Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription

Abstract

We have generated a WWW interface for automated comprehensive analyses of promoter regulatory motifs and the effect they exert on mRNA expression profiles. The server provides a wide spectrum of analysis tools that allow de novo discovery of regulatory motifs, along with refinement and in-depth investigation of fully or partially characterized motifs. The presented discovery and analysis tools are fundamentally different from existing tools in their basic rational, statistical background and specificity and sensitivity towards true regulatory elements. We thus anticipate that the service will be of great importance to the experimental and computational biology communities alike. The motif discovery and diagnosis workbench is available at http://longitude.weizmann.ac.il/rMotif/.

Figure 1

mRNA expression profiles of genes that contain the yeast sporulation motif Ndt80 measured during sporulation (A) (20) and during signaling through the MAPK pathway (B) (21). (C) The effect of multiple copies of a motif in promoters as demonstrated by the yeast cell cycle regulator, MCB. EC score was measured in six conditions: (1) cell cycle (26); (2) sporulation (20); (3) diauxic shift (27); (4) heat-shock (28); (5) MAPK signaling (21); and (6) DNA-damage response (29); for the genes that have one copy of the motif and for genes that have two or more copies of the motif in their promoters. The MCB position specific weight matrix (http://genetics.med.harvard.edu/~tpilpel/MotifList.html) was used to assign the motif to promoters using ScanACE (25) as reported previously (5). Conditions in which the EC score of the genes that have multiple copies is significantly higher than that of the genes that have a single copy are marked with ‘*’. The P-values on these hypotheses were calculated as before (11). (D) An example of three probability distributions of EC scores for random sets of genes of size 10 (blue), 30 (red) and 100 (green), obtained for the heat-shock experiment. (E and F) The effect of nucleotide substitutions at different positions within the motif on expression coherence. Shown in (E) are the averaged expression profiles, during sporulation, of genes that have the consensus Ndt80 motif (blue) and genes that have an A→T substitution relative to the consensus at the second position (red) and genes that have an A→G substitution relative to the consensus at the seventh position (green). (F) The averaged tolerance to substitution for each nucleotide position within the motif was defined as the averaged correlation coefficient between the averaged expression profiles of the genes that have a perfect match to the consensus motif and the averaged expression profiles of the genes that have each of the three possible substitutions relative to the consensus in that position.

Figure 2

A modified version of the Combinogram display designed to capture the effect of single nucleotide substitutions in regulatory regions on gene expression patterns. In this display, as in the original Combinograms, we represent the similarity of expression profiles between gene sets (1-correlation coefficients of their expression profiles, left side of the display) and within sets of genes (the EC score, right side of the display). The middle section displays the different promoter sequence elements shared among all the genes that are represented by each row of the display. The red motif is the consensus sequence and it represents all the genes that have a perfect match to it. The rest of the rows represent genes that have single substitutions relative to the consensus, with a ‘-’ indicating same nucleotide as the consensus, e.g. the bottom row represents the genes that have a GCCACAAAA motif instead of the consensus. The numbers next to the EC bars represent the number of genes that correspond to each row.