Single-cell genomics provides unprecedented potential for research on plant development and environmental responses. Here, researchers from the Max Delbrück Center for Molecular Medicine introduce a generic procedure for plant nuclei isolation combined with nanowell-based library preparation. This method enables the transcriptome analysis of thousands of individual plant nuclei. It serves as alternative to the use of protoplast isolation, which is currently a standard methodology for plant single-cell genomics, although it can be challenging for some plant tissues. The researchers show the applicability of their nuclei isolation method by using different plant materials from several species. The potential of this snRNA-seq method is shown through the characterization of transcriptomes of seedlings and developing flowers from Arabidopsis thaliana. The researchers evaluated the transcriptome dynamics during the early stages of anther development, identify stage-specific transcription factors regulating this process and the prediction of their target genes. This nuclei isolation procedure can be applied in different plant species and tissues, thus expanding the toolkit for plant single-cell genomics experiments.
Schematic overview of snRNA-seq experimental strategy