Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots

Abstract

Understanding how the expression of transcription factor (TF) genes is modulated is essential for reconstructing gene regulatory networks. There is increasing evidence that sequences other than upstream noncoding can contribute to modulating gene expression, but how frequently they do so remains unclear. Here, we investigated the regulation of TFs expressed in a tissue-enriched manner in Arabidopsis roots. For 61 TFs, we created GFP reporter constructs driven by each TF's upstream noncoding sequence (including the 5 UTR) fused to the GFP reporter gene alone or together with the TF's coding sequence. We compared the visually detectable GFP patterns with endogenous mRNA expression patterns, as defined by a genome-wide microarray root expression map. An automated image analysis method for quantifying GFP signals in different tissues was developed and used to validate our visual comparison method. From these combined analyses, we found that (i) the upstream noncoding sequence was sufficient to recapitulate the mRNA expression pattern for 80% (35͞44) of the TFs, and (ii) 25% of the TFs undergo posttranscriptional regulation via microRNA-mediated mRNA degradation (2͞24) or via intercellular protein movement (6͞24). The results suggest that, for Arabidopsis TFs, upstream noncoding sequences are major contributors to mRNA expression pattern establishment, but modulation of transcription factor protein expression pattern after transcription is relatively frequent. This study provides a systematic overview of regulation of TF expression at a cellular level. intercellular protein movement ͉ intergenic ͉ microRNA-mediated mRNA degradation ͉ transcriptional regulation

Analysis of Arabidopsis Transcription Factor Families Revealed Extensive Capacity for Cell-to-Cell Movement as Well as Discrete Trafficking Patterns

“…Interestingly, these data indicate that, of the 76 TFs investigated, 29% are NCATFs, a value similar to that reported by Lee et al (2006); i.e., 6 NCATFs out of a total of 24, or 25%. It is important to note that Lee et al (2006) employed endogenous promoters to analyze the movement potential of their 24 TFs. Although we used an enhancer trap system, our in silico expression analysis indi- Fig.…”

“…In a study conducted on Arabidopsis roots, Lee et al (2006) reported that among 24 TFs tested, 6 showed protein domains that extended beyond their sites of transcription. The Arabidopsis genome contains some 2000 TFs (1922 loci, 2290 gene models) that have been classified into 64 families based on DNA binding domain homologies (Guo et al, 2005).…”

MicroRNA promoter element discovery in Arabidopsis

“…While sequences other than the upstream non-coding ''promoter'' region of RNA Pol II transcribed genes can modulate gene expression, a recent study emphasizes that the sequences in the 59-upstream region of genes are of primary importance in Arabidopsis gene regulation (Lee et al 2006). Specifically, this study found that gene promoter sequences were sufficient to recapture the mRNA expression pattern for 80% of the TFs considered, confirming the important role RNA Pol II promoter regions in Arabidopsis gene expression.…”

An R2R3-type transcription factor gene AtMYB59 regulates root growth and cell cycle progression in Arabidopsis

“…Root growth and development are initiated from the root apical meristem and are regulated by transcription factors [32]. Mutations of SHR and SCR result in shorter roots.…”