Department of Biology.
Department of Computer Science, Indiana University, Bloomington, Indiana 47405, USA.
Genome Res. 2020 Jun;30(6):910-923. doi: 10.1101/gr.261545.120. Epub 2020 Jul 6.
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 reaction cleanups, a STRIPE-seq library can be constructed in about 5 h. We show application of STRIPE-seq to TSS profiling in yeast and human cells and show that it can also be effectively used for quantification of transcript levels and analysis of differential gene expression. In conjunction with our ready-to-use computational workflows, STRIPE-seq is a straightforward, efficient means by which to probe the landscape of transcriptional initiation.
准确绘制转录起始位点（TSS）对于理解转录调控至关重要。然而，目前用于全基因组 TSS 分析的方法既繁琐又昂贵。我们提出了一种简单、快速且经济高效的方法，即利用高通量测序进行启动子元件转录起始调查（STRIPE-seq），该方法可以从少至 50ng 总 RNA 中测序加帽 RNA 的 5' 端。包括非加帽 RNA 的耗尽和反应的清理，STRIPE-seq 文库可以在大约 5 小时内构建完成。我们将 STRIPE-seq 应用于酵母和人类细胞的 TSS 分析，并证明它也可以有效地用于转录本水平的定量和差异基因表达分析。结合我们现成的计算工作流程，STRIPE-seq 是一种简单、高效的方法，可以探测转录起始的全景。
