Although you may not appreciate them, or have even heard of them, throughout your body, countless microscopic machines called spliceosomes are hard at work. While you sit and read, they are faithfully and quickly rebuilding the broken information in your genes by removing sequences called “introns” so that your messenger RNAs can make the correct proteins your cells need.
Introns are perhaps one of the greatest mysteries of our genome. They are DNA sequences that disrupt sensitive protein-coding information in genes and need to be “cut.” The human genome has hundreds of thousands of introns, about 7 or 8 per gene, and each one is removed by a specialized RNA protein complex called a “spliceosome” that cuts out all the introns and joins together the remaining coding sequences, called exons. How this system of broken genes and the spliceosome evolved in our genomes is unknown.
Throughout his long career, Manny Ares, distinguished professor of molecular, cellular, and developmental biology at UC Santa Cruz, has made it his mission to learn everything he can about RNA splicing.
“I mean the splicing,” Ares said. “I just want to know everything the spliceosome does, even if I don’t know why it does it.”
In a new article published in the magazine Genes and development, Ares reports a surprising discovery about the spliceosome that could tell us more about the evolution of different species and the way cells have adapted to the strange problem of introns. The authors show that once the spliceosome finishes splicing the mRNA, it remains active and can participate in further reactions with the introns removed.
This discovery provides the strongest indication we have yet that spliceosomes could reinsert an intron into the genome at another location. This is a capability that spliceosomes were not previously thought to possess, but is a common feature of “Group II introns,” distant cousins of the spliceosome that exist primarily in bacteria.
The spliceosome and Group II introns are thought to share a common ancestor that was responsible for the spread of introns throughout the genome, but while Group II introns can separate from RNA and then return directly to DNA, the ” “Spliceosomal introns” found in most higher-level organisms require the spliceosome for splicing and are not thought to be reinserted into DNA. However, the Ares lab’s finding indicates that the spliceosome could still be reinserting introns into the genome today. This is an intriguing possibility to consider because introns being reintroduced into DNA add complexity to the genome, and understanding more about where these introns come from could help us better understand how organisms continue to evolve.
Taking advantage of an interesting discovery
An organism’s genes are made of DNA, in which four bases, adenine (A), cytosine (C), guanine (G), and thymine (T), are arranged in sequences that encode biological instructions, such as how to make specific proteins. in the body. needs. Before these instructions can be read, DNA is copied into RNA through a process known as transcription, and then the introns of that RNA must be removed before a ribosome can translate it into actual proteins.
The spliceosome removes introns through a two-step process that results in the intron RNA having one end attached to its center, forming a circle with a tail that looks like a “lasso” or cowboy lasso. This appearance has led to them being called “loop introns.” Recently, researchers at Brown University who were studying the locations of the binding sites on these loops made a strange observation: Some introns were actually circular rather than loop-shaped.
This observation immediately caught Ares’s attention. Something seemed to be interacting with the loop’s introns after they were removed from the RNA sequence to change its shape, and the spliceosome was the prime suspect.
“I thought it was interesting because of this very, very old idea about the origin of introns,” Ares said. “There is a lot of evidence that the RNA parts of the spliceosome, the snRNAs, are closely related to Group II introns.”
Because the chemical mechanism for splicing is very similar between spliceosomes and their distant cousins, Group II introns, many researchers have theorized that when the self-splicing process became too inefficient for Group II introns to completed reliably on their own, parts of these introns evolved into the spliceosome. While Group II introns were able to insert directly back into DNA, spliceosomal introns that required the help of spliceosomes were not thought to insert back into DNA.
“One of the questions that was kind of missing from this story in my mind was: Is it possible that the modern spliceosome is still capable of taking a lasso intron and inserting it somewhere in the genome?” Ares said. “Is he still able to do what the ancestor complex did?”
To begin to answer this question, Ares decided to investigate whether it was indeed the spliceosome that was making changes to the introns of the loop to eliminate their tails. His lab slowed down the splicing process in yeast cells and discovered that after the spliceosome released the mRNA from which it had finished splicing introns, it hung on the loops of introns and transformed them into true circles. Ares’ lab was able to reanalyze published RNA sequencing data from human cells and found that human spliceosomes also had this ability.
“We’re excited about this because, while we don’t know what this circular RNA might do, the fact that the spliceosome is still active suggests that it can catalyze the insertion of the Lariat intron back into the genome,” Ares said.
If the spliceosome is able to reinsert the intron into DNA, this would also add significant weight to the theory that spliceosomes and Group II introns shared a common ancestor long ago.
Testing a theory
Now that Ares and his lab have shown that the spliceosome has the catalytic ability to hypothetically place introns back into DNA like its ancestors did, the next step for researchers is to create an artificial situation in which they “feed” a strand of DNA to a splice that is still attached to a loop intron and see if they can actually get it to insert the intron somewhere, which would present a “proof of concept” for this theory.
If the spliceosome is able to reinsert introns into the genome, it is likely to be a very rare event in humans, because human spliceosomes are incredibly high in demand and therefore do not have much time to devote to the removed introns. However, in other organisms where the spliceosome is not as busy, intron reinsertion may be more frequent. Ares is working closely with UCSC biomolecular engineering professor Russ Corbett-Detig, who recently led a systematic and exhaustive search for new introns in the available genomes of all intron-containing species that was published in the journal Proceedings of the National Academy of Sciences (PNAS) last year.
The paper published in PNAS showed that intron “explosion” events far back in evolutionary history likely introduced thousands of introns into a genome at the same time. Ares and Corbett-Detig are now working to artificially recreate an explosion event, which would give them insight into how genomes reacted when this happened.
Ares said their interdisciplinary partnership with Corbett-Detig has opened the doors for them to really delve into some of the biggest mysteries about introns that would likely be impossible for them to fully understand without their combined expertise.
“It’s the best way to do things,” Ares said. “When you find someone who has the same kind of questions in mind but with a different set of methods, perspectives, prejudices and strange ideas, that becomes more exciting. That makes you feel like you can go out and solve a problem like this. which is very complex.”