The positions of ZFBS and ZFBS-Morph overlaps in the build canFam2 of the dog genome

<p>In the course of centuries, studies of canines have greatly contributed to our understanding of genetic basis of development processes in mammals.  However, not much is known about the influence of genomic imprinting in that species.  In mammals, genomic imprinting leads to the expression of a subset of genes in a parent-of-origin-specific fashion.  Studies of mouse and human genes have revealed that proteins that bind CpG containing sequences play central roles in numerous biological processes including the regulation of transcription and genomic imprinting.  Such proteins include ZFP57, MLL1/ KMT2A, and MLL2/ KMT2B.  While <em>in vitro</em> ZFP57 binds a methylated hexameric DNA sequence, MLL1 and MLL2 bind a set of nonmethylation CpG-rich motifs (the MLL1 morphemes) to regulate transcription. Bioinformatics studies have identified a set of composite-DNA-elements that occur often in the imprinting control regions (ICRs) and germline differentially methylated regions (gDMRs).  These elements consist of the ZFP57 binding site (ZFBS) overlapping a subset of the MLL1 morphemes.  It is thought that these DNA elements (ZFBS-Morph overlaps) could be a key feature that drives the recruitment of the DNMT3A andDNMT3L complex to the ICRs/ gDMRs for processive methylation of CpGs.</p>

<p>This publication provides a text file that lists the positions of ZFBS and ZFBS-Morph overlaps in the build canFam2 of the dog genome.  The file is in a format (bed.gz) suitable for upload at the UCSC genome browser to create a custom track.  To view the file as a custom track at the UCSC genome browser, follow the following 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 named:
<ul>
<li>Readme.txt and</li>
<li>BINA_ZFBS_Morph_ovlps_and_ZFBS_canFam2_v2.bed.gz</li>
</ul>
</li>
</ul>
</li>
<li>To view the plots at the UCSC genome browser, go to <a href="https://genome.ucsc.edu/">https://genome.ucsc.edu/</a>
<ul>
<li>Select the build canFam2 of the dog genome. </li>
<li>You will find a map displaying the default tracks.</li>
</ul>
</li>
<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>
</ul>
</li>
<li>On your computer, select the file named
<ul>
<li>BINA_ZFBS_Morph_ovlps_and_ZFBS_canFam2_v2.bed.gz
<ul>
<li>Subsequently, click on submit.</li>
</ul>
</li>
</ul>
</li>
</ul>

<p>Note: *- it works best if you change the custom tracks to dense.</p>

<p>*- In close-up views, choose  pack for ZFBS-Morph overlaps and dense for ZFP57 binding sites.</p>

<p>If you observe anomalies on this page and if you encounter a problem with downloading the bed file, please contact bina at purdue.edu.</p>