New genes on 'deteriorating' Y chromosome

New method brings momentum to the previously difficult identification of Y-linked genes

The Y chromosome has been a tough nut to crack in genome research. As it possesses only few functional genes, and these are embedded in repetitive DNA that is difficult to analyse, finding these genes is a challenge. "Only seven functional genes have been identified on the Y chromosome of Drosophila melanogaster. But we suspect that the number of functional genes as well as the actual transfer rate must be higher," says first author Ray Tobler. "We therefore developed a new analysis method that allows us to efficiently search for gene transfers onto the Y chromosome, so-called GeTYs." The researchers' trick consisted in sequencing the genome of males and females from a so-called inbred strain of fruit flies. These differ only in the Y chromosome sequence. "The key to our results was to search for variants in the males that do not exist among the females," says Tobler. "That means we worked without any known Y chromosome sequences that would usually be used for a comparison. This allowed us to trace the transferred genes back to so-called retrocopies, which are created when the RNA transcript of a gene is inserted into the Y chromosome."

Transferred RNA copies and important selection mechanisms identified for the first time

All previously described gene transfers onto the Y chromosome involved the transfer of a piece of the chromosome and not an RNA transcript. "The high number of validated gene transfers allowed us to statistically show that there were differences between Drosophila species," explains senior author Christian Schlötterer. "We only found genes originating from an RNA transcript in the closely related D. mauritiana and D. simulans, which suggests that the transfer mechanisms are species-specific."

New impetus for Y chromosome research in other species

A special surprise for the research team was that four of the 25 newly transferred genes on the Y chromosome have already assumed an important function there. "As these new genes can be found in all individuals of a species, the question arises as to which functions these new Y-linked genes could have," says Tobler. Until now, it has been still completely unclear if and how long these new genes can withstand the deterioration of the Y chromosome. As the new analysis method does not require a reference genome for the Y chromosome, it offers enormous potential to study the dynamics of new genes on the Y chromosome in many different species. "I expect many more exciting findings," concludes Christian Schlötterer.