Loop Extrusion Process Research Articles

Real-time imaging of DNA loop extrusion by condensin.

It has been hypothesized that SMC protein complexes such as condensin and cohesin spatially organize chromosomes by extruding DNA into large loops. We directly visualized the formation and processive extension of DNA loops by yeast condensin in real time. Our findings constitute unambiguous evidence for loop extrusion. We observed that a single condensin complex is able to extrude tens of kilobase pairs of DNA at a force-dependent speed of up to 1500 base pairs per second, using the energy of adenosine triphosphate hydrolysis. Condensin-induced loop extrusion was strictly asymmetric, which demonstrates that condensin anchors onto DNA and reels it in from only one side. Active DNA loop extrusion by SMC complexes may provide the universal unifying principle for genome organization.

Osmotic mechanism of the loop extrusion process.

The loop extrusion theory assumes that protein factors, such as cohesin rings, act as molecular motors that extrude chromatin loops. However, recent single molecule experiments have shown that cohesin does not show motor activity. To predict the physical mechanism involved in loop extrusion, we here theoretically analyze the dynamics of cohesin rings on a loop, where a cohesin loader is in the middle and unloaders at the ends. Cohesin monomers bind to the loader rather frequently and cohesin dimers bind to this site only occasionally. Our theory predicts that a cohesin dimer extrudes loops by the osmotic pressure of cohesin monomers on the chromatin fiber between the two connected rings. With this mechanism, the frequency of the interactions between chromatin segments depends on the loading and unloading rates of dimers at the corresponding sites.

Compaction and Segregation of Sister Chromatids by Loop-Extruding Enzymes

During cell division, two copies of each chromosome are segregated from each other and compacted more than hundred-fold into the canonical X-shaped structures. According to earlier microscopic observations and the recent Hi-C study, mitotic chromosomes are compacted into arrays of consecutive loops of ∼100 kb. Mechanisms leading to formation of such loop arrays are largely unknown. It has been proposed that SMC complexes involved in chromosome condensation can extrude chromatin loops, leading to formation of arrays of consecutive loops. Here, we use computer simulations to test whether the proposed loop-extruding activity of SMCs could compact and segregate sister chromatids. First, we model the system of loop-extruding SMCs on a chromatin fiber and show that it self-organizes into an array of consecutive dynamic loops. The structure of this array depends on microscopic properties of loop-extruding SMCs and can be predicted with a simple analytical model. Second, we model the process of loop extrusion in 3D and show that, coupled with the topo II strand-passing activity, it leads to robust compaction and segregation of sister chromatids. We show that loop-extruding proteins transform individual chromatids into bottle-brush structures consistent with the microscopic observations and Hi-C-based models. These bottle-brush chromatids repel each other allowing topo II to disentangle them. This mechanism of chromosomal condensation and segregation does not require additional proteins or specific DNA markup and is robust against variations in SMC number and properties.

Chromosome Compaction by Active Loop Extrusion

During cell division, chromosomes are compacted in length by more than a 100-fold. A wide range of experiments demonstrated that in their compacted state, mammalian chromosomes form arrays of closely stacked consecutive ∼100 kb loops. The mechanism underlying the active process of chromosome compaction into a stack of loops is unknown. Here we test the hypothesis that chromosomes are compacted by enzymatic machines that actively extrude chromatin loops. When such loop-extruding factors (LEF) bind to chromosomes, they progressively bridge sites that are further away along the chromosome, thus extruding a loop. We demonstrate that collective action of LEFs leads to formation of a dynamic array of consecutive loops. Simulations and an analytically solved model identify two distinct steady states: a sparse state, where loops are highly dynamic but provide little compaction; and a dense state, where there are more stable loops and dramatic chromosome compaction. We find that human chromosomes operate at the border of the dense steady state. Our analysis also shows how the macroscopic characteristics of the loop array are determined by the microscopic properties of LEFs and their abundance. When the number of LEFs are used that match experimentally based estimates, the model can quantitatively reproduce the average loop length, the degree of compaction, and the general loop-array morphology of compact human chromosomes. Our study demonstrates that efficient chromosome compaction can be achieved solely by an active loop-extrusion process.

Ciprofloxacin for treating urethral gonorrhoea in men.

The effectiveness of a single oral dose of ciprofloxacin in eradicating urethral gonorrhoea was assessed in 18 men who received 250 mg and 26 men who were given 100 mg. All patients, including two infected with beta lactamase (penicillinase) producing strains of Neisseria gonorrhoeae (PPNG), were cured. The drug had no effect on infection with Chlamydia trachomatis or on the incidence of post gonococcal urethritis. Ciprofloxacin may be useful in patients hypersensitive to penicillins and cephalosporins, and the drug may also be useful in urethral gonorrhoea caused by PPNG strains.