DNA free energy based promoter prediction and comparative analysis of Arabidopsis and rice genomes

Abstract

Cis-regulatory regions on DNA serve as binding sites for proteins such as transcription factors and RNA polymerase. The combinatorial interaction of these proteins plays a crucial role in transcription initiation, which is an important point of control in the regulation of gene expression. We present here an analysis of the performance of an in silico method for predicting cis-regulatory regions in the plant genomes Arabidopsis thaliana and Oryza sativa on the basis of free energy of melting of DNA. For protein coding genes, we achieve recall and precision of 96% and 42% for Arabidopsis and 97% and 31% for rice respectively. For ncRNA genes, the program gives recall and precision of 94% and 75% for Arabidopis and 95% and 90% for rice respectively. Moreover, 96% of the false positive predictions were located in non-coding regions of primary transcripts out of which 20% were found in the first intron alone, indicating possible regulatory roles. The predictions for orthologous genes from the two genomes showed a good correlation with respect to prediction scores and promoter organization. Comparison of our results with an existing program for promoter prediction in plant genomes indicates that our method shows improved prediction capability.