Paul Emily, Tirosh Itay, Lai William, Buck Michael J, Palumbo Michael J, Morse Randall H
Laboratory of Molecular Genetics, Wadsworth Center, New York State Department of Health, Albany, New York Department of Biomedical Science, University at Albany School of Public Health, Albany, New York.
Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
G3 (Bethesda). 2015 Mar 5;5(5):829-38. doi: 10.1534/g3.115.017418.
Previous studies have described a transcriptional "memory effect," whereby transcript levels of many Abf1-regulated genes in the budding yeast Saccharomyces cerevisiae are undiminished even after Abf1 has dissociated from its regulatory sites. Here we provide additional support for this effect and investigate its molecular basis. We show that the effect is observed in a distinct abf1 ts mutant from that used in earlier studies, demonstrating that it is robust, and use chromatin immunoprecipitation to show that Abf1 association is decreased similarly from memory effect and transcriptionally responsive genes at the restrictive temperature. We also demonstrate that the association of TATA-binding protein and Pol II decreases after the loss of Abf1 binding for transcriptionally responsive genes but not for memory effect genes. Examination of genome-wide nucleosome occupancy data reveals that although transcriptionally responsive genes exhibit increased nucleosome occupancy in abf1 ts yeast, the promoter regions of memory effect targets show no change in abf1 ts mutants, maintaining an open chromatin conformation even after Abf1 eviction. This contrasting behavior reflects different inherent propensity for nucleosome formation between the two classes, driven by the presence of A/T-rich sequences upstream of the Abf1 site in memory effect gene promoters. These sequence-based differences show conservation in closely related fungi and also correlate with different gene expression noise, suggesting a physiological basis for greater access to "memory effect" promoter regions. Thus, our results establish a conserved mechanism underlying a transcriptional memory effect whereby sequences surrounding Abf1 binding sequences affect local nucleosome occupancy following loss of Abf1 binding. Furthermore, these findings demonstrate that sequence-based differences in the propensity for nucleosome occupancy can influence the transcriptional response of genes to an altered regulatory signal.
先前的研究描述了一种转录“记忆效应”，即出芽酵母酿酒酵母中许多受Abf1调控的基因的转录水平，即使在Abf1与其调控位点解离后仍不会降低。在此，我们为这种效应提供了额外的支持，并研究了其分子基础。我们表明，在一个与早期研究中使用的不同的abf1温度敏感突变体中观察到了这种效应，证明它是强大的，并使用染色质免疫沉淀来表明，在限制温度下，Abf1与记忆效应基因和转录响应基因的结合同样减少。我们还证明，对于转录响应基因，在Abf1结合丧失后，TATA结合蛋白和Pol II的结合减少，但对于记忆效应基因则不然。对全基因组核小体占据数据的检查表明，尽管转录响应基因在abf1温度敏感酵母中表现出核小体占据增加，但记忆效应靶点的启动子区域在abf1温度敏感突变体中没有变化，即使在Abf1被驱逐后仍保持开放的染色质构象。这种不同的行为反映了两类基因之间核小体形成的不同内在倾向，这是由记忆效应基因启动子中Abf1位点上游富含A/T的序列驱动的。这些基于序列的差异在密切相关的真菌中具有保守性，并且还与不同的基因表达噪声相关，这表明更容易接近“记忆效应”启动子区域具有生理基础。因此，我们的结果建立了一种转录记忆效应的保守机制，即Abf1结合序列周围的序列在Abf1结合丧失后影响局部核小体占据。此外，这些发现表明，核小体占据倾向的基于序列的差异可以影响基因对改变的调控信号的转录反应。
