A genome-wide analysis identifies DIDO3 binding at active chromatin and topological boundaries in mouse stem cells

While chromatin structure influences gene expression, how chromatin readers exert transcriptional control is still not fully understood. DIDO3, an isoform of the Death Inducer Obliterator protein, has been implicated in cell differentiation and cancer, yet its precise genomic functions are unclear. Here we integrated ChIP-seq, RNA-seq and Hi-C analyses in mouse embryonic stem cells to reveal that DIDO3 predominantly binds to RNA polymerase II at topological domain boundaries and chromatin loops. We demonstrate that DIDO3 interacts with the architectural protein CTCF and that the N-terminal region of DIDO3 (DIDO3 1-528) also co-localizes with the histone marks H3K4me3 and H3K36me3. DIDO3 influences the expression of genes encoding chromatin remodeling components, as well as those involved in transcriptional dynamics and three-dimensional chromatin organization. These findings suggest that DIDO3 is associated with both transcriptional regulation and chromatin organization, with potential implications in terms of cell differentiation and tumorigenesis.