A combinatorial indexing strategy for low-cost epigenomic profiling of plant single cells

Understanding how cis-regulatory elements facilitate gene expression is a key question in biology.Recent advances in single-cell genomics have led to the discovery of cell-specific chromatin landscapes that underlie transcription programs in animal models.However,the high equipment and reagent costs of commercial systems limit their applications for many laboratories.In this study,we developed a combinatorial index and dual PCR barcode strategy to profile the Arabidopsis thaliana root single-cell epigenome without any specialized equipment.We generated chromatin accessibility profiles for 13576 root nuclei with an average of 12784 unique Tn5 integrations per cell.Integration of the single-cell assay for transposaseaccessible chromatin sequencing and RNA sequencing data sets enabled the identification of 24 cell clusters with unique transcription,chromatin,and cis-regulatory signatures.Comparison with single-cell data generated using the commercial microfluidic platform from 10X Genomics revealed that this low-cost combinatorial index method is capable of unbiased identification of cell-type-specific chromatin accessibility.We anticipate that,by removing cost,instrumentation,and other technical obstacles,this method will be a valuable tool for routine investigation of single-cell epigenomes and provide new insights into plant growth and development and plant interactions with the environment.