Myb is regulated by -81 enhancer eRNA transcript Myrlin through recruitment of MLL1 complex

The Myb proto-oncogene encodes the transcription factor c-MYB, which is critical for the proliferation and differentiation of hematopoietic stem and progenitor cells. Distant enhancers of Myb expression have been characterized but the regulation of Myb during hematopoiesis is still incompletely understood. Here we identified a novel nuclear Myb enhancer long intergenic non-coding RNA (Myrlin) that originates from the -81 kb murine Myb enhancer within the Myb ─ Hbs1l intergenic region. Myrlin and Myb are coordinately regulated in a developmental stage-specific fashion during maturation of erythroid progenitors and upon differentiation of MEL cells. CRISPR/Cas9 genome editing of the Myrlin transcription start site at the -81kb enhancer reduced both Myrlin and Myb expression. The deletion of Myrlin TSS reduces the occupancy of LDB1, which mediates chromatin looping, and compromises long-range contacts between the Myb promoter and enhancer and RNA Pol II occupancy decreases across the Myb locus. In contrast, silencing of Myrlin using CRISPRi similarly reduced both Myrlin and Myb expression but left the Myb enhancer hub undisturbed, separating chromatin looping from transcription activation of Myb. In unedited cells, we found that Myrlin interacts with MLL1 complex, a transcriptional coactivator that plays an essential role in regulating gene expression during hematopoiesis. Myrlin CRISPRi compromised MLL1 occupancy in the Myb locus and decreased CDK9 and RNA Pol II binding. Myrlin CRISPRi further resulted in pausing of RNA Pol II in the Myb first exon/intron. These data suggest that Myrlin directly participates in activating Myb transcription by recruiting MLL1.