Comparative Genomics in Eukaryotes IV GENE 330 CHROMOSOMES

Comparative Genomics in Eukaryotes IV. GENE 330

CHROMOSOMES Chromosome Number • Within species, the number of chromosomes is almost always an even multiple of a basic number • E. g. in humans the basic number is 23; mature eggs and sperm have this number of chromosomes. Most other types of human cells have twice as many (46). • The haploid, or basic chromosome number (n) defines a set of chromosomes called the haploid genome • Most somatic cells contain two of each the chromosomes in this set and are therefore diploid (2 n). • The basic number of chromosomes varies among spicies. • Chromosome number is not related to the size or biological complexity of an organism, with most species containing between 10 and 40 chromosomes in their genomes

Numbers of Pairs of Chromosomes in Different Species of Plants and Animals

SEX-DETERMINATION SYSTEM n n n A sex-determination system is a biological system that determines the development of sexual characteristics in an organism. Most sexual organisms have two sexes. In many cases, sex determination is genetic: males and females have different alleles or even different genes that specify their sexual morphology. In animals, this is often accompanied by chromosomal differences. In other cases, sex is determined by environmental variables (such as temperature) or social variables (the size of organism relative to other members of its population). The details of some sex-determination systems are not yet fully understood.

NON-GENETIC SEX-DETERMINATION SYSTEMS n n n In some species of reptiles, including alligators, some turtles, and the tuatara, sex is determined by the temperature at which the egg is incubated. Other species, such as some snails, practice sex change; adults start out male, then become female. In tropical clown fish, the dominant individual in a group becomes female while the other ones are male. Some species have no sex-determination system. Earthworms and some snails are hermaphrodites; a few species of lizard, fish, and insect are all female and reproduce by parthenogenesis. In some arthropods, sex is determined by infection, as when bacteria of the genus Wolbachia alter their sexuality; some species consist entirely of ZZ individuals (males), with sex determined by the presence of Wolbachia.

EVOLUTION OF SEX CHROMOSOMES n n n Sex chromosomes have arisen independently in many taxonomic groups. It is an interesting question whether the same mechanisms were involved each time. Similarities in sex chromosome evolution have been reported between birds and mammals (although in birds, females are the heterozygous sex). In one study has been uncovered striking parallels in the details of sex chromosome evolution between mammals and a far more distant group: plants! The theory of sex chromosome evolution holds that sex chromosomes were once homologs (a pair of equivalent autosomes) that evolved different morphology and gene content because they lost their ability to recombine. Suppression of recombination is thought to start around the sexdetermining region, but may eventually affect much of the sex chromosomes. Recombination is a key genetic process in which two chromosomes pair and exchange their sequences. In the absence of recombination, the two chromosomes of a pair evolve separately.

EVOLUTION OF SEX CHROMOSOMES n n n Sex chromosomes are an oddity in flowering plants. They are limited to dioecious species, a subset of plants that carry male and female organs on separate individuals (most flowering plants are hermaphrodites). In some genus e. g. Silene , which include the White Campion, includes both dioecious and hermaphrodite species. The X and Y chromosomes of dioecious Silene species are morphologically distinct, like those in mammals, and they also have a PAR (pseudoautosomal region) and nonrecombining region.

CHROMOSOMAL DETERMINATION n n XX/XY sex chromosomes In the XY sex-determination system individuals inheriting a Y chromosome become males, and XX individuals females. The XY sex chromosomes are different in shape and size from each other unlike the autosomes, and are termed allosomes/heterochromosomes. XX/X 0 sex determination In this variant of the XY system, XX individuals are females, and males are X 0 individuals. This system is observed in a number of insects, including grasshoppers and crickets and in cockroaches. The nematode C. elegans X 0 is male and XX is a hermaphrodite. ZW sex chromosomes The ZW sex-determination system is found in birds and some insects. System is reversed compare to the XY system - ZZ are males and ZW are females. Haplodiploidy System is found in insects – Hymenoptera – such as ants and bees. Unfertilized eggs develop into haploid males. Diploid individuals are generally female but may be sterile males.

CHROMOSOMES Cont… Sex Chromosomes • In other animals, e. g. human beings, males and females have the same number of chromosomes X X X Y

EVOLUTION OF THE HUMAN SEX CHROMOSOMES n n n The X and Y chromosomes of human and other mammalian species are heteromorphic. The human X chromosome is a submetacentric chromosome which contains about 165 Mb of DNA, whereas the Y chromosome is acrocentric and is much smaller – about 60 Mb of DNA. The human X chromosome contains numerous important genes: on the basis of its size alone, it might be expected to contain about 4000 genes. The bulk of the Y chromosome is genetically inert and is composed of constitutive heterochromatin consisting of different types of highly and moderately repetitive noncoding DNA. Only a very few functional genes are found on the Y chromosome, including some which have closely related homologues on the X chromosome. And several which are Y-specific and testis-expressed.

