Convergent gene pairs restrict chromatin looping in Dictyostelium discoideum, acting as directional barriers for extrusion

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 features of chromatin spatial organization remain unknown. Here, we report that the Dictyostelium 3D genome is organized into largely consecutive, non-hierarchical and weakly insulated loops positionally conserved at the onset of multicellular development. The transcription level within loops tends to be higher than in adjacent regions. Loops frequently contain functionally linked genes and genes which coherently change expression level during development. Genes at loop anchors are predominantly in the convergent orientation. Our data suggest that the loop profile may arise from the interplay between transcription and cohesin-driven chromatin extrusion. In particular, a convergent gene pair serves as a bidirectional extrusion barrier or a “diode” that controls passage of the cohesin extruder by relative transcription level of paired genes. Refer to individual Series