HOTTIP Dependent R-loop Formation Regulates CTCF Boundary Activity and TAD Integrity in Leukemia
Abstract: HOTTIP lncRNA is highly expressed in acute myeloid leukemia (AML) patients carrying MLL rearrangement or NPM1 mutation to facilitate the formation of HOXA topologically associated domains (TADs) and drive aberrant transcription. However, the mechanism through which HOTTIP accesses CTCF chromatin boundaries and regulates CTCF-mediated genome topology remains unknown. Here, we show that HOTTIP directly interacts 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 drives gene transcription. Either deleting CBS or targeting RNaseH to eliminate R-loop in CBS of beta-catenin TAD impaired CTCF boundary activity, inhibited promoter/enhancer interactomes, reduced beta-catenin target expression, and mitigated leukemogenesis in PDX mouse models with aberrant HOTTIP expression. Thus, HOTTIP-mediated R-loop formation directly reinforces CTCF chromatinboundary activity and TAD integrity to drive oncogene transcription and pathogenesis of leukemia.
Luo H, Zhu G, Eshelman M, Fung TK, Lai Q, Wang F, Zeisig BB, Lesperance J, Ma X, Chen S, Cesari N, Cogle C, Chen B, Xu B, Yang F-C, So E, Qiu Y, Xu M¶, Huang S¶.