Project description:Profiling 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.
Project description:Gene expression is controlled by the complex interaction of transcription factors binding to promoters and other regulatory DNA elements. One common characteristic of the genomic regions associated with regulatory proteins is a pronounced sensitivity to DNase I digestion. We reported genome-wide high resolution maps of DNase I hypersensitive (DH) sites from both seedling and flower tissues of Arabidopsis from the Columbia (Col) ecotype and the corresponding ddm1 (deficient in DNA methylation 1) mutant. We identified 38,290, 41,193, 38,313, and 38,153 DH sites in leaf (Col), flower (Col), ddm1 leaf, and ddm1 flower tissues, respectively. Approximately 45% of the DH sites in all tissue types were located within 1 kb of a transcription start site (TSS), which represents a putative promoter region. Pairwise comparisons of the DH sites derived from different tissue types revealed DH sites specific to each tissue. DH sites are significantly associated with long non-coding RNAs (lncRNAs) and conserved non-coding sequences (CNSs). The binding sites of MADS-domain transcription factors AP1 and SEP3 are highly correlated with DH sites.