Sex chromosomes, specifically through the genes ZFX and ZFY, play a key role in regulating gene expression throughout the body, a breakthrough study has revealed, challenging conventional views of their function. Human sex chromosomes originate from a pair of autosomes, ordinary or non-sex chromosomes, which comprise the majority of our genome and occur in pairs.
The ancestors of this pair of autosomes diverged into two different chromosomes - X and Y. Although X and Y have separated from each other and have unique functions - namely determining sex and driving sexual differences in males and females - they have also retained shared functions inherited from their common ancestor.
New research by Whitehead Institute member David Page, MIT biology professor and Howard Hughes Medical Institute Investigator, and Adrianna San Roman, a postdoc in his lab, reveals the collective role of sex chromosomes as influential gene regulators.
The study, published December 13 in the journal Cell Genomics, shows that genes expressed on the X and Y chromosomes affect cells throughout the body, not just those in the reproductive system, turning up or down the expression of thousands of genes on other chromosomes.
ZFX and ZFY: key gene regulators
In addition, the researchers also found that a pair of genes responsible for about half of the regulatory behaviors - ZFX and ZFY - are located on the X chromosome and Y chromosome respectively, and their regulatory functions are basically the same. This suggests that ZFX and ZFY inherited their roles as influential gene regulators from their common ancestor and independently maintained this role even as their respective chromosomes diverged, as this regulatory role is critical for human growth and development. Genes regulated by ZFX and ZFY are involved in a variety of important biological processes, suggesting that sex chromosomes make broad contributions beyond their functions related to sexual characteristics.
Effects of sex chromosomes on global gene expression
Page and Sanroman measured how the X and Y chromosomes affect overall gene expression by plotting how the expression of each gene in a cell changes as the number of X or Y chromosomes changes. For the study, they used tissue samples from people with natural variation in the number of sex chromosomes: people born with one to four X chromosomes and zero to four Y chromosomes. These sex chromosome variations are found throughout humans, and they can cause a variety of health disorders, but unlike duplications of most other chromosomes, they are compatible with life.
"By taking advantage of natural variation in sex chromosome composition in human populations, we are able to mathematically model how the number of X and Y chromosomes affects gene expression in an unprecedented way. Through this approach, we gain new insights into the dramatic impact that X and Y genes have across the genome." San Roman said.
In this project, the researchers studied two cell types—lymphoblasts (a type of immune cell) and skin cell-derived fibroblasts (which help form our connective tissue)—which they chose for ease of obtaining samples, and measured how gene expression in each cell type changed with the presence of each additional X or Y gene.
They found that thousands of genes change their expression levels as the number of X and/or Y chromosomes changes. These effects scale linearly, meaning that each additional X or Y chromosome changes gene expression to the same extent. Which genes are affected and to what extent each cell type is affected varies, suggesting that each type of cell in the body may have a unique response to genetic regulation of X and Y chromosome genes.
"With this approach, we gain new insights into the huge impact that X and Y genes have on the entire genome," Sanroman said.
Revealing surprising similarities and differences in gene regulation
However, for a specific gene in a specific cell type, the impact of an extra X gene is often similar to the impact of an extra Y gene. The discovery surprised researchers, who had thought that differences in the way X and Y genes regulate other genes might help explain some sex differences in health and disease. For example, men and women have different risks for certain diseases, have different symptoms of the same disease, and respond differently to certain medications. There are many differences between male and female cells that have yet to be explained, and it seems promising that the gene regulators on X and Y, which are adjusting gene expression throughout the body, are causing these differences.
Instead, Page and San-Roman narrowed their research and found that a pair of genes, ZFX and ZFY, were responsible for about half of the effects of X and Y on broad gene expression, and that the pair appeared to be functionally equivalent -- although ZFX sometimes had a slightly stronger effect than ZFY. Other genes on X and Y may also be regulators of a wide range of genes, accounting for the other half of the effect.
These other gene regulators may be X-Y gene pairs like ZFX and ZFY, playing essentially equivalent roles. After all, gene regulation is an important function, and the regulatory roles that X and Y inherited from their common ancestor may be required to achieve fetal survival in exactly the same way regardless of how X and Y grew apart.
However, the researchers suspect that certain X and Y genes must change gene expression in different ways, or to different extents, to explain many of the sex differences seen in male and female cells. The challenge is that because the strongest effects of the X and Y genes on broad gene expression are shared, it will be more difficult for researchers to pinpoint the different ways in which the two chromosomes affect gene expression.
"Effects on the genome may explain the sex differences, and this effect is more subtle than we previously predicted," Sanroman said. "One thing to watch in future studies is that although we see that the effects of X and Y on gene expression are highly correlated, we observe a larger effect of X relative to Y copy number, which may be one of the reasons for the sex differences."
Rethinking sex chromosomes: inactive X versus active X
One subtlety that Page and Samloman have not discussed so far is that when Page and Samloman think about sex chromosomes, they are no longer thinking about Xs, as most people think. Their work has convinced them that our current understanding of sex chromosomes is imprecise. Although human sex chromosomes are defined as X and Y, there are actually two types of X chromosomes, and typically only one differs between males and females. Everyone in the world has an "active X" chromosome. This chromosome, like an autologous chromosome, is ubiquitous and therefore exists regardless of gender.
The difference between typical males and females is the chromosome that pairs with the active X chromosome: Typical males have a Y chromosome, while typical females have an "inactive X" chromosome that has the same genes as the active X chromosome, but with most of the genes turned off. In people with atypical sex chromosome composition, any extra X chromosome will be an inactive X chromosome - so when researchers measure the effect of adding more X chromosomes, they are actually measuring the effect of adding more inactive X chromosomes.
The researchers found that inactive X and Y, rather than X and Y, more precisely the sex chromosomes, were changing widespread gene expression. In addition, Page and Sanroman found that both inactive X and Y regulate the expression of many genes on the active X chromosome, just as they do on all autosomes. (This is an extension of previous research on the relationship between inactive X and active X). In short, the active X chromosome behaves like an autosome, while the inactive X chromosome and Y chromosome are two sides of the same coin, serving as both sex chromosomes and gene regulators.
"These chromosomes, historically known as the 'inactive' X chromosome and the 'gene-poor' Y chromosome, have received little attention beyond their contribution to sexual differentiation, so we were shocked to see how widespread their network of effects was," Page said. "These chromosomes contain genes like ZFX and ZFY, which are global gene regulators, and I think as we learn more about them, it will revolutionize how we think about human X and Y chromosome genetics."
Compiled source: ScitechDaily