Tissue-Specific Profiling Reveals Transcriptome Alterations inArabidopsisMutants Lacking Morphological Phenotypes  

Abstract

Traditional genetic analysis relies on mutants with observable phenotypes. Mutants lacking visible abnormalities may nevertheless exhibit molecular differences useful for defining gene function. To examine this, we analyzed tissue-specific transcript profiles from Arabidopsis thaliana transcription factor gene mutants with known roles in root epidermis development, but lacking a single-gene mutant phenotype due to genetic redundancy. We discovered substantial transcriptional changes in each mutant, preferentially affecting root epidermal genes in a manner consistent with the known double mutant effects. Furthermore, comparing transcript profiles of single and double mutants, we observed remarkable variation in the sensitivity of target genes to the loss of one or both paralogous genes, including preferential effects on specific branches of the epidermal gene network, likely reflecting the pathways of paralog subfunctionalization during evolution. In addition, we analyzed the root epidermal transcriptome of the transparent testa glabra2 mutant to clarify its role in the network. These findings provide insight into the molecular basis of genetic redundancy and duplicate gene diversification at the level of a specific gene regulatory network, and they demonstrate the usefulness of tissue-specific transcript profiling to define gene function in mutants lacking informative visible changes in phenotype.

Integration of transcriptomic and proteomic analysis towards understanding the systems biology of root hairs

“…Genes involved in hair cell differentiation and tip growth are over‐represented as expected . Other genes that participate in protein phosphorylation and oxidative stress are also reported in some studies . Among different gene families, peroxidases are clearly over‐represented in these four species .…”

“…Over the past decades, extensive physiological and genetic studies have been undertaken to understand the biology of root hairs [7,8,10]. Meanwhile, with the development of new technology in transcriptional profiling, transcriptomic data sets of the root hairs at the whole-genome level provided rich information on the global gene expression changes of root hair development and the interactions between root hairs and their environment [13][14][15][16][17][18][19][20][21][22][23][24][25][26]. As proteins are the final executive actor of cell viability and function, exploring the global protein profiling of root hair is thus much more important for building the regulatory networks of root hairs [21,22,[27][28][29][30][31][32].…”

ArabidopsisTTG2 RegulatesTRYExpression through Enhancement of Activator Complex-Triggered Activation

“…Although less pronounced as found in our study for the trichome system, TRY expression in the root was reduced to 67% of the wild-type expression in ttg2 mutants (Simon et al, 2013). Thus, the role of TTG2 in enhancing the expression of TRY appears to also be relevant in the context of root hair patterning.…”

“…The analysis of the global expression changes in ttg2 cpc and try cpc mutants revealed similar phenotypes, suggesting that TTG2 promotes TRY expression (Simon et al, 2013). Although less pronounced as found in our study for the trichome system, TRY expression in the root was reduced to 67% of the wild-type expression in ttg2 mutants (Simon et al, 2013).…”

Root Hairs

“…Also, gene expression patterns suggest that the WRKY protein encoded by TRANSPARENT TESTA GLABRA2 (TTG2; At2g37260) acts in both trichome and non-root hair cell specification (Johnson et al, 2002;Ishida et al, 2007;Simon et al, 2013). Interestingly, the shoot and root epidermis employ functionally equivalent MYB proteins, WER (in the root) and GLABROUS1 (GL1: At3g27920) (in the shoot) to specify cell fate (Lee and Schiefelbein, 2001).…”