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However, how aneuploidy affects spatial genome organization remains less understood. In this study, we addressed this question by utilizing the previously established isogenic wild\u2010type (WT) and trisomic mouse embryonic stem cells (mESCs). We employed a combination of Hi\u2010C, RNA\u2010seq, chromosome painting and nascent RNA imaging technologies to compare the spatial genome structures and gene transcription among these cells. We found that trisomy has little effect on spatial genome organization at the level of A\/B compartment or topologically associating domain (TAD). Inter\u2010chromosomal interactions are associated with chromosome regions with high gene density, active histone modifications and high transcription levels, which are confirmed by imaging. Imaging also revealed contracted chromosome volume and weakened transcriptional activity for trisomic chromosomes, suggesting potential implications for the transcriptional output of these chromosomes. Our data resources and findings may contribute to a better understanding of the consequences of aneuploidy from the angle of spatial genome organization.<\/jats:p>","DOI":"10.1111\/cpr.13639","type":"journal-article","created":{"date-parts":[[2024,3,30]],"date-time":"2024-03-30T04:39:29Z","timestamp":1711773569000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["The effect of trisomic chromosomes on spatial genome organization and global transcription in embryonic stem cells"],"prefix":"10.1111","volume":"57","author":[{"given":"Mengfan","family":"Li","sequence":"first","affiliation":[{"name":"Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking\u2010Tsinghua Center for Life Sciences Peking University  Beijing China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junsheng","family":"Yang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of 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