NDLI: Use of a Drosophila Genome-Wide Conserved Sequence Database to Identify Functionally Related cis-Regulatory Enhancers

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Use of a Drosophila Genome-Wide Conserved Sequence Database to Identify Functionally Related cis-Regulatory Enhancers

Content Provider	PubMed Central
Author	Brody, Thomas Yavatkar, Amarendra S. Kuzin, Alexander Kundu, Mukta Tyson, Leonard J. Ross, Jermaine Lin, Tzu-yang Lee, Chi-hon Awasaki, Takeshi Lee, Tzumin Odenwald, Ward F.
Copyright Year	2011
Abstract	Background: Phylogenetic footprinting has revealed that cis-regulatory enhancers consist of conserved DNA sequence clusters (CSCs). Currently, there is no systematic approach for enhancer discovery and analysis that takes full-advantage of the sequence information within enhancer CSCs. Results: We have generated a Drosophila genome-wide database of conserved DNA consisting of >100,000 CSCs derived from EvoPrints spanning over 90% of the genome. cis-Decoder database search and alignment algorithms enable the discovery of functionally related enhancers. The program first identifies conserved repeat elements within an input enhancer and then searches the database for CSCs that score highly against the input CSC. Scoring is based on shared repeats as well as uniquely shared matches, and includes measures of the balance of shared elements, a diagnostic that has proven to be useful in predicting cis-regulatory function. To demonstrate the utility of these tools, a temporally-restricted CNS neuroblast enhancer was used to identify other functionally related enhancers and analyze their structural organization. Conclusions: cis-Decoder reveals that co-regulating enhancers consist of combinations of overlapping shared sequence elements, providing insights into the mode of integration of multiple regulating transcription factors. The database and accompanying algorithms should prove useful in the discovery and analysis of enhancers involved in any developmental process. Developmental Dynamics 241:169–189, 2012. © 2011 Wiley Periodicals, Inc.
Related Links	http://dx.doi.org/10.1002/dvdy.22728
Ending Page	189
Page Count	21
Starting Page	169
File Format	PDF
ISSN	10588388
e-ISSN	10970177
Journal	Developmental Dynamics
Issue Number	1
Volume Number	241
Language	English
Publisher	Wiley-Liss, Inc.
Publisher Date	2012-01-01
Access Restriction	Open
Rights Holder	Wiley-Liss, Inc.
Subject Keyword	Developmental Biology Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Developmental Biology

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