Casein Kinase 2 Mediated Phosphorylation of Spt6 Modulates Histone dynamics and Regulates Spurious Transcription (RNA-Seq)

CK2 is an essential protein kinase implicated in various cellular processes. In this study, we address a potential role of this kinase in chromatin modulations associated with transcription. We found that CK2 depletion from yeast cells leads to replication-independent increase of histone H3K56 acetylation and global activation of H3 turnover in coding regions. This suggests a positive role of CK2 in maintenance/recycling of the histone H3/H4 tetramers during transcription. Interestingly, strand-specific RNA-seq analyses show that CK2 inhibits global cryptic promoters driving both sense and antisense transcription. This further indicates a role of CK2 in the modulation of chromatin during transcription. Next, we showed that CK2 interacts with the major histone chaperone Spt6, and phosphorylates it in vivo and in vitro. CK2 phosphorylation of Spt6 is required for its cellular levels, for the suppression of histone H3 turnover and for the inhibition of spurious transcription. Finally, we show that CK2 and Spt6 phosphorylation sites are important to various transcriptional responses suggesting that cryptic intragenic and antisense transcript production may have an impact on cell adaptation to environmental cues. Altogether, our data indicate that CK2 mediated phosphorylation of Spt6 regulates chromatin dynamics associated with transcription, and prevents aberrant transcription.CK2是一类关键蛋白激酶（protein kinase），参与调控多种细胞生理过程。本研究聚焦该激酶在与转录相关的染色质调控中的潜在功能。我们发现，从酵母细胞中敲除CK2会导致不依赖复制的组蛋白H3K56乙酰化（histone H3K56 acetylation）水平上调，以及编码区组蛋白H3的全局替换速率被激活。上述结果提示，CK2在转录过程中组蛋白H3/H4四聚体的维持与循环过程中发挥正向调控作用。有趣的是，链特异性RNA测序（strand-specific RNA-seq）分析显示，CK2能够抑制驱动正义与反义转录的全局隐蔽启动子（cryptic promoters）活性，这进一步表明CK2在转录过程中参与染色质的动态调控。后续实验证实，CK2可与核心组蛋白伴侣（histone chaperone）Spt6相互结合，并在体内（in vivo）与体外（in vitro）对其进行磷酸化修饰。CK2介导的Spt6磷酸化对于维持其细胞水平、抑制组蛋白H3替换速率，以及阻断异常转录（spurious transcription）均不可或缺。最后，我们证实CK2与Spt6的磷酸化位点对多种转录应答过程均具有重要意义，提示基因内隐蔽转录与反义转录的产生可能会影响细胞对环境信号的适应性。综上，本研究数据表明，CK2介导的Spt6磷酸化可调控与转录相关的染色质动态变化，并防止异常转录的发生。