A robust method of nuclei isolation for single-cell RNA sequencing of solid plant tissues

Single-cell transcriptome analysis has been extensively applied in humans and animal models to uncover gene expression heterogeneity between the different cell types of a tissue or an organ. It demonstrated its capability to discover key regulatory elements that determine cell fate during developmental programs. Single-cell analysis requires the isolation and labeling of the messenger RNA (mRNA) derived from each cell. These challenges were primarily addressed in mammals by developing microfluidic-based approaches. For plant species whose cells contain cell walls, these approaches have generally required the generation of isolated protoplasts. Many plant tissues’ secondary cell wall hinders enzymatic digestion required for individual protoplast isolation, resulting in an unequal representation of cell types in a protoplast population. This limitation is especially critical for cell types located in the inner layers of a tissue or the inner tissues of an organ. Consequently, single-cell RNA sequencing (scRNA-seq) studies using microfluidic approaches in plants have mainly been restricted to Arabidopsis roots, for which well-established procedures of protoplast isolation are available.

University of Florida researchers have developed a simple alternative approach to generating high-quality protoplasts from plant tissue by characterizing the mRNA extracted from individual nuclei instead of whole cells. The researchers developed the protocol using two different plant materials with varying cellular complexity levels and cell wall structure, Populus shoot apices, and more lignified stems. Using the 10× Genomics Chromium technology, they show that this procedure results in intact mRNA isolation and limited leakage, with a broad representation of individual cell transcriptomes.

Nuclei isolation workflow

Workflow diagram showing the nuclei isolation and snRNA-seq library construction procedure from Populus shoots and stem.

Conde D, Triozzi PM, Balmant KM, Doty AL, Miranda M, Boullosa A, et al. (2021) A robust method of nuclei isolation for single-cell RNA sequencing of solid tissues from the plant genus Populus. PLoS ONE 16(5): e0251149. [article]

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