Escape from X inactivation in mouse tissues (RNA-Seq)

X chromosome inactivation (XCI) silences most genes on one X chromosome in female mammals, but some genes escape XCI. To identify escape gene in vivo and to explore molecular mechanisms that regulate this process we analyzed the allele-specific expression and chromatin structure of X-linked genes in mouse tissues and cells with skewed XCI and distinguishable alleles based on single nucleotide polymorphisms. Using a new method to estimate allelic expression, we demonstrate a continuum between complete silencing and significant expression from the inactive X (Xi). Few genes (2-3%) escape XCI to a significant level and only a minority differs between mouse tissues, suggesting stringent silencing and escape controls. Allelic profiles of DNase I hypersensitivity and RNA polymerase II occupancy of genes on the Xi correlate with escape from XCI. Allelic binding profiles of the DNA binding protein CCCTC-binding factor (CTCF) in different cell types indicate that CTCF binding at the promoter correlates with escape. Importantly, CTCF binding at the boundary between escape and silenced domains may prevent the spreading of active escape chromatin into silenced domains. Examination of allelic expression in mouse hybrid tissues.

X染色体失活（X chromosome inactivation, XCI）会使雌性哺乳动物一条X染色体上的绝大多数基因发生沉默，但部分基因可逃逸XCI。为在体内鉴定逃逸XCI的基因，并探索调控该过程的分子机制，我们基于单核苷酸多态性（single nucleotide polymorphisms）区分等位基因，对具有偏斜XCI的小鼠组织和细胞中的X连锁基因的等位基因特异性表达与染色质结构进行了分析。通过一种全新的等位基因表达量估算方法，我们证实失活X染色体（inactive X, Xi）上的基因表达存在连续谱系，从完全沉默到显著表达均有分布。仅有极少数基因（2%-3%）可显著逃逸XCI，且仅少数基因的逃逸情况在小鼠不同组织间存在差异，这表明XCI的沉默与逃逸过程受到严格的调控。失活X染色体上基因的DNase I超敏性等位基因谱与RNA聚合酶II结合占有率，均与XCI逃逸存在相关性。不同细胞类型中DNA结合蛋白CCCTC结合因子（CCCTC-binding factor, CTCF）的等位基因结合谱显示，启动子区域的CTCF结合与XCI逃逸存在关联。尤为重要的是，逃逸区域与沉默区域边界处的CTCF结合，可阻止活性逃逸染色质向沉默区域扩散。我们还对小鼠杂交组织中的等位基因表达情况进行了检测。