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Positions of ZFBS and ZFBS-Morph overlaps in the build mm9 of the mouse genome

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By Minou Bina1, Phillip Wyss1, Xiaohui Song2

1. Purdue University, Department of Chemistry 2. Information Technology at Purdue University

Supplementary materials for the publication entitled “Imprinted Control Regions Include Composite DNA Elements consisting of the ZFP57 Binding Site overlapping MLL1 Morphemes” Bina M. Genomics, in press

Version 1.0 - published on 24 Apr 2017 doi:10.4231/R7C82782 - cite this Archived on 25 May 2017

Licensed under CC0 1.0 Universal

Description

Expression of mammalian genes is regulated by many proteins.  Examples include proteins that repress transcription, and proteins (i.e. MLL1, MLL2, and CXXC1) that contribute to the formation of chromatin states that support gene activation.  The structure of MLL1, MLL2, and CXXC1 includes a domain that binds nonmethylated DNA.  DNA sequences that bind MLL1 are known as MLL1 morphemes.  Repressors of gene expression include enzymes that methylate DNA (i.e. DNMT3A and DNMT3L), and proteins that associate with specific methylated DNA sequences (i.e. ZFP57).  

In mammals, regulation of gene expression also includes a process known as genomic imprinting: a subset of genes is imprinted (by CpG methylation) producing parent-of-origin-specific gene expression.  Genomic imprinting requires collective actions of many proteins including TRIM28, ZFP57, DNMT3A and DNMT3L. Since the ZFP57 binding site (ZFBS) occurs frequently along chromosomal DNA, additional sequence features might be required for the selective association of ZFP57 with the Imprinting Control Regions (ICRs) and Germline Differentially Methylated Regions (gDMRs).    

We have identified a group of composite DNA elements (ZFBS-Morph overlaps) consisting of the ZFP57 binding site overlapping a subset of the MLL1 morphemes.  Data evaluations revealed that ZFBS-Morph overlaps significantly reduced chromosomal occurrences of ZFP57 binding site, thus facilitating localization of ICRs/gDMRs in chromosomal DNA. 

This publication provides a text file that lists the positions of ZFBS and ZFBS-Morph overlaps in the build mm9 of the mouse genome.  The file is in a format (.bed) suitable for uploading and creating a custom track at the UCSC genome browser. 

  • At the top right corner of the page, click on download to obtain and save a copy of the bed file.
  • If you observe anomalies on this page and if you encounter a problem with downloading the bed file, please contact bina@ purdue.edu

    View data in the UCSC genome browser.

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