Developmental Biology, Department of Biology, Biocenter, University of Cologne, Cologne, Germany.
Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg, Cologne, Germany.
J Exp Bot. 2019 Aug 7;70(15):3867-3879. doi: 10.1093/jxb/erz181.
Fluorescence-activated cell sorting (FACS) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) were combined to analyse the chromatin state of lateral organ founder cells (LOFCs) in the peripheral zone of the Arabidopsis apetala1-1 cauliflower-1 double mutant inflorescence meristem. On a genome-wide level, we observed a striking correlation between transposase hypersensitive sites (THSs) detected by ATAC-seq and DNase I hypersensitive sites (DHSs). The mostly expanded DHSs were often substructured into several individual THSs, which correlated with phylogenetically conserved DNA sequences or enhancer elements. Comparing chromatin accessibility with available RNA-seq data, THS change configuration was reflected by gene activation or repression and chromatin regions acquired or lost transposase accessibility in direct correlation with gene expression levels in LOFCs. This was most pronounced immediately upstream of the transcription start, where genome-wide THSs were abundant in a complementary pattern to established H3K4me3 activation or H3K27me3 repression marks. At this resolution, the combined application of FACS/ATAC-seq is widely applicable to detect chromatin changes during cell-type specification and facilitates the detection of regulatory elements in plant promoters.
荧光激活细胞分选（FACS）和转座酶可及染色质的高通量测序（ATAC-seq）分析相结合，研究了拟南芥花椰菜花叶 1 号 1 cauliflower-1 双突变体花序分生组织周围区侧生器官起始细胞（LOFC）的染色质状态。在全基因组水平上，我们观察到 ATAC-seq 检测到的转座酶超敏位点（THSs）与 DNase I 超敏位点（DHSs）之间存在显著相关性。大多数扩展的 DHS 通常被细分为几个单独的 THS，这些 THS 与系统发育保守的 DNA 序列或增强子元件相关。将染色质可及性与可用的 RNA-seq 数据进行比较，THS 变化的结构反映了基因的激活或抑制，以及 LOFCs 中基因表达水平直接相关的染色质区域获得或失去转座酶的可及性。这在转录起始点上游最为明显，全基因组 THS 以互补的模式丰富，与已建立的 H3K4me3 激活或 H3K27me3 抑制标记相对应。在这种分辨率下，FACS/ATAC-seq 的联合应用广泛适用于检测细胞类型特化过程中的染色质变化，并有助于检测植物启动子中的调控元件。
