Stepwise reorganization of chromosome conformation and nuclear organization during stem cell differentiation [RNA-Seq]

Compared with differentiated cells, pluripotent stem cells exhibit markedly distinct nuclear architecture at multiple levels, including chromosome folding, lamina association, histone modification landscapes and nuclear body organization. Although individual aspects of this reorganization have been characterized, how and in what order these features are remodeled as cells commit to a lineage remains poorly understood.

Here, we temporally map nuclear reorganization across five stages of an in vitro differentiation of human embryonic stem cells through definitive endoderm and hepatoblast intermediates into hepatocytes. By integrating Hi-C, RNA-seq, ATAC-seq, ChIP-seq, and CUT&RUN data, we establish a genome-wide framework linking structural, epigenetic, and transcriptional changes across differentiation. Combined with immunofluorescence imaging, chromosome painting, liquid chromatin Hi-C (LC-Hi-C) and physical modeling, we show that nuclear reorganization proceeds in a stepwise and temporally ordered manner through three major transitions.