Rat and mouse imprintomes (allele-specific transcriptomes)

The rat is a widely used model for human physiology and psychology. However, due to their longer gestation periods and husbandry costs relative to mice, as well as the availability of superior molecular techniques to manipulate the mouse genome, relatively few genome-wide studies have been conducted in the rat. As such, a comprehensive analysis of genomic imprinting, which impacts complex traits such as growth and behaviour, has yet to be conducted in the rat. Towards this end, we systematically profiled embryonic and extra-embryonic tissue gene expression and DNA methylation with allele-specific resolution. We identified 14 embryonic and 26 extra-embryonic imprinted genes in the rat. Comparative analyses with mouse revealed that orthologous imprinted gene expression and associated canonical DNA methylation imprints are conserved in the embryo proper of the Muridae family. However, only 3 paternally expressed imprinted genes in the extra-embryonic embryo are conserved in Muridae, all of which are associated with non-canonical H3K27me3 imprints. The discovery of 8 novel candidate non-canonical imprinted genes unique to the rat is consistent with more rapid evolution of extra-embryonic imprinting. Cross-species analysis of novel rat imprinted genes with mouse and human revealed multiple mechanisms by which species-specific imprinted expression may be established, including H3K27me3 deposition in the oocyte, the birth of ZFP57 binding motifs and the insertion of endogenous retroviral promoters. Thus, characterization of the rat imprintome provides insights into the conservation of imprinted gene expression and the etiology of species-specific imprinting. Strand-specific RNA-seq of epiblasts (EBs) and ectoplacental cones (EPCs) from rat and mouse embryos.大鼠是广泛应用于人类生理学与心理学研究的经典模式生物。然而，相较于小鼠，大鼠妊娠期更长、饲养成本更高，加之用于操控小鼠基因组的分子技术更为成熟，目前针对大鼠开展的全基因组研究相对匮乏。 正因如此，针对会影响生长、行为等复杂性状的基因组印记（genomic imprinting）的全面分析，在大鼠中仍未完成。为此，我们以等位基因特异性分辨率（allele-specific resolution）系统分析了胚胎组织与胚外组织的基因表达及DNA甲基化谱式，并在大鼠中鉴定出14个胚胎印记基因与26个胚外印记基因。 与小鼠的比较分析显示，鼠科（Muridae）动物胚胎本体中，同源印记基因的表达及其相关的经典DNA甲基化印记具有保守性。然而，仅3个在胚外组织中父本表达的印记基因在鼠科动物中保守，且这些基因均与非经典H3K27me3印记相关。 本次发现的8个大鼠特有的新型候选非经典印记基因，与胚外印记进化速率更快的结论相符。通过与小鼠、人类的跨物种分析，我们揭示了物种特异性印记表达可能的多种建立机制，包括卵母细胞中的H3K27me3沉积、ZFP57结合基序的产生，以及内源性逆转录病毒启动子的插入。 因此，对大鼠印记组（imprintome）的表征，为理解印记基因表达的保守性以及物种特异性印记的成因提供了全新视角。本研究还对大鼠与小鼠胚胎的上胚层（epiblasts, EBs）及外胎盘锥（ectoplacental cones, EPCs）开展了链特异性RNA测序（strand-specific RNA-seq）。