ArticleBMC molecular biology2007
Prediction of highly expressed genes in microbes based on chromatin accessibility.
Article in BMC molecular biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 17 citations in OpenAlex.
- DNA structural features and variability of complete MHC locus sequences.Frontiers in bioinformatics · 2024Review
- Does the eclipse limit bacterial nucleoid complexity and cell width?Synthetic and systems biotechnology · 2017Review
- A genome-wide identification of genes undergoing recombination and positive selection in Neisseria.BioMed research international · 2014Article
- PerPlot & PerScan: tools for analysis of DNA curvature-related periodicity in genomic nucleotide sequences.Microbial informatics and experimentation · 2011Article
- Complete genome sequence of the marine fish pathogen Vibrio anguillarum harboring the pJM1 virulence plasmid and genomic comparison with other virulent strains of V. anguillarum and V. ordalii.Infection and immunity · 2011Article
- Concept and application of a computational vaccinology workflow.Immunome research · 2010Article
- Comparative analysis of sequence periodicity among prokaryotic genomes points to differences in nucleoid structure and a relationship to gene expression.Journal of bacteriology · 2010Article
- Genome-wide analyses reveal lineage specific contributions of positive selection and recombination to the evolution of Listeria monocytogenes.BMC evolutionary biology · 2008Article
- Prediction of highly expressed genes in microbes based on chromatin accessibility.BMC molecular biology · 2007Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIt is well known that gene expression is dependent on chromatin structure in eukaryotes and it is likely that chromatin can play a role in bacterial gene expression as well. Here, we use a nucleosomal position preference measure of anisotropic DNA flexibility to predict highly expressed genes in microbial genomes. We compare these predictions with those based on codon adaptation index (CAI) values, and also with experimental data for 6 different microbial genomes, with a particular interest in experimental data from Escherichia coli. Moreover, position preference is examined further in 328 sequenced microbial genomes.
resultsWe find that absolute gene expression levels are correlated with the position preference in many microbial genomes. It is postulated that in these regions, the DNA may be more accessible to the transcriptional machinery. Moreover, ribosomal proteins and ribosomal RNA are encoded by DNA having significantly lower position preference values than other genes in fast-replicating microbes.
conclusionThis insight into DNA structure-dependent gene expression in microbes may be exploited for predicting the expression of non-translated genes such as non-coding RNAs that may not be predicted by any of the conventional codon usage bias approaches.
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