Yao Shengze, Jeon Yesu, Kesner Barry, Lee Jeannie T
Department of Molecular Biology, Massachusetts General Hospital, Boston, United States.
Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, United States.
Elife. 2025 Jun 9;13:RP101197. doi: 10.7554/eLife.101197.
a pivotal player in X chromosome inactivation (XCI), has long been perceived as a cis-acting long noncoding RNA that binds exclusively to the inactive X chromosome (Xi). However, 's ability to diffuse under select circumstances has also been documented, leading us to suspect that RNA may have targets and functions beyond the Xi. Here, using female mouse embryonic stem cells (ES) and mouse embryonic fibroblasts (MEF) as models, we demonstrate that RNA indeed can localize beyond the Xi. However, its binding is limited to ~100 genes in cells undergoing XCI (ES cells) and in post-XCI cells (MEFs). The target genes are diverse in function but are unified by their active chromatin status. binds discretely to promoters of target genes in neighborhoods relatively depleted for Polycomb marks, contrasting with the broad, Polycomb-enriched domains reported for human RNA. We find that binding is associated with down-modulation of autosomal gene expression. However, unlike on the Xi, binding does not lead to full silencing and also does not spread beyond the target gene. Over-expressing in transgenic ES cells similarly leads to autosomal gene suppression, while deleting 's Repeat B motif reduces autosomal binding and perturbs autosomal down-regulation. Furthermore, treating female ES cells with the inhibitor, X1, leads to loss of autosomal suppression. Altogether, our findings reveal that targets ~100 genes beyond the Xi, identify Repeat B as a crucial domain for its in-trans function in mice, and indicate that autosomal targeting can be disrupted by a small molecule inhibitor.
作为X染色体失活（XCI）中的关键因子，长期以来一直被视为一种顺式作用的长链非编码RNA，它仅与失活的X染色体（Xi）结合。然而，也有文献记载了其在特定情况下的扩散能力，这使我们怀疑该RNA可能具有Xi之外的靶点和功能。在这里，我们以雌性小鼠胚胎干细胞（ES）和小鼠胚胎成纤维细胞（MEF）为模型，证明该RNA确实可以定位于Xi之外。然而，其结合仅限于正在进行XCI的细胞（ES细胞）和XCI后细胞（MEF）中的约100个基因。这些靶基因功能多样，但因其活跃的染色质状态而统一。该RNA离散地结合到聚梳蛋白标记相对较少的区域中靶基因的启动子上，这与报道的人类该RNA广泛的、富含聚梳蛋白的结构域形成对比。我们发现该RNA的结合与常染色体基因表达的下调有关。然而，与在Xi上不同，该RNA的结合不会导致完全沉默，也不会扩散到靶基因之外。在转基因ES细胞中过表达该RNA同样会导致常染色体基因抑制，而删除该RNA的重复B基序会减少常染色体结合并扰乱常染色体下调。此外，用该RNA抑制剂X1处理雌性ES细胞会导致常染色体抑制的丧失。总之，我们的研究结果表明，该RNA在Xi之外靶向约100个基因，确定重复B基序是其在小鼠中反式功能的关键结构域，并表明小分子抑制剂可以破坏常染色体靶向。
