Scientists have solved the mystery of male rats without Y chromosomes

Collecting samples from Amami spiny rats

The Amami spiny rat is a critically endangered rodent that can only be found on Amami Oshima in Japan. It is one of only four animals known to lack a Y chromosome, along with the Tokunoshima spiny rat, the Transcaucasian mole vole, and the Zaisan mole vole.

The study team led by Professor Asato Kuroiwa examined tissue samples from three male and three female Amami spiny rats to create genomic sequences for each person. A DNA sequence duplication that was only present in the males was discovered after extensive investigation. On chromosome 3, this duplicated region was situated before the Sox9 gene.

The researchers discovered that the Amami spiny rats' sequence duplication constituted a new regulatory element that elevated Sox9 in the absence of Sry. They were able to map its position on the chromosomes in relation to Sox9, and it was shown to be similar to Enh14, a possible Sox9 enhancer in mice.

They believe that the two copies of Enh14 work together to increase the expression of Sox9. When they inserted the sequence into the genomes of mice using gene editing techniques, female (XX) mice embryos displayed gene expression that caused testis development.

It is the first discovery

This study is the first discovery of a male-specific genetic element directly related to a sex-determining mechanism in mammals that is independent of Sry. Future research will concentrate on determining the precise method by which Enh14 functions, as well as other components of this novel system. It is unclear, nevertheless, if this method applies to the four rodent species that are Y-chromosome-less, particularly the distantly related mole voles. In addition, according to the scientists who conducted the research, this study may also help future studies on humans.

The study was published in PNAS on November 28.

Study abstract:

Mammalian sex chromosomes are highly conserved, and sex is determined by SRY on the Y chromosome. Two exceptional rodent groups in which some species lack a Y chromosome and Sry offer insights into how novel sex genes can arise and replace Sry, leading to sex chromosome turnover. However, intensive study over three decades has failed to reveal the identity of novel sex genes in either of these lineages. We here report our discovery of a male-specific duplication of an enhancer of Sox9 in the Amami spiny rat Tokudaia osimensis, in which males and females have only a single X chromosome (XO/XO) and the Y chromosome and Sry are completely lost. We performed a comprehensive survey to detect sex-specific genomic regions in the spiny rat. Sex-related genomic differences were limited to a male-specific duplication of a 17-kb unit located 430 kb upstream of Sox9 on an autosome. Hi-C analysis using male spiny rat cells showed the duplicated region has potential chromatin interaction with Sox9. The duplicated unit harbored a 1,262-bp element homologous to mouse enhancer 14 (Enh14), a candidate Sox9 enhancer that is functionally redundant in mice. Transgenic reporter mice showed that the spiny rat Enh14 could function as an embryonic testis enhancer in mice. Embryonic gonads of XX mice in which Enh14 was replaced by the duplicated spiny rat Enh14 showed increased Sox9 expression and decreased Foxl2 expression. We propose that male-specific duplication of this Sox9 enhancer substituted for Sry function, defining a novel Y chromosome in the spiny rat.