RNA polymerases as moving barriers to condensin loop extrusion

Significance Genomic DNA must be compacted to fit in the cell but must simultaneously remain accessible for transcription. While genome organization influences gene expression, the impact of transcription on genome organization remains to be understood. The process of “loop extrusion” is central to chromosome organization. In bacteria, the condensin SMC complex performs extrusion by translocating along arms of the chromosome. During translocation, condensins encounter bulky transcription machinery, which could interfere with loop extrusion. This work investigates the interplay between 2 important active processes; it demonstrates that extruding SMCs can efficiently bypass transcribing RNA polymerases within mere seconds, thus allowing spatial organization of the transcriptionally active genome, and predicts that extruding SMC complexes have a mechanism to bypass other bulky DNA-bound obstacles. To separate replicated sister chromatids during mitosis, eukaryotes and prokaryotes have structural maintenance of chromosome (SMC) condensin complexes that were recently shown to organize chromosomes by a process known as DNA loop extrusion. In rapidly dividing bacterial cells, the process of separating sister chromatids occurs concomitantly with ongoing transcription. How transcription interferes with the condensin loop-extrusion process is largely unexplored, but recent experiments have shown that sites of high transcription may directionally affect condensin loop extrusion. We quantitatively investigate different mechanisms of interaction between condensin and elongating RNA polymerases (RNAPs) and find that RNAPs are likely steric barriers that can push and interact with condensins. Supported by chromosome conformation capture and chromatin immunoprecipitation for cells after transcription inhibition and RNAP degradation, we argue that translocating condensins must bypass transcribing RNAPs within ∼1 to 2 s of an encounter at rRNA genes and within ∼10 s at protein-coding genes. Thus, while individual RNAPs have little effect on the progress of loop extrusion, long, highly transcribed operons can significantly impede the extrusion process. Our data and quantitative models further suggest that bacterial condensin loop extrusion occurs by 2 independent, uncoupled motor activities; the motors translocate on DNA in opposing directions and function together to enlarge chromosomal loops, each independently bypassing steric barriers in their path. Our study provides a quantitative link between transcription and 3D genome organization and proposes a mechanism of interactions between SMC complexes and elongating transcription machinery relevant from bacteria to higher eukaryotes.