Department of Development and Regeneration, Laboratory of Cellular Reprogramming and Epigenetic Regulation, KU Leuven - University of Leuven, Herestraat 49, 3000, Leuven, Belgium.
KU Leuven Institute for Single Cell Omics (LISCO), 3000, Leuven, Belgium.
Genome Biol. 2021 Nov 1;22(1):302. doi: 10.1186/s13059-021-02518-5.
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.
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 雌性体细胞表现出其单个活性 X 染色体的转录 X 染色体上调，而另一个 X 染色体则处于非活性状态。此外，在胚胎内细胞团和生殖细胞中，通过 X 染色体重新激活，非活性 X 染色体在发育过程中被重新激活，这可以通过体细胞重编程为多能性来在体外进行研究。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 染色体重新激活期间的 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，在雌性胚胎成纤维细胞中和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 染色体上的可及性在重编程过程中被擦除，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 染色体重新激活过程中表征了基因调控网络，揭示了调控状态的变化。我们的数据表明，ZFP42/REX1 是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 染色体重新激活和多能性之间存在进化联系。
我们的数据揭示了内在补偿机制的存在，这些机制涉及调节染色质可及性以抵消由于进化或体外 X 染色体丢失和哺乳动物细胞中 X 染色体失活引起的 X 染色体与常染色体基因剂量失衡。
