An overview of peak positions –in plots of ZFBS-morph-overlap density– with respect to known ICRs/gDMRs 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:10.4231/32C9-G644 - cite this Archived on 04 Jul 2020

Licensed under CC0 1.0 Universal

Description

In mammalian genomes, Imprinting Control Regions (ICRs) regulate parent-of-origin specific expression of a subset of genes.  Previously, a report offered a dataset for displaying the density of ZFBS-morph overlaps in the built mm9 of the mouse genome —Bina et al. Purdue University Research Repository. doi:10.4231/R7W37TJH (https://purr.purdue.edu/publications/2961/1).  The density-plots are results of bioinformatic studies aimed at de novo discovery candidate ICRs and imprinted genes.  To assess the validity of the strategy, I have examined peak-positions 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.

To offer an overview, I have complied a series of snapshots that I have obtained at the UCSC genome browser.  You can access a PDF of the images by clicking on download –on the top right-side of this page.  By browsing through the file, you could view: the relative distribution of peak along the chromosomal bands; and peak-positions with respect to the known ICRs and results of ChIPs reported for H3K9me3, ZFP57, and KAP1.  Note that peak intensities depend on the number of ZFBS-morph overlaps in a sliding 850-base window moving along chromosomal DNA.  Peaks covering 2 overlaps could be true or false-positives.  Those covering 3 overlaps are more robust.  Also note that since the overlaps are CpG-rich, robust-peaks occur infrequently along the DNA. 

If you observe anomalies on this page please contact bina@ purdue.edu.

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