Along the Bos taurus genome, uncover candidate imprinting control regions

Abstract

Background In mammals, Imprinting Control Regions (ICRs) regulate a subset of genes in a parent-of-origin-specific manner. In both human and mouse, previous studies identified a set of CpG-rich motifs occurring as clusters in ICRs and germline Differentially Methylated Regions (gDMRs). These motifs consist of the ZFP57 binding site (ZFBS) overlapping a subset of MLL binding units known as MLL morphemes. MLL or MLL1 (Mixed Lineage Leukemia 1) is a relatively large multidomain protein that plays a central role in the regulation of transcription. The structures of both MLL1 and MLL2 include a domain (MT) that binds CpG-rich DNA and a conserved domain (SET) that methylates lysine 4 in histone H3 producing H3K4me3 marks in chromatin. Results Since genomic imprinting impacts many developmental and key physiological processes, we followed a previous bioinformatics strategy to pinpoint ICR positions in the Bos taurus genome. Initial genome-wide analyses involved finding the positions of ZFP57 binding sites, and the CpG-rich motifs (ZFBS-morph overlaps) along cattle chromosomal DNA. By creating plots displaying the density of ZFBS-morph overlaps, we removed background noise and thus improved signal detection. With the density-plots, we could view the positions of peaks locating known and candidate ICRs in cattle DNA. Our evaluations revealed the correspondence of peaks in plots to reported known and inferred ICRs/DMRs in cattle. Beside peaks pinpointing such ICRs, the density-plots also revealed additional peaks. Since evaluations validated the robustness of our approach, we inferred that the additional peaks may correspond to candidate ICRs for imprinted gene expression. Conclusion Our bioinformatics strategy offers the first genome-wide approach for systematically localizing candidate ICRs. Furthermore, we have tailored our datasets for upload onto the UCSC genome browser so that researchers could find known and candidate ICRs with respect to a wide variety of annotations at all scales: from the positions of Single Nucleotide Polymorphisms (SNPs), to positions of genes, transcripts, and repeated DNA elements. Furthermore, the UCSC genome browser offers tools to produce enlarged views: to uncover the genes in the vicinity of candidate ICRs and thus discover potential imprinted genes for experimental validations.

Defining Candidate Imprinted loci in Bos taurus

“…In LOS induced by ART, ZAC1 was biallelically expressed in fetuses [16]. In the PLAGL1 locus in Bos taurus, a peak in plots is within the experimentally defined imprinted DMR [48]. Thus, my strategy correctly located an imprinted DMR in nearly 106 Mb long cattle chromosomal DNA (Figure 1).…”

“…A whole-genome assembly of Bos taurus [50] offered the opportunity to perform genome-wide analyses to discover ICRs in domestic cattle [48]. Briefly, from the UCSC genome browser, I downloaded the build bosTau8 assembly.…”

“…To date, my strategy correctly pinpointed the genomic positions of a substantial fraction of fully characterized ICRs/gDMRs in three mammalian species [46][47][48]. The strategy is based on studies demonstrating that in emouse, nearly 90% of ICRs/gDMRs include composite DNA elements consisting of the ZFP57 binding site (ZFBS) overlapping a subset of the MLL1 morphemes [52].…”

“…A third track shows peak positions in the density plots (Figure 1). Peak positions are markers of known, inferred, and predicted ICRs along chromosomal DNA sequences [46][47][48].…”

“…To date, I have applied my genome-wide studies to three different mammals: mouse [46], human [47], and Bos taurus [48]. In this report, I focus on demonstrating that my strategy could identify candidate ICRs for potential imprinted genes important to spermatogenesis in bulls, and myogenesis in Bos taurus.…”