Fig. 1

Allele-specific mapping of Zfp57 binding sites. a Schematic diagram of the experimental design. Example polymorphisms are shown for the maternal allele-specific binding of ZFP57 over BL6 (A)–Cast (G) SNP. BL6 allele (blue line) is bound by ZFP57 in BC and Cast (brown line) in the CB line. ASAP allele-specific alignment pipeline devised to map genome-specific reads; ESC embryonic stem cell. b Total number of peaks identified as being biallelic, parental origin-specific (maternal (Mat) and paternal (Pat)) and strain-specific (BL6 and Cast) based on Fisher’s exact test analysis of allele-specific reads under each peak. NI refers to non-informative sites due to lack of SNP spanning reads. c UCSC genome browser views (mm9 assembly) of data showing parental allele-specific binding at the paternally methylated IG-DMR (top left), maternally methylated Snrpn ICR (bottom left), biallelic binding site within Pank4 gene intron on chromosome 4 (top right) and a strain-specific monoallelic binding within the Cmtm4 gene intron on chromosome 8 (bottom right). Tracks in each panel show the following (top-down): histone modification profiles for H3K4me3, H3K9me3 and H4K20me3 [28]; combined read densities for BC and CB ZFP57 ChIP; Bl6/Cast SNPs [24]; density plots for allele-specific reads in BC and CB ChIP; position of known ICRs where found; annotated UCSC genes in the region