Nature Communications: “Genetic Junk” Helps Chromosomes Find Their Correct Partners

Scientists at ETH Zurich have discovered how chromosomes find their matching partners before germ cells divide. A study in fruit flies has revealed an unexpected role for so-called “junk DNA”—repetitive regions of the genome that were long considered to have little or no function.

In humans and other animals, cells normally contain two copies of each chromosome, one inherited from the mother and one from the father. During the formation of eggs and sperm, this number must be reduced by half. This process, known as meiosis, is essential for restoring the normal paired set of chromosomes after fertilization. Before they separate, corresponding maternal and paternal chromosomes must recognize each other and pair up. Errors at this stage can lead to abnormal distribution of genetic material.

Researchers led by Professor Madhav Jagannathan and doctoral student Lena Skrutle studied this mechanism during egg development in fruit flies (Drosophila). They discovered that satellite DNA—numerous repetitive sequences previously often dismissed as “genetic junk”—plays a crucial role in the chromosome recognition process.

According to the study, published in Nature Communications, sets of satellite DNA on different chromosome pairs act like genetic “barcodes.” They help chromosomes identify their appropriate partners among the many other chromosomes inside the cell nucleus.

When the scientists removed these sequences from two different chromosomes, the recognition system broke down. The chromosomes began pairing with incorrect partners. The researchers also identified a protein called D1 that acts as a kind of molecular “glue”: it recognizes matching regions of satellite DNA and helps bring the corresponding chromosomes together.

If the “barcode” of one chromosome is altered by a mutation or partially lost, however, D1 may connect incompatible chromosomes, disrupting normal pairing.

The findings could also shed light on how new species arise. Satellite DNA evolves more rapidly than many other parts of the genome. If a population becomes geographically isolated, its genetic “barcodes” may gradually diverge so extensively that, when the populations encounter each other again, their chromosomes can no longer pair properly. This could result in hybrid infertility and, ultimately, contribute to the division of one population into two distinct species.

The authors emphasize that the mechanism has so far been demonstrated only in Drosophila. It remains unknown whether the same process operates in humans.