by Jongmin Nam, Ping Dong, Ryan Tarpine, Sorin Istrail, Eric H. Davidson
Abstract:
Gene expression is controlled by interactions between trans-regulatory factors and cis-regulatory DNA sequences, and these interactions constitute the essential functional linkages of gene regulatory networks (GRNs). Validation of GRN models requires experimental cis-regulatory tests of predicted linkages to authenticate their identities and proposed functions. However, cis-regulatory analysis is, at present, at a severe bottleneck in genomic system biology because of the demanding experimental methodologies currently in use for discovering cis-regulatory modules (CRMs), in the genome, and for measuring their activities. Here we demonstrate a high-throughput approach to both discovery and quantitative characterization of CRMs. The unique aspect is use of DNA sequence tags to ???barcode??? CRM expression constructs, which can then be mixed, injected together into sea urchin eggs, and subsequently deconvolved. This method has increased the rate of cis-regulatory analysis by >100-fold compared with conventional one-by-one reporter assays. The utility of the DNA-tag reporters was demonstrated by the rapid discovery of 81 active CRMs from 37 previously unexplored sea urchin genes. We then obtained simultaneous high-resolution temporal characterization of the regulatory activities of more than 80 CRMs. On average 2???3 CRMs were discovered per gene. Comparison of endogenous gene expression profiles with those of the CRMs recovered from each gene showed that, for most cases, at least one CRM is active in each phase of endogenous expression, suggesting that CRM recovery was comprehensive. This approach will qualitatively alter the practice of GRN construction as well as validation, and will impact many additional areas of regulatory system biology.
Reference:
Jongmin Nam, Ping Dong, Ryan Tarpine, Sorin Istrail, Eric H. Davidson, "Functional cis-regulatory genomics for systems biology", In Proceedings of the National Academy of Sciences, vol. 107, no. 8, pp. 3930-3935, 2010.
Bibtex Entry:
@ARTICLE{Nam2010,
author = {Nam, Jongmin and Dong, Ping and Tarpine, Ryan and Istrail, Sorin
and Davidson, Eric H.},
title = {Functional cis-regulatory genomics for systems biology},
journal = {Proceedings of the National Academy of Sciences},
year = {2010},
volume = {107},
pages = {3930--3935},
number = {8},
abstract = {Gene expression is controlled by interactions between trans-regulatory
factors and cis-regulatory DNA sequences, and these interactions
constitute the essential functional linkages of gene regulatory networks
(GRNs). Validation of GRN models requires experimental cis-regulatory
tests of predicted linkages to authenticate their identities and
proposed functions. However, cis-regulatory analysis is, at present,
at a severe bottleneck in genomic system biology because of the demanding
experimental methodologies currently in use for discovering cis-regulatory
modules (CRMs), in the genome, and for measuring their activities.
Here we demonstrate a high-throughput approach to both discovery
and quantitative characterization of CRMs. The unique aspect is use
of DNA sequence tags to ???barcode??? CRM expression constructs,
which can then be mixed, injected together into sea urchin eggs,
and subsequently deconvolved. This method has increased the rate
of cis-regulatory analysis by >100-fold compared with conventional
one-by-one reporter assays. The utility of the DNA-tag reporters
was demonstrated by the rapid discovery of 81 active CRMs from 37
previously unexplored sea urchin genes. We then obtained simultaneous
high-resolution temporal characterization of the regulatory activities
of more than 80 CRMs. On average 2???3 CRMs were discovered per gene.
Comparison of endogenous gene expression profiles with those of the
CRMs recovered from each gene showed that, for most cases, at least
one CRM is active in each phase of endogenous expression, suggesting
that CRM recovery was comprehensive. This approach will qualitatively
alter the practice of GRN construction as well as validation, and
will impact many additional areas of regulatory system biology.},
date = {February 23, 2010},
doi = {10.1073/pnas.1000147107},
owner = {Derek},
timestamp = {2012.05.08},
url = {http://www.brown.edu/Research/Istrail_Lab/papers/PNAS-2010-Nam-3930-5.pdf},
category = {Regulatory Genomics}
}