Retrotransposon protects ribosomal DNA from shrinkage

New findings from a study conducted by Whitehead Institute Member Yukiko Yamashita and postdoc Jonathan Nelson shed light on the safeguarding mechanism of ribosomal DNA (rDNA) sequences. These sequences, crucial components of various organisms’ genomes, are prone to shrinking over time, potentially leading to cell death if they diminish excessively. In the case of germ cells responsible for producing eggs and sperm, significant shrinkage of rDNA can result in infertility and, ultimately, the extinction of lineages.

Previously, scientists had been uncertain about the factors that preserve the integrity of rDNA across generations. However, the recent research reveals an unexpected defender for rDNA—retrotransposons. Retrotransposons are genetic elements often labeled as genetic parasites due to their seemingly self-replicating nature.

The study, published on May 30, 2023, in the journal PNAS, demonstrates how these so-called parasites actually serve a vital role in upholding rDNA and ensuring fertility over time. The newfound understanding highlights the intricate and interconnected mechanisms at play in maintaining the stability of genetic material.

The puzzle of why rDNA does not disappear

The function of rDNA is to produce the RNA subunits that make up ribosomes, the cellular machinery responsible for protein synthesis. Since cells require numerous ribosomes to produce the proteins essential for their function, rDNA contains multiple repeated copies of the sequence required for ribosome assembly.

The challenge with repetitive DNA like rDNA is that during cell division, there is a risk of inadvertently deleting some of the identical repeats while replicating the genome. Over time and multiple cell divisions, it is expected that the number of repeats would progressively decrease.

This issue becomes particularly significant in aging individuals and germ cells—the only cells passed from one generation to the next. If there were no mechanism in place to restore the missing repeats, each subsequent generation would begin with fewer repeats than the previous one. Eventually, a generation could have insufficient repeats to produce viable germ cells, leading to the extinction of that population.

Yukiko Yamashita, who is a professor of biology at the Massachusetts Institute of Technology and an Investigator with the Howard Hughes Medical Institute, focuses her research on the immortality of germ cells in male fruit flies (Drosophila melanogaster). She investigates how germ cells can continually generate healthy sperm and eggs across multiple generations.

Unlike other cell types that perish with the organism, germ cells must carefully maintain their rDNA to avoid accumulating errors in their genomes over successive generations and preserve their immortality.

Although germ cells can replenish lost rDNA repeats, the mechanism behind this process remained unknown. Yamashita and Nelson embarked on a quest to unravel this mystery.

The repetitive nature of ribosomal DNA makes it susceptible to loss, which logically implies that all individuals should lose rDNA in their germ cells, ultimately leading to the complete disappearance of future generations. Yamashita acknowledges the magnitude of this question, which often goes unnoticed due to the assumption that something must be preserving rDNA. However, once they recognized the existence of the question, they embarked on a mission to discover the answer.

Retrotransposons: Not so selfish after all

The researchers made a significant discovery regarding the role of a retrotransposon called R2 in the restoration of rDNA. Retrotransposons are genetic sequences that primarily focus on replicating themselves, often at the expense of the rest of the genome. While they have been referred to as genetic parasites, their behavior resembles that of a virus, which manipulates cells into producing copies of itself. Retrotransposons achieve replication by reversing the typical process of gene expression.

When the DNA encoding a retrotransposon is transcribed into RNA, that RNA can be reverse-transcribed back into DNA. The retrotransposon then cleaves open the cell’s genome and inserts its new DNA, effectively adding another copy of itself to the genome. This process not only expands the size of a species’ genome over generations (almost half of the human genome consists of transposable elements), but it can also cause damage to individual cells.

When a retrotransposon cleaves the genome, especially if it inserts itself into a vital DNA sequence, it can render essential genes nonfunctional.

However, Nelson and Yamashita discovered that the retrotransposon R2, which typically duplicates and inserts itself into fruit fly rDNA, can also benefit cells. During cell division, each chromosome has two copies—one for each new daughter cell. R2 cleaves open both copies of the chromosome containing rDNA. As the cell repairs these breaks, the repetitive nature of rDNA can cause it to lose its original position. Consequently, a segment of rDNA repeats from one copy of the chromosome is stitched into the other copy.

This process results in one daughter cell having more repeats in its rDNA than the original cell, while the other daughter cell has fewer repeats. To preserve immortality, germ cells ensure that the cell with more repeats in its rDNA becomes the one responsible for perpetuating the germline.

In a previous study from Yamashita’s lab published in 2022, the researchers identified a gene named Indra, which produces a protein that binds to the chromosome with more rDNA repeats. This protein marks the daughter cell containing that chromosome to remain a stem cell, while the other daughter cell proceeds towards spermatogenesis.

Germ cells employ these mechanisms to transfer rDNA repeats from one chromosome to another and selectively designate the cell with more repeats, thereby constantly replenishing the level of rDNA in the germline. This ensures that the population of germ cells maintains a sufficient number of rDNA repeats, preserving the lineage of cells and the individuals carrying them.

The work of Nelson and Yamashita highlights that R2 is not solely a selfish parasite but plays a vital role in the rejuvenation of germline rDNA. However, as a retrotransposon, R2 is also capable of causing damage. Nelson found that germ cells keep R2 inactive except in cases where the number of rDNA repeats becomes critically low.

By activating R2 only when necessary, cells can maximize the benefits and minimize the risks associated with the retrotransposon. This suggests a mutually beneficial relationship between the cell and R2. The researchers speculate that other transposable elements may also provide unknown advantages to cells.

While transposable elements are often regarded as existing because their replication in the genome surpasses the host’s defense mechanisms, they make up large genomic regions that are commonly considered non-functional. However, Yamashita and Nelson propose that the abundance of transposable elements may be due to their contribution to functions that are not yet fully understood.

Nelson remarks, “These elements make up large regions of the genome that we think of as non-functional, but what if the reason why there are so many of them is because they contribute some function that we just don’t understand yet?”

Source: Whitehead Institute for Biomedical Research

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