Heat shock response and transposon control in plant shoot stem cells [Bisulfite-seq]

Post-embryonic plant development must be coordinated in response to and with environmental feedback. Development of above-ground organs is orchestrated from stem cells in the center of the shoot apical meristem (SAM). Heat can pose significant abiotic stress to plants and induce a rapid heat shock response, developmental alterations, chromatin decondensation, and activation of transposable elements (TEs). However, most plant heat-stress studies are conducted with seedlings, and we know very little about cell-type-specific responses. Here we use fluorescent-activated nuclear sorting to isolate and characterize stem cells of wild type and mutants defective in TE defense and chromatin compaction after heat shock and after a long recovery. Our results indicate that stem cells can suppress heat shock response pathways to maintain developmental programs. Furthermore, mutants defective in DNA methylation fail to recover efficiently from heat stress and persistently activate heat shock factors and heat-inducible TEs. Heat stress also induces DNA methylation epimutations, especially in the CHG context, and we find hundreds of DNA methylation changes three weeks after stress. Our results underline the importance of disentangling cell type-specific environmental responses for understanding plant development. Overall design: Six-day old wt, poliv and, ddm1 plants were exposed to 37 celsius degree for 1 day (D7), then plants were transferred to soil to grow for 21 more days (D28). The plants stem cell nuclei at D28 were collected for bisulfite-seq.

植物胚后发育必须响应环境反馈并与之协同调控。地上器官的发育由茎尖分生组织（shoot apical meristem, SAM）中心的干细胞协同调控。高温会对植物造成严重的非生物胁迫，可诱导快速的热激响应、发育异常、染色质解凝以及转座因子（transposable elements, TEs）的激活。然而，当前绝大多数植物热胁迫研究均以幼苗为实验材料，我们对细胞类型特异性的热响应机制仍知之甚少。本研究借助荧光激活细胞核分选技术（fluorescent-activated nuclear sorting），分离并鉴定了野生型以及转座因子防御与染色质压缩缺陷突变体在热激处理及长期恢复阶段的干细胞。本研究结果显示，干细胞可通过抑制热激响应通路以维持自身发育程序。此外，DNA甲基化缺陷突变体无法从热胁迫中有效恢复，且会持续激活热激因子与热诱导型转座因子。热胁迫还可诱发DNA甲基化表观突变，尤其在CHG序列背景下；我们在胁迫处理三周后检测到数百个DNA甲基化位点的改变。本研究结果凸显了解析细胞类型特异性环境响应机制对于理解植物发育的重要性。实验设计：将生长6天的野生型（wild type, wt）、polⅣ与ddm1突变体植株置于37摄氏度环境下处理1天（记为D7），随后移栽至土壤中继续生长21天（记为D28）；于D28阶段收集植株干细胞细胞核，用于亚硫酸氢盐测序（bisulfite-seq）。