HOTTIP-dependent R-loop formation regulates CTCF boundary activity and TAD integrity in leukemia

Huacheng Luo, Ganqian Zhu, Melanie A. Eshelman, Tsz Kan Fung, Qian Lai, Fei Wang, Bernd B. Zeisig, Julia Lesperance, Xiaoyan Ma, Shi Chen, Nicholas Cesari, Christopher Cogle, Baoan Chen, Bing Xu, Feng Chun Yang, Chi Wai Eric So, Yi Qiu, Mingjiang Xu, Suming Huang

Research output: Contribution to journalArticlepeer-review

41 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)833-851.e11
JournalMolecular Cell
Issue number4
StatePublished - Feb 17 2022


  • AML leukemogenesis
  • CTCF chromatin boundary
  • R-loops
  • TAD formation
  • canonical Wnt transcription
  • cohesin complex
  • enhancer/promoter interactions

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology


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