Sequence-based prediction of transcription upregulation by auxin in plants

Abstract

Auxin is one of the main regulators of growth and development in plants. Prediction of auxin response based on gene sequence is of high importance. We found the TGTCNC consensus of 111 known natural and artificially mutated auxin response elements (AuxREs) with measured auxin-caused relative increase in genes' transcription levels, so-called either "a response to auxin" or "an auxin response." This consensus was identical to the most cited AuxRE motif. Also, we found several DNA sequence features that correlate with auxin-caused increase in genes' transcription levels, namely: number of matches with TGTCNC, homology score based on nucleotide frequencies at the consensus positions, abundances of five trinucleotides and five B-helical DNA features around these known AuxREs. We combined these correlations using a four-step empirical model of auxin response based on a gene's sequence with four steps, namely: (1) search for AuxREs with no auxin; (2) stop at the found AuxRE; (3) repression of the basal transcription of the gene having this AuxRE; and (4) manifold increase of this gene's transcription in response to auxin. Independently measured increases in transcription levels in response to auxin for 70 Arabidopsis genes were found to significantly correlate with predictions of this equation (r = 0.44, p < 0.001) as well as with TATA-binding protein (TBP)'s affinity to promoters of these genes and with nucleosome packing of these promoters (both, p < 0.025). Finally, we improved our equation for prediction of a gene's transcription increase in response to auxin by taking into account TBP-binding and nucleosome packing (r = 0.53, p < 10(-6)). Fisher's F-test validated the significant impact of both TBP/promoter-affinity and promoter nucleosome on auxin response in addition to those of AuxRE, F = 4.07, p < 0.025. It means that both TATA-box and nucleosome should be taken into account to recognize transcription factor binding sites upon DNA sequences: in the case of the TATA-less nucleosome-rich promoters, recognition scores must be higher than in the case of the TATA-containing nucleosome-free promoters at the same transcription activity.

How to Use SNP_TATA_Comparator to Find a Significant Change in Gene Expression Caused by the Regulatory SNP of This Gene’s Promoter via a Change in Affinity of the TATA-Binding Protein for This Promoter

“…Additionally, we compiled a set of SNPs in the TBP-binding sites associated with human diseases [ 54 ], including the AIDS pandemic [ 55 ], and with commercially important traits of plants and animals [ 56 ]. Then, we confirmed the three-step predictions by means of these SNPs [ 57 ] and by means of transcriptomes of the human brain [ 58 ], the auxin response in plants [ 59 , 60 ], and the data from 68 independent experiments (for review, see [ 61 ]). To finalize this comprehensive verification of the three-step model of TBP binding to a promoter [ 47 , 49 ], we created a freely available Web service [ 62 ] for users who wish to apply this bioinformatics application to data on the TBP/promoter-complexes in humans: http://beehive.bionet.nsc.ru/cgi-bin/mgs/tatascan/start.pl .…”

A Core Regulatory Pathway Controlling Rice Tiller Angle Mediated by the LAZY1-Dependent Asymmetric Distribution of Auxin

“…In Arabidopsis, AtWOX11 and AtWOX12, orthologs of rice WOX6 and WOX11, respectively, are reported to play roles in root development (Liu et al, 2014;Hu and Xu, 2016;Sheng et al, 2017). We found that both WOX6 and WOX11 contain auxin response elements, TGTCNC (Ponomarenko and Ponomarenko, 2015), in their promoter regions (Supplemental Figure 9). We further verified that WOX6 and WOX11 were not only responsive to NAA treatment, but also displayed an asymmetrical expression pattern like that of IAA20 during shoot gravitropism under light ( Figures 6C and 6D).…”

Auxin response factors

“…This refined auxin‐responsive motif was more predictive of auxin responsiveness compared with using the canonical DR5 motif within the first 500 bp of the promoter sequence; however, it has not been functionally tested in vivo . Modelling of auxin responses based on promoter motifs is not only powerful in confirming known AuxREs, but correlations using 111 natural or artificially tested AuxREs showed a positive correlation between auxin inducibility and the abundance of five trinucleotides and five β ‐helical DNA features around these known AuxREs, confirming that in addition to ARF sequence specificity, TATA‐binding protein affinity for DNA and nucleosomal packing is also important in modelling auxin response at the promoter level (Ponomarenko & Ponomarenko ). Enigmatically, many auxin‐regulated genes lack AuxREs in their promoters (Goda et al .…”