Booth Gregory T, Wang Isabel X, Cheung Vivian G, Lis John T
Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853-2703, USA;
Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA.
Genome Res. 2016 Jun;26(6):799-811. doi: 10.1101/gr.204578.116. Epub 2016 May 12.
Complex regulation of gene expression in mammals has evolved from simpler eukaryotic systems, yet the mechanistic features of this evolution remain elusive. Here, we compared the transcriptional landscapes of the distantly related budding and fission yeast. We adapted the Precision Run-On sequencing (PRO-seq) approach to map the positions of RNA polymerase active sites genome-wide in Schizosaccharomyces pombe and Saccharomyces cerevisiae. Additionally, we mapped preferred sites of transcription initiation in each organism using PRO-cap. Unexpectedly, we identify a pause in early elongation, specific to S. pombe, that requires the conserved elongation factor subunit Spt4 and resembles promoter-proximal pausing in metazoans. PRO-seq profiles in strains lacking Spt4 reveal globally elevated levels of transcribing RNA Polymerase II (Pol II) within genes in both species. Messenger RNA abundance, however, does not reflect the increases in Pol II density, indicating a global reduction in elongation rate. Together, our results provide the first base-pair resolution map of transcription elongation in S. pombe and identify divergent roles for Spt4 in controlling elongation in budding and fission yeast.
哺乳动物基因表达的复杂调控是从更简单的真核生物系统进化而来的，然而这种进化的机制特征仍然难以捉摸。在这里，我们比较了远缘的出芽酵母和裂殖酵母的转录图谱。我们采用精确连续测序（PRO-seq）方法，在全基因组范围内绘制粟酒裂殖酵母和酿酒酵母中RNA聚合酶活性位点的位置。此外，我们使用PRO-cap绘制了每种生物体中转录起始的偏好位点。出乎意料的是，我们发现了裂殖酵母特有的早期延伸过程中的停顿，这需要保守的延伸因子亚基Spt4，并且类似于后生动物中启动子近端的停顿。缺乏Spt4的菌株中的PRO-seq图谱显示，两个物种的基因内转录RNA聚合酶II（Pol II）的水平普遍升高。然而，信使RNA丰度并未反映Pol II密度的增加，表明延伸速率整体下降。总之，我们的结果提供了粟酒裂殖酵母转录延伸的首张碱基对分辨率图谱，并确定了Spt4在控制出芽酵母和裂殖酵母延伸中的不同作用。
