美国芝加哥大学何川课题组开发出一种乙氧二羟丁酮辅助的单链DNA测序技术，可捕获全局转录动态和原位增强子活性。该成果于2020年4月6日在线发表在《自然—方法学》杂志上。

研究人员表示，转录是一个高度动态的过程，会在基因组中生成“转录气泡”的单链DNA（ssDNA）。

研究人员基于N3-乙氧二羟丁酮和鸟嘌呤在ssDNA中快速而特异性的反应，报道了一种乙氧二羟丁酮辅助的单链DNA测序（KAS-seq）方法。KAS-seq可快速（在5分钟内）地在全基因组范围内捕获和定位由转录活性RNA聚合酶或其他原位过程产生的ssDNA，所使用的细胞数可低至1000个。

KAS-seq可以定义一组增强子，其为单链，并具有独特的序列基序。这些增强子与特定的转录因子结合相关，并且比典型的增强子表现出更多的增强子-启动子相互作用。在抑制蛋白质聚集的条件下，KAS-seq揭示了一组从启动子中RNA聚合酶II（Pol II）的快速释放。因此，KAS-seq有助于以低输入和高通量方式同时快速、准确地分析转录动态和增强子活性。

附：英文原文

Title: Kethoxal-assisted single-stranded DNA sequencing captures global transcription dynamics and enhancer activity in situ

Author: Tong Wu, Ruitu Lyu, Qiancheng You, Chuan He

Issue&Volume: 2020-04-06

Abstract: Transcription is a highly dynamic process that generates single-stranded DNA (ssDNA) in the genome as ‘transcription bubbles’. Here we describe a kethoxal-assisted single-stranded DNA sequencing (KAS-seq) approach, based on the fast and specific reaction between N3-kethoxal and guanines in ssDNA. KAS-seq allows rapid (within 5min), sensitive and genome-wide capture and mapping of ssDNA produced by transcriptionally active RNA polymerases or other processes in situ using as few as 1,000 cells. KAS-seq enables definition of a group of enhancers that are single-stranded and enrich unique sequence motifs. These enhancers are associated with specific transcription-factor binding and exhibit more enhancer–promoter interactions than typical enhancers do. Under conditions that inhibit protein condensation, KAS-seq uncovers a rapid release of RNA polymerase II (Pol II) from a group of promoters. KAS-seq thus facilitates fast and accurate analysis of transcription dynamics and enhancer activities simultaneously in both low-input and high-throughput manner.

DOI: 10.1038/s41592-020-0797-9

Source: https://www.nature.com/articles/s41592-020-0797-9