COMPUTATIONAL ANALYSIS AND FUNCTIONAL ANNOTATION OF AP2/ERF TRANSCRIPTION FACTOR BINDING SITES IN ARABIDOPSIS THALIANA L. GENOME
The plant hormone ethylene regulates both developmental processes and various stress responses in plants. Ethylene perception in plants is followed by activation of some transcription factors from the large family of APETALA2/ETHYLENE response factors (ERFs). ERF TF binding sites contain a specific...
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| Format: | Article |
| Language: | English |
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Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders
2015-01-01
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| Series: | Вавиловский журнал генетики и селекции |
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| Online Access: | https://vavilov.elpub.ru/jour/article/view/318 |
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| _version_ | 1832575319896227840 |
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| author | O. A. Chernykh V. G. Levitsky N. A. Omelyanchuk V. V. Mironova |
| author_facet | O. A. Chernykh V. G. Levitsky N. A. Omelyanchuk V. V. Mironova |
| author_sort | O. A. Chernykh |
| collection | DOAJ |
| description | The plant hormone ethylene regulates both developmental processes and various stress responses in plants. Ethylene perception in plants is followed by activation of some transcription factors from the large family of APETALA2/ETHYLENE response factors (ERFs). ERF TF binding sites contain a specific GCCGCC motif, called GCC-box. In this study, we applied TF binding site recognition tools oPWM and SiteGA for sequence analysis of experimentally proven GCC-boxes. We carried out GCC box recognition and tested its distribution in the Arabidopsis thaliana L. genome. Functional annotation and microarray data analysis of the genes possessing predicted GCC-boxes elucidated their role in ethylene response. |
| format | Article |
| id | doaj-art-a6b6da7c83b34c81a294279991cf40fb |
| institution | Kabale University |
| issn | 2500-3259 |
| language | English |
| publishDate | 2015-01-01 |
| publisher | Siberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and Breeders |
| record_format | Article |
| series | Вавиловский журнал генетики и селекции |
| spelling | doaj-art-a6b6da7c83b34c81a294279991cf40fb2025-02-01T09:58:01ZengSiberian Branch of the Russian Academy of Sciences, Federal Research Center Institute of Cytology and Genetics, The Vavilov Society of Geneticists and BreedersВавиловский журнал генетики и селекции2500-32592015-01-01184/2887897301COMPUTATIONAL ANALYSIS AND FUNCTIONAL ANNOTATION OF AP2/ERF TRANSCRIPTION FACTOR BINDING SITES IN ARABIDOPSIS THALIANA L. GENOMEO. A. Chernykh0V. G. Levitsky1N. A. Omelyanchuk2V. V. Mironova3Institute of Cytology and Genetics SB RAS, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RAS, Novosibirsk, Russia Novosibirsk National Research State University, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RAS, Novosibirsk, RussiaInstitute of Cytology and Genetics SB RAS, Novosibirsk, Russia Novosibirsk National Research State University, Novosibirsk, RussiaThe plant hormone ethylene regulates both developmental processes and various stress responses in plants. Ethylene perception in plants is followed by activation of some transcription factors from the large family of APETALA2/ETHYLENE response factors (ERFs). ERF TF binding sites contain a specific GCCGCC motif, called GCC-box. In this study, we applied TF binding site recognition tools oPWM and SiteGA for sequence analysis of experimentally proven GCC-boxes. We carried out GCC box recognition and tested its distribution in the Arabidopsis thaliana L. genome. Functional annotation and microarray data analysis of the genes possessing predicted GCC-boxes elucidated their role in ethylene response.https://vavilov.elpub.ru/jour/article/view/318ethylenetranscription factorbinding sitearabidopsis thaliana |
| spellingShingle | O. A. Chernykh V. G. Levitsky N. A. Omelyanchuk V. V. Mironova COMPUTATIONAL ANALYSIS AND FUNCTIONAL ANNOTATION OF AP2/ERF TRANSCRIPTION FACTOR BINDING SITES IN ARABIDOPSIS THALIANA L. GENOME Вавиловский журнал генетики и селекции ethylene transcription factor binding site arabidopsis thaliana |
| title | COMPUTATIONAL ANALYSIS AND FUNCTIONAL ANNOTATION OF AP2/ERF TRANSCRIPTION FACTOR BINDING SITES IN ARABIDOPSIS THALIANA L. GENOME |
| title_full | COMPUTATIONAL ANALYSIS AND FUNCTIONAL ANNOTATION OF AP2/ERF TRANSCRIPTION FACTOR BINDING SITES IN ARABIDOPSIS THALIANA L. GENOME |
| title_fullStr | COMPUTATIONAL ANALYSIS AND FUNCTIONAL ANNOTATION OF AP2/ERF TRANSCRIPTION FACTOR BINDING SITES IN ARABIDOPSIS THALIANA L. GENOME |
| title_full_unstemmed | COMPUTATIONAL ANALYSIS AND FUNCTIONAL ANNOTATION OF AP2/ERF TRANSCRIPTION FACTOR BINDING SITES IN ARABIDOPSIS THALIANA L. GENOME |
| title_short | COMPUTATIONAL ANALYSIS AND FUNCTIONAL ANNOTATION OF AP2/ERF TRANSCRIPTION FACTOR BINDING SITES IN ARABIDOPSIS THALIANA L. GENOME |
| title_sort | computational analysis and functional annotation of ap2 erf transcription factor binding sites in arabidopsis thaliana l genome |
| topic | ethylene transcription factor binding site arabidopsis thaliana |
| url | https://vavilov.elpub.ru/jour/article/view/318 |
| work_keys_str_mv | AT oachernykh computationalanalysisandfunctionalannotationofap2erftranscriptionfactorbindingsitesinarabidopsisthalianalgenome AT vglevitsky computationalanalysisandfunctionalannotationofap2erftranscriptionfactorbindingsitesinarabidopsisthalianalgenome AT naomelyanchuk computationalanalysisandfunctionalannotationofap2erftranscriptionfactorbindingsitesinarabidopsisthalianalgenome AT vvmironova computationalanalysisandfunctionalannotationofap2erftranscriptionfactorbindingsitesinarabidopsisthalianalgenome |