Genome-wide maps of Usp16, ubH2A and gene expression profiles in wild type and Usp16 knock out mouse embryonic stem cells (ESCs) and embryoid bodies (EBs)

Polycomb Repressive Complex 1 and histone H2A ubiquitination (ubH2A) contribute to embryonic stem cell (ESC) pluripotency by repressing lineage-specific gene expression. However, whether active deubiquitination co-regulates ubH2A levels in ESCs and during differentiation is not known. Here, we report that the histone H2A deubiquitinase Usp16 regulates H2A deubiquitination and gene expression in ESCs, and importantly, is required for ESC differentiation. Usp16 knockout is embryonic lethal in mice, but does not affect ESC viability or identity. Usp16 binds to the promoter regions of a large number of genes in ESCs and Usp16 binding is inversely correlated with ubH2A levels and positively correlated with gene expression levels. Intriguingly, Usp16-/- ESCs fail to differentiate due to ubH2A-mediated repression of lineage-specific genes. Finally, Usp16, but not the enzymatically inactive mutant, rescues the differentiation defects of Usp16-/- ESCs. Therefore, this study identifies Usp16 and H2A deubiquitination as critical regulators of ESC gene expression and differentiation.

多梳抑制复合体1（Polycomb Repressive Complex 1）与组蛋白H2A泛素化（ubH2A）可通过抑制谱系特异性基因表达，参与维持胚胎干细胞（ESC）的多能性。然而，在胚胎干细胞及细胞分化过程中，是否存在活跃的去泛素化过程协同调控ubH2A水平，目前尚不清楚。本研究发现，组蛋白H2A去泛素化酶泛素特异性蛋白酶16（Usp16）可调控胚胎干细胞内的H2A去泛素化进程与基因表达，且其对胚胎干细胞的分化不可或缺。小鼠体内Usp16基因敲除会导致胚胎致死，但该操作不会影响胚胎干细胞的存活特性与细胞身份。Usp16可结合胚胎干细胞中大量基因的启动子区域，其结合水平与ubH2A水平呈负相关，而与基因表达水平呈正相关。有趣的是，Usp16敲除（Usp16-/-）的胚胎干细胞因ubH2A介导的谱系特异性基因抑制而无法完成分化。最后，唯有野生型Usp16（而非酶活失活的突变体）可挽救Usp16敲除胚胎干细胞的分化缺陷。综上，本研究证实Usp16及H2A去泛素化是调控胚胎干细胞基因表达与分化的关键调控因子。