The vast length of DNA in every cell must be meticulously organized to fit within the microscopic nucleus. This packaging is a dynamic process that allows the cell to access genetic information as needed. A primary mechanism in this folding process is cohesin loop extrusion, where a protein complex actively shapes DNA into functional loops. Understanding this process reveals how cells control which genes are turned on or off, ensuring proper function and development.
Understanding the Cohesin Complex
At the heart of DNA organization is cohesin, a molecular machine from the Structural Maintenance of Chromosomes (SMC) family of proteins. Its core is a ring-like structure formed by four main protein subunits. Two of these, SMC1 and SMC3, are long proteins that connect at one end through a flexible “hinge” domain, forming a V-shape. The other ends of these SMC proteins feature head domains that use ATP for energy.
This V-shaped structure is closed into a complete ring by a third component, a kleisin subunit called RAD21. RAD21 acts as a clasp, bridging the two head domains of the SMC proteins. The fourth core subunit, a STAG protein, attaches to RAD21 and helps regulate the complex’s function. This assembly creates a ring large enough to physically encircle DNA strands.
The interfaces where the subunits connect, particularly where RAD21 binds to the SMC heads, can open and close. This gating mechanism allows DNA to enter and exit the cohesin ring. This process is fundamental to its role in holding DNA strands together and actively reshaping the genome through loop extrusion.
How Cohesin Forms DNA Loops
The process of forming DNA loops begins when the cohesin ring is loaded onto a DNA strand, a step facilitated by a protein complex called NIPBL-MAU2. Once loaded, cohesin begins to actively translocate along the DNA, reeling in the fiber from both sides to enlarge a loop. This motor activity is powered by ATP hydrolysis at the SMC head domains, which drives changes in the cohesin complex that pull the DNA through its ring.
This active reeling of DNA is often compared to a winch pulling in a rope, causing the loop of DNA it holds to grow progressively larger. Single-molecule imaging has directly visualized this process, showing a single cohesin complex extruding thousands of base pairs of DNA. The cycle is regulated and involves both loading and removal; a protein called WAPL is responsible for releasing cohesin from the DNA, ensuring that loops are not permanent.
The growth of these DNA loops is not limitless. Loop extrusion is halted when the cohesin complex encounters specific barrier elements on the DNA. The most well-known of these are sites bound by the protein CTCF. When an extruding cohesin complex meets a CTCF protein bound in a specific orientation, its progress is blocked, establishing a defined boundary that sets the loop’s final size and position.
Shaping the Genome Through Loop Extrusion
Cohesin’s formation of DNA loops organizes the genome into a functional, three-dimensional structure by establishing distinct architectural units called Topologically Associating Domains (TADs). TADs are regions where internal DNA sequences interact more frequently with each other than with sequences in neighboring domains. These domains form as cohesin extrudes a DNA loop that is then anchored at its base by boundary elements like CTCF.
The creation of TADs directly impacts gene regulation. By folding the DNA, loop extrusion brings distant genetic elements into close physical proximity. For example, an enhancer—a DNA region that increases gene transcription—might be located far from its target gene’s promoter. Loop extrusion can bring the enhancer and promoter together, allowing regulatory proteins to interact and activate the gene.
This precise spatial organization is important for cellular function, differentiation, and maintaining cell identity. By packaging the genome into insulated neighborhoods, TADs ensure that enhancers activate only their intended target genes. This prevents inappropriate interactions with genes in adjacent domains, allowing different cell types to express unique gene sets from the same genetic blueprint.
Impact of Cohesin Loop Extrusion Errors
Malfunctions in the cohesin complex or its regulatory machinery can significantly impact genome architecture and human health. Errors in loop extrusion disrupt chromosome folding, leading to altered gene expression and developmental disorders. These conditions, which stem from mutations in genes for cohesin or its regulators, are known as cohesinopathies.
The most well-studied cohesinopathy is Cornelia de Lange Syndrome (CdLS). This rare genetic disorder is characterized by a wide range of developmental abnormalities, including growth delays, intellectual disability, and distinctive facial features. The majority of CdLS cases are caused by mutations in the NIPBL gene, which codes for the protein responsible for loading cohesin onto DNA. With impaired cohesin loading, loop extrusion is compromised, leading to a disorganized genome and widespread gene dysregulation.
Mutations in other cohesin-related genes, such as SMC1A, SMC3, and RAD21, are also linked to CdLS, typically resulting in milder forms of the syndrome. The disruption of proper TAD boundaries and enhancer-promoter contacts is a central molecular defect in these conditions.