DNA deformability changes of single base pair mutants within CDE binding sites in S. Cerevisiae centromere DNA correlate with measured chromosomal loss rates and CDE binding site symmetries

BACKGROUND: The centromeres in yeast (S. cerevisiae) are organized by short DNA sequences (125 bp) on each chromosome consisting of 2 conserved elements: CDEI and CDEIII spaced by a CDEII region. CDEI and CDEIII are critical sequence specific protein binding sites necessary for correct centromere formation and following assembly with proteins, are positioned near each other on a specialized nucleosome. Hegemann et al. BioEssays 1993, 15: 451–460 reported single base DNA mutants within the critical CDEI and CDEIII binding sites on the centromere of chromosome 6 and quantitated centromere loss of function, which they measured as loss rates for the different chromosome 6 mutants during cell division. Olson et al. Proc Natl Acad Sci USA 1998, 95: 11163–11168 reported the use of protein-DNA crystallography data to produce a DNA dinucleotide protein deformability energetic scale (PD-scale) that describes local DNA deformability by sequence specific binding proteins. We have used the PD-scale to investigate the DNA sequence dependence of the yeast chromosome 6 mutants' loss rate data. Each single base mutant changes 2 PD-scale values at that changed base position relative to the wild type. In this study, we have utilized these mutants to demonstrate a correlation between the change in DNA deformability of the CDEI and CDEIII core sites and the overall experimentally measured chromosome loss rates of the chromosome 6 mutants. RESULTS: In the CDE I and CDEIII core binding regions an increase in the magnitude of change in deformability of chromosome 6 single base mutants with respect to the wild type correlates to an increase in the measured chromosome loss rate. These correlations were found to be significant relative to 10(5 )Monte Carlo randomizations of the dinucleotide PD-scale applied to the same calculation. A net loss of deformability also tends to increase the loss rate. Binding site position specific, 4 data-point correlations were also created using the wild type sequence and the 3 associated alternate base mutants at each binding site position. These position specific slope magnitudes, or sensitivities, correlated with and reflected the underlying position symmetry of the DNA binding sequences. CONCLUSION: These results suggest the utility of correlating quantitative aspects of sequence specific protein-DNA complex single base mutants with changes in the easily calculated PD-deformability scale of the individual DNA sequence mutants. Using this PD approach, it may be possible in the future to understand the magnitude of biological or energetic functional effects of specific DNA sequence mutants within DNA-protein complexes in terms of their effect on DNA deformability

DNA deformability changes of single base pair mutants within CDE binding sites in centromere DNA correlate with measured chromosomal loss rates and CDE binding site symmetries-5

<p><b>Copyright information:</b></p><p>Taken from "DNA deformability changes of single base pair mutants within CDE binding sites in centromere DNA correlate with measured chromosomal loss rates and CDE binding site symmetries"</p><p>BMC Molecular Biology 2006;7():12-12.</p><p>Published online 16 Mar 2006</p><p>PMCID:PMC1434758.</p><p></p>rnate base mutant data points along with the wild type data point for the CDEI position 5. This position possesses unusually good correlations for both unsignedPD (A) and signedPD (B) plots

DNA deformability changes of single base pair mutants within CDE binding sites in centromere DNA correlate with measured chromosomal loss rates and CDE binding site symmetries-2

<p><b>Copyright information:</b></p><p>Taken from "DNA deformability changes of single base pair mutants within CDE binding sites in centromere DNA correlate with measured chromosomal loss rates and CDE binding site symmetries"</p><p>BMC Molecular Biology 2006;7():12-12.</p><p>Published online 16 Mar 2006</p><p>PMCID:PMC1434758.</p><p></p>B) signedPD. Correlation values, R, are shown within text boxes. The position of the wild type data point is plotted as a 'W'. Dashed lines show 95% confidence intervals for average predicted values

DNA deformability changes of single base pair mutants within CDE binding sites in centromere DNA correlate with measured chromosomal loss rates and CDE binding site symmetries-3

