Cause of selective male deafness discovered

The DFNY1 Pedigree Males, squares; females, circles; diagonal line, deceased. Filled symbols indicate hearing impairment (including from family records); question marks indicate two individuals whose hearing phenotype is unknown; and asterisks indicate individuals who are on the affected branch but who were below the age of onset of symptoms at the time of examination. Arrows indicate the two individuals whose Y chromosomes were sequenced. The structural rearrangement occurred during one of the four meioses marked by red stars. Spouses are omitted in generations VII-IX and in generation VI on the unaffected branch. [Credit: American Journal of Human Genetics: http://dx.doi.org/10.1016/j.ajhg.2012.12.015]

The DFNY1 Pedigree Males, squares; females, circles; diagonal line, deceased. Filled symbols indicate hearing impairment (including from family records); question marks indicate two individuals whose hearing phenotype is unknown; and asterisks indicate individuals who are on the affected branch but who were below the age of onset of symptoms at the time of examination. Arrows indicate the two individuals whose Y chromosomes were sequenced. The structural rearrangement occurred during one of the four meioses marked by red stars. Spouses are omitted in generations VII-IX and in generation VI on the unaffected branch. [Credit: American Journal of Human Genetics: http://dx.doi.org/10.1016/j.ajhg.2012.12.015%5D

13 February 2013

By Yali Xue

I’m sure many of us can remember a discussion like this between our parents:

Mum: “Could you put the rubbish out, please dear?”

Dad watches TV.

Mum: “Could you put the rubbish out now, please?”

Dad carries on watching TV.

Mum shouts: “I said, ‘Could you put the rubbish out, now!’”

Dad: “Hmm? Of course, no need to shout”

Men can be rather good at not hearing sometimes, and you might wonder if they have ‘selective deafness’ or not. But in one family, at least, male selective deafness is real.

In this family, all the men, but not the women, become deaf as adults. This is because the men carry a genetic mutation on their Y chromosomes (the male-only sex chromosome) that produces hearing loss. For them, deafness is inherited as a male-specific Mendelian trait.

To appreciate just how novel and interesting this family and their genetic condition are, we need to look back at the history of ‘male-only’ genetic conditions. Over the years many male-specific traits – the most famous of which is ‘hairy ears’ – have been suggested as being passed down on the Y chromosome in a Mendelian fashion. However, subsequent investigation has always excluded this inheritance pattern for all such candidate conditions.

So when, in 2004, our collaborator Professor Qiuju Wang discovered a family where only the males inherited adult hearing loss, she immediately appreciated their importance. Quiju was also able to trace back the family even further and found another branch without the deafness but sharing the same Y chromosome and a common ancestor seven generations ago.

We were first contacted about the family in 2006 by Quiju, we were excited about the possibility of understanding the basis of this unique form of deafness. Even before starting the work, we realized that the cause must be unusual. Mendelian traits are often due to inactivation of a gene, but there are people who have lost the entire Y chromosome and all its genes and they have not gone deaf. People lacking a Y chromosome have a recognizable set of physical problems (known as Turner Syndrome), but deafness is not one of them. Similarly, people with an extra copy of the Y chromosome and duplication of all its genes do not suffer deafness.

In 2006, the best way to investigate seemed to be two techniques, using whole-genome aCGH (array comparative genomic hybrization), and aCGH focusing in detail on the Y chromosome. These techniques look for repeating areas or missing areas within the genome. We carried out both, and detected a partial duplication within the Y chromosome, including some of the testes-specific protein Y-encoded genes or TSPY genes. However, this finding alone did not seem to explain the deafness.

Then, in 2007, new sequencing technology and sequencing the whole Y chromosome became possible. So, we took advantage of the chromosome sorting facility we have here to sort the two Y chromosomes – one from the branch of the family with deafness and one from the branch without – and then sequenced them. By comparing the sequencing data, we found that three regions of the Y chromosome were duplicated, just as we had seen using aCGH.  But we wanted to know more, to know where these duplications were arranged on the chromosome.

