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
Cite this work
Researchers should cite this work as follows:
- Bina, M. (2020). Positions of known ICRs/gDMRs with respect to peaks in plots of ZFBS-morph-overlap density in the mouse genome. Purdue University Research Repository. doi:10.4231/V87T-4X79