Chromatin accessibility dynamics during kidney organoid induction from human embryonic stem cells

Human kidney development remains incompletely characterized at the level of chromatin accessibility. Here, we investigate chromatin accessibility dynamics (CAD) during the differentiation of human embryonic stem cells (hESCs) into kidney organoids (E-iKOs). Time-course ATAC-seq reveals progressive remodeling of pluripotency-associated chromatin landscapes toward an intermediate mesoderm state, followed by metanephric mesenchyme specification and early nephron epithelialization. These transitions are accompanied by increased accessibility at genomic regions enriched for binding motifs of transcription factors, including SIX, HOX, LHX, PAX, EBF, RFX, WT1, HNF1B, and TEAD. Functional analyses demonstrate that HNF1β is required for tubular differentiation, as HNF1β deficiency results in severe defects in tubule formation while podocytes remain detectable. Integrative analysis of chromatin accessibility and time-course transcriptomics further identifies the histone H3K79 methyltransferase DOT1L as a regulator required for nephron progenitor induction and epithelial differentiation. DOT1L deficiency is associated with widespread alterations in chromatin accessibility and gene expression, particularly at regions enriched for SIX, HOX, PAX, EBF, WT1, HNF1B, and TEAD motifs, accompanied by impaired mesenchymal-to-epithelial transition. Together, this study provides a valuable resource describing chromatin accessibility dynamics during human kidney organoid differentiation and a foundation for future studies of human nephrogenesis in vitro.