Imprinting Control Regions (ICRs) regulate the expression of a subset of genes in a parent-of-origin-specific manner. Previous studies have established that imprinted ICRs include sites for interactions with ZFP57. We have shown that a significant fraction of the known Differentially Methylated Regions (gDMRs) often encompass clusters of composite-DNA-elements consisting of the ZFP57 binding site (ZFBS) overlapping a subset of the MLL1 morphemes. These elements are known as ZFBS-Morph overlaps.
We wrote a Perl script in order to facilitate locating the genomic positions of clusters of ZFBS-Morph overlaps along the mammalian chromosomes. This script produces density-plots, in which peaks mark the position of ZFBS-Morph-overlap clusters. This publication offers a file that includes the density-plots obtained for the build mm9 of the mouse genome. These plots are in a format (wig.gz) suitable for display as a custom track, at the UCSC genome browser.
To obtain a copy of the file (BINA_Dens_ZFBS-Morph_overlaps_mm9.wig.gz), follow the listed steps:
- At the top right corner of this page, click on download bundle; the file is compressed.
- After download, decompress the file.
- You will find two files: Readme.txt and a copy of BINA_Dens_ZFBS-Morph_overlaps_mm9.wig.gz
To view the plots at the UCSC genome browser (https://genome.ucsc.edu/), select the build mm9 of the mouse genome. You will find a map displaying the default tracks.
- Under the map, click on "manage custom tracks”
- Afterward, click on "add custom track"
- Then click on choose file (on your computer select the file named BINA_Dens_ZFBS-Morph_overlaps_mm9.wig.gz), then click on submit.
The plot will display the density-peaks as brown vertical bars along the genomic DNA.
- NOTE: the track will indicate “no data” for the genomic regions that do not include any density-peak.
- In evaluations, we found that reliable peaks encompassed 3 or more ZFBS-Morph overlaps. Peaks encompassing 2 overlaps could be true or false positive.
In our studies, density-peaks correctly localized ~ 90% of the known ICRs/gDMRs in the mouse genome. Therefore, these plots could offer a relatively robust strategy for locating candidate ICRs for novel imprinted genes.
If you observe anomalies on this page, please contact bina@ purdue.edu
Cite this work
Researchers should cite this work as follows:
- Bina, M., Wyss, P. J., Song, X. C. (2018). Density of ZFBS-Morph overlaps in the build mm9 of the mouse genome. Purdue University Research Repository. doi:10.4231/R7W37TJH