Identification of eukaryotic promoter regulatory elements using nonhomologous random recombination

Understanding the regulatory logic of a eukaryotic promoter requires the elucidation of the regulatory elements within that promoter. Current experimental or computational methods to discover regulatory motifs within a promoter can be labor intensive and may miss redundant, unprecedented or weakly a...

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Main Authors:	Doyon, Jeffrey B., Liu, David R.
Format:	Online
Language:	English
Published:	Oxford University Press 2007
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2034452/

id	pubmed-2034452
recordtype	oai_dc
spelling	pubmed-20344522007-10-24 Identification of eukaryotic promoter regulatory elements using nonhomologous random recombination Doyon, Jeffrey B. Liu, David R. Molecular Biology Understanding the regulatory logic of a eukaryotic promoter requires the elucidation of the regulatory elements within that promoter. Current experimental or computational methods to discover regulatory motifs within a promoter can be labor intensive and may miss redundant, unprecedented or weakly activating elements. We have developed an unbiased combinatorial approach to rapidly identify new upstream activating sequences (UASs) in a promoter. This approach couples nonhomologous random recombination with an in vivo screen to efficiently identify UASs and does not rely on preconceived hypotheses about promoter regulation or on similarity to known activating sequences. We validated this method using the unfolded protein response (UPR) in yeast and were able to identify both known and potentially novel UASs involved in the UPR. One of the new UASs discovered using this approach implicates Crz1 as a possible activator of Hac1, a transcription factor involved in the UPR. This method has several advantages over existing methods for UAS discovery including its speed, potential generality, sensitivity and lack of false positives and negatives. Oxford University Press 2007-09 2007-08-24 /pmc/articles/PMC2034452/ /pubmed/17720707 http://dx.doi.org/10.1093/nar/gkm634 Text en © 2007 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Doyon, Jeffrey B. Liu, David R.
spellingShingle	Doyon, Jeffrey B. Liu, David R. Identification of eukaryotic promoter regulatory elements using nonhomologous random recombination
author_facet	Doyon, Jeffrey B. Liu, David R.
author_sort	Doyon, Jeffrey B.
title	Identification of eukaryotic promoter regulatory elements using nonhomologous random recombination
title_short	Identification of eukaryotic promoter regulatory elements using nonhomologous random recombination
title_full	Identification of eukaryotic promoter regulatory elements using nonhomologous random recombination
title_fullStr	Identification of eukaryotic promoter regulatory elements using nonhomologous random recombination
title_full_unstemmed	Identification of eukaryotic promoter regulatory elements using nonhomologous random recombination
title_sort	identification of eukaryotic promoter regulatory elements using nonhomologous random recombination
description	Understanding the regulatory logic of a eukaryotic promoter requires the elucidation of the regulatory elements within that promoter. Current experimental or computational methods to discover regulatory motifs within a promoter can be labor intensive and may miss redundant, unprecedented or weakly activating elements. We have developed an unbiased combinatorial approach to rapidly identify new upstream activating sequences (UASs) in a promoter. This approach couples nonhomologous random recombination with an in vivo screen to efficiently identify UASs and does not rely on preconceived hypotheses about promoter regulation or on similarity to known activating sequences. We validated this method using the unfolded protein response (UPR) in yeast and were able to identify both known and potentially novel UASs involved in the UPR. One of the new UASs discovered using this approach implicates Crz1 as a possible activator of Hac1, a transcription factor involved in the UPR. This method has several advantages over existing methods for UAS discovery including its speed, potential generality, sensitivity and lack of false positives and negatives.
publisher	Oxford University Press
publishDate	2007
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2034452/
_version_	1611405298315034624

Identification of eukaryotic promoter regulatory elements using nonhomologous random recombination

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