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.
Cite this work
Researchers should cite this work as follows:
- Bina, M. (2020). An overview of peak positions –in plots of ZFBS-morph-overlap density– with respect to known ICRs/gDMRs in the mouse genome. Purdue University Research Repository. doi:10.4231/32C9-G644