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 t...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.展开更多
基金funded with support from the NSFC for Young Scientists(32100438)the China Postdoctoral Science Foundation(2020M672858 and 2021T140677)(to X.T.)+5 种基金Hong Kong GRF-14104119,GRF-14109420and AoE/M-403/16funding from the State Key Laboratory of Agrobiotechnology(to S.Z.)the NSF(IOS-1856627)the UGA Office of Research(to R.J.S.)an NSF postdoctoral fellowship in biology(DBI-1905869 to A.P.M.).
文摘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.
