PURR may experience downtime this Thursday (10/17) in the afternoon for scheduled maintenance. We apologize for the inconvenience. close

Density of ZFBS-Morph overlaps in the build mm9 of the mouse genome

Listed in Datasets

By Minou Bina1, Phillip J. Wyss1, Xiaohui Carol Song1

Purdue University

Supplementary material for the publication entitled “Imprinted Control Regions include composite DNA elements consisting of the ZFP57 binding site overlapping MLL1 Morphemes” Bina M.  Genomics, 109: 265–273 (2017).

Version 1.0 - published on 25 Apr 2018 doi:10.4231/R7W37TJH - cite this Archived on 25 May 2018

Licensed under CC0 1.0 Universal

Description

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:

Tags

The Purdue University Research Repository (PURR) is a university core research facility provided by the Purdue University Libraries, the Office of the Executive Vice President for Research and Partnerships, and Information Technology at Purdue (ITaP).