Principles of chromosome loop formation by cohesin and condensin protein complexes

Abstract

Chromosome polymers from all organisms must be compacted to fit inside their cells while remaining accessible for other cell biological processes such as transcription. Chromosome compaction is achieved by a process of DNA looping by a family of protein complexes called the Structural Maintenance of Chromosomes (SMC). Looping is important not only for chromosome compaction, but also in the process of DNA damage repair, regulation of gene expression, and cell division. It remained unclear, however, how SMC complexes create chromosomal loops. For example: Are they active molecular complexes (using energy to drive DNA looping), or passive (facilitating chromosomal looping by a diffusive mechanism, or by coupling with other enzymes)? What are the rules by which SMC complexes engage with the chromosomal substrate? How do SMC complexes interact with one another? And how do they interact with other proteins, such as RNA polymerases? This thesis aims to elucidate the dynamics by which SMC complexes organize chromosomes in living cells. Herein there are four projects, presented in chronological order of publication, which use a combination of experimental data coming from chromosome conformation capture (Hi-C), chromatin immunoprecipitation (ChIP-seq) experiments, theory and polymer simulations to address the questions above. We find that SMC complexes extrude DNA loops in an energy-driven process, we develop methodologies to infer the sizes and numbers of SMC complex-mediated loops from Hi-C data, and we uncover an unexpected, but seemingly general principle of DNA organization by SMCs: the ability to bypass barriers and points of collision.