Mechanism, Regulation and Functions of DNA Loop Extrusion by SMC complexes

Introduction

Life and evolution of organisms relies on the maintenance, integration, propagation, and readout of genetic information. This information is stored in chromosomes that have a specific three-dimensional structure, a condensed yet accessible form of DNA that is dynamically folded during the lifespan of cells.

The Mystery of DNA Folding

How DNA is folded within chromosomes has, however, remained a mystery. It has been proposed that this is achieved by a process of loop extrusion in which SMC (Structural Maintenance of Chromosomes) complexes that are multi-subunit ATPases present in all kingdoms of life, including condensin and cohesin, reel DNA into loops, thereby organizing genomic DNA into higher-order structures.

Recent Discoveries

Recent in vitro single-molecule studies, stimulated by our initial discovery on condensin, provided direct evidence that both condensin and cohesin can indeed generate chromatin loops by extrusion. However, the most fundamental questions relating to this process remain unanswered:

1. What is the molecular mechanism of loop extrusion?
2. How is this process regulated?
3. What are the functional roles of SMC-mediated loop extrusion beyond condensation?

Research Objectives

To address these questions, we will synergistically combine our single-molecule loop extrusion assay with correlative light and electron tomography and force spectroscopy to reveal both dynamic and structural aspects of loop extrusion and SMC proteins.

Specific Aims

Specifically, we will resolve:

• How SMC complexes function as molecular motors
• How regulatory factors modulate the kinetics of loop extrusion
• How loop extrusion impacts cellular functions like chromosome segregation and gene recombination, all at the single molecule level.

Long-term Impact

In the long term, our findings will provide vital insights into the basic packaging structure of the genome which directly governs its biological function.