sj-docx-5-cpc-10.1177_10556656221125392 - Supplemental material for <i>MMP16</i> as NSCL ± P Susceptible Gene in Western Han Chinese

Supplemental material, sj-docx-5-cpc-10.1177_10556656221125392 for MMP16 as NSCL ± P Susceptible Gene in Western Han Chinese by Yansong Lin, Jiayu Shi, Bing Shi and Zhonglin Jia in The Cleft Palate-Craniofacial Journal</p

Correlation coefficients and significant values (P values) of miRNA conservation and sequence features (F1-F12) in six species. Features F1–F4 are the base contents of A, C, G, and U of miRNA precursors.

<p>Features F5–F8 are the base contents of A, C, G, and U of mature miRNAs. Features F9–F12 are the base contents of A, C, G, and U of non-mature sequences. Correlation analysis was performed for each miRNA feature and miRNA conservation for each species. The numbers in each cell mean the correlation coefficient and p value of the correlation analysis.</p

A diagram indicating the significance of different base preferences at the 5′ end for conserved miRNAs and less-conserved miRNAs in human.

<p>The blue curve is the random distribution of the difference of the base U fraction between conserved miRNAs and less-conserved miRNAs. The red arrow represents the real difference of the base U fraction between conserved miRNAs and less-conserved miRNAs.</p

sj-tif-1-cpc-10.1177_10556656221125392 - Supplemental material for <i>MMP16</i> as NSCL ± P Susceptible Gene in Western Han Chinese

Supplemental material, sj-tif-1-cpc-10.1177_10556656221125392 for MMP16 as NSCL ± P Susceptible Gene in Western Han Chinese by Yansong Lin, Jiayu Shi, Bing Shi and Zhonglin Jia in The Cleft Palate-Craniofacial Journal</p

Sequence Fingerprints of MicroRNA Conservation

<div><p>It is known that the conservation of protein-coding genes is associated with their sequences both various species, such as animals and plants. However, the association between microRNA (miRNA) conservation and their sequences in various species remains unexplored. Here we report the association of miRNA conservation with its sequence features, such as base content and cleavage sites, suggesting that miRNA sequences contain the fingerprints for miRNA conservation. More interestingly, different species show different and even opposite patterns between miRNA conservation and sequence features. For example, mammalian miRNAs show a positive/negative correlation between conservation and AU/GC content, whereas plant miRNAs show a negative/positive correlation between conservation and AU/GC content. Further analysis puts forward the hypothesis that the introns of protein-coding genes may be a main driving force for the origin and evolution of mammalian miRNAs. At the 5′ end, conserved miRNAs have a preference for base U, while less-conserved miRNAs have a preference for a non-U base in mammals. This difference does not exist in insects and plants, in which both conserved miRNAs and less-conserved miRNAs have a preference for base U at the 5′ end. We further revealed that the non-U preference at the 5′ end of less-conserved mammalian miRNAs is associated with miRNA function diversity, which may have evolved from the pressure of a highly sophisticated environmental stimulus the mammals encountered during evolution. These results indicated that miRNA sequences contain the fingerprints for conservation, and these fingerprints vary according to species. More importantly, the results suggest that although species share common mechanisms by which miRNAs originate and evolve, mammals may develop a novel mechanism for miRNA origin and evolution. In addition, the fingerprint found in this study can be predictor of miRNA conservation, and the findings are helpful in achieving a clearer understanding of miRNA function and evolution.</p> </div

sj-tif-2-cpc-10.1177_10556656221125392 - Supplemental material for <i>MMP16</i> as NSCL ± P Susceptible Gene in Western Han Chinese

Supplemental material, sj-tif-2-cpc-10.1177_10556656221125392 for MMP16 as NSCL ± P Susceptible Gene in Western Han Chinese by Yansong Lin, Jiayu Shi, Bing Shi and Zhonglin Jia in The Cleft Palate-Craniofacial Journal</p

sj-docx-3-cpc-10.1177_10556656221125392 - Supplemental material for <i>MMP16</i> as NSCL ± P Susceptible Gene in Western Han Chinese

Supplemental material, sj-docx-3-cpc-10.1177_10556656221125392 for MMP16 as NSCL ± P Susceptible Gene in Western Han Chinese by Yansong Lin, Jiayu Shi, Bing Shi and Zhonglin Jia in The Cleft Palate-Craniofacial Journal</p

A comparison of the silencing mechanism distribution in old miRNAs (highly conserved miRNAs) and young miRNAs (lowly conserved miRNAs).

<p>A comparison of the silencing mechanism distribution in old miRNAs (highly conserved miRNAs) and young miRNAs (lowly conserved miRNAs).</p

A comparison of the miRNA conservation score between intronic miRNAs and non-intronic miRNAs.

<p>A comparison of the miRNA conservation score between intronic miRNAs and non-intronic miRNAs.</p

Clustering heatmap of the correlation patterns between base content and miRNA conservation in six species.

<p>A red element indicates a positive correlation between the corresponding sequence features and miRNA conservation for a given species. In contrast, a green element indicates a negative correlation, and a black one represents a non-significant correlation. Features F1–F4 are the base contents of A, C, G, and U of the miRNA precursors. Features F5–F8 are the base contents of A, C, G, and U of the mature miRNAs. Features F9–F12 are the base contents of A, C, G, and U of non-mature miRNAs.</p