To map the duplications we took advantage of the skills of the Sanger Institute’s cytogenetics facility. Fengtang Yang’s group used fibre-FISH (fluorescence in-situ hybridisation) to show where the duplications were arranged on the Y. This technique reveals duplicated areas by producing segments of the Y chromosome, adding a fluorescent tag to these segments, and then allowing the pieces to bind to their twins on the original Y chromosome. Not only did the technique reveal the position of the three duplications, it showed us something even more intriguing.

The fibre-FISH technique revealed that there was an unknown region within the duplication on the Y chromosome that did not belong to the Y chromosome. Where had this ‘foreign’ region of DNA come from and how had it ended up the Y chromosome?

Dr. Yujun Zhang, working at the Sanger Institute at the time, was able to contribute his expertise to help solve the mystery. He cleverly applied Tail-PCR to dig into this question. This technique uses the known part of the Y chromosome as a primer and uses different random primers to find the unknown part. It showed that the foreign DNA region had come from chromosome 1 (see diagram below).

The affected Y chromosome has an inserted segment from Chromosome 1. (A) The structure of the unaffected Y chromosome. Grey and black: errors and gaps, respectively, in the GRCH37 assembly. Blue: region matching the reference sequence at the level of resolution used. Shown below are part of theTSPY1 array (blue arrowheads) and the location of BAC clone signals. (B) Structure of the affected Y chromosome. This chromosome contains a segment that is not in the unaffected chromosome; this segment is derived from duplications of sequences from both chromosome 1 (yellow) and the Y chromosome (blue). Again, the gene content and BAC signals are shown below. The arrowheads above indicate the orientation of the duplicated segments relative to the reference sequence. (C) Detailed view of the two chromosome 1-Y junctions studied at the sequence level, showing the difference between the simple structure of junction 1 and the complex structure of junction 2 [Credit: American Journal of Human Genetics: http://dx.doi.org/10.1016/j.ajhg.2012.12.015]

The affected Y chromosome has an inserted segment from Chromosome 1. (A) The structure of the unaffected Y chromosome. Grey and black: errors and gaps, respectively, in the GRCH37 assembly. Blue: region matching the reference sequence at the level of resolution used. Shown below are part of theTSPY1 array (blue arrowheads) and the location of BAC clone signals. (B) Structure of the affected Y chromosome. This chromosome contains a segment that is not in the unaffected chromosome; this segment is derived from duplications of sequences from both chromosome 1 (yellow) and the Y chromosome (blue). Again, the gene content and BAC signals are shown below. The arrowheads above indicate the orientation of the duplicated segments relative to the reference sequence. (C) Detailed view of the two chromosome 1-Y junctions studied at the sequence level, showing the difference between the simple structure of junction 1 and the complex structure of junction 2 [Credit: American Journal of Human Genetics: http://dx.doi.org/10.1016/j.ajhg.2012.12.015%5D

This result made us really excited because, combined the sequencing data, a quick check showed that the region of chromosome 1 that had been translocated to the Y chromosome had come from an area known to be associated with deafness (DFNA49). So the selective male adult deafness in the family was not due to a Y chromosome gene, but the addition of a chromosome 1 gene to the Y chromosome.

It really was a unique experience for me to be involved in this project, which called upon so many different genomic techniques and the skills of so many teams. What amuses me is that, given the size of the chromosome 1 fragment that is translocated, this ‘foreign’ region in the Y chromosome should have been detected in the first whole-genome aCGH experiment we carried out, but for some reason it was not. Instead, it made us chase its existence through a whole range of routes before we discovered the truth.

Yali Xue is senior staff scientist in the Human Evolution group at the Wellcome Trust Sanger Institute. Initially interested in using variation on the Y chromosome to provide insights into aspects of human history and evolution more…

Related Links

Research paper: Wang Q et al. Genetic basis of Y-linked hearing impairment. AJHG 2013 Available online 24 January 2013
http://dx.doi.org/10.1016/j.ajhg.2012.12.015