A Simple Method for Gene Expression and Chromatin Profiling of Individual Cell Types within a Tissue

SummaryUnderstanding the production and function of specialized cells during development requires the isolation of individual cell types for analysis, but this is currently a major technical challenge. Here we describe a method for cell type-specific RNA and chromatin profiling that circumvents many of the limitations of current methods for cell isolation. We used in vivo biotin labeling of a nuclear envelope protein in individual cell types followed by affinity isolation of labeled nuclei to measure gene expression and chromatin features of the hair and non-hair cell types of the Arabidopsis root epidermis. We identified hundreds of genes that are preferentially expressed in each cell type and show that genes with the largest expression differences between hair and non-hair cells also show differences between cell types in the trimethylation of histone H3 at lysines 4 and 27. This method should be applicable to any organism that is amenable to transformation.Video Abstract To view the video inline, enable JavaScript on your browser. However, you can download and view the video by clicking on the icon belowHelp with MP4 filesOptionsDownload video (71583 K)

► An affinity-based method was developed to purify nuclei from specific cell types
► High yield and purity of nuclei were obtained from each of the tested cell types
► Gene expression and chromatin profiles of individual root cell types were generated
► This method does not require specialized equipment and should be widely applicable