barcoded dna-tag reporters for multiplex cis-regulatory analysis条形码dna-tag记者对多路顺式分析.pdfVIP

Barcoded DNA-Tag Reporters for Multiplex Cis- Regulatory Analysis Jongmin Nam*, Eric H. Davidson* Division of Biology, California Institute of Technology, Pasadena, California, United States of America Abstract 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. Citation: Nam J, Davidson EH (2012) Barcoded DNA-Tag Reporters for Multiplex Cis-Regulatory Analysis. PLoS ONE 7(4): e35934. doi:10.1371/ journal.pone.0035934 Editor: Ferenc Mueller, University of Birmingham, United Kingdom Received November 3, 2011; Accepted March 26, 2012; Published April 26, 2012 Copyright: 2012 Nam, Davidson. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This project was supported by American Recovery and Reinvestment Act (ARRA) funds through grant number RC1 HG005332 to (E.H.D.) from the Na