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Determination of the Optimal Chromosomal Location(s) for a DNA Element in Escherichia coli Using a Novel Transposon-mediated Approach
Published on: September 11, 2017
Comparative genomics study of inverted repeats in bacteria
Fabrizio Lillo1, Salvatore Basile, Rosario N Mantegna
1Istituto Nazionale per la Fisica della Materia, Unità di Palermo, Viale delle Scienze, I-90128, Palermo, Italy.
Bioinformatics (Oxford, England)
|July 16, 2002
Summary
Bacterial genomes contain more inverted repeats (IRs) than expected, often located near coding regions. While some IRs may form hairpin structures, not all meet the criteria for rho-independent transcription termination.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Comparative genomics analyzes DNA differences across species.
- Inverted repeats (IRs) in DNA can form hairpin structures in messenger RNA.
- Some hairpin structures function as rho-independent intrinsic terminators.
Purpose of the Study:
- To investigate the occurrence and genomic location of inverted repeats in bacterial genomes.
- To compare observed IR numbers with predictions from Markovian models.
- To determine the relationship between IRs and coding regions, and their potential role in transcription termination.
Main Methods:
- Analysis of inverted repeat (IR) distribution in 37 complete bacterial genomes.
- Comparison of observed IR frequencies with Markovian DNA sequence models.
- Genomic location analysis of IRs relative to coding regions and gene orientations.
- Utilizing the TransTerm program to predict rho-independent transcription terminators.
Main Results:
- Most eubacteria exhibit a higher number of IRs than predicted by Markovian models.
- IRs longer than 8 nucleotides preferentially locate near the 3' end of coding regions.
- IRs with longer stems are found in short non-coding regions between convergent genes.
- Only a subset of observed IRs satisfy the criteria for rho-independent termination.
Conclusions:
- Bacterial genomes possess a distinct pattern of inverted repeat distribution.
- The location of IRs suggests functional roles beyond simple sequence modeling.
- A portion of bacterial IRs are potential rho-independent transcription terminators, but not all.
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