<p><b>Copyright information:</b></p><p>Taken from "DNA deformability changes of single base pair mutants within CDE binding sites in centromere DNA correlate with measured chromosomal loss rates and CDE binding site symmetries"</p><p>BMC Molecular Biology 2006;7():12-12.</p><p>Published online 16 Mar 2006</p><p>PMCID:PMC1434758.</p><p></p> is marked by a triangle along the x-axis. Shaded dual tail areas correspond to probabilities of better correlations than the actual value reported in Table 1. The normal curve, superimposed on each of the histograms using the mean and standard deviation of the distribution, reveals the normal character of the CDEI distributions (A) & (C) and contrasts with the bimodal CDEIII distributions (B) & (D)

DNA deformability changes of single base pair mutants within CDE binding sites in centromere DNA correlate with measured chromosomal loss rates and CDE binding site symmetries-1

<p><b>Copyright information:</b></p><p>Taken from "DNA deformability changes of single base pair mutants within CDE binding sites in centromere DNA correlate with measured chromosomal loss rates and CDE binding site symmetries"</p><p>BMC Molecular Biology 2006;7():12-12.</p><p>Published online 16 Mar 2006</p><p>PMCID:PMC1434758.</p><p></p> in both core binding areas are shown as squares with the mutant base placed above the corresponding base in the wild type sequence

DNA deformability changes of single base pair mutants within CDE binding sites in centromere DNA correlate with measured chromosomal loss rates and CDE binding site symmetries-4

<p><b>Copyright information:</b></p><p>Taken from "DNA deformability changes of single base pair mutants within CDE binding sites in centromere DNA correlate with measured chromosomal loss rates and CDE binding site symmetries"</p><p>BMC Molecular Biology 2006;7():12-12.</p><p>Published online 16 Mar 2006</p><p>PMCID:PMC1434758.</p><p></p>). The actual values obtained from the true PD-scale are indicated by arrows and marked by '+' signs. The probabilities of better pair values in the respective quadrants are .0001 and .0044 for unsignedPD and signedPD respectively

DNA deformability changes of single base pair mutants within CDE binding sites in centromere DNA correlate with measured chromosomal loss rates and CDE binding site symmetries-6

<p><b>Copyright information:</b></p><p>Taken from "DNA deformability changes of single base pair mutants within CDE binding sites in centromere DNA correlate with measured chromosomal loss rates and CDE binding site symmetries"</p><p>BMC Molecular Biology 2006;7():12-12.</p><p>Published online 16 Mar 2006</p><p>PMCID:PMC1434758.</p><p></p>sites are marked with an asterisk and palindromic regions with bolded arrows. In the case of CDEI, symmetry is between positions 5 and 6. For CDEIII, symmetry centers on position 14, the central conserved cytosine

DNA deformability changes of single base pair mutants within CDE binding sites in centromere DNA correlate with measured chromosomal loss rates and CDE binding site symmetries-0

<p><b>Copyright information:</b></p><p>Taken from "DNA deformability changes of single base pair mutants within CDE binding sites in centromere DNA correlate with measured chromosomal loss rates and CDE binding site symmetries"</p><p>BMC Molecular Biology 2006;7():12-12.</p><p>Published online 16 Mar 2006</p><p>PMCID:PMC1434758.</p><p></p> asterisks. The flanking palindrome areas of CDEIII are indicated by lighter arrows. Below each of the wild type sequences, the different mutant bases tested for each wild type base position are shown. Beneath each mutant, the bold vertical line indicates it's relative log(loss) rate, of magnitude indicated by the log scale shown. These data are recreated from Hegemann et al [7] Figure 3. The inset depicts a model of the yeast centromere showing the modified nucleosome formed by wrapping the CDEI site into close proximity to CDEIII. Also shown are their associated protein complexes that along with additional binding proteins form the kinetochore, which bind the spindle microtubule [2]