Transposons, DNA sequences that can self-replicate and move (jump) across the genome, are widespread and can affect cell survival if left unchecked. Cells control these “jump genes” by silencing them, but little was known about how cells recognize and protect themselves from invading transposons. Scientists at St. Jude Children’s Research Hospital answered that question by showing that cells sense aberrant RNA patterns produced by invading transposons and respond by activating pathways that silence them. Additionally, this process extends to any invading DNA as long as it generates enough RNA interference for the cell to detect. This research today nature communicationsprovides insight into genetic phenomena that are central to diversity and evolution.
Researchers led by corresponding author Mario Harrick, PhD, of St. Jude’s Department of Structural Biology, discovered that fission yeast cells use two routes to silence invading transposons. The first is RNA interference, which silences genes by destroying messenger RNA. A second mechanism of silencing utilizes heterochromatin, a highly condensed form of DNA. Heterochromatin physically blocks transcription factors from engaging the DNA, thus stopping gene expression. Cells use both RNA interference and heterochromatin to detect and silence transposons. Recognition efficiency is based on insertion location (where the transposon is in the genome) and copy number (the number of copies of the transposon).
Although this study was conducted in yeast, similar defense mechanisms are thought to exist in higher organisms, especially germline cells (sperm and eggs) that are particularly vulnerable to transposon-induced disruption.
All living things try to protect themselves from transposon invasion. They can multiply uncontrollably and occupy large portions of the genome, slowing growth and negatively impacting gene expression. Such defense systems are usually restricted to germline cells where strong defenses are essential. Otherwise, transposons can multiply dramatically within just a few generations. ”
Dr. Mario Harrick, St. Jude Department of Structural Biology
Transposon silencing works against all invading DNA
For their study, the researchers introduced an invasive transposon into cells and watched it pop into different locations within the yeast genome. They then sequenced those locations and measured DNA copy numbers and RNA levels to see how efficiently they were silenced. As the researchers point out, yeast strains that produced more RNA from the initially invading DNA were found to be more effective at detecting and silencing it, but the systems to control this are high-risk, high-reward.
“Heterochromatin has a spreading habit, silencing not only transposons but also nearby genes,” Harrick says. “Yeast cells that silence transposons in this way initially grow slowly, which is a disadvantage, but become beneficial once the transposon grows. This may explain why human adult cells use a safer, more targeted system instead of this broad silencing mechanism.”
Using RNA interference and heterochromatin, cells can rapidly silence new transposons without sequence recognition and instead identify transposons through disruption of expression patterns. These findings provide important insights into how developing cells protect themselves from invasive gene sequences.
“What excited us most was discovering that cells can not only silence transposons, but also any invading DNA as long as they produce enough RNA,” said co-first author Yinxia Yang, Ph.D., Department of Structural Biology. “This showed that the cellular defense system is even smarter than we thought.”
sauce:
St. Jude Children’s Research Hospital
Reference magazines:
Salvi, L. others. (2026). Recognition and silencing of new transposable elements. nature communications. DOI: 10.1038/s41467-026-72981-w. https://www.nature.com/articles/s41467-026-72981-w
