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Title: De Novo Identification of Regulatory Regions in Intergenic Spaces of Prokaryotic Genomes

Abstract

This project was begun to implement, test, and experimentally validate the results of a novel algorithm for genome-wide identification of candidate transcription-factor binding sites in prokaryotes. Most techniques used to identify regulatory regions rely on conservation between different genomes or have a predetermined sequence motif(s) to perform a genome-wide search. Therefore, such techniques cannot be used with new genome sequences, where information regarding such motifs has not yet been discovered. This project aimed to apply a de novo search algorithm to identify candidate binding-site motifs in intergenic regions of prokaryotic organisms, initially testing the available genomes of the Yersinia genus. We retrofitted existing nucleotide pattern-matching algorithms, analyzed the candidate sites identified by these algorithms as well as their target genes to screen for meaningful patterns. Using properly annotated prokaryotic genomes, this project aimed to develop a set of procedures to identify candidate intergenic sites important for gene regulation. We planned to demonstrate this in Yersinia pestis, a model biodefense, Category A Select Agent pathogen, and then follow up with experimental evidence that these regions are indeed involved in regulation. The ability to quickly characterize transcription-factor binding sites will help lead to a better understanding of how known virulence pathways aremore » modulated in biodefense-related organisms, and will help our understanding and exploration of regulons--gene regulatory networks--and novel pathways for metabolic processes in environmental microbes.« less

Authors:
; ; ;
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
902275
Report Number(s):
UCRL-TR-228471
TRN: US200717%%518
DOE Contract Number:
W-7405-ENG-48
Resource Type:
Technical Report
Country of Publication:
United States
Language:
English
Subject:
99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; 59 BASIC BIOLOGICAL SCIENCES; ALGORITHMS; EXPLORATION; GENE REGULATION; GENES; NUCLEOTIDES; SCREENS; TARGETS; TESTING; VIRULENCE

Citation Formats

Chain, P, Garcia, E, Mcloughlin, K, and Ovcharenko, I. De Novo Identification of Regulatory Regions in Intergenic Spaces of Prokaryotic Genomes. United States: N. p., 2007. Web. doi:10.2172/902275.
Chain, P, Garcia, E, Mcloughlin, K, & Ovcharenko, I. De Novo Identification of Regulatory Regions in Intergenic Spaces of Prokaryotic Genomes. United States. doi:10.2172/902275.
Chain, P, Garcia, E, Mcloughlin, K, and Ovcharenko, I. Tue . "De Novo Identification of Regulatory Regions in Intergenic Spaces of Prokaryotic Genomes". United States. doi:10.2172/902275. https://www.osti.gov/servlets/purl/902275.
@article{osti_902275,
title = {De Novo Identification of Regulatory Regions in Intergenic Spaces of Prokaryotic Genomes},
author = {Chain, P and Garcia, E and Mcloughlin, K and Ovcharenko, I},
abstractNote = {This project was begun to implement, test, and experimentally validate the results of a novel algorithm for genome-wide identification of candidate transcription-factor binding sites in prokaryotes. Most techniques used to identify regulatory regions rely on conservation between different genomes or have a predetermined sequence motif(s) to perform a genome-wide search. Therefore, such techniques cannot be used with new genome sequences, where information regarding such motifs has not yet been discovered. This project aimed to apply a de novo search algorithm to identify candidate binding-site motifs in intergenic regions of prokaryotic organisms, initially testing the available genomes of the Yersinia genus. We retrofitted existing nucleotide pattern-matching algorithms, analyzed the candidate sites identified by these algorithms as well as their target genes to screen for meaningful patterns. Using properly annotated prokaryotic genomes, this project aimed to develop a set of procedures to identify candidate intergenic sites important for gene regulation. We planned to demonstrate this in Yersinia pestis, a model biodefense, Category A Select Agent pathogen, and then follow up with experimental evidence that these regions are indeed involved in regulation. The ability to quickly characterize transcription-factor binding sites will help lead to a better understanding of how known virulence pathways are modulated in biodefense-related organisms, and will help our understanding and exploration of regulons--gene regulatory networks--and novel pathways for metabolic processes in environmental microbes.},
doi = {10.2172/902275},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Tue Feb 20 00:00:00 EST 2007},
month = {Tue Feb 20 00:00:00 EST 2007}
}

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