Journal Article

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

Hansen, Anders S, Cattoglio, Claudia, Darzacq, Xavier, Tjian, Robert, Pustova, Iryna

2017

Overview

Folding of mammalian genomes into spatial domains is critical for gene regulation. The insulator protein CTCF and cohesin control domain location by folding domains into loop structures, which are widely thought to be stable. Combining genomic and biochemical approaches we show that CTCF and cohesin co-occupy the same sites and physically interact as a biochemically stable complex. However, using single-molecule imaging we find that CTCF binds chromatin much more dynamically than cohesin (~1–2 min vs. ~22 min residence time). Moreover, after unbinding, CTCF quickly rebinds another cognate site unlike cohesin for which the search process is long (~1 min vs. ~33 min). Thus, CTCF and cohesin form a rapidly exchanging 'dynamic complex' rather than a typical stable complex. Since CTCF and cohesin are required for loop domain formation, our results suggest that chromatin loops are dynamic and frequently break and reform throughout the cell cycle. A human cell contains about 2 meters of DNA tightly packed in a compartment called the nucleus. Within the space inside the nucleus, different parts of the DNA fold into distinct bundles known as domains. These domains are important for organising the genome and are crucial for regulating gene expression, by stimulating specific DNA segments to activate certain genes. Previous research has shown that DNA segments within the same domain frequently interact, whereas DNA segments in different domains rarely do. The domains are often folded into loops that are held together by a ring-shaped protein complex called cohesin, while another protein called CTCF positions cohesin and thereby sets the boundaries between the domains. Some mutations are known to disrupt these boundaries, which allows certain DNA segments to activate the wrong genes. This can lead to cancer or cause defects when embryos are developing. However, we do not currently understand how these domains are formed or maintained. In particular, it was unclear whether these loop domains are stable or dynamic structures. Hansen et al. addressed these questions in embryonic stem cells from mice and human cancer cells. It was found that cohesin and CTCF form a complex that binds to the DNA and likely holds the loops together. In further experiments, single molecules of cohesin and CTCF were tracked inside cells using super-resolution microscopy. The results showed that CTCF and cohesin bind to DNA with different dynamics: CTCF binds the DNA for about a minute, whereas cohesin binds the DNA for about 20–25 minutes. Once CTCF detaches from DNA, it quickly rebinds DNA at another site, but cohesin takes much longer. These observations suggest that rather than remaining static, chromatin domains are held together by a dynamic protein complex, with a molecular composition that exchanges over time. This results suggests that DNA loop domains, which were generally assumed to be very stable anchor points, are in fact highly dynamic structures that frequently fall apart and reform. The next challenge will be to understand how the dynamic nature of these loop domains contribute to gene regulation. This may, one day, enable us to manipulate the domains to correct faulty folding of DNA in cancer and other diseases.

• Publisher: eLife Sciences Publications Ltd,eLife Sciences Publications, Ltd
• Subject: Animals / Binding sites / biophysics / Biophysics and Structural Biology / CCCTC-Binding Factor - metabolism / Cell cycle / Cell Cycle Proteins - metabolism / Cells, Cultured / Chromatin / Chromatin - metabolism / Chromosomal Proteins, Non-Histone - metabolism / Cohesin / Cohesins / CTCF / Deoxyribonucleic acid / DNA / Experiments / Gene regulation / Genes and Chromosomes / genome organization / Genomes / imaging / Kinetics / Labeling / Ligands / Mice / Protein Binding / Protein folding / Protein Interaction Mapping / Proteins / single-molecule / Stem cells / Tumors