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Barcoded DNA-Tag Reporters for Multiplex Cis-Regulatory Analysis

Nam, Jongmin and Davidson, Eric H. (2012) Barcoded DNA-Tag Reporters for Multiplex Cis-Regulatory Analysis. PLoS ONE, 7 (4). Art. No. e35934. ISSN 1932-6203. PMCID PMC3339872. doi:10.1371/journal.pone.0035934. https://resolver.caltech.edu/CaltechAUTHORS:20120710-115422137

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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.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1371/journal.pone.0035934DOIArticle
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0035934PublisherArticle
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3339872/PubMed CentralArticle
Additional Information:© 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. Received November 3, 2011; Accepted March 26, 2012; Published April 26, 2012. Editor: Ferenc Mueller, University of Birmingham, United Kingdom. Funding: This project was supported by American Recovery and Reinvestment Act (ARRA) funds through grant number RC1 HG005332 to (E.H.D.) from the National Human Genome Research Institute, National Institute of Health. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The authors thank the following individuals for their contributions to this work: Ping Dong for cloning Nanotag vectors and other technical assistance; Miki Yun for sequencing; Julius Barsi, Sagar Damle, Smadar Ben-Tabou DeLeon, and Stefan Materna for their comments on an earlier version of the manuscript; and Stephen Jackson in the NanoString Inc. for his support from the inception of the project. Author Contributions: Conceived and designed the experiments: JN. Performed the experiments: JN. Analyzed the data: JN. Contributed reagents/materials/analysis tools: JN EHD. Wrote the paper: JN EHD.
Funders:
Funding AgencyGrant Number
American Recovery and Reinvestment Act (ARRA)UNSPECIFIED
NIHRC1 HG005332
Issue or Number:4
PubMed Central ID:PMC3339872
DOI:10.1371/journal.pone.0035934
Record Number:CaltechAUTHORS:20120710-115422137
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20120710-115422137
Official 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
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:32329
Collection:CaltechAUTHORS
Deposited By: Jason Perez
Deposited On:10 Jul 2012 20:45
Last Modified:09 Nov 2021 21:26

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