Myeloid leukemia dependency MYNRL15 exemplifies class of CTCF-bound lncRNA loci [ATAC-Seq]

The noncoding genome presents a largely untapped source of new biological insights, including thousands of long noncoding RNA (lncRNA) loci. While some produce bona fide functional transcripts, others exert transcript-independent regulatory effects, and the lack of predictive features renders mechanistic dissection a major challenge. Here, we describe MYNRL15: a noncoding regulatory locus on chromosome 15 and pan-myeloid leukemia dependency identified by a CRISPR screen of lncRNA signatures from hematopoietic stem and progenitor cells (HSPCs) and acute myeloid leukemia (AML) samples We demonstrate that the loss of cis-regulatory DNA elements in the locus, rather than its transcriptional products, drives its perturbation phenotype, triggering a global downregulation of oncogenic pathways, coordinated dysregulation of chromosome 15 neighborhoods, and formation of a tumor-suppressive, long-range chromatin interaction with the base of a distal loop. In addition, MYNRL15 perturbation selectively impaired primary AML blasts over normal HSPCs in vitro, and depleted patient-derived xenografts in vivo, providing evidence for oncogenic vulnerabilities at chromatin-regulating, noncoding loci. MYNRL15 is characterized by elevated CTCF binding, low expression, and short span - features shared by hundreds of lncRNA genes, nearly half of which associate with clinical aspects in AML patient cohorts. We propose these as a new class of functional genetic elements carrying both therapeutic potential for AML and profound implications for cancer pathophysiology in general, as exemplified by MYNRL15. NG Capture-C combines 3C library preparation with oligonucleotide capture to enrich for interactions involving regions of interest. In this case, one of the two cis-regulatory elements in MYNRL15 (C1) was used as the viewpoint. This method was applied to K562 and ML-2 cells, with and without Cas9-mediated MYNRL15 perturbation, as well as to differentiated monocytic cells.