Wyss Phillip, Bina Minou
Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
BMC Genomics. 2025 Jul 30;26(1):704. doi: 10.1186/s12864-025-11801-9.
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) dispersed across autosomal chromosomal DNA. An unresolved question is how to discover candidate ICRs across the entire canine genome. Previously, bioinformatics analyses found a significant fraction of well-known ICRs 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 approach is creating density plots to mark cluster positions as peaks. In genome-wide analyses, peaks in plots effectively discovered candidate ICRs along chromosomal DNA sequences of the Canis 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 the 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.
在哺乳动物中，基因组印记限制了两个亲本等位基因之一中一部分基因的表达。该过程由分散在常染色体DNA上的印记控制区域（ICR）调控。一个尚未解决的问题是如何在整个犬类基因组中发现候选ICR。此前，生物信息学分析在小鼠、人类和牛中发现了相当一部分知名的ICR。分析基于找到几个富含CpG的基序簇（称为ZFBS-形态重叠）的基因组位置。这些基序是复合DNA元件。在本报告中，我们进行了类似的研究以确定犬类基因组中的候选ICR。生物信息学方法的一个关键特征是创建密度图，将簇位置标记为峰值。在全基因组分析中，图中的峰值有效地发现了家犬品种拳师犬染色体DNA序列上的候选ICR。关于非犬类参考序列基因，一些候选ICR位于与小鼠DNA、人类DNA或两者中的ICR位置类似的区域。在拳师犬基因组中，例子包括MEST同工型PEG1、INPP5F_V2、PLAGL1同工型ZAC1、IGF2R、PEG3和GNAS基因座的亲本特异性表达的候选ICR。在小鼠中，这些基因座中的印记基因在发育和生理过程中起重要作用。
