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

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By Minou Bina

Purdue University, Department of Chemistry

Supplementary material for the publication entitled “Simultaneous discovery of candidate imprinted genes and Imprinting Control Regions in the mouse genome” Bina M., and Wyss P. bioRxiv doi: https://doi.org/10.1101/780551 (2019).

Version 1.0 - published on 04 Jun 2020 doi:10.4231/V87T-4X79 - cite this Archived on 04 Jul 2020

Licensed under CC0 1.0 Universal

Description

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 Purdue University Research Repository doi:10.4231/R7W37TJH (https://purr.purdue.edu/publications/2961/1).  The goal of the project is to create a framework for de novo discovery of candidate ICRs and imprinted genes. 

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 via a link listed in the GEO series GSE77444 —Riso et al. Nucleic Acids Res 44, 8165-8178 (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 via Purdue University Research Repository doi:10.4231/32C9-G644 (https://purr.purdue.edu/publications/3493/1).

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. 

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

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