GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE331nnn/GSE331340/primary200OKTranscriptomicsArabidopsis thalianaExpression profiling by high throughput sequencinghttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE331340GEOGSEfalseHormone-treatment (ABA, SA) timecourse of Arabidopsis thaliana rootProfiling of binding sites for hundreds of A. thaliana transcription factors genome-wide revealed an unexpected enrichment of conserved TF binding sites (TFBSs) in coding sequence (CDS) for specific TF families, yet little association with cell type-specific gene expression. To differentiate between possible explanations for this, gene expression was profiled using bulk RNA-seq in response to hormone-induced stress. Abscisic Acid (ABA) treatment time-course data revealed that TFs known to activate transcription in response to ABA were significantly up-regulated, and most target genes of these TFs were upregulated as well - with the exception being target genes with TFBSs exclusively in coding sequence, which showed no significant expression change. Salicylic acid (SA) treatment further confirmed that target genes of known SA-responsive activators were induced only when TFBSs were found outside the coding region. However a key SA-responsive repressor (ABR1) showed strong repression of genes with CDS binding sites, suggesting a mechanism for rapid antagonistic response. Moreover, integration with chromatin accessibility data from the same tissues revealed strong links between constitutive TFBS accessibility and stress-induced target gene expression, suggesting that rapid, tissue-wide regulatory responses might preferentially operate through constitutively accessible sites primarily located close to transcription start sites.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 thaliana