, Volume 126, Issue 6, pp 741–751 | Cite as

Unique XCI evolution in Tokudaia: initial XCI of the neo-X chromosome in Tokudaia muenninki and function loss of XIST in Tokudaia osimensis

  • Hideki Zushi
  • Chie Murata
  • Shusei Mizushima
  • Chizuko Nishida
  • Asato KuroiwaEmail author
Original Article


X chromosome inactivation (XCI) is an essential mechanism to compensate gene dosage in mammals. Here, we show that XCI has evolved differently in two species of the genus Tokudaia. The Amami spiny rat, Tokudaia osimensis, has a single X chromosome in males and females (XO/XO). By contrast, the Okinawa spiny rat, Tokudaia muenninki, has XX/XY sex chromosomes like most mammals, although the X chromosome has acquired a neo-X region by fusion with an autosome. BAC clones containing the XIST gene, which produces the long non-coding RNA XIST required for XCI, were obtained by screening of T. osimensis and T. muenninki BAC libraries. Each clone was mapped to the homologous region of the X inactivation center in the X chromosome of the two species by BAC-FISH. XIST RNAs were expressed in T. muenninki females, whereas no expression was observed in T. osimensis. The sequence of the XIST RNA was compared with that of mouse, showing that the XIST gene is highly conserved in T. muenninki. XIST RNAs were localized to the ancestral X region (Xq), to the heterochromatic region (pericentromeric region), and partially to the neo-X region (Xp). The hybridization pattern correlated with LINE-1 accumulation in Xq but not in Xp. Dosage of genes located on the neo-X chromosome was not compensated, suggesting that the neo-X region is in an early state of XCI. By contrast, many mutations were observed in the XIST gene of T. osimensis, indicating its loss of function in the XO/XO species.


X chromosome inactivation XIST Dosage compensation Evolution Neo-Y 



The authors thank C. Nishiyama for gene cloning and I. Yoshida for helpful suggestion for analyzing data.

Authors’ contribution

HZ conducted most experiments and sequence analysis. CM contributed RNA-seq experiment and the analysis. SM contributed northern blotting analysis. CN performed cell culture and chromosome preparation. AK designed the study and analyzed the data, and wrote the manuscript. All authors discussed the results and approved the final version of the manuscript.

Compliance with ethical standards

Ethical approval

All the animal experiments in this study were approved by Institutional Animal Care and Use Committee of National University Corporation Hokkaido University and were performed in accordance with the Guidelines for the Care and Use of Laboratory Animals, Hokkaido University. This article does not contain any studies on human participants by any of the authors.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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Fig. S1

Sequence alignment of the Xist/XIST genes between mouse, T. muenninki and T. osimensis. (a) Sequence alignment of A-repeat. Yellow boxes and red rounded rectangles indicate the motif sequence of A-repeat and AUCG tetraloop, respectively. One copy is consisted with two A-repeat motif. (b) Sequence alignment of F-repeat. Yellow boxes mean the motif sequence. (c) Sequence alignment of B-repeat. Red rectangles indicate the motif sequence. (d) Sequence alignment of C-repeat. Yellow and blue boxes indicate LNA-C1 and LNA-C2, respectively. (e, f) Sequence alignment of P1 and P2 promoter regions. Yellow boxes indicate P1 (e) and P2 (f) promoter region. (g) Sequence alignment of YY1 binding sites. Yellow boxes indicate YY1 binding sites. Red colored nucleotide was supposed to reduce transcription activity of XIST in a previous study (Jeon and Lee 2011). (JPEG 428 kb)

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Copyright information

© Springer-Verlag GmbH Germany 2017

Authors and Affiliations

  • Hideki Zushi
    • 1
  • Chie Murata
    • 2
    • 3
  • Shusei Mizushima
    • 3
  • Chizuko Nishida
    • 3
  • Asato Kuroiwa
    • 3
    Email author
  1. 1.Graduate School of Life ScienceHokkaido UniversitySapporoJapan
  2. 2.Department of Human Genetics, Tokushima University Graduate SchoolInstitute of Biomedical SciencesTokushimaJapan
  3. 3.Department of Biological Sciences, Faculty of ScienceHokkaido UniversitySapporoJapan

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