Division of Pediatric Hematology/Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
Department of Molecular Medicine, the University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3904, USA.
Mol Cell. 2022 Feb 17;82(4):833-851.e11. doi: 10.1016/j.molcel.2022.01.014.
HOTTIP lncRNA is highly expressed in acute myeloid leukemia (AML) driven by MLL rearrangements or NPM1 mutations to mediate HOXA topologically associated domain (TAD) formation and drive aberrant transcription. However, the mechanism through which HOTTIP accesses CCCTC-binding factor (CTCF) chromatin boundaries and regulates CTCF-mediated genome topology remains unknown. Here, we show that HOTTIP directly interacts with and regulates a fraction of CTCF-binding sites (CBSs) in the AML genome by recruiting CTCF/cohesin complex and R-loop-associated regulators to form R-loops. HOTTIP-mediated R-loops reinforce the CTCF boundary and facilitate formation of TADs to drive gene transcription. Either deleting CBS or targeting RNase H to eliminate R-loops in the boundary CBS of β-catenin TAD impaired CTCF boundary activity, inhibited promoter/enhancer interactions, reduced β-catenin target expression, and mitigated leukemogenesis in xenograft mouse models with aberrant HOTTIP expression. Thus, HOTTIP-mediated R-loop formation directly reinforces CTCF chromatin boundary activity and TAD integrity to drive oncogene transcription and leukemia development.
HOTTIP lncRNA 在由 MLL 重排或 NPM1 突变驱动的急性髓系白血病（AML）中高度表达，介导 HOXA 拓扑关联域（TAD）形成并驱动异常转录。然而，HOTTIP 如何访问 CCCTC 结合因子（CTCF）染色质边界并调节 CTCF 介导的基因组拓扑结构的机制尚不清楚。在这里，我们表明 HOTTIP 通过募集 CTCF/黏合复合物和 R 环相关调节剂与 AML 基因组中的一部分 CTCF 结合位点（CBS）直接相互作用并调节它们，形成 R 环。HOTTIP 介导的 R 环增强了 CTCF 边界，并促进 TAD 的形成以驱动基因转录。无论是删除 CBS 还是靶向 RNase H 以消除β-连环蛋白 TAD 边界 CBS 中的 R 环，都会损害 CTCF 边界活性，抑制启动子/增强子相互作用，降低β-连环蛋白靶基因表达，并减轻携带异常 HOTTIP 表达的异种移植小鼠模型中的白血病发生。因此，HOTTIP 介导的 R 环形成直接增强了 CTCF 染色质边界活性和 TAD 完整性，以驱动癌基因转录和白血病的发生发展。
