Insights into the role of the germline in de novo mutation

The male reproductive system is a hotspot for the introduction of new genes. Perhaps that might assist in understanding why fathers tend to pass on more new mutations than mothers do. However, it does not explain why older fathers pass on more mutations than younger fathers.

Insights into the role of the germline in de novo mutation
A photo of fruit fly testes as rendered by Deep Dream AI. Image Credit: Sigi Benjamin; Processing: Evan Witt.

The processes underlying these well-documented trends have long been a mystery. A new study published in the journal Nature Ecology & Evolution by Rockefeller University researchers explains why older male fruit flies are more likely to pass mutations onto their progeny, perhaps shedding light on the risk of genetic disease in humans.

Scientists in Li Zhao’s lab analyzed mutations that take place during spermatogenesis, the process of producing sperm from germline cells. They discovered that mutations are widespread in both young and old fruit flies’ testes, but are more prevalent in older flies from the start.

Furthermore, many of these mutations appear to be repaired by the body’s genomic repair mechanisms in younger fruit flies during spermatogenesis, but they fail to be rectified in older flies’ testes.

We were trying to test whether the older germline is less efficient at mutation repair, or whether the older germline just starts out more mutated. Our results indicate that it’s actually both. At every stage of spermatogenesis, there are more mutations per RNA molecule in older flies than in younger flies.”

Evan Witt, Study First Author and Computational Biologist, Biomarin Pharmaceuticals

Evan Witt is a former graduate student of Li Zhao‘s lab.

Self-care at the genetic level

Genomes keep themselves tidy by employing a variety of repair mechanisms. Testes must work extra hard since they have the highest rate of gene expression of any organ. Furthermore, genes that are strongly expressed during spermatogenesis have fewer mutations than those that are not.

This may appear to be irrational, but it makes sense: One explanation proposes that the testes express so many genes as a kind of genomic surveillance mechanism—a technique to detect and then remove undesirable mutations.

The weed-whacker, however, appears to sputter out when it comes to older sperm, according to the researchers. Earlier study implies that a malfunctioning transcription-coupled repair mechanism, which only repairs transcribed genes, could be to blame.

Inherited or new mutations?

To obtain these findings, researchers from the Laboratory of Evolutionary Genetics and Genomics performed single-cell sequencing on the RNA from the testes of approximately 300 fruit flies, roughly half of which were young (48 hours old) and half of which were old (25 days old), progressing a line of inquiry they began in 2019.

They sequenced the genome of each fly to determine if the mutations they discovered were somatic, inherited from the flies’ parents, or de novo (arising in the particular fly’s germline). They were able to prove that each mutation was a true original.

We can directly say this mutation was not present in the DNA of that same fly in its somatic cells. We know that it’s a de novo mutation,” adds Evan Witt.

Scientists were able to associate mutations to the cell type in which they originated thanks to their unconventional approach of inferring genomic mutations using single-cell RNA sequencing and then contrasting them to genomic data.

It’s a good way to compare mutational load between cell types, because you can follow them throughout spermatogenesis.”

Evan Witt, Study First Author and Computational Biologist, Biomarin Pharmaceuticals

The human connection

The next step is to broaden the analysis to include more age groups of flies, evaluate whether or not this transcription repair mechanism can happen, and if it does, pinpoint the pathways in charge.

Witt adds, “What genes are really driving the difference between old and young flies in terms of mutation repair?

Since fruit flies reproduce rapidly, Zhao believes that studying their mutation patterns can provide fresh insights into the impact of novel mutations on human health and evolution.

It’s largely unknown whether a more mutated male germline is more or less fertile than a less mutated one. There’s not been very much research on it except for at a population level. And if people inherit more mutations from aging fathers, that increases the odds of de novo genetic disorders or certain types of cancers.”

Evan Witt, Study First Author and Computational Biologist, Biomarin Pharmaceuticals

Source:
Journal reference:

Witt, E., et al. (2023) Transcriptional and mutational signatures of the Drosophila ageing germline. Nature Ecology & Evolution. doi.org/10.1038/s41559-022-01958-x.

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