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Cells Use Loop Extrusion to Keep DNA Optimized

Photo credit: Gelpgim22, CC BY-SA 3.0 , via Wikimedia Commons.

Loop extrusion is a technique used in various machines for repairs and maintenance. Here are a few examples from the early days of computing and other technologies:

  • Audio technicians would extrude audio tapes in reels and cassettes to fix wrinkles or splice broken ends together.
  • Typists would pull out segments of ink reels to straighten kinks or to wind the tape past defective spots.
  • Computer operators could spin the reels of computer tapes in opposite directions to extrude loops for inspection or repair of tape, or to re-align the tape around guide posts.

These operations could be done by hand or could sometimes be automated. The general principle is that loop extrusion allows for inspection and repair when a physical tape has a problem. 

In high-speed operations with computer tape, loop extrusion was also a built-in mechanism to buffer differences in tension between the two reels. Rapid changes in direction would otherwise have broken the tape. In some advanced computer tape systems, the loops could be several feet long. Operators could see the loops taking up the slack as the reels stopped and started rapidly.

Distant Memories

These examples are distant memories to those who worked on computers and audio systems in days before everything migrated to hard drives, SSDs, MP3 files, and cloud computing. Nevertheless, any time a physical tape must move rapidly, loop extrusion is a good idea. It turns out that cells had been using loop extrusion long before humans thought of it.

In Nature, Arnould et al. report that cells use “Loop extrusion as a mechanism for formation of DNA damage repair foci.” Double-stranded breaks are particularly dangerous if not repaired, leading to cancer and cell death. The team found that molecular machines latch onto the DNA on both sides of the break and extrude loops that expose the DNA to phosphorylation machines necessary to call in other damage repair machines. The loops can be huge, covering a million base pairs.

The repair of DNA double-strand breaks (DSBs) is essential for safeguarding genome integrity. When a DSB forms, the PI3K-related ATM kinase rapidly triggers the establishment of megabase-sized, chromatin domains decorated with phosphorylated histone H2AX (γH2AX), which act as seeds for the formation of DNA-damage response foci. It is unclear how these foci are rapidly assembled to establish a ‘repair-prone’ environment within the nucleus. Topologically associating domains are a key feature of 3D genome organization that compartmentalize transcription and replication, but little is known about their contribution to DNA repair processes. Here we show that topologically associating domains are functional units of the DNA damage response, and are instrumental for the correct establishment of γH2AX–53BP1 chromatin domains in a manner that involves one-sided cohesin-mediated loop extrusion on both sides of the DSB. We propose a model in which H2AX-containing nucleosomes are rapidly phosphorylated as they actively pass by DSB-anchored cohesin. Our work highlights the importance of chromosome conformation in the maintenance of genome integrity and demonstrates the establishment of a chromatin modification by loop extrusion. [Emphasis added.]

A General Principle in Genome Maintenance

In the same issue of Nature, Leonid A. Mirny found this case fascinating. It amplifies what he had known about loop extrusion in the formation of chromosomes. 

Cells neatly compact their spaghetti of DNA in several ways. In cells with a nucleus, the DNA is first wrapped around cores of histone proteins to make structures called nucleosomes, which together form a chromatin fibre that looks like beads on a string. Loop extrusion is the subsequent compaction process, whereby a molecular motor binds a chromatin fibre and reels it in from the sides, forcing out a progressively larger loop in between (Fig. 1a).

A look at Fig. 1a shows something very interesting: gears that do the extruding. Mirny does not mean to suggest that the molecular machines that do loop extrusion are actual gears. It’s just a handy way to show that molecular motors turning in opposite directions can extrude a loop. That’s apparently what SMC motors do (“Structural Maintenance of Chromosomes”). This family of enzymes in the nucleus, “once thought to be passive rings or staples — are actually loop-extruding motors.”

Meanwhile, Elsewhere in the Nucleus

Looking beyond the cases of DSB repair and SMC action, Mirny sees evidence of loop extrusion elsewhere in the nucleus. It might even by a general principle behind several otherwise mysterious processes.

Cellular processes often multitask. So, could this ubiquitous mechanism for weaving the genome have other functions? During cell division, the formation of loops is key to compacting chromosomes to enable accurate passing of genetic material into daughter cells. But the role of extrusion during interphase — the period during which cells duplicate their DNA and grow in preparation for the next division — is yet to be understood.

There are several possibilities. One of these is in regulating gene expression: extrusion can bring together distant genomic elements (such as enhancers and promoters, which regulate transcription) that are not separated by a CTCF barrier. Such barriers can also turn extrusion into genomic tracking. To explain, when a cohesin protein stalls on one CTCF, it can continue reeling DNA in on the other side, thereby tracking over long genomic regions….

Unveiling this smart way of buffering DNA strands against breaks and also inspecting them quickly is thus leading to new insights into the physical mechanisms that cells use to maintain their genetic “tapes.” He notes that another study showed bacteria able to extrude at a rate of 150,000 bases per minute.

Cohesin, he says, should no longer be thought of as a passive ring around the DNA. It well could be a set of motors using loop extrusion for its varied functions.

It is also possible that the roles of cohesin and other SMCs in repairing breaks go beyond γH2AX spreading. Cohesin has long been implicated in DNA repair, but was thought to be a passive ring, keeping together duplicated chromosomes for repair. The findings suggest more-active roles, for example in enabling the search for a region of DNA that can act as a template for repair. What’s more, the recruitment of SMCs to breaks, and the central role of cohesin in other processes that deal with DSBs (such as a type of division called meiosis and immunoglobulin-gene regulation), suggests that these motors might be important in detecting and managing broken DNA during many normal cellular processes. So, SMC complexes — master weavers of the genome— might be in charge not only of making loops, but also of finding and tying together broken fibres.

An Ingenious Invention

A vista opens for viewing motors in the nucleus as loop extruders with multiple functions: taking care of double-stranded breaks, compacting the genome, bringing promoters and enhancers together, and ensuring “structural maintenance of chromosomes.” How any primitive cell could have survived without these functions is hard to imagine.

Cells mastered loop extrusion as an ingenious way of inspecting, repairing, and compacting the genome. They have mastered the technique of loop extrusion far beyond what any computer operator, typist, or audio engineer ever imagined. When one considers that DNA is not a solid tape but a double helix with delicate hydrogen bonds holding the strands together, it becomes apparent just how careful these motors must be to perform their tasks rapidly and flawlessly almost all the time. 

Loop extrusion represents another physical mechanism, using molecular motors, that humans can relate to from their own creativity with handling tapes — only the cell’s mechanisms are far more sophisticated than anything humans ever made. It is one more wonder that should make us stand in awe of the designer’s intelligence and wisdom.