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For information about chromosomes in genetic algorithms, see chromosome (genetic algorithm).

For a non-technical introduction to the topic, see Introduction to genetics.

Diagram of a duplicated and condensed (metaphase) eukaryotic chromosome. (1) Chromatid - one of the two identical parts of the chromosome after S phase. (2) Centromere - the point where the two chromatids touch, and where the microtubules attach. (3) Short arm. (4) Long arm.

Chromosomes are organized structures of DNA and proteins that are found in cells. A chromosome is a singular piece of DNA, which contains many genes, regulatory elements and other nucleotide sequences. Chromosomes also contain DNA-bound proteins, which serve to package the DNA and control its functions. The word chromosome comes from the Greek χρῶμα (chroma, color) and σῶμα (soma, body) due to their property of being stained very strongly by some dyes.

Chromosomes vary extensively between different organisms. The DNA molecule may be circular or linear, and can contain anything from tens of kilobase pairs to hundreds of megabase pairs. Typically eukaryotic cells (cells with nuclei) have large linear chromosomes and prokaryotic cells (cells without defined nuclei) have smaller circular chromosomes, although there are many exceptions to this rule. Furthermore, cells may contain more than one type of chromosome; for example, mitochondria in most eukaryotes and chloroplasts in plants have their own small chromosomes.

In eukaryotes, nuclear chromosomes are packaged by proteins into a condensed structure called chromatin. This allows the very long DNA molecules to fit into the cell nucleus. The structure of chromosomes and chromatin varies through the cell cycle. Chromosomes may exist as either duplicated or unduplicated—unduplicated chromosomes are single linear strands, whereas duplicated chromosomes (copied during synthesis phase) contain two copies joined by a centromere. Compaction of the duplicated chromosomes during mitosis and meiosis results in the classic four-arm structure (pictured to the right).

"Chromosome" is a rather loosely defined term. In prokaryotes, a small circular DNA molecule may be called either a plasmid or a small chromosome. These small circular genomes are also found in mitochondria and chloroplasts, reflecting their bacterial origins. The simplest chromosomes are found in viruses: these DNA or RNA molecules are short linear or circular chromosomes that often lack any structural proteins.

History

This is a brief history of research in a complex field where each advance was hard won, and often hotly disputed at the time.

Visual discovery of chromosomes. Textbooks have often said that chromosomes were first observed in plant cells by a Swiss botanist named Karl Wilhelm von Nägeli in 1842. However, this opinion has been challenged, perhaps decisively, by Henry Harris, who has freshly reviewed the primary literature. In his opinion the claim of Nägeli to have seen spore mother cells divide is mistaken, as are some of his interpretations. Harris considers other candidates, especially Wilhelm Hofmeister, whose publications in 1848-9 include plates that definitely show mitotic events. Hofmeister was also the choice of Cyril Darlington.

The work of other cytologists such as Walther Flemming, Eduard Strasburger, Otto Bütschli, Oskar Hertwig and Carl Rabl should be acknowledged. The use of basophilic aniline dyes was a new technique for effectively staining the chromatin material in the nucleus. Their behavior in animal (salamander) cells was later described in detail by Walther Flemming, who in 1882 "provided a superb summary of the state of the field." The name chromosome was invented in 1888 by Heinrich von Waldeyer. However, van Beneden's monograph of 1883 on the fertilised eggs of the parasitic roundworm Ascaris megalocephala was the outstanding work of this period. His conclusions are classic:

• Thus there is no fusion between the male chromatin and the female chromatin at any stage of division....
• The elements of male origin and those of female origin are never fused together in a cleavage nucleus, and perhaps they remain distinct in all the nuclei derived from them. [tranl: Harris p162]

"It is not easy to identify who first discerned chromosomes during mitosis, but there is no doubt that those who first saw them had no idea of their significance... [but] with the work of Balbiani and van Beneden we move away from... the mechanism of cell division to a precise delineation of chromosomes and what they do during the division of the cell."

Van Beneden's master work was closely followed by that of Carl Rabl, who reached similar conclusions. This more or less concludes the first period, in which chromosomes were visually sighted and the morphological stages of mitosis were described. Coleman also gives a useful review of these discoveries.

Nucleus as the seat of heredity. The origin of this epoch-making idea lies in a few sentences tucked away in Ernst Haeckel's Generelle Morphologie of 1866. The evidence for this insight gradually accumulated until, after twenty or so years, two of the greatest in a line of great German scientists spelled out the concept. August Weismann proposed that the germ line is separate from the soma, and that the cell nucleus is the repository of the hereditary material, which, he proposed, is arranged along the chromosomes in a linear manner. Furthermore, he proposed that at fertilisation a new combination of chromosomes (and their hereditary material) would be formed. This was the explanation for the reduction division of meiosis (first described by van Beneden).

