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-type-specific 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 (sNucATAC-seq) 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.

与其他复杂的生物体类似，植物由多种特殊的细胞类型组成。这些不同细胞类型的独特生物学功能的获得是建立细胞类型特异性转录程序的结果。作为深入了解控制植物基因表达的调控机制的必要步骤，我们报告了单核 RNA 测序 (sNucRNA-seq) 和单核检测转座酶可及染色质测序 (sNucATAC-seq) 技术的使用拟南芥根。我们的单核转录组与已发表的原生质体转录组的比较证实了使用细胞核作为生物实体来建立植物细胞类型特异性转录组。此外，我们的 sNucRNA-seq 结果揭示了未被单细胞 RNA-seq 识别的其他细胞亚型的转录组。与我们的转录组学方法类似，sNucATAC-seq 方法导致拟南芥的分布细胞核分成不同的簇，表明细胞组之间染色质的可及性根据它们的身份不同。为了揭示染色质可及性对基因表达的影响，我们整合了 sNucRNA-seq 和 sNucATAC-seq 数据，并证明细胞类型特异性标记基因显示染色质可及性的细胞类型特异性模式。我们的数据表明，差异染色质可及性是在细胞类型水平上调节基因活性的关键机制。