LDB1-mediated regulation of gene expression and chromatin structure in development

Authors

• D Dey
• A Swaminathan
• A Leroux
• K Merikangas

Abstract

The Lim domain binding protein 1 (LDB1) is essential for cell identity determination and cell-specific gene expression regulation through promoter-enhancer looping. In erythropoiesis, the activation of the β-globin gene relies on the LDB1 complex, which enables interaction with the distant locus control region (LCR) enhancer. However, the precise mechanisms by which LDB1 contributes to gene regulation and chromatin structure modification during erythrocyte development stages are not well understood. Using CRISPR/Cas9 gene editing, we generated LDB1-deleted mouse embryonic stem cells (ESCs) to investigate LDB1's role in erythropoiesis. LDB1 deletion impaired embryoid body formation and hindered erythrocyte differentiation in ESCs. Knocking out LDB1 significantly reduced the levels of key transcription factors involved in stem cell regulation, including Sox2, Oct4, and KLF4, and revealed an interaction between LDB1 and KLF4. LDB1 deficiency also affected erythrocyte differentiation after ESCs transitioned to embryoid bodies, as indicated by decreased expression of Ter119 and CD71 markers. Additionally, ATAC-sequencing and CUT&TAG analysis showed reduced accessibility and H3K27ac modification at the Sox2 locus following LDB1 deletion. Transcriptomic analysis revealed upregulated expression of Lin28b, a gene typically suppressed during erythroid progenitor differentiation and loss of self-renewal capacity. Moreover, reduced transcription of let-7 microRNA, a Lin28 target, mirrored effects observed with Lin28b overexpression in hematopoietic stem cells. These findings highlight the critical role of LDB1 in maintaining both ESC stemness and promoting differentiation through its influence on gene expression and genome organization. LDB1 may also mediate developmentally timed changes in hematopoietic stem cell self-renewal capacity by regulating Lin28.

Scientific Focus Area: Chromosome Biology

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