{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,14]],"date-time":"2025-05-14T03:35:11Z","timestamp":1747193711245,"version":"3.40.5"},"reference-count":54,"publisher":"S. Karger AG","issue":"1","license":[{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/karger.com\/pages\/terms-and-conditions"},{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/karger.com\/pages\/terms-and-conditions"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cytogenet Genome Res"],"published-print":{"date-parts":[[2024]]},"abstract":"<b><i>Introduction:<\/i><\/b> 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 <i>Xist<\/i> is the key regulator. However, little is known about the Xic in species with unusual sex chromosomes. The genus <i>Tokudaia<\/i> includes three rodent species endemic to Japan. <i>Tokudaia osimensis<\/i> and <i>Tokudaia tokunoshimensis<\/i> lost the Y chromosome (XO\/XO), while <i>Tokudaia muenninki<\/i> (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 <i>Tokudaia<\/i> species. <b><i>Methods:<\/i><\/b> Gene structure of nine genes in Xic was predicted, and the gene location and genome sequences of Xic were compared between mouse and <i>Tokudaia<\/i> species. The expression level of the gene was confirmed by transcripts per million calculation using RNA-seq data. <b><i>Results:<\/i><\/b> Compared to mouse, the Xic gene order and location were conserved in <i>Tokudaia<\/i> species. However, remarkable structure changes were observed in lncRNA genes, <i>Xist<\/i> and <i>Tsix<\/i>, in the XO\/XO species. In <i>Xist,<\/i> 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 <i>Xist<\/i> and <i>Tsix<\/i> were confirmed in TMU, however, not in the XO\/XO species. Additionally, three deletions and one inversion were confirmed in the intergenic region between <i>Jpx<\/i> and <i>Ftx<\/i> in the XO\/XO species. <b><i>Conclusion:<\/i><\/b> Our findings indicate that even if the <i>Xist<\/i> and <i>Tsix<\/i> 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 <i>Jpx<\/i>-<i>Ftx<\/i> resulted in the inability to perform the XCI, and, as a result, a lack of <i>Xist<\/i> 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. <\/jats:p>","DOI":"10.1159\/000539294","type":"journal-article","created":{"date-parts":[[2024,5,16]],"date-time":"2024-05-16T21:01:48Z","timestamp":1715893308000},"page":"23-32","source":"Crossref","is-referenced-by-count":0,"title":["Loss of One X and the Y Chromosome Changes the Configuration of the X Inactivation Center in the Genus <i>Tokudaia<\/i>"],"prefix":"10.1159","volume":"164","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8777-7047","authenticated-orcid":false,"given":"Luisa","family":"Matiz-Ceron","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Miki","family":"Okuno","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Takehiko","family":"Itoh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ikuya","family":"Yoshida","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shusei","family":"Mizushima","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Atsushi","family":"Toyoda","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Takamichi","family":"Jogahara","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Asato","family":"Kuroiwa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"127","published-online":{"date-parts":[[2024,5,16]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","DOI":"10.1038\/s41580-021-00438-7"},{"key":"ref2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.genet.42.110807.091711"},{"key":"ref3","doi-asserted-by":"publisher","DOI":"10.1016\/j.gde.2007.08.001"},{"key":"ref4","doi-asserted-by":"publisher","DOI":"10.1038\/newbio232229a0"},{"key":"ref5","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0005616"},{"key":"ref6","doi-asserted-by":"publisher","DOI":"10.3106\/041.035.0404"},{"key":"ref7","doi-asserted-by":"publisher","DOI":"10.1266\/jjg.52.247"},{"key":"ref8","doi-asserted-by":"publisher","DOI":"10.1266\/jjg.53.297"},{"key":"ref9","doi-asserted-by":"publisher","DOI":"10.1007\/s10577-010-9142-y"},{"key":"ref10","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2211574119"},{"key":"ref11","doi-asserted-by":"publisher","DOI":"10.1007\/s10577-011-9268-6"},{"key":"ref12","doi-asserted-by":"publisher","DOI":"10.3390\/genes8110306"},{"key":"ref13","doi-asserted-by":"publisher","DOI":"10.1159\/000104771"},{"key":"ref14","doi-asserted-by":"publisher","DOI":"10.1101\/gr.201665.115"},{"key":"ref15","doi-asserted-by":"publisher","DOI":"10.1101\/gr.152902"},{"key":"ref16","doi-asserted-by":"publisher","DOI":"10.1038\/nrg2987"},{"key":"ref17","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1002248"},{"key":"ref18","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2118182119"},{"key":"ref19","doi-asserted-by":"publisher","DOI":"10.1038\/7734"},{"key":"ref20","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(92)90520-m"},{"key":"ref21","doi-asserted-by":"publisher","DOI":"10.1101\/gr.174901"},{"key":"ref22","doi-asserted-by":"publisher","DOI":"10.1101\/gad.389006"},{"key":"ref23","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddi089"},{"key":"ref24","doi-asserted-by":"publisher","DOI":"10.1042\/BST20210253"},{"key":"ref25","doi-asserted-by":"publisher","DOI":"10.1016\/s0092-8674(01)80012-x"},{"key":"ref26","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.1000276"},{"key":"ref27","doi-asserted-by":"publisher","DOI":"10.1038\/sj.emboj.7601187"},{"key":"ref28","doi-asserted-by":"publisher","DOI":"10.1261\/rna.2747411"},{"key":"ref29","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2011.06.026"},{"key":"ref30","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1009785107"},{"key":"ref31","doi-asserted-by":"publisher","DOI":"10.1007\/s00412-017-0639-4"},{"key":"ref32","doi-asserted-by":"publisher","DOI":"10.1159\/000531275"},{"key":"ref33","doi-asserted-by":"publisher","DOI":"10.1038\/s41597-023-02845-1"},{"key":"ref34","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3317"},{"key":"ref35","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1009730"},{"key":"ref36","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1883"},{"key":"ref37","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl158"},{"key":"ref38","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bti310"},{"key":"ref39","doi-asserted-by":"publisher","DOI":"10.1101\/gr.229202"},{"key":"ref40","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"ref41","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/30.11.2478"},{"key":"ref42","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts635"},{"key":"ref43","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-12-323"},{"key":"ref44","doi-asserted-by":"publisher","DOI":"10.1006\/bbrc.1999.0681"},{"key":"ref45","doi-asserted-by":"publisher","DOI":"10.15252\/embr.201948019"},{"key":"ref46","doi-asserted-by":"publisher","DOI":"10.1101\/gad.295907.117"},{"key":"ref47","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-019-0412-0"},{"key":"ref48","doi-asserted-by":"publisher",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