LDB1 regulates gene expression and chromatin structure in pluripotency and lineage differentiation

Chromatin organization is a pivotal factor in stem cell pluripotency and differentiation. However, the role of enhancer looping protein LDB1 in stem cells has not been explored. We generated Ldb1(-/-) embryonic stem cells (ESC) using CRISPR/Cas9 editing and observed a reduction in key stem cell factors SOX2 and KLF4 upon LDB1 loss. Embryoid bodies (EB) derived from Ldb1(-/-) ESC displayed reduced expression of lineage-specific markers and impaired ability to undergo terminal differentiation to erythroblasts. Differential gene expression, including of the Lin28-mediated self-renewal pathway genes, was observed between WT and Ldb1(-/-) ESC and EB but was most pronounced after differentiation to erythroblasts. LDB1 occupied super enhancers, including those of pluripotency genes, in ESC together with pluripotency factors. LDB1 loss resulted in globally decreased chromatin accessibility in ESC and EB. Conditional LDB1-deficient mice displayed reduced hematopoietic stem cell markers on bone marrow cells, and dysregulation of the Lin28 pathway. Thus, LDB1 function is critical for ESC and EB development and becomes progressively more important during differentiation to erythroblasts.