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PLoS One 2012 Jan 01;74:e35934. doi: 10.1371/journal.pone.0035934.
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Barcoded DNA-tag reporters for multiplex cis-regulatory analysis.

Nam J , Davidson EH .

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.

PubMed ID: 22563420
PMC ID: PMC3339872
Article link: PLoS One
Grant support: [+]

Species referenced: Echinodermata
Genes referenced: gata6 LOC100887844 LOC100888549 LOC115919910 LOC583082 nodall

Article Images: [+] show captions
References [+] :
Amit, Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. 2009, Pubmed