Precise gene dosage of the X chromosomes is critical for normal development and cellular function. In mice, XX female somatic cells show transcriptional X chromosome upregulation of their single active X chromosome, while the other X chromosome is inactive. Moreover, the inactive X chromosome is reactivated during development in the inner cell mass and in germ cells through X chromosome reactivation, which can be studied in vitro by reprogramming of somatic cells to pluripotency. How chromatin processes and gene regulatory networks evolved to regulate X chromosome dosage in the somatic state and during X chromosome reactivation remains unclear. Using genome-wide approaches, allele-specific ATAC-seq and single-cell RNA-seq, in female embryonic fibroblasts and during reprogramming to pluripotency, we show that chromatin accessibility on the upregulated mammalian active X chromosome is increased compared to autosomes. We further show that increased accessibility on the active X chromosome is erased by reprogramming, accompanied by erasure of transcriptional X chromosome upregulation and the loss of increased transcriptional burst frequency. In addition, we characterize gene regulatory networks during reprogramming and X chromosome reactivation, revealing changes in regulatory states. Our data show that ZFP42/REX1, a pluripotency-associated gene that evolved specifically in placental mammals, targets multiple X-linked genes, suggesting an evolutionary link between ZFP42/REX1, X chromosome reactivation, and pluripotency. Our data reveal the existence of intrinsic compensatory mechanisms that involve modulation of chromatin accessibility to counteract X-to-Autosome gene dosage imbalances caused by evolutionary or in vitro X chromosome loss and X chromosome inactivation in mammalian cells.

中文翻译：

---

增强的染色质可及性有助于哺乳动物 X 染色体剂量补偿

X 染色体的精确基因剂量对于正常发育和细胞功能至关重要。在小鼠中，XX 雌性体细胞显示其单个活跃 X 染色体的转录 X 染色体上调，而另一个 X 染色体不活跃。此外，无活性的 X 染色体在内细胞团和生殖细胞发育过程中通过 X 染色体重新激活被重新激活，这可以通过将体细胞重新编程为多能性进行体外研究。染色质过程和基因调控网络如何进化以调节体细胞状态和 X 染色体再激活期间的 X 染色体剂量仍不清楚。使用全基因组方法、等位基因特异性 ATAC-seq 和单细胞 RNA-seq，在女性胚胎成纤维细胞中和在重编程为多能性期间，我们表明，与常染色体相比，上调的哺乳动物活性 X 染色体上的染色质可及性增加。我们进一步表明，活性 X 染色体上增加的可及性通过重编程被擦除，伴随着转录 X 染色体上调的擦除和增加的转录突发频率的丧失。此外，我们在重编程和 X 染色体再激活过程中描述了基因调控网络，揭示了调控状态的变化。我们的数据显示 ZFP42/REX1，一种在胎盘哺乳动物中特异性进化的多能性相关基因，靶向多个 X 连锁基因，表明 ZFP42/REX1、X 染色体再激活和多能性之间存在进化联系。