Modifying Proteins Have Low Levels of Promoter Polymorphism: A Study of 1000 Genomes Project Data
The expression level of each gene is controlled by its regulatory regions, which determine the precise regulation in a tissue-specific manner, according to the developmental stage of the body and the necessity of a response to external stimuli. Nucleotide substitutions in regulatory gene regions may...
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| Format: | Article |
| Language: | English |
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Wiley
2015-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2015/260159 |
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| author | Elena V. Ignatieva Victor G. Levitsky Nikolay A. Kolchanov |
| author_facet | Elena V. Ignatieva Victor G. Levitsky Nikolay A. Kolchanov |
| author_sort | Elena V. Ignatieva |
| collection | DOAJ |
| description | The expression level of each gene is controlled by its regulatory regions, which determine the precise regulation in a tissue-specific manner, according to the developmental stage of the body and the necessity of a response to external stimuli. Nucleotide substitutions in regulatory gene regions may modify the affinity of transcription factors to their specific DNA binding sites, affecting the transcription rates of genes. In our previous research, we found that genes controlling the sensory perception of smell and genes involved in antigen processing and presentation were overrepresented significantly among genes with high SNP contents in their promoter regions. The goal of our study was to reveal functional features of human genes containing extremely small numbers of SNPs in promoter regions. Two functional groups were found to be overrepresented among genes whose promoters did not contain SNPs: (1) genes involved in gene-specific transcription and (2) genes controlling chromatin organization. We revealed that the 5′-regulatory regions of genes encoding transcription factors and chromatin-modifying proteins were characterized by reduced genetic variability. One important exception from this rule refers to genes encoding transcription factors with zinc-coordinating DNA-binding domains (DBDs), which underwent extensive expansion in vertebrates, particularly, in primate evolution. Hence, we obtained new evidence for evolutionary forces shaping variability in 5′-regulatory regions of genes. |
| format | Article |
| id | doaj-art-8705391fa7d44f689d780e5dd72a7171 |
| institution | OA Journals |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2015-01-01 |
| publisher | Wiley |
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| series | International Journal of Genomics |
| spelling | doaj-art-8705391fa7d44f689d780e5dd72a71712025-08-20T02:08:35ZengWileyInternational Journal of Genomics2314-436X2314-43782015-01-01201510.1155/2015/260159260159Human Genes Encoding Transcription Factors and Chromatin-Modifying Proteins Have Low Levels of Promoter Polymorphism: A Study of 1000 Genomes Project DataElena V. Ignatieva0Victor G. Levitsky1Nikolay A. Kolchanov2Laboratory of Evolutionary Bioinformatics and Theoretical Genetics, Federal State Research Center Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, RussiaLaboratory of Evolutionary Bioinformatics and Theoretical Genetics, Federal State Research Center Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, RussiaDepartment of Natural Science, Novosibirsk State University, Novosibirsk 630090, RussiaThe expression level of each gene is controlled by its regulatory regions, which determine the precise regulation in a tissue-specific manner, according to the developmental stage of the body and the necessity of a response to external stimuli. Nucleotide substitutions in regulatory gene regions may modify the affinity of transcription factors to their specific DNA binding sites, affecting the transcription rates of genes. In our previous research, we found that genes controlling the sensory perception of smell and genes involved in antigen processing and presentation were overrepresented significantly among genes with high SNP contents in their promoter regions. The goal of our study was to reveal functional features of human genes containing extremely small numbers of SNPs in promoter regions. Two functional groups were found to be overrepresented among genes whose promoters did not contain SNPs: (1) genes involved in gene-specific transcription and (2) genes controlling chromatin organization. We revealed that the 5′-regulatory regions of genes encoding transcription factors and chromatin-modifying proteins were characterized by reduced genetic variability. One important exception from this rule refers to genes encoding transcription factors with zinc-coordinating DNA-binding domains (DBDs), which underwent extensive expansion in vertebrates, particularly, in primate evolution. Hence, we obtained new evidence for evolutionary forces shaping variability in 5′-regulatory regions of genes.http://dx.doi.org/10.1155/2015/260159 |
| spellingShingle | Elena V. Ignatieva Victor G. Levitsky Nikolay A. Kolchanov Human Genes Encoding Transcription Factors and Chromatin-Modifying Proteins Have Low Levels of Promoter Polymorphism: A Study of 1000 Genomes Project Data International Journal of Genomics |
| title | Human Genes Encoding Transcription Factors and Chromatin-Modifying Proteins Have Low Levels of Promoter Polymorphism: A Study of 1000 Genomes Project Data |
| title_full | Human Genes Encoding Transcription Factors and Chromatin-Modifying Proteins Have Low Levels of Promoter Polymorphism: A Study of 1000 Genomes Project Data |
| title_fullStr | Human Genes Encoding Transcription Factors and Chromatin-Modifying Proteins Have Low Levels of Promoter Polymorphism: A Study of 1000 Genomes Project Data |
| title_full_unstemmed | Human Genes Encoding Transcription Factors and Chromatin-Modifying Proteins Have Low Levels of Promoter Polymorphism: A Study of 1000 Genomes Project Data |
| title_short | Human Genes Encoding Transcription Factors and Chromatin-Modifying Proteins Have Low Levels of Promoter Polymorphism: A Study of 1000 Genomes Project Data |
| title_sort | human genes encoding transcription factors and chromatin modifying proteins have low levels of promoter polymorphism a study of 1000 genomes project data |
| url | http://dx.doi.org/10.1155/2015/260159 |
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