Abstract
BackgroundQuantitative 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.ResultsHere, 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.ConclusionsThe 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.
Highlights
Quantitative information on gene activity at single cell-type resolution is essential for the understanding of how cells work and interact
In five-day-old seedlings carrying a construct containing the expansin 7 (EXP7) promoter sequence positioned upstream of a green fluorescent protein (GFP) reporter, expression of the pEXP7-GFP chimera was observable in developing and mature root hairs, but no expression was detected before the initiation of bulge formation (Figure 1)
Expression of EXP7 was restricted to trichoblasts, and no GFP signal was seen in non-hair cells (Figure 1a,c)
Summary
Quantitative information on gene activity at single cell-type resolution is essential for the understanding of how cells work and interact. Trichoblasts, tubular-shaped outgrowths of specialized cells in the epidermis, represent an ideal model for cell fate acquisition and differentiation in plants. Root hairs, which differentiate from specialized cells in the epidermis, represent a well-explored model for cell differentiation and growth. 10,492 genes were detected in the root, and mapped to five different tissues in three developmental root zones This analysis was later extended into a spatiotemporal expression atlas of Arabidopsis roots, investigating 14 non-overlapping cell types and 13 root sections representing different developmental stages. Cell type-specific expression profiling in response to environmental conditions identified coordinated responses in distinct cell types and showed that this approach dramatically increases the detection sensitivity for transcriptional changes compared with studies using whole roots as experimental material [10]. It was further shown that cell type-specific transcription is largely dependent on environmental conditions, with the epidermis showing the least conserved gene expression when the transcriptional profile of stressed plants was compared with that of plants grown under standard conditions [11]
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