Density of ZFBS-Morph overlaps in the build mm9 of the mouse genome

<p>Imprinting Control Regions (ICRs) regulate the expression of a subset of genes in a parent-of-origin-specific manner.  Previous studies have established that imprinted ICRs include sites for interactions with ZFP57.  We have shown that a significant fraction of the known Differentially Methylated Regions (gDMRs) often encompass clusters of composite-DNA-elements consisting of the ZFP57 binding site (ZFBS) overlapping a subset of the MLL1 morphemes.  These elements are known as ZFBS-Morph overlaps. </p>

<p>We wrote a Perl script in order to facilitate locating the genomic positions of clusters of ZFBS-Morph overlaps along the mammalian chromosomes.  This script produces density-plots, in which peaks mark the position of ZFBS-Morph-overlap clusters.  This publication offers a file that includes the density-plots obtained for the build mm9 of the mouse genome.  These plots are in a format (wig.gz) suitable for display as a custom track, at the UCSC genome browser.</p>

<p>To obtain a copy of the file (BINA_Dens_ZFBS-Morph_overlaps_mm9.wig.gz), follow the listed steps:</p>

<ul>
<li>At the top right corner of this page, click on download bundle; the file is compressed.</li>
<li>After download, decompress the file.
<ul>
<li>You will find two files: Readme.txt and a copy of BINA_Dens_ZFBS-Morph_overlaps_mm9.wig.gz</li>
</ul>
</li>
</ul>

<p>To view the plots at the UCSC genome browser (<a href="https://genome.ucsc.edu/">https://genome.ucsc.edu/</a>), select the build mm9 of the mouse genome.  You will find a map displaying the default tracks.</p>

<ul>
<li>Under the map, click on "manage custom tracks”</li>
<li>Afterward, click on "add custom track"</li>
<li>Then click on choose file (on your computer select the file named BINA_Dens_ZFBS-Morph_overlaps_mm9.wig.gz), then click on submit.</li>
</ul>

<p>The plot will display the density-peaks as brown vertical bars along the genomic DNA.</p>

<ul>
<li>NOTE:  the track will indicate “no data” for the genomic regions that do not include any density-peak.</li>
<li>In evaluations, we found that reliable peaks encompassed 3 or more ZFBS-Morph overlaps.  Peaks encompassing 2 overlaps could be true or false positive.</li>
</ul>

<p>In our studies, density-peaks correctly localized ~ 90% of the known ICRs/gDMRs in the mouse genome.  Therefore, these plots could offer a relatively robust strategy for locating candidate ICRs for novel imprinted genes. </p>

<p>If you observe anomalies on this page, please contact bina@ purdue.edu</p>

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