Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
Nature. 2012 Jan 18;483(7389):295-301. doi: 10.1038/nature10799.
Transcription and regulation of genes originate from transcription pre-initiation complexes (PICs). Their structural and positional organization across eukaryotic genomes is unknown. Here we applied lambda exonuclease to chromatin immunoprecipitates (termed ChIP-exo) to examine the precise location of 6,045 PICs in Saccharomyces. PICs, including RNA polymerase II and protein complexes TFIIA, TFIIB, TFIID (or TBP), TFIIE, TFIIF, TFIIH and TFIIK were positioned within promoters and excluded from coding regions. Exonuclease patterns were in agreement with crystallographic models of the PIC, and were sufficiently precise to identify TATA-like elements at so-called TATA-less promoters. These PICs and their transcription start sites were positionally constrained at TFIID-engaged downstream +1 nucleosomes. At TATA-box-containing promoters, which are depleted of TFIID, a +1 nucleosome was positioned to be in competition with the PIC, which may allow greater latitude in start-site selection. Our genomic localization of messenger RNA and non-coding RNA PICs reveals that two PICs, in inverted orientation, may occupy the flanking borders of nucleosome-free regions. Their unambiguous detection may help distinguish bona fide genes from transcriptional noise.
基因的转录和调控源于转录起始前复合物（PICs）。它们在真核生物基因组中的结构和位置组织尚不清楚。在这里，我们应用 λ 核酸外切酶对染色质免疫沉淀（称为 ChIP-exo）进行分析，以检查酿酒酵母中 6045 个 PIC 的精确位置。PICs 包括 RNA 聚合酶 II 和蛋白质复合物 TFIIA、TFIIB、TFIID（或 TBP）、TFIIE、TFIIF、TFIIH 和 TFIIK，它们定位于启动子内，而排除在编码区之外。核酸外切酶的模式与 PIC 的晶体结构模型一致，并且足够精确，可以在所谓的无 TATA 启动子中识别 TATA 样元件。这些 PICs 及其转录起始位点在 TFIID 结合的下游+1 核小体处受到位置限制。在含有 TATA 框的启动子中，TFIID 被耗尽，+1 核小体被定位在与 PIC 竞争的位置，这可能允许在起始位点选择方面有更大的自由度。我们对信使 RNA 和非编码 RNA PICs 的基因组定位表明，两个 PIC 可能以反转方向占据无核小体区域的侧翼边界。它们的明确检测可能有助于区分真正的基因和转录噪声。
