Division of Biology, California Institute of Technology, Pasadena, California, United States of America.
PLoS One. 2012;7(4):e35934. doi: 10.1371/journal.pone.0035934. Epub 2012 Apr 26.
Cis-regulatory DNA sequences causally mediate patterns of gene expression, but efficient experimental analysis of these control systems has remained challenging. Here we develop a new version of "barcoded" DNA-tag reporters, "Nanotags" that permit simultaneous quantitative analysis of up to 130 distinct cis-regulatory modules (CRMs). The activities of these reporters are measured in single experiments by the NanoString RNA counting method and other quantitative procedures. We demonstrate the efficiency of the Nanotag method by simultaneously measuring hourly temporal activities of 126 CRMs from 46 genes in the developing sea urchin embryo, otherwise a virtually impossible task. Nanotags are also used in gene perturbation experiments to reveal cis-regulatory responses of many CRMs at once. Nanotag methodology can be applied to many research areas, ranging from gene regulatory networks to functional and evolutionary genomics.
顺式调控 DNA 序列能够因果介导基因表达模式，但有效的实验分析这些控制系统一直具有挑战性。在这里，我们开发了一种新的“条形码” DNA 标记报告基因，“Nanotags”，它可以同时定量分析多达 130 个不同的顺式调控模块（CRMs）。通过 NanoString RNA 计数方法和其他定量程序，在单个实验中测量这些报告基因的活性。我们通过同时测量来自海胆胚胎发育过程中 46 个基因的 126 个 CRM 的每小时时间活性来证明 Nanotag 方法的效率，否则这几乎是不可能完成的任务。Nanotags 也可用于基因干扰实验，以一次性揭示许多 CRM 的顺式调控反应。Nanotag 方法学可应用于许多研究领域，从基因调控网络到功能和进化基因组学。
