Outline of the ergosterol synthesis pathway in yeast.

<p>(+) the corresponding gene is present in <i>C. elegans</i> and <i>D. melanogaster</i>, according to our exploration. (−) the corresponding gene is absent. (?) not convincing evidence for the presence of the ortholog.</p

Segments of the <i>Drosophila</i> paralogs CG1998 and CG11162 (homologs of Erg25) and the corresponding conceptual translations.

<p>The interruption of the open reading frames of both genes, by their last intron, is shown by vertical lines.</p

Expressional correlation among <i>D. melanogaster ERG</i> orthologs.

<p>The analyses were performed using data downloaded from the Gene expression-Omnibus database (<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgiCMDsearchDBgeo" target="_blank">http://www.ncbi.nlm.nih.gov/entrez/query.fcgiCMDsearchDBgeo</a>). We considered the datasets GDS192 (wing imaginal disc spatial gene expression), GDS653 (neurotransmitter-specific neuronal gene expression), GDS664 (splicing factor mutant at permissive and restrictive temperatures) and GDS667 (mRNA splicing factor knock-down) which contain 51 data points for 14 000 transcripts.</p

Functional clustering of genes whose expression profiles stronlgy correlate with those of dLBR and CG1998 (using the DAVID classification tool at Medium stringency).

<p>ER: endoplasmic reticulum, HSP: heat shock protein, SRP: signal recognition particle. At high stringency, only the first functional cluster is obtained.</p

Isoelectric points (pI) of the ERGp orthologs in <i>C. elegans</i> and <i>D. melanogaster</i>.

<p>The mean pI values (and standard deviations –std) of the orthologous proteins in cholesterol prototrophs are shown for comparison. “pI (w/o)” stands for means +/− std calculated <b>w</b>ith<b>o</b>ut taking into account the orthologs in <i>C. elegans</i> and <i>D. melanogaster</i> while “pI (w)” stands for means +/− std calculated including the orthologs in <i>C. elegans</i> and <i>D. melanogaster</i>. “n” is the number of orthologs in cholesterol prototrophs used to calculate the means.</p

Details of the BLAST analysis that allowed the detection of <i>ERG</i> orthologs in <i>C. elegans</i> and <i>D. melanogaster</i>.

<p>The comparisons were performed in the directions indicated by the arrows (i.e. Yeast→Human represents a BLASTp search with an ERG protein from yeast in the division <i>Homo sapiens</i> of Genbank). Low Scores S and high E-values (>10⁻⁶) are classically considered as non-significant (unrelated or divergent sequences). The small tables display the S and E-values for the comparisons using the species-specific divisions of Genbank.</p

Hydrophobic profiles of several potential ERG orthologous proteins.

<p>A way to show a structural relationship is to predict the hydrophobic profiles of the relevant proteins. Here we have used the TopPred program <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002883#pone.0002883-Claros1" target="_blank">[36]</a> as implemented in the server of Pasteur Institute (<a href="http://www.pasteur.fr" target="_blank">http://www.pasteur.fr</a>). Left panels show the results for the potential homologs of ERG2p while the right panels display the profiles for ERG28p homologs (using the Kyte-Doolitle scale, with the default parameters). Negative (positive) values represent hydrophobic (hydrophilic) segments. A way to statistically assess the similarity of two profiles is to calculate their correlation coefficient R. R-values for pairwise comparisons with the human sequence are reported. We tried to maximize the R-value by slightly sliding one profile over the other (that is why the frames of the profiles are not perfectly aligned).</p

Correlation between methylation profile and gestational age.

<p>Bisulphite pyrosequencing results for each CpG dinucleotide of the <i>AMOT</i> promoter CpG island. Dots represent methylation values (y-axis) at each CpG for the corresponding gestational age in weeks (x-axis). We used this two variables as quantitative to estimate the relationship. The "cor" value for each plot represents the Pearson correlation coefficient that estimates the link between the two variables and P-values correspond to statistical relevance of the "cor" coefficient. The red lines correspond to the linear regression of the methylation profile as function of gestational age to illustrate the correlation in the plot. A negative value of the cor coefficient corresponds to a deacreasing of the methylation as function of the gestational age for the linear model (decreasing red line). Statistical were performed using R statistical tools.</p

Correlation between methylation profile and gestational age.

<p>Bisulphite pyrosequencing results for each CpG dinucleotide of the <i>AMOT</i> promoter CpG island. Dots represent methylation values (y-axis) at each CpG for the corresponding gestational age in weeks (x-axis). We used this two variables as quantitative to estimate the relationship. The "cor" value for each plot represents the Pearson correlation coefficient that estimates the link between the two variables and P-values correspond to statistical relevance of the "cor" coefficient. The red lines correspond to the linear regression of the methylation profile as function of gestational age to illustrate the correlation in the plot. A negative value of the cor coefficient corresponds to a deacreasing of the methylation as function of the gestational age for the linear model (decreasing red line). Statistical were performed using R statistical tools.</p

Modulation of <i>AMOT</i> gene expression.

<p>Changes in AMOT expression were assessed by qPCR on 6 cord blood ECFC from preterm neonates or their control counterparts. Each bar represents an individual sample. Each RNA from preterm ECFC was matched against an RNA from a control. Results were normalized to the values obtained with RPL13 expression.</p