Abstract
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.
Highlights
The hormone auxin is a major regulator of plant growth and development
Recognition of potential Auxin Responsive Elements To apply methods for Auxin responsive elements (AuxRE) recognition, we collected from published papers (a) the nucleotide sequences of experimentally proven AuxREs (Training set; 25 sequences 106-nt in length with centrally located TGTCNN hexamer, Additional file 1) and (b) extended promoters [-2000;-1] of auxin-regulated genes (Positive set; 44 sequences)
We established the thresholds for genomewide AuxRE recognition as those allowed to predict potential AuxREs in about 30% of promoters from the Positive set by both Optimized PWM (oPWM) and SiteGA
Summary
The hormone auxin is a major regulator of plant growth and development. The influence of auxin on gene transcription is primarily mediated by its binding to TIR1/AFB receptors [1,2]. Auxin changes the conformation of receptors and thereby promotes their interaction with Aux/IAA proteins. These proteins form heterodimers with Auxin Response Transcription Factors (ARFs) making them inactive. ARFs bind in target promoters to the specific sites called AuxREs (Auxin Response Elements) with the TGTCNN (most frequently TGTCTC) consensus core sequence [3,4,5]. It has been shown, that the TGTCGG motif is more effective in binding ARF1 and ARF5 [6]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
