Conservation of transcription factor binding specificities across 600 million years of bilateria evolution
Divergent morphology of species has largely been ascribed to genetic differences in the tissue-specific expression of proteins, which could be achieved by divergence in cis-regulatory elements or by altering the binding specificity of transcription factors (TFs). The relative importance of the latte...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2015-03-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/04837 |
| _version_ | 1811181069962051584 |
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| author | Kazuhiro R Nitta Arttu Jolma Yimeng Yin Ekaterina Morgunova Teemu Kivioja Junaid Akhtar Korneel Hens Jarkko Toivonen Bart Deplancke Eileen E M Furlong Jussi Taipale |
| author_facet | Kazuhiro R Nitta Arttu Jolma Yimeng Yin Ekaterina Morgunova Teemu Kivioja Junaid Akhtar Korneel Hens Jarkko Toivonen Bart Deplancke Eileen E M Furlong Jussi Taipale |
| author_sort | Kazuhiro R Nitta |
| collection | DOAJ |
| description | Divergent morphology of species has largely been ascribed to genetic differences in the tissue-specific expression of proteins, which could be achieved by divergence in cis-regulatory elements or by altering the binding specificity of transcription factors (TFs). The relative importance of the latter has been difficult to assess, as previous systematic analyses of TF binding specificity have been performed using different methods in different species. To address this, we determined the binding specificities of 242 Drosophila TFs, and compared them to human and mouse data. This analysis revealed that TF binding specificities are highly conserved between Drosophila and mammals, and that for orthologous TFs, the similarity extends even to the level of very subtle dinucleotide binding preferences. The few human TFs with divergent specificities function in cell types not found in fruit flies, suggesting that evolution of TF specificities contributes to emergence of novel types of differentiated cells. |
| first_indexed | 2024-04-11T09:13:28Z |
| format | Article |
| id | doaj.art-11fa20f60f5d445aa2130f64f79fb476 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-11T09:13:28Z |
| publishDate | 2015-03-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-11fa20f60f5d445aa2130f64f79fb4762022-12-22T04:32:26ZengeLife Sciences Publications LtdeLife2050-084X2015-03-01410.7554/eLife.04837Conservation of transcription factor binding specificities across 600 million years of bilateria evolutionKazuhiro R Nitta0Arttu Jolma1Yimeng Yin2Ekaterina Morgunova3Teemu Kivioja4Junaid Akhtar5Korneel Hens6https://orcid.org/0000-0002-0362-7007Jarkko Toivonen7Bart Deplancke8Eileen E M Furlong9Jussi Taipale10Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, SwedenDepartment of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden; Genome-Scale Biology Program, University of Helsinki, Helsinki, FinlandDepartment of Biosciences and Nutrition, Karolinska Institutet, Stockholm, SwedenDepartment of Biosciences and Nutrition, Karolinska Institutet, Stockholm, SwedenGenome-Scale Biology Program, University of Helsinki, Helsinki, FinlandGenome Biology Unit, European Molecular Biology Laboratory, Heidelberg, GermanyInstitute of Bioengineering, School of Life Sciences, Swiss Federal Institute of Technology, Lausanne, SwitzerlandDepartment of Computer Science, University of Helsinki, Helsinki, FinlandInstitute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, SwitzerlandGenome Biology Unit, European Molecular Biology Laboratory, Heidelberg, GermanyDepartment of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden; Genome-Scale Biology Program, University of Helsinki, Helsinki, FinlandDivergent morphology of species has largely been ascribed to genetic differences in the tissue-specific expression of proteins, which could be achieved by divergence in cis-regulatory elements or by altering the binding specificity of transcription factors (TFs). The relative importance of the latter has been difficult to assess, as previous systematic analyses of TF binding specificity have been performed using different methods in different species. To address this, we determined the binding specificities of 242 Drosophila TFs, and compared them to human and mouse data. This analysis revealed that TF binding specificities are highly conserved between Drosophila and mammals, and that for orthologous TFs, the similarity extends even to the level of very subtle dinucleotide binding preferences. The few human TFs with divergent specificities function in cell types not found in fruit flies, suggesting that evolution of TF specificities contributes to emergence of novel types of differentiated cells.https://elifesciences.org/articles/04837transcription factorevolutionary conservationDNA binding specificityHT-SELEX |
| spellingShingle | Kazuhiro R Nitta Arttu Jolma Yimeng Yin Ekaterina Morgunova Teemu Kivioja Junaid Akhtar Korneel Hens Jarkko Toivonen Bart Deplancke Eileen E M Furlong Jussi Taipale Conservation of transcription factor binding specificities across 600 million years of bilateria evolution eLife transcription factor evolutionary conservation DNA binding specificity HT-SELEX |
| title | Conservation of transcription factor binding specificities across 600 million years of bilateria evolution |
| title_full | Conservation of transcription factor binding specificities across 600 million years of bilateria evolution |
| title_fullStr | Conservation of transcription factor binding specificities across 600 million years of bilateria evolution |
| title_full_unstemmed | Conservation of transcription factor binding specificities across 600 million years of bilateria evolution |
| title_short | Conservation of transcription factor binding specificities across 600 million years of bilateria evolution |
| title_sort | conservation of transcription factor binding specificities across 600 million years of bilateria evolution |
| topic | transcription factor evolutionary conservation DNA binding specificity HT-SELEX |
| url | https://elifesciences.org/articles/04837 |
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