School of BioSciences, The University of Melbourne, Melbourne, VIC, 3010, Australia.
Department of Anatomy, University of Otago, Dunedin, New Zealand.
Epigenetics Chromatin. 2024 Sep 28;17(1):29. doi: 10.1186/s13072-024-00552-8.
Genomic imprinting results in parent-of-origin-specific gene expression and, among vertebrates, is found only in therian mammals: marsupials and eutherians. A differentially methylated region (DMR), in which the methylation status of CpG dinucleotides differs between the two alleles, can mark the parental identity of imprinted genes. We developed a computational pipeline that detected CpG islands (CGIs) marked by both methylated and unmethylated signals in whole genome bisulfite sequencing data. This approach identified candidate marsupial DMRs in a publicly available koala methylome. One of these candidate DMRs was associated with PRKACB, a gene encoding the protein kinase A catalytic subunit beta. Nothing is known about the imprinting status of PRKACB in eutherian mammals although mutations of this gene are associated with endocrine neoplasia and other developmental disorders.
In the tammar wallaby and brushtail possum there was parent-of-origin-specific DNA methylation in the PRKACB DMR in which the maternal allele was methylated and the paternal allele was unmethylated. There were multiple RNAs transcribed from this locus. Allele-specific expression analysis identified paternal expression of a PRKACB lncRNA and an mRNA isoform. Comparison of the PRKACB gene start site between marsupials and eutherians demonstrated that the CGI is longer in marsupials. The PRKACB gene product functions in the same signalling pathway as the guanine nucleotide-binding protein alpha subunit encoded at the GNAS locus, a known eutherian imprinted gene. In a mouse methylome Gnas had three differentially methylated CGIs, while in the koala methylome the GNAS locus had two unmethylated CGIs.
We conclude that PRKACB is a novel, DMR-associated marsupial imprinted gene. Imprinting of PRKACB in marsupials and GNAS in eutherians may indicate a conserved selection pressure for imprinting of the protein kinase A signalling pathway in therians with the two lineages adapting by imprinting different genes.
基因组印迹导致了亲源特异性基因表达，在脊椎动物中，仅在有袋类哺乳动物和真兽类中发现。差异甲基化区域（DMR）中，CpG 二核苷酸的甲基化状态在两个等位基因之间存在差异，可以标记印迹基因的亲本身份。我们开发了一种计算管道，该管道可以在全基因组亚硫酸氢盐测序数据中检测到同时被甲基化和非甲基化信号标记的 CpG 岛（CGI）。这种方法在公开的考拉甲基组中鉴定了候选有袋类 DMR。其中一个候选 DMR 与 PRKACB 相关，PRKACB 编码蛋白激酶 A 催化亚基β。尽管该基因的突变与内分泌肿瘤和其他发育障碍有关，但在真兽类哺乳动物中，PRKACB 的印迹状态尚不清楚。
在塔马尔袋鼠和帚尾袋貂中，PRKACB DMR 中存在亲源特异性 DNA 甲基化，其中母本等位基因甲基化，而父本等位基因未甲基化。该基因座有多个 RNA 转录。等位基因特异性表达分析鉴定出 PRKACB lncRNA 和 mRNA 异构体的父本表达。在有袋类和真兽类之间比较 PRKACB 基因起始位点表明，CGI 在有袋类中更长。PRKACB 基因产物在相同的信号通路中起作用，该通路由 GNAS 基因座编码的鸟嘌呤核苷酸结合蛋白α亚基编码，这是一个已知的真兽类印迹基因。在小鼠甲基组中，GNAS 有三个差异甲基化 CGI，而在考拉甲基组中，GNAS 基因座有两个非甲基化 CGI。
我们得出结论，PRKACB 是一个新的、与 DMR 相关的有袋类印迹基因。PRKACB 在有袋类中的印迹和 GNAS 在真兽类中的印迹可能表明，蛋白激酶 A 信号通路的印迹在有袋类和真兽类中受到保守的选择压力，而这两个谱系通过印迹不同的基因来适应。
