RNA polymerases as moving barriers to condensin loop extrusion

Area of Science:

• Molecular Biology
• Genomics
• Biophysics

Background:

• Structural Maintenance of Chromosome (SMC) condensin complexes organize chromosomes via DNA loop extrusion in both prokaryotes and eukaryotes.
• Sister chromatid separation during mitosis occurs alongside ongoing transcription in rapidly dividing bacterial cells.
• The interference of transcription with condensin-mediated loop extrusion is not well understood, though high transcription sites may directionally influence it.

Purpose of the Study:

• To quantitatively investigate the mechanisms of interaction between condensin and elongating RNA polymerases (RNAPs).
• To determine how transcription impacts the condensin loop-extrusion process in bacteria.
• To propose a model for how condensin bypasses RNAPs during DNA loop extrusion.

Main Methods:

• Quantitative investigation of condensin-RNAP interactions.
• Chromosome conformation capture (3C) experiments.
• Chromatin immunoprecipitation (ChIP) assays following transcription inhibition and RNAP degradation.
• Development of quantitative models for DNA loop extrusion.

Main Results:

• RNAPs act as steric barriers that can push and interact with condensins.
• Condensins must bypass transcribing RNAPs within seconds at rRNA genes (1-2s) and protein-coding genes (∼10s).
• Individual RNAPs have minimal effect, but long, highly transcribed operons significantly impede loop extrusion.
• Bacterial condensin loop extrusion involves two independent, uncoupled motor activities that enlarge loops by bypassing steric barriers.

Conclusions:

• Condensin-mediated DNA loop extrusion is quantitatively linked to transcription.
• A mechanism is proposed where condensin motors independently bypass RNAPs during loop extrusion.
• Findings are relevant to genome organization in bacteria and higher eukaryotes.