Sex – phenotypically different males and females making sperm or eggs which must fuse to make a new diploid individual – is almost ubiquitous in animals because there are big advantages in mixing gene variants to produce fitter progeny. The discovery of sex chromosomes, and the strange patterns of inheritance (sex linkage) of genes on the X, provided the first clues about how sex is determined. Meiosis, the specialized division that halves the chromosome number and separates the X and Y in males, ensures a 1:1 sex ratio in the progeny, which can be subverted. Here I discuss classical studies of the human X chromosome, and the diseases caused by mutations of X-borne genes, then the technical leaps that enabled construction of detailed genetic and physical maps of the human X chromosome, and the progressive compilation of its gene content. Early characterization of the human Y revealed a much smaller, gene poor and repeat-ridden little chromosome that pairs with the X at male meiosis only over a tiny terminal pseudoautosomal region.

The discovery that the SRY gene represents the long-sought testis determining factor (TDF) excited expectations that it would be easy to identify its target and elucidate the whole sex-determining pathway in mammals. But it took more than 20 years to discover the targets of SRY and how they interact with other pathways to effect differentiation of the testis in XY embryos and an ovary in XX embryos. It required a mixture of biochemical studies of the transcript, the protein and its binding partners, and of genes identified from mutant mice and patients with atypical sexual differentiation. The sex-determining pathway is not a simple linear pathway, nor is there a simple on-off switch that determines whether the male or the female pathway will be followed. Rather, it is a network, full of checks and balances between antagonistic genes. Here I summarize the work that has led us, at last, to an understanding of the network of pathways that control sexual differentiation in humans and other mammals.

The whole point of sex chromosomes, the reason they have evolved and differentiated, is that they specify the sex of an individual and the type of gametes (eggs or sperm) that they produce. Here I review the profound biological differences between men and women, the role of sex hormones and the differentiation of either a testis or an ovary in the embryo. I describe the classic experiments that show that testis development is the key factor in human sex determination. I discuss the evidence that sex differences between men and women, are triggered by a single gene (the mysterious ‘testis determining factor’ TDF on the Y chromosome) that sends gonad development down the testis-determining pathway. The testis makes hormones, and these male hormones make the baby a boy. In the absence of TDF, an ovary forms, and female hormones ensure female development. I describe the search for TDF on the human Y chromosome – the false starts and eventual successful identification of the SRY gene.

Here I describe how molecular techniques have been applied to mammalian sex chromosomes, and the remarkable insights they have provided into the structure, sequence and gene content of the X and Y in humans and other mammals. Mammal species share an XY sex chromosome pair, with a medium-sized X, and a much smaller Y bearing few genes and a lot of repetitive DNA. To zero in on sex chromosomes, molecular scale maps of the X and Y chromosomes were constructed for humans and other mammals, which built on the genetic and physical maps described in Chapter 2. This paved the way to applying the rapidly developing DNA sequencing methods to reveal the most intimate molecular details of human sex chromosomes as part of the Human Genome Project. This revealed not only the gene content of the X and Y, but peculiarities of their structure. The tips of the X and Y were homologous over a pseudoautosomal region, which paired and recombined at male meiosis. The Y, in particular, bore genes that had become specialized and often greatly amplified within ‘palindrome’ loops.

We know that the mammal Y chromosome is quite young, and SRY is not shared with non-mammal vertebrates, or even with monotreme mammals. Here I describe the discovery of different sex-determining genes in other vertebrates, and investigations of how they work to determine sex. I distinguish four basic chromosomal sex-determining systems, defined either by a dominant gene on the sex-specific chromosome, or by dosage differences of a gene on the shared sex chromosome. I examine the gathering evidence that sex gene networks are basically conserved, but are triggered by many different sex-determining genes in different vertebrate lineages. I examine the examples of sex gene turnover, in which an old sex-determining gene has been replaced by a different gene, and show how easy it is to make a novel sex-determining gene by mutation of a gene or regulatory sequence, chromosome rearrangement, gene copying and even epigenetic change. I discuss how environmental factors such as temperature interact with sex-determining genes, and how sudden flip-flops between genetic and temperature sex determination can speed up the evolution of new systems.

Intense study of the molecular mechanisms of X inactivation revealed cooperation between molecular changes at many levels. Transcriptional inactivation of genes on the inactive X correlates with binding with several modified histones that are associated with inactivation, and loss of modified histones associated with activation. DNA methylation is associated with silencing, and removing methyl groups causes reactivation. The inactive X is held in a very atypical 3D conformation which obliterates the topological domains obvious on the active X and autosomes. A breakthrough was the discovery that the X inactivation centre contained a gene that was transcribed into a long noncoding RNA only on the inactive X; this XIST gene appears to coordinate modification of DNA and of histones, and binding to membranes, nuclear structures and many protein cofactors.

Sexual reproduction is almost universal amongst eukaryotes. Gametes are produced in the gonad (eggs in the ovary of a female, sperm in the testis of a male) then fuse to form an individual with unique combinations of parental traits. In mammals, birds, snakes and most other vertebrates, most insects and a few plants, sex of an individual is determined by a gene on specialized sex chromosomes which trigger either the male or the female developmental pathway. Sex chromosomes are peculiarly fascinating. Firstly, because they bear the genes that determine sex. But also because they possess unique features imposed upon them by their possession of this control gene. Understanding the organization, function and evolution of sex chromosomes requires some fundamental knowledge of biology and genetics. In this chapter, I will skim lightly across the critical concepts and some of the methods we use to test them, for readers who do not have a background in biology. I will also introduce mammals and other vertebrates on which this book focuses.

Sex is the most dramatic normal human polymorphism. A single gene triggers remarkable physical differences in gonads and gametes, in anatomy and behaviour of men and women via a network of genes that induce a ridge of cells to become either a testis or an ovary. These very different gonads make hormones that activate other whole networks of genes in far-flung tissues and organs. Here I explore the role of sex differences in health, longevity, reproduction and evolution, societal roles and discrimination. Sex is genetically complex, and wide variation results from variation in genes of the sex pathway, in hormone-producing genes, and in downstream genes that receive these messages in other tissues. This throws up ethical dilemmas of whether, or how, to treat, babies with atypical sexual development. And how to create a ‘level playing field’ for sport. Some variants may influence gender identity, and mate choice so that transgender and homosexual, may both be seen as simply the edges of normal curves of male and female sexual development. I conclude with the hope that we are heading for a more enlightened world in which variation in sexual development and behaviour, and sexual identity is accepted and celebrated.

Here I discuss how X chromosome inactivation might have evolved in mammals to compensate for the progressive loss of alleles from the Y chromosome. We can exploit genetic differences between species in the expression and the molecular mechanism of X inactivation to explore how the several layers of silencing could have evolved to build the extraordinarily stable silencing of the inactive X in eutherian mammals. I describe how dosage compensation works (or doesn’t work) in other vertebrates that have differentiated sex chromosomes; monotremes, birds, snakes, even frogs and fish. We must ask the question – how essential is dosage compensation anyway? Are there other ways of coping with dosage inequities brought on by sex chromosome differentiation? I then describe briefly some of the best-known dosage compensation systems, in our invertebrate models, revealing many ancient silencing mechanisms whose components we recognize in fish, flies and humans. These mechanisms are there in all sorts of other systems in which epigenetic silencing has been selected for, constituting an ancient molecular toolbox full of ways to regulate the activities of genes, or of whole regions of the genome.