Prediction of highly expressed genes in microbes based on chromatin accessibility.
BACKGROUND
It 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.


RESULTS
We 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.


CONCLUSIONS
This 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.
Willenbrock
Hanni
H
Center for Biological Sequence Analysis, BioCentrum, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark. hanni@cbs.dtu.dk <hanni@cbs.dtu.dk>
Ussery
David W
DW
D001271:Atlases as Topic; D002843:Chromatin / Q000235:genetics*; D004926:Escherichia coli / Q000235:genetics*; D005544:Forecasting; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D016680:Genome, Bacterial / Q000235:genetics*; D012313:RNA / Q000235:genetics; D012269:Ribosomal Proteins / Q000235:genetics; D014178:Translocation, Genetic
D002843:Chromatin; D012269:Ribosomal Proteins; D012313:RNA