The lncRNA DUBR is regulated by CTCF and coordinates chromatin landscape and gene expression in hematopoietic cells [ChIP-Seq]

Master hematopoietic transcription factors (TFs) and long non-coding RNAs (lncRNAs) coordinate shaping lineage-specific gene expression programs during hematopoietic differentiation. The architectural protein CCCTC-binding factor (CTCF) has emerged as a pivotal regulator of gene expression in cell differentiation. However, the relationship and its regulatory effect of CTCF on lncRNA genes in hematopoiesis remains elusive. We demonstrated that CTCF constrains DUBR transcription throughout erythroid differentiation. DUBR is highly expressed in human hematopoietic stem and progenitor cells (HSPC) but depleted in erythroblasts. DUBR perturbation dysregulates the expression of hematopoietic-erythroid cell differentiation genes and facilitates genome-wide activation of regulatory elements. A genomic map of RNA occupancy revealed that DUBR directly regulates a set of TFs involved in regulating hematopoietic differentiation, including the erythroid repressor HES1, which in turn targets a subset of regulatory elements of DUBR-dysregulated genes. Our results support the role of DUBR as a regulator of a hematopoietic differentiation gene program, by coordinating the expression of TFs and influencing the chromatin regulatory landscape. Overall design: To analyze the contribution of lncRNA DUBR in hematopoietic gene expression, we targeted DUBR by CRISPR-Cas9-mediated gene editing in K562 cells and analyzed histone marks associated with regulatory elements.