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Mapping gene activity of Arabidopsis root hairs

Ping Lan1, Wenfeng Li1, Wen-Dar Lin1, Simonetta Santi2 and Wolfgang Schmidt134*

Author affiliations

1 Institute of Plant and Microbial Biology, Academia Sinica, 11529 Taipei, Taiwan

2 Dipartimento di Scienze Agrarie e Ambientali, Universit√° degli Studi di Udine, Via delle Scienze 206, I-33100 Udine, Italy

3 Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan

4 Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei, Taiwan

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Citation and License

Genome Biology 2013, 14:R67  doi:10.1186/gb-2013-14-6-r67

Published: 25 June 2013

Abstract

Background

Quantitative information on gene activity at single cell-type resolution is essential for the understanding of how cells work and interact. Root hairs, or trichoblasts, tubular-shaped outgrowths of specialized cells 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 by paired-end RNA sequencing and LC/MS-MS analysis of protoplasts from plants containing a pEXP7-GFP reporter construct. In total, transcripts of 23,034 genes were detected in root hairs. High-resolution proteome analysis led to the reliable identification of 2,447 proteins, 129 of which were differentially expressed between root hairs and non-root hair tissue. Dissection of pre-mRNA splicing patterns showed that all types of alternative splicing were cell type-dependent, and less complex in EXP7-expressing cells when compared to non-root hair cells. Intron retention was repressed in several transcripts functionally related to root hair morphogenesis, indicative of a cell type-specific control of gene expression by alternative splicing of pre-mRNA. Concordance between mRNA and protein expression 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, multilayered regulatory mechanisms that allow for a cell type-specific composition of functional components.