To better understand human RNA polymerase II (Pol II) promoters in the context of promoter-proximal pausing and local chromatin organization, 5′ and 3′ ends of nascent capped transcripts and the locations of nearby nucleosomes were accurately identified through sequencing at exceptional depth. High-quality visualization tools revealed a preferred sequence that defines over 177 000 core promoters with strengths varying by >10 000-fold. This sequence signature encompasses and better defines the binding site for TFIID and is surprisingly invariant over a wide range of promoter strength. We identified a sequence motif associated with promoter-proximal pausing and demonstrated that cap methylation only begins once transcripts are about 30 nt long. Mapping also revealed a ∼150 bp periodic downstream sequence element (PDE) following the typical pause location, strongly suggestive of a +1 nucleosome positioning element. A nuclear run-off assay utilizing the unique properties of the DNA fragmentation factor (DFF) coupled with sequencing of DFF protected fragments demonstrated that a +1 nucleosome is present downstream of paused Pol II. Our data more clearly define the human Pol II promoter: a TFIID binding site with built-in downstream information directing ubiquitous promoter-proximal pausing and downstream nucleosome location.

中文翻译：

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人RNA聚合酶II启动子的序列和功能组织的统一视图。

为了更好地理解人RNA聚合酶II（Pol II）启动子在启动子附近的暂停和局部染色质组织的背景下，通过在异常深度进行测序，可以准确识别新生的有帽转录本的5'和3'末端以及附近核小体的位置。高质量的可视化工具揭示了一个优选序列，该序列定义了超过177 000个核心启动子，其强度相差> 10,000倍。该序列标记涵盖并更好地定义了TFIID的结合位点，并且令人惊讶地在很大范围的启动子强度上不变。我们确定了与启动子近端暂停相关的序列基序，并证明仅在转录物长约30 nt时才开始帽甲基化。定位还显示在典型的停顿位置之后有一个约150 bp的周期性下游序列元件（PDE），强烈暗示着+1核小体定位元件。利用DNA断裂因子（DFF）的独特特性与DFF保护的片段的测序相结合的核径流试验表明，在暂停的Pol II下游存在+1核小体。我们的数据更清楚地定义了人类Pol II启动子：具有内置下游信息的TFIID结合位点，该信息指导普遍存在的启动子-近端暂停和下游核小体位置。利用DNA断裂因子（DFF）的独特特性与DFF保护的片段的测序相结合的核径流试验表明，在暂停的Pol II下游存在+1核小体。我们的数据更清楚地定义了人类Pol II启动子：具有内置下游信息的TFIID结合位点，该信息指导普遍存在的启动子-近端暂停和下游核小体位置。利用DNA断裂因子（DFF）的独特特性与DFF保护的片段的测序相结合的核径流试验表明，在暂停的Pol II下游存在+1核小体。我们的数据更清楚地定义了人类Pol II启动子：具有内置下游信息的TFIID结合位点，该信息指导普遍存在的启动子-近端暂停和下游核小体位置。