Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.
Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA.
Genome Biol. 2019 Aug 20;20(1):170. doi: 10.1186/s13059-019-1777-1.
Circadian rhythms modulate growth and development in all organisms through interlocking transcriptional-translational feedback loops. The transcriptional loop involves chromatin modifications of central circadian oscillators in mammals and plants. However, the molecular basis for rhythmic epigenetic modifications and circadian regulation is poorly understood.
Here we report a feedback relationship between diurnal regulation of circadian clock genes and histone modifications in Arabidopsis. On one hand, the circadian oscillators CCA1 and LHY regulate diurnal expression of genes coding for the eraser (JMJ14) directly and writer (SDG2) indirectly for H3K4me3 modification, leading to rhythmic H3K4me3 changes in target genes. On the other hand, expression of circadian oscillator genes including CCA1 and LHY is associated with H3K4me3 levels and decreased in the sdg2 mutant but increased in the jmj14 mutant. At the genome-wide level, diurnal rhythms of H3K4me3 and another histone mark H3K9ac are associated with diurnal regulation of 20-30% of the expressed genes. While the majority (86%) of H3K4me3 and H3K9ac target genes overlap, only 13% of morning-phased and 22% of evening-phased genes had both H3K4me3 and H3K9ac peaks, suggesting specific roles of different histone modifications in diurnal gene expression.
Circadian clock genes promote diurnal regulation of SDG2 and JMJ14 expression, which in turn regulate rhythmic histone modification dynamics for the clock and its output genes. This reciprocal regulatory module between chromatin modifiers and circadian clock oscillators orchestrates diurnal gene expression that governs plant growth and development.
昼夜节律通过互锁的转录-翻译反馈环调节所有生物体的生长和发育。转录环涉及哺乳动物和植物中中央生物钟振荡器的染色质修饰。然而，节律性表观遗传修饰和生物钟调节的分子基础还知之甚少。
本文报道了拟南芥中昼夜节律钟基因的调控与组蛋白修饰之间的反馈关系。一方面，昼夜节律钟 CCA1 和 LHY 直接调控编码擦除酶（JMJ14）的基因的昼夜表达，并间接调控编码 H3K4me3 修饰的写入酶（SDG2）的基因的昼夜表达，从而导致靶基因中 H3K4me3 的节律性变化。另一方面，CCA1 和 LHY 等生物钟基因的表达与 H3K4me3 水平相关，在 sdg2 突变体中降低，但在 jmj14 突变体中增加。在全基因组水平上，H3K4me3 和另一种组蛋白标记 H3K9ac 的昼夜节律与 20-30%表达基因的昼夜调控相关。虽然大多数（86%）H3K4me3 和 H3K9ac 的靶基因重叠，但只有 13%的早晨相和 22%的傍晚相基因同时具有 H3K4me3 和 H3K9ac 峰，表明不同组蛋白修饰在昼夜基因表达中具有特定的作用。
生物钟基因促进了 SDG2 和 JMJ14 表达的昼夜调控，而后者又调节了生物钟及其输出基因的节律性组蛋白修饰动力学。染色质修饰物和生物钟振荡器之间的这种互反馈调节模块协调了昼夜基因表达，从而控制植物的生长和发育。
