An enhancer RNA recruits MLL1 to regulate transcription ofMyb

Abstract

TheMybproto-oncogene encodes the transcription factor c-MYB, which is critical for the proliferation and differentiation of hematopoietic stem and progenitor cells. Distant enhancers ofMybexpression form a hub of interactions with theMybpromoter but the regulation ofMybduring hematopoiesis is still incompletely understood. Here we identified a novel nuclearMyblong non-coding enhancer RNA (Myrlin) that originates from the -81 kb murineMybenhancer within theMyb ─ Hbs1lintergenic region.MyrlinandMybare coordinately regulated in a developmental stage-specific fashion during maturation of erythroid progenitors and upon differentiation of MEL cells. CRISPR/Cas9 genome editing of theMyrlintranscription start site at the -81kb enhancer reduced bothMyrlinandMybexpression. Deletion of theMyrlinTSS reduced occupancy by the looping protein LDB1, compromising long-range hub contacts between theMybpromoter and its enhancer and reducing RNA Pol II occupancy across theMyblocus. In contrast, silencing ofMyrlinusing CRISPRi, while similarly reducing bothMyrlinandMybexpression, left theMybenhancer hub undisturbed, revealing that chromatin looping and transcription activation ofMybcan be decoupled. Investigating a role forMyrlin,per se, we found thatMyrlininteracts with MLL1 complex, a transcriptional coactivator that plays an essential role in regulating gene expression during hematopoiesis.MyrlinCRISPRi compromised MLL1 occupancy in theMyblocus and decreased CDK9 and RNA Pol II binding.MyrlinCRISPRi further resulted in pausing of RNA Pol II in theMybfirst exon/intron. These data document that Myrlin directly participates in activatingMybtranscription by recruiting MLL1.