背景:X染色体失活(XCI)是哺乳动物中雌性和雄性之间剂量补偿的重要机制。在女性中,XCI是由一个复杂的控制,保守的基因座称为X失活中心(XIC),其中lncRNAXist是关键调节因子。然而,对具有不寻常性染色体的物种的Xic知之甚少。Tokudaia属包括日本特有的三种啮齿动物。德州岛(TOS)和德州岛(TTO)失去了Y染色体(XO/XO),而Tokudaiamuenninki(TMU)通过X染色体和常染色体(XX/XY)的融合获得了neo-X区域。我们比较了Tokudaia物种中Xic的基因位置和结构。
方法:预测了Xic中9个基因的基因结构,并比较了小鼠和Tokudaia物种之间Xic的基因位置和基因组序列。使用RNA-seq数据通过TPM计算确认基因的表达水平。
结果:与鼠标相比,在Tokudaia物种中,Xic基因的顺序和位置是保守的。然而,在lncRNA基因中观察到显着的结构变化,Xist和Tsix,在XO/XO物种中。在Xist,重要的功能重复,B-,C-,D-,和E重复,由于这些物种的缺失而部分或完全丢失。RNA-seq数据显示,在TMU中证实了Xist和Tsix的女性特异性表达模式,然而不在XO/XO物种中。此外,在XO/XO物种的Jpx和Ftx之间的基因间区域中确认了三个缺失和一个倒位。
结论:我们的发现表明,即使Xist和TsixlncRNAs表达,它们无法在XO/XO物种中产生成功且持久的XCI。我们假设Jpx-Ftx基因间区域的显著结构变化导致X染色体失活,and,因此,缺乏Xist的表达。我们的结果共同表明,Xic的结构变化发生在XO/XO物种的祖先谱系中,可能是由于一个X染色体和Y染色体的丢失以及XCI系统降解的结果。
BACKGROUND: X chromosome inactivation (XCI) is an essential mechanism for dosage compensation between females and males in mammals. In females, XCI is controlled by a complex, conserved locus termed the X inactivation center (Xic), in which the lncRNA Xist is the key regulator. However, little is known about the Xic in species with unusual sex chromosomes. The genus Tokudaia includes three rodent species endemic to Japan. Tokudaia osimensis and Tokudaia tokunoshimensis lost the Y chromosome (XO/XO), while Tokudaia muenninki (TMU) acquired a neo-X region by fusion of the X chromosome and an autosome (XX/XY). We compared the gene location and structure in the Xic among Tokudaia species.
METHODS: Gene structure of nine genes in Xic was predicted, and the gene location and genome sequences of Xic were compared between mouse and Tokudaia species. The expression level of the gene was confirmed by transcripts per million calculation using RNA-seq data.
RESULTS: Compared to mouse, the Xic gene order and location were conserved in Tokudaia species. However, remarkable structure changes were observed in lncRNA genes, Xist and Tsix, in the XO/XO species. In Xist, important functional repeats, B-, C-, D-, and E-repeats, were partially or completely lost due to deletions in these species. RNA-seq data showed that female-specific expression patterns of Xist and Tsix were confirmed in TMU, however, not in the XO/XO species. Additionally, three deletions and one inversion were confirmed in the intergenic region between Jpx and Ftx in the XO/XO species.
CONCLUSIONS: Our findings indicate that even if the Xist and Tsix lncRNAs are expressed, they are incapable of producing a successful and lasting XCI in the XO/XO species. We hypothesized that the significant structure change in the intergenic region of Jpx-Ftx resulted in the inability to perform the XCI, and, as a result, a lack of Xist expression. Our results collectively suggest that structural changes in the Xic occurred in the ancestral lineage of XO/XO species, likely due to the loss of one X chromosome and the Y chromosome as a consequence of the degradation of the XCI system.