Barcoded DNA-tag reporters for multiplex cis-regulatory analysis.

PloS One
Jongmin Nam, Eric H Davidson

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.

References

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Dec 24, 2008·Proceedings of the National Academy of Sciences of the United States of America·Joel Smith, Eric H Davidson
Feb 10, 2010·Proceedings of the National Academy of Sciences of the United States of America·Jongmin NamEric H Davidson
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May 31, 2011·Nature·Isabelle S Peter, Eric H Davidson

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Citations

Mar 13, 2014·Nature Reviews. Genetics·Daria ShlyuevaAlexander Stark
Jan 31, 2016·Developmental Biology·Ellen V Rothenberg
Jun 15, 2015·Genomics·Felix MuerdterCosmas D Arnold
Oct 3, 2015·Advanced Drug Delivery Reviews·K D HankensonM Shaughnessy
Nov 24, 2012·Genesis : the Journal of Genetics and Development·Andrea StreitClaudio D Stern
Feb 24, 2015·Wiley Interdisciplinary Reviews. Developmental Biology·Kushal Suryamohan, Marc S Halfon
Jul 17, 2015·Developmental Dynamics : an Official Publication of the American Association of Anatomists·Jingchen Chen, Andrea Streit
Dec 25, 2012·Developmental Biology·Stefan C MaternaEric H Davidson
Feb 12, 2017·Developmental Biology·Gregory A Cary, Veronica F Hinman
May 25, 2021·STAR Protocols·Ruth M Williams, Tatjana Sauka-Spengler

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Methods Mentioned

BETA
PCR
in vitro transcription
fusion
PCRs

Software Mentioned

FastPCR
Nanostring
SoxB1 MASO
HesC MASO
Nanotag
Nodal MASO
NanoString nCounter

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