Chromosomes as vectors of heredity. In a series of outstanding experiments, Theodor Boveri gave the definitive demonstration that chromosomes are the vectors of heredity. His two principles were:

The continuity of chromosomes

The individuality of chromosomes.

It is the second of these principles that was so original. Boveri was able to test the proposal put forward by Wilhelm Roux, that each chromosome carries a different genetic load, and showed that Roux was right. Upon the rediscovery of Mendel, Boveri was able to point out the connection between the rules of inheritance and the behaviour of the chromosomes. It is interesting to see that Boveri influenced two generations of American cytologists: Edmund Beecher Wilson, Walter Sutton and Theophilus Painter were all influenced by Boveri (Wilson and Painter actually worked with him). In his famous textbook The Cell, Wilson linked Boveri and Sutton together by the Boveri-Sutton theory. Mayr remarks that the theory was hotly contested by some famous geneticists: William Bateson, Wilhelm Johannsen, Richard Goldschmidt and T.H. Morgan, all of a rather dogmatic turn-of-mind. Eventually complete proof came from chromosome maps – in Morgan's own lab.

Chromosomes in eukaryotes

Eukaryotes (cells with nuclei such as plants, yeast, and animals) possess multiple large linear chromosomes contained in the cell's nucleus. Each chromosome has one centromere, with one or two arms projecting from the centromere, although, under most circumstances, these arms are not visible as such. In addition, most eukaryotes have a small circular mitochondrial genome, and some eukaryotes may have additional small circular or linear cytoplasmic chromosomes.

In the nuclear chromosomes of eukaryotes, the uncondensed DNA exists in a semi-ordered structure, where it is wrapped around histones (structural proteins), forming a composite material called chromatin.

Chromatin

Main article: Chromatin

Fig. 2: The major structures in DNA compaction; DNA, the nucleosome, the 10nm "beads-on-a-string" fibre, the 30nm fibre and the metaphase chromosome.

Chromatin is the complex of DNA and protein found in the eukaryotic nucleus which packages chromosomes. The structure of chromatin varies significantly between different stages of the cell cycle, according to the requirements of the DNA.

Interphase chromatin

During interphase (the period of the cell cycle where the cell is not dividing) two types of chromatin can be distinguished:

• Euchromatin, which consists of DNA that is active, e.g., expressed as protein.
• Heterochromatin, which consists of mostly inactive DNA. It seems to serve structural purposes during the chromosomal stages. Heterochromatin can be further distinguished into two types:
  • Constitutive heterochromatin, which is never expressed. It is located around the centromere and usually contains repetitive sequences.
  • Facultative heterochromatin, which is sometimes expressed.

Individual chromosomes cannot be distinguished at this stage - they appear in the nucleus as a homogeneous tangled mix of DNA and protein.

Metaphase chromatin and division

See also: mitosis and meiosis

Human chromosomes during metaphase.

In the early stages of mitosis or meiosis (cell division), the chromatin strands become more and more condensed. They cease to function as accessible genetic material (transcription stops) and become a compact transportable form. This compact form makes the individual chromosomes visible, and they form the classic four arm structure, a pair of sister chromatids attached to each other at the centromere. The shorter arms are called p arms (from the French petit, small) and the longer arms are called q arms (q follows p in the Latin alphabet). This is the only natural context in which individual chromosomes are visible with an optical microscope.

During divisions long microtubules attach to the centromere and the two opposite ends of the cell. The microtubules then pull the chromatids apart, so that each daughter cell inherits one set of chromatids. Once the cells have divided, the chromatids are uncoiled and can function again as chromatin. In spite of their appearance, chromosomes are structurally highly condensed, which enables these giant DNA structures to be contained within a cell nucleus (Fig. 2).

The self-assembled microtubules form the spindle, which attaches to chromosomes at specialized structures called kinetochores, one of which is present on each sister chromatid. A special DNA base sequence in the region of the kinetochores provides, along with special proteins, longer-lasting attachment in this region.

Chromosomes in prokaryotes

The prokaryotes - bacteria and archaea - typically have a single circular chromosome, but many variations do exist. Most bacteria have a single circular chromosome that can range in size from only 160,000 base pairs in the endosymbiotic bacteria Candidatus Carsonella ruddii, to 12,200,000 base pairs in the soil-dwelling bacteria Sorangium cellulosum. Spirochaetes of the genus Borrelia are a notable exception to this arrangement, with bacteria such as Borrelia burgdorferi, the cause of Lyme disease, containing a single linear chromosome.

Structure in sequences

Prokaryotes chromosomes have less sequence-based structure than eukaryotes. Bacteria typically have a single point (the origin of replication) from which replication starts, whereas some archaea contain multiple replication origins. The genes in prokaryotes are often organized in operons, and do not contain introns, unlike eukaryotes.

