Transcription and loop extrusion cooperatively shape the 3D genome of developing slime mold Dictyostelium discoideum [RNA-seq]

Dictyostelium discoideum is a unicellular slime mold developing into a multicellular fruiting body upon starvation. Development is accompanied by large-scale shifts in gene expression program, but underlying rearrangements of chromatin structure remain unknown. Here, we report a unique Dictyostelium 3D genome organization represented by largely consecutive, non-hierarchical and weakly insulated loops of diverse morphology conserved at the onset of multicellular development. Loops are chromosomal neighborhoods facilitating transcription and frequently containing functionally-linked genes which coherently change expression level during development. Loop anchors are enriched with convergent gene pairs, putative enhancers and boundaries of synteny gene blocks that point at their role in genome function and evolution. Our data suggest that the loop profile arises from the interplay between transcription and cohesin-driven chromatin extrusion. In this confunction, a convergent gene pair serves as a “diode” effectively passing the extruder from upstream or downstream direction in dependence on transcription level of the paired genes. Overall design: Total RNA-seq on developing D. discoideum