Density of ZFBS-Morph overlaps in the build bosTau8 of the Bos taurus genome

<p>Genomic imprinting results in the expression of a subset of genes from either the maternal or paternal allele.  This complex process is regulated by Imprinting Control Regions (ICRs), dispersed along the mammalian autosomal chromosomes.  In the mouse and the human genomes, the ICRs often encompass composite DNA elements consisting of the ZFP57 binding site (ZFBS) overlapping a subset of the MLL1 morphemes.  These elements (ZFBS-Morph overlaps) occur often as clusters of 2 or more in the ICRs and the germline Differentially Methylated Regions (gDMRs).  To enhance detection of such clusters, we developed a Perl script for viewing the density of ZFBS-Morph overlaps in the build bosTau8 of the cow genome.  In a sliding window (consisting of 850 bases), the script counted and reported the number of ZFBS-Morph overlaps while ignoring isolated occurrences of such overlaps.             </p>

<p>This publication provides a file (in wig.gz format) for displaying the density of ZFBS-Morph overlaps at the UCSC genome browser.  Follow the steps listed below to obtain a copy of the file for creating a custom track at the browser.</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 named:
<ul>
<li>Readme.txt and</li>
<li>BINA_Dens_ZFBS-Morph_overlaps_bosTau8.wig.gz</li>
</ul>
</li>
</ul>
</li>
</ul>

<ul>
<li>To view the plots at the UCSC genome browser, go to <a href="https://genome.ucsc.edu/">https://genome.ucsc.edu/</a></li>
</ul>

<ul>
<li>Select the build bosTau8 of the cow genome. 
<ul>
<li>You will find a map displaying the default tracks.</li>
</ul>
</li>
</ul>

<ul>
<li>Under the map, click on "manage custom tracks”
<ul>
<li>Afterward, click on "add custom track"</li>
<li>Then click on choose file.</li>
<li>*On your computer, select the file named
<ul>
<li>BINA_Dens_ZFBS-Morph_overlaps_bosTau8.wig.gz</li>
</ul>
</li>
<li>Subsequently, click on submit.</li>
</ul>
</li>
</ul>

<p>At the browser, the plot will display the density-peaks as brown vertical bars.</p>

<ul style="list-style-type:circle;">
<li>NOTE: the track will indicate “no data” in regions that do not include any density-peak.</li>
</ul>

<p>In evaluations, we found that reliable peaks encompassed 3 or more ZFBS-Morph overlaps.  Peaks encompassing 2 overlaps could be true or false positive.</p>

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