EVOLUTION OF THE HUMAN SEX CHROMOSOMES n n The X and Y chromosomes are able to pair during meiosis in male cells, and to exchange sequence information. Sequence exchange occur within certain small region of homology between X and Y chromosomes, known as pseudoautosomal regions (PAR), which do not show strict sex-linked inheritance. In the human sex chromosomes, there are two PARs: * The PAR 1(the major pseudoautosomal region) extends over 2. 6 Mb at the extreme tips of the short arms of the X and Y chromosomes. It is the site of an obligate crossover during male meiosis which is thought to be required for correct meiotic segregation. This region is remarkable for its high recombination frequency – approximately 10 times the normal recombination frequency. * The PAR 2 (the minor pseudoautosomal region) extends over 320 kb at the extreme tips of the long arms of the X and Y chromosomes. Crossover between the X and Y in this region is not so frequent, and is neither necessary for successful male meiosis.

GENES OUTSIDE PAR n n n n Although 95% of the Y chromosome lies between the PAR, fewer than 80 genes have been found here. Over half of this region is genetically-barren heterochromatin. Of the 80 -odd genes found in the euchromatin , some encode proteins used by all cells. The others encode proteins that appear to function only in the testes. A key player in this latter group is SRY (for sex-determining region Y) is a gene located on short (p) arm just outside the pseudoautosomal region. It is the master switch that triggers the events that converts the embryo into a male. Without this gene, you get a female instead. So femaleness is the “default” program.

X-INACTIVATION n n n X inactivation occurs early in embryonic development. In a given cell, which of a female’s X chromosome becomes inactivated and converted into a Barr body is a matter of chance (except in marsupials like a kangaroo, where it is always the father’s X chromosome that is inactivated). After inactivation has occurred all the descendants of that cell will have the same chromosome inactivated. Thus X-inactivation creates clones with differing effective gene content. An organism whose cells vary in effective gene content and hence in the expression of a trait, is called a genetic mosaic.

MECHANISM OF X-INACTIVATION Inactivation of an X chromosome requires a gene on that chromosome called XIST. n XIST encodes a large molecule of RNA n XIST RNA accumulates along the X chromosome containing the active XIST gene and proceeds to inactive all (or almost all) of the other hundreds of genes on that chromosome. n XIST RNA does not travel over to any other X chromosome in the nucleus. n Barr bodies are inactive X chromosomes “painted” with XIST RNA.

Bar body in a human female cell stained with cresyl violet

CHROMOSOMES Cont… Sex Chromosomes • In other animals, e. g. human beings, males and females have the same number of chromosomes, due the presence of Y chromosome in males which pairs with X during meiosis. • The Y chromosome is morphologically distinct from the X chromosome. e. g. in humans the Y chromosome is much shorter than X chromosome and its centromere is located closer to one of the ends. • The common regions to human X and Y chromosoms is at the extreme tips of the arms(short and long) near the end of the chromosomes. • During meiosis in the male, the X and Y chromosomes separate from each other producing two kinds of sperm, X bearing and Y bearing; the frequencies of the two types are approximately equal. • XX females produce only one kind of egg, which is X-bearing. • If fertilization were to occur randomly, approximately half the zygotes would be XX, leading to 1: 1 sex ratio at conception

CHROMOSOMES Cont… Sex Chromosomes • However, in humans, Y-bearing sperm have a fertilization advantage, and the zygotic sex ratio is about 1. 3 : 1. • During development, the excess of males is diminished by differential viability of XX and XY embryos, and at birth, males are only slightly more numerous than females (sex ratio 1. 07. 1 • By the age of production, the excess of males is essentially eliminated and the sex ratio is very close to 1: 1. • The X and Y chromosomes are called sex chromosomes and all other chromosomes in the genome are called autosomes

CHROMOSOMES Cont… Sex Chromosomes • Some animals such as grasshoppers females have one or more chromosome than males This extra chromosome is called the X chromosome • Females of such chromosomes have 2 X chromosomes and males have only 1. Thus males are cyctologically XX and males XO • During meiosis in the female, the two X chromosomes pair and then separate, producing eggs that contain a single X chromosome. • In the males, the solitary X chromosome moves independently of all the other chromosomes and is incorporated into half the sperm; the other half receive no X chromosome • Thus, the sperm and eggs unite, two kinds of zygotes are produced: XX, which develop into females, and XO, which develop into males. • In these animals, the reproductive mechanism preserves a 1: 1 ratio of males to females in these species

CHROMOSOMES Cont… Sex Chromosomes X X X O