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Mapping gene activity of Arabidopsis root hairs

By Ping Lan, Wenfeng Li, Wen-Dar Lin, Simonetta Santi and Wolfgang Schmidt

Abstract

Background: Quantitative information on gene activity at single cell-type resolution is essential for theunderstanding of how cells work and interact. Root hairs, or trichoblasts, tubular-shaped outgrowths of specializedcells in the epidermis, represent an ideal model for cell fate acquisition and differentiation in plants.Results: Here, we provide an atlas of gene and protein expression in Arabidopsis root hair cells, generated bypaired-end RNA sequencing and LC/MS-MS analysis of protoplasts from plants containing a pEXP7-GFP reporterconstruct. In total, transcripts of 23,034 genes were detected in root hairs. High-resolution proteome analysis led tothe reliable identification of 2,447 proteins, 129 of which were differentially expressed between root hairs and nonroothair tissue. Dissection of pre-mRNA splicing patterns showed that all types of alternative splicing were celltype-dependent, and less complex in EXP7-expressing cells when compared to non-root hair cells. Intron retentionwas repressed in several transcripts functionally related to root hair morphogenesis, indicative of a cell type-specificcontrol of gene expression by alternative splicing of pre-mRNA. Concordance between mRNA and proteinexpression was generally high, but in many cases mRNA expression was not predictive for protein abundance.Conclusions: The integrated analysis shows that gene activity in root hairs is dictated by orchestrated, multilayeredregulatory mechanisms that allow for a cell type-specific composition of functional components.BackgroundSystems-wide exploration of ‘omics’ data obtained at differentmolecular levels provides a way to understandphysiological or developmental processes. The fidelity oflarge-scale analysis of gene activity has dramaticallyincreased because of new technologies in transcriptionalprofiling such as RNA sequencing (RNA-seq) and advancesin mass spectrometry (MS) techniques for protein profiling,allowing more accurate detection of expressed genes. Inmulticellular organisms, the correct assembly of disparatedatasets derived from parallel profiling experiments isoften obscured by an amalgam of different tissues or celltypes, compromising the comparability of these data.Despite the technical improvements in high-throughputassays, genome-wide exploration of gene activity at theresolution of single cell types is still a challenging task.Root hairs, which differentiate from specialized cells inthe epidermis, represent a well-explored model for cell differentiationand growth

Year: 2014
DOI identifier: 10.1186/gb-2013-14-6-r67
OAI identifier: oai:ir.lib.nchu.edu.tw:11455/85120

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