"LDB1 Contributions to Enhancer Chromatin Looping and Erythroid Gene Activation"

Distal enhancers control cell-specific transcriptomes through contacting target genes. Interactions between lineage specific activators bound to enhancers and target promoters can account for the cell-type specificity of gene activation. One example is the dimerization of LDB1 bound at the -globin LCR and gene promoter as part of an erythroid complex including GATA1, LMO2 and TAL1. The dimerization domain of LDB1 is both necessary and sufficient to mediate this chromatin looping. Moreover, the LDB1 dimerization domain provides a transcription activating function through which it is required for recruitment of RNA pol II to a looped -globin locus. Genome-wide mapping in murine primary hematopoietic cells revealed a large cohort of erythroid genes regulated by LDB1, suggesting it can function broadly to affect lineage commitment, potentially through enhancer looping. However, only about 15% of erythroid genes have promoters bound by the LDB1 complex. We identified a subset of erythroid genes with CTCF-bound promoters that interact with LDB1-bound known or putative enhancers. LDB1 and CTCF interact directly to mediate enhancer-gene contact. CRISPR-Cas9 deletion of select enhancers compromises gene transcription, validating enhancer function and generalizing the contribution of LDB1-CTCF interaction to enhancer looping. Thus, in addition to self-interaction, LDB1 can co-opt CTCF into cell type specific enhancer looping interactions to specify an erythroid transcriptome.