LOUP Mediates Opposing Regulatory Effects of RUNX 1 and RUNX 1-ETO in 1 t ( 8 ; 21 ) AML 2

45 The mechanism underlying cell type-specific gene induction conferred by ubiquitous transcription 46 factors as well as disruptions caused by their chimeric derivatives in leukemia is not well understood. 47 Here we investigate whether RNAs coordinate with transcription factors to drive myeloid gene 48 transcription. In an integrated genome-wide approach surveying for gene loci exhibiting concurrent 49 RNAand DNA-interactions with the broadly expressed transcription factor RUNX1, we identified the 50 long noncoding RNA LOUP. This myeloid-specific and polyadenylated lncRNA induces myeloid 51 differentiation and inhibits cell growth, acting as a transcriptional inducer of the myeloid master 52 regulator PU.1. Mechanistically, LOUP recruits RUNX1 to both the PU.1 enhancer and the promoter, 53 leading to the formation of an active chromatin loop. In t(8;21) acute myeloid leukemia, wherein RUNX1 54 is fused to ETO, the resulting oncogenic fusion protein RUNX1-ETO limits chromatin accessibility at the 55 LOUP locus, causing inhibition of LOUP and PU.1 expression. These findings highlight the important 56 role of the interplay between cell type-specific RNAs and transcription factors as well as their oncogenic 57 derivatives in modulating lineage-gene activation and raise the possibility that RNA regulators of 58 transcription factors represent alternative targets for therapeutic development. 59 60 INTRODUCTION 61 Lineage-control genes that dictate cellular identities are often expressed in dynamic and 62 hierarchical patterns.1-3 Disturbance of these established normal patterns results in anomalies.4 In the 63 blood system, the ETS-family transcription factor PU.1 (also known as Spi-1) is essential for myeloid 64 differentiation. PU.1 is silent in most tissues and cell types but expressed at highest levels in myeloid 65 cells including granulocytes and monocytes.5 Downregulation of PU.1 impairs myeloid cell 66 differentiation leading to acute myeloid leukemia (AML).6,7 PU.1 is a major downstream transcriptional 67 was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this preprint (which this version posted July 25, 2020. ; https://doi.org/10.1101/2020.07.24.220020 doi: bioRxiv preprint