Similar to other complex organisms,plants consist of diverse and specialized cell types.The gain of unique biological functions of these different cell types is the consequence of the establishment of cell-typespecifi...Similar to other complex organisms,plants consist of diverse and specialized cell types.The gain of unique biological functions of these different cell types is the consequence of the establishment of cell-typespecific transcriptional programs.As a necessary step in gaining a deeper understanding of the regulatory mechanisms controlling plant gene expression,we report the use of single-nucleus RNA sequencing(sNucRNA-seq)and single-nucleus assay for transposase accessible chromatin sequencing(sNucATACseq)technologies on Arabidopsis roots.The comparison of our single-nucleus transcriptomes to the published protoplast transcriptomes validated the use of nuclei as biological entities to establish plant cell-type-specific transcriptomes.Furthermore,our sNucRNA-seq results uncovered the transcriptomes of additional cell subtypes not identified by single-cell RNA-seq.Similar to our transcriptomic approach,the sNucATAC-seq approach led to the distribution of the Arabidopsis nuclei into distinct clusters,suggesting the differential accessibility of chromatin between groups of cells according to their identity.To reveal the impact of chromatin accessibility on gene expression,we integrated sNucRNA-seq and sNucATAC-seq data and demonstrated that cell-type-specific marker genes display cell-type-specific patterns of chromatin accessibility.Our data suggest that the differential chromatin accessibility is a critical mechanism to regulate gene activity at the cell-type level.展开更多
基金This work was supported by a grant to M.L.from the U.S.National Science Foundation(IOS#1339194 and 1854326)by grants to J.S.from the U.S.National Science Foundation(IOS#1923589)+1 种基金the Department of Energy(DE-SC0020358)by the Center for Plant Science Innovation,and by the Department of Agronomy and Horticulture at the University of Nebraska-Lincoln.
文摘Similar to other complex organisms,plants consist of diverse and specialized cell types.The gain of unique biological functions of these different cell types is the consequence of the establishment of cell-typespecific transcriptional programs.As a necessary step in gaining a deeper understanding of the regulatory mechanisms controlling plant gene expression,we report the use of single-nucleus RNA sequencing(sNucRNA-seq)and single-nucleus assay for transposase accessible chromatin sequencing(sNucATACseq)technologies on Arabidopsis roots.The comparison of our single-nucleus transcriptomes to the published protoplast transcriptomes validated the use of nuclei as biological entities to establish plant cell-type-specific transcriptomes.Furthermore,our sNucRNA-seq results uncovered the transcriptomes of additional cell subtypes not identified by single-cell RNA-seq.Similar to our transcriptomic approach,the sNucATAC-seq approach led to the distribution of the Arabidopsis nuclei into distinct clusters,suggesting the differential accessibility of chromatin between groups of cells according to their identity.To reveal the impact of chromatin accessibility on gene expression,we integrated sNucRNA-seq and sNucATAC-seq data and demonstrated that cell-type-specific marker genes display cell-type-specific patterns of chromatin accessibility.Our data suggest that the differential chromatin accessibility is a critical mechanism to regulate gene activity at the cell-type level.
