Transcriptional clusters follow a conserved condensation-dispersal sequence during stem cell differentiation

Abstract

Spatiotemporal organization of transcription is essential for organism development. Most eukaryotic genes are transcribed by RNA polymerase II (Pol II). In stem cells, Pol II forms prominent clusters, which gradually disappear during differentiation, such that only smaller clusters remain. Here, we ask whether the formation and loss of large Pol II clusters is a stereotypical process explicable by changes in the Pol II transcriptional state during differentiation. We assess clusters by super-resolution microscopy in differentiating mouse embryonic stem cells, sperm precursor formation in fruit flies, and germ layer induction in zebrafish. In all cases, Pol II clusters first become larger and rounder, then unfold, and finally disperse into small clusters. These shape changes are accompanied by initial increase in recruited Pol II, subsequent transition into transcript elongation, and finally reduction of active enhancers. We reproduce these observations using a biophysical surface condensation model, where enhancers support Pol II cluster formation, and transcriptional activity unfolds clusters. Our work indicates that changes in enhancer marks and transcriptional activity during differentiation define a stereotyped trajectory through a generally applicable space of cluster shapes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=189 HEIGHT=200 SRC="FIGDIR/small/547621v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1fb769borg.highwire.dtl.DTLVardef@27f6a0org.highwire.dtl.DTLVardef@1b0ab7corg.highwire.dtl.DTLVardef@1ca932d_HPS_FORMAT_FIGEXP M_FIG C_FIG