Linking dosage compensation and X chromosome nuclear organization in C. elegans

Dosage compensation in Bombyx mori is achieved by partial repression of both Z chromosomes in males

Genes on sex chromosomes (i.e. human chX) are regulated differently in males and females to balance gene expression levels between sexes (XY vs. XX). This sex-specific regulation is called dosage compensation (DC). DC is achieved by altering the shape and compaction of sex chromosomes specifically in one sex. In this study, we use Oligopaints to examine DC in silkworms. This study visualizes this phenomenon in a species with ZW sex chromosomes, which evolved independently of XY. Our data support a long-standing model for how DC mechanisms evolved across species, and we show potential similarity between DC in silkworms and nematodes, suggesting that this type of DC may have emerged multiple independent times throughout evolution.

Interphase chromatin is organized precisely to facilitate accurate gene expression. The structure–function relationship of chromatin is epitomized in sex chromosome dosage compensation (DC), where sex-linked gene expression is balanced between males and females via sex-specific alterations to three-dimensional chromatin structure. Studies in ZW-bearing species suggest that DC is absent or incomplete in most lineages except butterflies and moths, where male (ZZ) Z chromosome (chZ) expression is reduced by half to equal females (ZW). However, whether one chZ is inactivated (as in mammals) or both are partially repressed (as in Caenorhabditis elegans) is unclear. Using Oligopaints in the silkworm, Bombyx mori, we visualize autosomes and chZ in somatic cells from both sexes. We find that B. mori chromosomes are highly compact relative to Drosophila. We show that in B. mori males, both chZs are similar in size and shape and are more compact than autosomes or the female chZ after DC establishment, suggesting both male chZs are partially and equally downregulated. We also find that in the early stages of DC in females, chZ chromatin becomes more accessible and Z-linked expression increases. Concomitant with these changes, the female chZ repositions toward the nuclear center, revealing nonsequencing-based support for Ohno’s hypothesis. These studies visualizing interphase genome organization and chZ structure in Lepidoptera uncover intriguing similarities between DC in B. mori and C. elegans, despite these lineages harboring evolutionarily distinct sex chromosomes (ZW/XY), suggesting a possible role for holocentricity in DC mechanisms.

When Down Is Up: Heterochromatin, Nuclear Organization and X Upregulation

Organisms with highly differentiated sex chromosomes face an imbalance in X-linked gene dosage. Male Drosophila solve this problem by increasing expression from virtually every gene on their single X chromosome, a process known as dosage compensation. This involves a ribonucleoprotein complex that is recruited to active, X-linked genes to remodel chromatin and increase expression. Interestingly, the male X chromosome is also enriched for several proteins associated with heterochromatin. Furthermore, the polytenized male X is selectively disrupted by the loss of factors involved in repression, silencing, heterochromatin formation or chromatin remodeling. Mutations in many of these factors preferentially reduce male survival or enhance the lethality of mutations that prevent normal recognition of the X chromosome. The involvement of primarily repressive factors in a process that elevates expression has long been puzzling. Interestingly, recent work suggests that the siRNA pathway, often associated with heterochromatin formation and repression, also helps the dosage compensation machinery identify the X chromosome. In light of this finding, we revisit the evidence that links nuclear organization and heterochromatin to regulation of the male X chromosome.

Chromosome-wide mechanisms to decouple gene expression from gene dose during sex-chromosome evolution

Changes in chromosome number impair fitness by disrupting the balance of gene expression. Here we analyze mechanisms to compensate for changes in gene dose that accompanied the evolution of sex chromosomes from autosomes. Using single-copy transgenes integrated throughout the Caenorhabditis elegans genome, we show that expression of all X-linked transgenes is balanced between XX hermaphrodites and XO males. However, proximity of a dosage compensation complex (DCC) binding site (rex site) is neither necessary to repress X-linked transgenes nor sufficient to repress transgenes on autosomes. Thus, X is broadly permissive for dosage compensation, and the DCC acts via a chromosome-wide mechanism to balance transcription between sexes. In contrast, no analogous X-chromosome-wide mechanism balances transcription between X and autosomes: expression of compensated hermaphrodite X-linked transgenes is half that of autosomal transgenes. Furthermore, our results argue against an X-chromosome dosage compensation model contingent upon rex-directed positioning of X relative to the nuclear periphery.

