Computational analysis of auxin responsive elements in the Arabidopsis thalianaL. genome

BMC Genomics

Research

Nadezda A Omelyanchuk¹  Victor G Levitsky²  Daniil S Wiebe²  Victoria V Mironova² 

[1]Institute of Cytology and Genetics SB RAS, 10 Lavrentyeva avenue, 630090, Novosibirsk, Russia

[2]Institute of Cytology and Genetics SB RAS, 10 Lavrentyeva avenue, 630090, Novosibirsk, Russia

[3]Novosibirsk State University, 2 Pirogova street, 630090, Novosibirsk, Russia

关键词: Plant hormone;    primary response;    transcription regulation;    composite element;    bioinformatics;   

DOI  :  10.1186/1471-2164-15-S12-S4

来源: Springer

【 摘 要 】

Auxin responsive elements (AuxRE) were found in upstream regions of target genes for ARFs (Auxin response factors). While Chip-seq data for most of ARFs are still unavailable, prediction of potential AuxRE is restricted by consensus models that detect too many false positive sites. Using sequence analysis of experimentally proven AuxREs, we revealed both an extended nucleotide context pattern for AuxRE itself and three distinct types of its coupling motifs (Y-patch, AuxRE-like, and ABRE-like), which together with AuxRE may form the composite elements. Computational analysis of the genome-wide distribution of the predicted AuxREs and their impact on auxin responsive gene expression allowed us to conclude that: (1) AuxREs are enriched around the transcription start site with the maximum density in 5'UTR; (2) AuxREs mediate auxin responsive up-regulation, not down-regulation. (3) Directly oriented single AuxREs and reverse multiple AuxREs are mostly associated with auxin responsiveness. In the composite AuxRE elements associated with auxin response, ABRE-like and Y-patch are 5'-flanking or overlapping AuxRE, whereas AuxRE-like motif is 3'-flanking. The specificity in location and orientation of the coupling elements suggests them as potential binding sites for ARFs partners.

【 授权许可】

CC BY   
© Mironova et al.; licensee BioMed Central Ltd. 2014