Myeloid leukemia vulnerabilities at CTCF-enriched long noncoding RNA loci

The noncoding genome presents a largely untapped source of biological insights, including thousands of long noncoding RNA (lncRNA) loci. While some produce bona fide lncRNAs, others exert transcript-independent cis-regulatory effects, and a lack of predictive features renders mechanistic dissection challenging. Here, we describe MYNRL15, a CTCF-enriched lncRNA locus and pan-myeloid leukemia dependency initially identified by expression-guided CRISPR interference screens. We show that accessibility and integrity of the MYNRL15 locus is required for myeloid leukemia maintenance; its perturbation selectively impairs acute myeloid leukemia (AML) cells compared to hematopoietic stem and progenitor cells in vitro, and depletes AML xenografts in vivo. While the MYNRL15 transcript and neighboring protein-coding genes appear dispensable, dense CRISPR tiling of the locus revealed two crucial candidate cis-regulatory DNA elements which drive the perturbation phenotype. Disruption of these elements triggers the formation of a tumor-suppressive, long-range chromatin interaction. By integrating transcriptome profiling with a CRISPR-Cas9 knockout screen of genes from the gained interaction region, we pinpointed two downregulated, potent cancer dependency genes as effectors of MYNRL15 disruption: WDR61 and IMP3. Finally, guided by distinctive features of the MYNRL15 locus, we find that elevated CTCF density characterizes a set of lncRNA loci enriched in leukemia vulnerabilities (22.6-24.2% essentiality rate). A catalog of CTCF-enriched lncRNA loci (C-LNCs) in 18 cell types representing different cancer entities and tissues is provided with this study, towards refining the search for noncoding oncogenic vulnerabilities in leukemia and other malignancies.