DNA packaging

Prokaryotes do not possess nuclei. Instead, their DNA is organized into a structure called the nucleoid. The nucleoid is a distinct structure and occupies a defined region of the bacterial cell. This structure is, however, dynamic and is maintained and remodeled by the actions of a range of histone-like proteins, which associate with the bacterial chromosome. In archaea, the DNA in chromosomes is even more organized, with the DNA packaged within structures similar to eukaryotic nucleosomes.

Bacterial chromosomes tend to be tethered to the plasma membrane of the bacteria. In molecular biology application, this allows for its isolation from plasmid DNA by centrifugation of lysed bacteria and pelleting of the membranes (and the attached DNA).

Prokaryotic chromosomes and plasmids are, like eukaryotic DNA, generally supercoiled. The DNA must first be released into its relaxed state for access for transcription, regulation, and replication.

Number of chromosomes in various organisms

Main article: List of number of chromosomes of various organisms

Eukaryotes

These tables give the total number of chromosomes (including sex chromosomes) in a cell nucleus. For example, human cells are diploid and have 22 different types of autosomes, each present as two copies, and two sex chromosomes. This gives 46 chromosomes in total. Other organisms have more than two copies of their chromosomes, such as Bread wheat, which is hexaploid and has six copies of seven different chromosomes - 42 chromosomes in total.

Chromosome numbers in some plants Plant Species # Arabidopsis thaliana (diploid) 10 Rye (diploid) 14 Maize (diploid) 20 Einkorn wheat (diploid) 14 Durum wheat (tetraploid) 28 Bread wheat (hexaploid) 42 Potato (tetraploid) 48 Cultivated tobacco (diploid) 48 Adder's Tongue Fern (diploid) approx 1,440

Chromosome numbers (2n) in some animals Species # Species # Common fruit fly 8 Guinea Pig 64 Dove 16 Garden snail 54 Earthworm Octodrilus complanatus 36 Tibetan fox 36 Domestic cat 38 Domestic pig 38 Lab mouse 40 Lab rat 42 Rabbit 44 Syrian hamster 44 Hare 46 Human 46 Gorillas, Chimpanzees 48 Domestic sheep 54 Elephants 56 Cow 60 Donkey 62 Horse 64 Dog 78 Kingfisher 132 Goldfish 100-104 Silkworm 56

