Specific chromatin changes mark lateral organ founder cells in the Arabidopsis inflorescence meristem
Specific chromatin changes mark lateral organ founder cells in the Arabidopsis inflorescence meristem
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DOI：
10.1093/jxb/erz181
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发表时间：
2019-08-01
影响因子：
6.9
通讯作者：
Werr, Wolfgang
中科院分区：
文献类型：
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作者：
Frerichs, Anneke;Engelhorn, Julia;Werr, Wolfgang
采用流式细胞仪（FACS）和转座酶可及染色质高通量测序（ATAC-seq）相结合的方法，对拟南芥apetala 1 -1花椰菜-1双突变体花序分生组织周边区侧生器官形成细胞（LOFCs）的染色质状态进行了分析。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（THS）与DNA酶I超敏位点（DHS）之间存在显著相关性。大多数扩增的DHS通常被亚结构化为几个单独的THS，这些THS与遗传上保守的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变化构型通过基因激活或抑制以及染色质区域获得或丧失转座酶可及性来反映，其与LOFC中的基因表达水平直接相关。这是最明显的转录开始，其中全基因组的THS是丰富的互补模式建立H3 K4 me 3激活或H3 K27 me 3抑制标记的上游。在此分辨率下，FACS/ATAC-seq的组合应用广泛适用于检测细胞类型特化期间的染色质变化，并有助于检测植物启动子中的调控元件。
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.