小柯机器人

美国康奈尔大学Haiyuan Yu和John T. Lis研究组合作的最新研究对在全基因组水平鉴定活性增强子的实验和分析方法进行了比较。2022年2月17日出版的《自然-生物技术》发表了这项成果。

研究人员比较了K562细胞中13全基因组RNA测序(RNA-seq)的数据，并表明核连续加帽选择测定(GRO/PRO-cap)在增强子RNA检测和活性增强子鉴定方面具有优势。研究人员还编写了新的程序，即新生转录起始的峰值标识符(PINTS)，以识别全基因组中的活性启动子和增强子，并确定5'转录起始位点的精确位置。

最后，研究人员依据从120种细胞和组织类型中鉴定的增强子RNA (eRNA)转录起始位点(TSS)编写了一个综合的增强子筛选库，可通过 https://pints.yulab.org访问。凭借对最佳可用分析和数据的计算，这种对候选增强子的大规模注释将为便捷选择和表征增强子的功能铺平道路。

研究人员表示，越来越多的证据表明在活性增强子鉴别中转录模式是比组蛋白标记更为具体的标志。然而，尚未确定通过实验和计算识别活性增强子的最佳方法。

附：英文原文

Title: A comparison of experimental assays and analytical methods for genome-wide identification of active enhancers

Author: Yao, Li, Liang, Jin, Ozer, Abdullah, Leung, Alden King-Yung, Lis, John T., Yu, Haiyuan

Issue&Volume: 2022-02-17

Abstract: Mounting evidence supports the idea that transcriptional patterns serve as more specific identifiers of active enhancers than histone marks; however, the optimal strategy to identify active enhancers both experimentally and computationally has not been determined. Here, we compared 13genome-wide RNA sequencing (RNA-seq) assays in K562 cells and show that nuclear run-on followed by cap-selection assay (GRO/PRO-cap) has advantages in enhancer RNA detection and active enhancer identification. We also introduce a tool, peak identifier for nascent transcript starts (PINTS), to identify active promoters and enhancers genome wide and pinpoint the precise location of 5′transcription start sites. Finally, we compiled a comprehensive enhancer candidate compendium based on the detected enhancer RNA (eRNA) transcription start sites (TSSs) available in 120cell and tissue types, which can be accessed at https://pints.yulab.org. With knowledge of the best available assays and pipelines, this large-scale annotation of candidate enhancers will pave the way for selection and characterization of their functions in a time- and labor-efficient manner.

DOI: 10.1038/s41587-022-01211-7

Source: https://www.nature.com/articles/s41587-022-01211-7

Nature Biotechnology：《自然—生物技术》，创刊于1996年。隶属于施普林格·自然出版集团，最新IF：68.164
官方网址：https://www.nature.com/nbt/
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