Candidate imprinting control regions in dog genome

In mammals, genomic imprinting restricts the expression of a subset of genes from one of the two parental alleles. The process is regulated by imprinting control regions (ICRs) and gDMRs (germline Differentially Methylated Regions) dispersed across autosomal chromosomal DNA. An unresolved question is how to discover candidate ICRs in canine DNA genome wide. Previously, bioinformatics analyses found a significant fraction of well-known ICRs/gDMRs in mouse, human, and Bos taurus. Analyses were based on finding the genomic positions of clusters of several CpG-rich motifs known as ZFBS-morph overlaps. These motifs are composite DNA elements. For this report, we performed similar studies to pinpoint candidate ICRs in the dog genome. A key feature of the bioinformatics strategy is creating density plots to mark cluster positions. In genome-wide analyses, peaks in plots effectively discovered candidate ICRs along chromosomal DNA sequences of Canis lupus familiaris breed Boxer. With respect to Non-Dog RefSeq Genes, several candidate ICRs are in regions analogous to ICR positions in mouse DNA, in human DNA, or both. In Boxer genome, examples include candidate ICRs for parent-of-origin-specific expression of the MEST isoform PEG1, INPP5F_V2, the PLAGL1 isoform ZAC1, IGF2R, PEG3, and GNAS loci. In mouse, imprinted genes in these loci play important roles in developmental and physiological processes.