Positions of known ICRs/gDMRs with respect to peaks in plots of ZFBS-morph-overlap density in the mouse genome

<p>In mammalian genomes, a subset of genes is imprinted to produce parent-of-origin-specific expression.  This process is regulated by ICRs/gDMRs.  Previously, I demonstrated that in the mouse genome, the ICRs/gDMRs often encompass clusters of a set of composite-DNA-elements known as ZFBS-morph overlaps.  These elements  are CpG-rich.  They consist of the ZFP57 binding site (ZFBS) overlapping a subset of the MLL1 morphemes.  In order to facilitate the detection of such clusters, a publication offered a dataset for displaying the density of ZFBS-morph overlaps in the built mm9 of the mouse genome.  You can access and download this dataset via <em>Purdue University Research Repository</em> doi:10.4231/R7W37TJH (<a href="https://purr.purdue.edu/publications/2961/1">https://purr.purdue.edu/publications/2961/1</a>).  The goal of the project is to create a framework for <em>de</em> <em>novo</em> discovery of candidate ICRs and imprinted genes. </p>

<p>To investigate the validity of my strategy, initially I obtained snapshots of peak positions in plots of the entire chromosomal DNA sequences.  The plots were displayed with respect to known ICRs/gDMRs and results of ChIPs (chromatin (immunoprecipitation assays) performed using mouse embryonic stem cells (ESCs) E14.  I obtained the experimental data <em>via</em> a link listed in the GEO series GSE77444 —Riso et al. <em>Nucleic Acids Res</em> 44, <a href="tel:[phone]">8165-8178</a> (2016).  From the extensive experimental datasets, I selected the track displaying the genomic positions of the known ICRs/gDMRs, and tracks displaying results of ChIPs corresponding to ZFP57, KAP1, and H3K9me3.  You can access and download these plots <em>via</em> <em>Purdue University Research Repository </em>doi:10.4231/32C9-G644 (<a href="https://purr.purdue.edu/publications/3493/1">https://purr.purdue.edu/publications/3493/1</a>).</p>

<p>Here, I provide a series of snapshots, showing closeup views of peak-positions in the density-plots, with respect to the known ICRs/gDMRs and results of ChIPs.  These plots clearly demonstrate that peaks in plots correctly located the known ICRs/gDMRs with respect to experimental results.  You can access a PDF of the images by clicking on download –on the top right-side of this page. </p>

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