Simple and efficient measurement of transcription initiation and transcript levels with STRIPE-seq

Accurate mapping of transcription start sites (TSSs) is key for understanding transcriptional regulation. However, current protocols for genome-wide TSS profiling are laborious and/or expensive. We present Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a simple, rapid, and cost-effective protocol for sequencing capped RNA 5’-ends from as little as 50 ng total RNA. Including depletion of uncapped RNA and SPRI bead cleanups, a STRIPE-seq library can be constructed in approximately four hours. We demonstrate application of STRIPE-seq to TSS profiling in yeast and human cells and show that it can also be effectively used for measuring transcript levels and for differential gene expression analysis. In conjunction with our ready-to-use computational analysis workflows, STRIPE-seq is a straightforward, efficient means by which to probe the landscape of transcriptional initiation.精准定位转录起始位点（transcription start sites, TSSs）是解析转录调控机制的核心所在。然而，当前用于全基因组TSS谱型分析的实验方案往往耗时费力且成本高昂。我们开发了启动子元件转录起始位点高通量测序调查技术（STRIPE-seq，Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing），该方案可从低至50 ng的总RNA样本中对带帽RNA的5'端进行测序，具有操作简便、快速高效且成本可控的优势。该流程包含无帽RNA去除与SPRI磁珠纯化步骤，STRIPE-seq文库的构建仅需约4小时即可完成。我们将STRIPE-seq应用于酵母与人类细胞的TSS谱型分析，结果表明该技术还可有效用于转录本水平检测与差异基因表达分析。结合我们提供的即用型计算分析流程，STRIPE-seq可成为一种简便高效的工具，用于解析转录起始的整体调控图谱。