ITHACA, New York – In the same way that Lego pieces can be arranged in new ways to build a variety of structures, genetic elements can be mixed and matched to create new genes, according to new research.
A long-proposed mechanism of gene synthesis, called exon shuffling, works by mixing functional blocks of DNA sequences into new genes that express proteins.
A study entitled “Repetitive Evolution of Vertebrate Transcription Factors by Transposase Capture” was published on February 19 Science, Looks at how genetic elements called transposons, or “jumpers,” are added to the mix during evolution to collect new genes through exon shuffling.
Transposons were first discovered in the 1940s by Cornell Alum and Nobel Prize Laureate Barbara McClintock 23, MA ’25, Ph.D. ’27, they are abundant components of the genome – making up half of human DNA – and have the ability to hop and replicate selfishly in the genome. Some transposons contain their own genes that code for enzymes called transposes proteins, which cut and paste genetic material from one chromosomal site to another.
The study that focused on tetrapods (four-legged vertebrates) is important because it shows that transposons are an important force in the formation of new genes during evolution. The work also explains how genes essential to human development were born.
“We think it’s very likely that this mechanism extends far beyond vertebrates and could be an underlying mechanism that occurs in non-vertebrates as well,” said first author Rachel Cosby, PhD. 19, Postdoctoral Researcher at the National Institutes of Health. Cosby is a former graduate student in the lead author’s lab Cedric Viscott, professor in the Department of Molecular Biology and Genetics in the College of Agriculture and Life Sciences.
“You’re placing bricks in a different way and you’re building something completely new,” said Fishut. We are looking at the question of how genes are born. Originally, we are looking at the role of transposons in the formation of proteins with a new function in evolution. “
In the study, the researchers first extracted existing databases of tetrapod genomes, because the genomes of more than 500 species were completely sequenced. Cosby and colleagues searched for combinations of DNA sequences known as transposon properties fused into host sequences to find good candidates for the study. Then they selected the genes that evolved relatively recently – within tens of millions of years – so that they could trace the history of gene evolution through the vertebrate tree of life.
Although the genes incorporated into these transposons are relatively rare, researchers have found them throughout the vertebrate tree of life. Researchers have identified more than 100 distinct genes merging with transposons that were born in the past 350 million years along lineages of different species, including those in birds, reptiles, frogs, bats and koalas, and a total of 44 genes generated this way in the human genome.
Cosby and colleagues selected four recently evolved genes and conducted a wide range of experiments in cell culture to understand their functions. They found that proteins derived from these genes are able to bind to specific sequences of DNA and stop gene expression. These genes are known as transcription factors and serve as major regulator genes of development and primary physiology. One of these genes, PAX6, has been well studied, plays a major role as a key regulator in ophthalmic formation in all animals and is highly preserved throughout evolution.
“If the PAX6 gene was developed from a mouse in a fruit fly [fruit fly]Viscott said. Although others have previously suggested that PAX6 is a derivative of transposase fusion, the researchers in this study validated the hypothesis.
Cosby and colleagues isolated one of these genes that had recently evolved in bats, called the Kraabiner, and then used CRISPR to modify genes to remove it from the bat genome and see which genes were affected, before adding it again. The experiment revealed that when KRABINER was removed, hundreds of genes were disrupted, and when they were restored, normal performance returned. Cosby said that the protein expressed by the Krabner gene is linked to other related transpositions in the bat genome.
“The experiment revealed that it controls a large network of other genes that have been delivered via previous scattering of related transposons throughout the bat genome – resulting in not just the gene but what is known as the gene regulatory network,” Viscott said.
Current and former Feschotte Lab members Julius Judd, Ruiling Zhang ’20, Alan Zhong ’19, Nathaniel Garry ’21 and collaborator Ellen Pritham are co-authors of the paper.
The study was funded by the National Institutes of Health.