A bioconductor based workflow for Z-DNA region detection and biological inference

Abstract

Z-DNA is an alternative conformation of the DNA molecule implied in regulation of gene expression. However, the exact role of this structure in cell metabolism is not yet fully understood. Here we present a novel Z-DNA analysis workflow using the R software environment which aims to investigate Z-DNA forming regions (ZDRs) throughout the genome. It combines thermodynamic analysis of the well-known software Z-Catcher with biological data manipulation capabilities of several Bioconductor packages. We employed our methodology in the human chromosome 14 as a case study. With that, we established a correlation of ZDRs with transcription start sites (TSSs) which is in agreement with previous reports. In addition, our workflow was able to show that ZDRs which are positioned inside genes tend to occur in intronic sequences rather than exonic and that ZDRs upstream to TSSs may have a positive correlation with the up-regulation of RNA polymerase activity. © 2012 Springer-Verlag.