Department of Plant and Microbial Biology, University of California, Berkeley, California, 94720, USA.
Plant Gene Expression Center, Agriculture Research Service, US Department of Agriculture, Albany, California, 94710, USA.
Plant Physiol. 2022 Oct 27;190(3):1915-1926. doi: 10.1093/plphys/kiac282.
The phytochrome (phy)-PHYTOCHROME-INTERACTING FACTOR (PIF) sensory module perceives and transduces light signals to direct target genes (DTGs), which then drive the adaptational responses in plant growth and development appropriate to the prevailing environment. These signals include the first exposure of etiolated seedlings to sunlight upon emergence from subterranean darkness and the change in color of the light that is filtered through, or reflected from, neighboring vegetation ("shade"). Previously, we identified three broad categories of rapidly signal-responsive genes: those repressed by light and conversely induced by shade; those repressed by light, but subsequently unresponsive to shade; and those responsive to shade only. Here, we investigate the potential role of epigenetic chromatin modifications in regulating these contrasting patterns of phy-PIF module-induced expression of DTGs in Arabidopsis (Arabidopsis thaliana). Using RNA-seq and ChIP-seq to determine time-resolved profiling of transcript and histone 3 lysine 4 trimethylation (H3K4me3) levels, respectively, we show that, whereas the initial dark-to-light transition triggers a rapid, apparently temporally coincident decline of both parameters, the light-to-shade transition induces similarly rapid increases in transcript levels that precede increases in H3K4me3 levels. Together with other recent findings, these data raise the possibility that, rather than being causal in the shade-induced expression changes, H3K4me3 may function to buffer the rapidly fluctuating shade/light switching that is intrinsic to vegetational canopies under natural sunlight conditions.
光敏色素（phy）-PHYTOCHROME-INTERACTING FACTOR（PIF）感觉模块感知并转换光信号，以直接靶向基因（DTG），从而驱动植物生长和发育的适应反应，以适应当前的环境。这些信号包括：幼苗出土后首次暴露在阳光下，以及透过或反射周围植被的光的颜色变化（“遮荫”）。此前，我们确定了三类快速信号反应基因：受光抑制而被遮荫诱导的基因；受光抑制但随后对遮荫无反应的基因；以及仅对遮荫有反应的基因。在这里，我们研究了表观遗传染色质修饰在调节这些相反的 phy-PIF 模块诱导 DTG 表达模式中的潜在作用，在拟南芥（Arabidopsis thaliana）中进行了研究。我们使用 RNA-seq 和 ChIP-seq 分别确定了时间分辨的转录物和组蛋白 3 赖氨酸 4 三甲基化（H3K4me3）水平的概况，结果表明，虽然从黑暗到光照的初始转换会触发这两个参数的快速、明显的时间巧合下降，但从光照到遮荫的转换会引起类似的快速转录物水平增加，然后才增加 H3K4me3 水平。结合其他最近的发现，这些数据提出了这样一种可能性，即 H3K4me3 可能不是遮荫诱导表达变化的因果关系，而是在自然阳光条件下，植被冠层中固有的快速波动的遮荫/光照转换中起到缓冲作用。
