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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Main Authors: O. A. Chernykh, V. G. Levitsky, N. A. Omelyanchuk, V. V. Mironova
Format: Article
Language:English
Published: 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
Series:Вавиловский журнал генетики и селекции
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Online Access:https://vavilov.elpub.ru/jour/article/view/318
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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
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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
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AT vglevitsky computationalanalysisandfunctionalannotationofap2erftranscriptionfactorbindingsitesinarabidopsisthalianalgenome
AT naomelyanchuk computationalanalysisandfunctionalannotationofap2erftranscriptionfactorbindingsitesinarabidopsisthalianalgenome
AT vvmironova computationalanalysisandfunctionalannotationofap2erftranscriptionfactorbindingsitesinarabidopsisthalianalgenome