title: Tissue-specific profiling reveals transcriptome alterations in Arabidopsis mutants 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.
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, University of Michigan, An Arbor, Michigan 48109.
authors.forename: Marissa
authors.initials: M
authors.lastname: Simon
authors.forename: Angela
authors.initials: A
authors.lastname: Bruex
authors.forename: Raghunandan M
authors.initials: RM
authors.lastname: Kainkaryam
authors.forename: Xiaohua
authors.initials: X
authors.lastname: Zheng
authors.forename: Ling
authors.initials: L
authors.lastname: Huang
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Woolf
authors.forename: John
authors.initials: J
authors.lastname: Schiefelbein
mesh_terms: D017360:Arabidopsis / Q000033:anatomy & histology / Q000235:genetics* / Q000254:growth & development; D029681:Arabidopsis Proteins / Q000235:genetics*; D002454:Cell Differentiation; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D017930:Genes, Reporter; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D009928:Organ Specificity; D010641:Phenotype; D019441:Plant Epidermis / Q000033:anatomy & histology / Q000235:genetics / Q000254:growth & development; D018517:Plant Roots / Q000033:anatomy & histology / Q000235:genetics / Q000254:growth & development; D014157:Transcription Factors / Q000235:genetics; D059467:Transcriptome
chemical_list: D029681:Arabidopsis Proteins; D014157:Transcription Factors