Inactive X chromosome moves from second fiddle to the conductor’s podium

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Humans have twenty-three pairs of chromosomes, and twenty-two of these pairs contain identical copies. The twenty-third pair is the sex chromosomes. Males typically have one X and one Y sex chromosome. Females typically have two X chromosomes, and these are genetically identical, but the output from each X is quite different. The expression, or protein production, of most of the genes on one of the X chromosomes, known as the inactive X chromosome, is dialed down or turned off completely. Because of this, the inactive X is often treated as a passive copy playing second fiddle to its partner, the active X chromosome. However, research from Whitehead Institute Member David Page and postdoc Adrianna San Roman shows that the so-called inactive X chromosome does much more than was previously thought. This work will help researchers to better understand the contributions of the sex chromosomes to sex differences in health and disease.

Even though the inactive X chromosome had been thought for many decades to contribute much less to X chromosome gene expression than the active X, San Roman and Page wanted to understand exactly what it did contribute. In order to quantify inactive X’s contributions to gene expression, they compared gene activity in cells from people with different numbers of X chromosomes. Everyone has one active X chromosome, and while humans typically have zero (in the case of XY males) or one (in the case of XX females) inactive X chromosomes, some individuals may have up to four. The researchers measured how much the expression of X chromosome genes changed with the presence of each additional inactive X chromosome.

They found that the change in expression caused by inactive X chromosomes is modular: every inactive X contributes in the same way as the one before it (for example, each inactive X might increase expression of a certain gene by 20% of the original level). However, the ways in which they affect gene expression were surprising. One might expect that the expression of a gene that is off on the inactive X chromosome would not change no matter how many inactive X chromosomes a person had, but this was not always the case. One might expect that the addition of more X chromosomes could only increase expression of X chromosome genes, but sometimes it decreased expression.

These paradoxical differences in gene expression led the researchers to a startling conclusion: the inactive X chromosome regulates expression of genes on the active X chromosome. This is how the addition of an inactive X chromosome can affect the expression level of a gene that the chromosome does not itself express—by altering that gene’s expression on the active X. Far from playing second fiddle to the active X, the inactive X can not only harmonize with but even conduct its partner. The researchers found that 38% of X chromosome genes in the two cell types that they tested are affected by the presence of inactive X chromosomes. This means that the inactive X contributes to the expression of many more genes than previously thought.

The researchers’ discoveries caused them to reframe how they view the sex chromosomes. The active X chromosome is present in people of all sexes. The only chromosome difference between typical males and females is that males have a Y chromosome and females have an inactive X. Therefore, Page and San Roman now see the inactive X chromosome, specifically, as the female sex chromosome and counterpart to the male Y. The researchers think that changing the framing in this way will help to focus questions about sex chromosomes and their impacts on sex differences in health and disease. The researchers are continuing to investigate the inactive X chromosome’s regulatory effects throughout the genome, and their consequent health impacts throughout the body. They anticipate that the more they learn, the more apparent it will become that the inactive X chromosome is in fact a very active player in cellular processes and sex differences in health and disease.