Technologies for systems-level analysis of specific cell types in plants

The study of biological processes at cell type resolution requires the isolation of the specific cell types from an organism, but this presents a great technical challenge. In recent years a number of methods have been developed that allow deep analyses of the epigenome, transcriptome, and ribosome-associated mRNA populations in individual cell types. The application of these methods has lead to a clearer understanding of important issues in plant biology, including cell fate specification and cell type-specific responses to the environment. In this review, we discuss current mechanical- and affinity-based technologies available for isolation and analysis of individual cell types in a plant. The integration of these methods is proposed as a means of achieving a holistic view of cellular processes at all levels, from chromatin dynamics to metabolomics. Finally, we explore the limitations of current methods and the needs for future technological development.

► Multiple methods exist for analyzing specific cell types, each with their own virtues and limitations.
► Each of these methods is suitable for measuring one or a few cellular characteristics.
► Integrating such methods will allow cell type-specific profiling of numerous cellular features, from the epigenome to the metabolome.
► We propose new approaches that could overcome the limitations of current methods.