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

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

  BibTex | EndNote

1. Chemistry
2. Chemistry (Dept)
3. Codes in DNA
4. DMRs
5. Gene Regulation
6. Genomic imprinting
7. Germline DMRs
8. ICRs
9. Imprinting Control Regions