About PlantcisProm

Introduction

The process of transcription begins with the RNA polymerase (RNAP) binding to the DNA at the promoter region, which is in the vicinity of transcription start site (TSS). Promoter regions have several common features, such as lower stability, higher curvature and less bendability compared with their neighboring regions. Based on the difference in stability between neighboring upstream and downstream regions in the vicinity of experimentally determined TSS, a promoter prediction algorithm, PromPredict, has been developed (Kanhere A and Bansal M 2005a, 2005b, and Rangannan V and Bansal M 2007, 2009). PromPredict has been successfully applied to predict promoter regions in prokaryotes and the results are displayed in PromBase. We have used PromPredict for predicting cis-regulatory regions in eukaryotes Arabidopsis thaliana and Oryza sativa genomes, since the regions in the vicinity of the TSS in these genomes show similar features as prokaryotes. Plantcisprom provides a genome browser for visualizing the predictions in the entire genome of these plants.

PlantcisProm is a database of predicted promoter regions for 12 rice chromosomes (Oryza sativa L. ssp. japonica cultivar Nipponbare) and 5 Arabidopsis chromosomes (Arabidopsis thaliana). Sequence information for rice was downloaded from the Rice Annotation Project Database (RAP-DB Build 4) which provides the genome sequence assembly for the International Rice Genome Sequencing Project (IRGSP). The Arabidopsis genome sequences were downloaded from The Arabidopsis Information Resource (TAIR 9) Database. RAP-DB and TAIR contains annotated gene information which is presented in the genome browser along with the predictions.

Promoter prediction methodology

The program detects relative differences in free energy and applies cutoffs based on GC content of sequence. It compares the free energy of two adjacent sequences and predicts a cis-regulatory region at the upstream sequence if the two criteria - (a) free energy of the upstream sequence (E1 value); and (b) the difference in free energy between the two sequences (D value) - are greater than pre-determined cut-off values.
The predictions are categorized according to their scores (Dmax value) into five score classes from highest to lowest score as (a) Highest (b) Very high (c) High (d) Medium (e) Low.

Free energy (stability) calculation

The stability of a double stranded DNA molecule can be expressed as sum of free energy of its constituent base paired dinucleotides. In the present study free energy over a long continuous stretch of DNA sequence was calculated by dividing the sequence into overlapping windows of 15 base pairs (or 14 dinucleotide steps). The energy values corresponding to the 16 dinucleotide steps (10 unique dinucleotides) are taken from the unified parameters obtained from melting studies on 108 oligonucleotides (Allawi and SantaLucia 1997; SantaLucia 1998). Details are described in Rangannan V and Bansal M 2009, 2010 and PromPredict.

 

Dinucleotide step	Free energy(kcal/mol)
AA	-1.0
TT	-1.0
AT	-0.88
TA	-0.58
CA	-1.45
TG	-1.45
AC	-1.44
GT	-1.44
CT	-1.28
AG	-1.28
GA	-1.30
TC	-1.30
CG	-2.17
GC	-2.24
GG	-1.84
CC	-1.84