DOI:http://dx.doi.org/10.7554/eLife.17365.001

DNA inside cells is packaged into structures called chromosomes, each of which contains numerous genes. Many organisms, including humans, have two copies of most chromosomes in their cells. If the process of cell division goes awry, cells can end up with too many or too few copies of their chromosomes, which can cause serious illnesses.

Sex chromosomes pose a conundrum for cells. In humans, females have two copies of the X chromosome, whereas males only have one. This means that males have half the copy number (dose) of genes on the X chromosome. Human cells correct this imbalance by suppressing the activity, or expression, of most of the genes on one of the X chromosomes in females.

“Dosage compensation” also occurs in the roundworm species Caenorhabditis elegans, because male worms have one X chromosome whilst hermaphrodites have two. The dosage compensation mechanism in roundworms differs from that in humans. It involves turning down the expression of both hermaphrodite X chromosomes by half. The process is enacted by a dosage compensation complex that binds to specific sites along both hermaphrodite X chromosomes.

Dosage compensation mechanisms that reduce X chromosome expression in females cause sex chromosomes to have lower gene expression than non-sex chromosomes. Modern sex chromosomes evolved from a pair of non-sex chromosomes, and males lost one copy of all of the genes located on those ancestral chromosomes. This evolutionary history causes both sexes to have lower gene expression from X chromosomes than the other chromosomes, raising the question of whether a mechanism exists to balance out the difference in gene expression between sex chromosomes and non-sex chromosomes.

Wheeler et al. now show that the expression of any foreign gene artificially added to the X chromosomes of C. elegans is equalized between males and hermaphrodites despite the difference in gene dose. The equalization works regardless of where on the X chromosome the new gene is added. The foreign gene does not need to be adjacent to a binding site for the dosage compensation complex. These results indicate that dosage compensation mechanisms regulate gene expression on a chromosome-wide scale.

Wheeler et al. also show that genes added to X chromosomes are expressed at half the level as the same genes added to non-sex chromosomes. These results mean that no chromosome-wide mechanism balances gene expression levels between the X chromosome and the non-sex chromosomes.

It remains unknown how C. elegans, and many other living organisms, evolved to tolerate a lower level of gene expression from the sex chromosomes. Instead of a chromosome-wide mechanism, it is likely that individual genes evolved different ways to alter their expression levels. Working out what these mechanisms are remains a challenge for further research.

DOI:http://dx.doi.org/10.7554/eLife.17365.002

Dosage compensation of the sex chromosomes and autosomes

Males are XY and females are XX in most mammalian species. Other species such as birds have a different sex chromosome make-up: ZZ in males and ZW in females. In both types of organisms one of the sex chromosomes, Y or W, has degenerated due to lack of recombination with its respective homolog X or Z. Since autosomes are present in two copies in diploid organisms the heterogametic sex has become a natural "aneuploid" with haploinsufficiency for X- or Z-linked genes. Specific mechanisms have evolved to restore a balance between critical gene products throughout the genome and between males and females. Some of these mechanisms were co-opted from and/or added to compensatory processes that alleviate autosomal aneuploidy. Surprisingly, several modes of dosage compensation have evolved. In this review we will consider the evidence for dosage compensation and the molecular mechanisms implicated.

Dosage compensation and nuclear organization: cluster to control chromosome-wide gene expression

In many species, male and female animals differ in the number of X chromosomes they possess. As a consequence, large scale differences in gene dosage exist between sexes; a phenomenon that is rarely tolerated by the organism for changes in autosome dosage. Several strategies have evolved independently to balance X-linked gene dosage between sexes, named dosage compensation (DC). The molecular basis of DC differs among the three best-studied examples: mammals, fruit fly and nematodes. In this short review, we summarize recent microscopic and chromosome conformation capture data that reveal key features of the compensated X chromosome and highlight the events leading to the establishment of a functional, specialized nuclear compartment, the X domain.