A lariat intron is a looped structure of RNA that forms during the cellular process of gene splicing. For many years, these molecules were considered transient byproducts destined for quick disposal. However, emerging research reveals that some lariats are more stable than previously thought and may have functions of their own. The evolving view of these structures highlights how what was once considered cellular debris is now being investigated for potential biological roles.
Genes, Messages, and Editing: The Basics of Splicing
The instructions for building an organism are stored within DNA in segments called genes. For a gene to be used, its code is copied into a temporary message molecule called pre-messenger RNA (pre-mRNA). In many organisms, including humans, genes contain sections called exons, which hold protein-building instructions, interrupted by non-coding sequences called introns.
Before the RNA message can be used to create a protein, the introns must be removed and the exons stitched together in a process called RNA splicing. This ensures that only the relevant information is sent to the cell’s protein-building machinery. Think of pre-mRNA as rough film footage, with exons as the main scenes and introns as extraneous material that is edited out.
During splicing, the removed intron is formed into a looped shape, creating the lariat intron. The removal of introns and the joining of exons must be exact, as a mistake of even a single nucleotide could lead to a faulty protein with damaging consequences for the cell.
Forming the Lariat: A Key Step in RNA Processing
RNA splicing is carried out by a molecular machine called the spliceosome, which is assembled from small nuclear RNAs and proteins. The spliceosome recognizes specific sequences at the boundaries of introns and exons, guiding the two sequential chemical reactions, known as transesterification steps, that cut the intron and join the exons.
The lariat structure forms during the first of these reactions. The spliceosome brings one end of the intron, the 5′ splice site, to a specific point within the intron called the branch point. This branch point contains an adenosine (A) nucleotide, and a chemical reaction cleaves the intron’s 5′ end, forming a new bond between it and the branch point adenosine.
This connection is a 2′-5′ phosphodiester bond, distinct from the usual 3′-5′ bonds that link nucleotides in a linear RNA chain. This bond creates a closed loop with a tail, resembling a cowboy’s lasso, which is why it is called a lariat. Once the lariat is formed, the second reaction joins the exons and releases the intron.
The Usual Fate: Degradation of Lariat Introns
Once released from the spliceosome, the lariat intron is considered cellular waste. These excised introns are quickly eliminated from the cell’s nucleus, which prevents the non-coding RNA from accumulating and allows the cell to recycle its building blocks.
Degradation begins with the debranching enzyme, or DBR1, which targets the 2′-5′ phosphodiester bond at the branch point. DBR1 breaks this bond, opening the loop and converting the lariat into a linear RNA molecule. This step is necessary because the lariat’s structure makes it resistant to standard degradation machinery.
After the intron is linearized, other enzymes like exonucleases and endonucleases rapidly degrade it into its constituent nucleotides. This degradation pathway was long considered the universal fate for all lariat introns.
Unexpected Functions: When Lariats Stick Around
Scientific understanding of lariat introns is expanding, with research revealing that not all of them are immediately destroyed. Studies have identified stable lariat introns that escape the degradation pathway and persist within the cell. These stable lariats have been found in the cytoplasm of cells from organisms like humans, mice, and zebrafish, suggesting they have conserved biological roles.
One proposed role is in the regulation of gene expression, where some stable lariats may act as precursors for other small regulatory RNA molecules. Examples include circular RNAs or small nucleolar RNAs. The stability of these lariats appears linked to specific features in their sequence or structure that make them resistant to the debranching enzyme DBR1.
This area of research is active, with some evidence suggesting lariats could interact with proteins or act as molecular sponges, binding to other molecules like microRNAs to influence their activity. The discovery that lariat introns can have a life beyond their excision challenges the traditional view of these molecules as simple cellular debris.