Chromosome numbers in other organisms Species Large Chromosomes Intermediate Chromosomes Small Chromosomes Trypanosoma brucei 11 6 ~100 Chicken 8 2 sex chromosomes 60 Normal members of a particular eukaryotic species all have the same number of nuclear chromosomes (see the table). Other eukaryotic chromosomes, i.e., mitochondrial and plasmid-like small chromosomes, are much more variable in number, and there may be thousands of copies per cell. The 24 human chromosome territories during prometaphase in fibroblast cells. Asexually reproducing species have one set of chromosomes, which is the same in all body cells. Sexually reproducing species have somatic cells (body cells), which are diploid [2n] having two sets of chromosomes, one from the mother and one from the father. Gametes, reproductive cells, are haploid [n]: They have one set of chromosomes. Gametes are produced by meiosis of a diploid germ line cell. During meiosis, the matching chromosomes of father and mother can exchange small parts of themselves (crossover), and thus create new chromosomes that are not inherited solely from either parent. When a male and a female gamete merge (fertilization), a new diploid organism is formed. Some animal and plant species are polyploid [Xn]: They have more than two sets of homologous chromosomes. Plants important in agriculture such as tobacco or wheat are often polyploid, compared to their ancestral species. Wheat has a haploid number of seven chromosomes, still seen in some cultivars as well as the wild progenitors. The more-common pasta and bread wheats are polyploid, having 28 (tetraploid) and 42 (hexaploid) chromosomes, compared to the 14 (diploid) chromosomes in the wild wheat. Prokaryotes Prokaryote species generally have one copy of each major chromosome, but most cells can easily survive with multiple copies. For example, Buchnera, a symbiont of aphids has multiple copies of its chromosome, ranging from 10–400 copies per cell. However, in some large bacteria, such as Epulopiscium fishelsoni up to 100,000 copies of the chromosome can be present. Plasmids and plasmid-like small chromosomes are, as in eukaryotes, very variable in copy number. The number of plasmids in the cell is almost entirely determined by the rate of division of the plasmid - fast division causes high copy number, and vice versa. Karyotype Main article: Karyotype Figure 3: Karyogram of a human male In general, the karyotype is the characteristic chromosome complement of a eukaryote species. The preparation and study of karyotypes is part of cytogenetics. Although the replication and transcription of DNA is highly standardized in eukaryotes, the same cannot be said for their karotypes, which are often highly variable. There may be variation between species in chromosome number and in detailed organization. In some cases, there is significant variation within species. Often there is 1. variation between the two sexes; 2. variation between the germ-line and soma (between gametes and the rest of the body); 3. variation between members of a population, due to balanced genetic polymorphism; 4. geographical variation between races; 5. mosaics or otherwise abnormal individuals. Also, variation in karyotype may occur during development from the fertilised egg. The technique of determining the karyotype is usually called karyotyping. Cells can be locked part-way through division (in metaphase) in vitro (in a reaction vial) with colchicine. These cells are then stained, photographed, and arranged into a karyogram, with the set of chromosomes arranged, autosomes in order of length, and sex chromosomes (here XY) at the end: Fig. 3. Like many sexually reproducing species, humans have special gonosomes (sex chromosomes, in contrast to autosomes). These are XX in females and XY in males. Historical note Investigation into the human karyotype took many years to settle the most basic question. How many chromosomes does a normal diploid human cell contain? In 1912, Hans von Winiwarter reported 47 chromosomes in spermatogonia and 48 in oogonia, concluding an XX/XO sex determination mechanism. Painter in 1922 was not certain whether the diploid number of man is 46 or 48, at first favouring 46. He revised his opinion later from 46 to 48, and he correctly insisted on man's having an XX/XY system. New techniques were needed to definitively solve the problem: 1. Using cells in culture 2. Pretreating cells in a hypotonic solution, which swells them and spreads the chromosomes 3. Arresting mitosis in metaphase by a solution of colchicine 4. Squashing the preparation on the slide forcing the chromosomes into a single plane 5. Cutting up a photomicrograph and arranging the result into an indisputable karyogram. It took until the mid-1950s until it became generally accepted that the human karyotype include only 46 chromosomes. Considering the techniques of Winiwarter and Painter, their results were quite remarkable. Chimpanzees (the closest living relatives to modern humans) have 48 chromosomes. Chromosomal aberrations Main articles: Chromosome abnormalities and aneuploidy The three major single chromosome mutations; deletion (1), duplication (2) and inversion (3). The two major two-chromosome mutations; insertion (1) and translocation (2). In Down syndrome, there are three copies of chromosome 21 Chromosomal aberrations are disruptions in the normal chromosomal content of a cell, and are a major cause of genetic conditions in humans, such as Down syndrome. Some chromosome abnormalities do not cause disease in carriers, such as translocations, or chromosomal inversions, although they may lead to a higher chance of birthing a child with a chromosome disorder. Abnormal numbers of chromosomes or chromosome sets, aneuploidy, may be lethal or give rise to genetic disorders. Genetic counseling is offered for families that may carry a chromosome rearrangement. The gain or loss of chromosome material can lead to a variety of genetic disorders. Human examples include: Cri du chat, which is caused by the deletion of part of the short arm of chromosome 5. "Cri du chat" means "cry of the cat" in French, and the condition was so-named because affected babies make high-pitched cries that sound like those of a cat. Affected individuals have wide-set eyes, a small head and jaw, and are moderately to severely mentally retarded and very short. Wolf-Hirschhorn syndrome, which is caused by partial deletion of the short arm of chromosome 4. It is characterized by severe growth retardation and severe to profound mental retardation. Down's syndrome, usually is caused by an extra copy of chromosome 21 (trisomy 21). Characteristics include decreased muscle tone, stockier build, asymmetrical skull, slanting eyes and mild to moderate mental retardation. Edwards syndrome, which is the second-most-common trisomy; Down syndrome is the most common. It is a trisomy of chromosome 18. Symptoms include mental and motor retardation and numerous congenital anomalies causing serious health problems. Ninety percent die in infancy; however, those that live past their first birthday usually are quite healthy thereafter. They have a characteristic clenched hands and overlapping fingers. Patau Syndrome, also called D-Syndrome or trisomy-13. Symptoms are somewhat similar to those of trisomy-18, but they do not have the characteristic hand shape. Idic15, abbreviation for Isodicentric 15 on chromosome 15; also called the following names due to various researches, but they all mean the same; IDIC(15), Inverted dupliction 15, extra Marker, Inv dup 15, partial tetrasomy 15 Jacobsen syndrome, also called the terminal 11q deletion disorder. This is a very rare disorder. Those affected have normal intelligence or mild mental retardation, with poor expressive language skills. Most have a bleeding disorder called Paris-Trousseau syndrome. Klinefelter's syndrome (XXY). Men with Klinefelter syndrome are usually sterile, and tend to have longer arms and legs and to be taller than their peers. Boys with the syndrome are often shy and quiet, and have a higher incidence of speech delay and dyslexia. During puberty, without testosterone treatment, some of them may develop gynecomastia. Turner syndrome (X instead of XX or XY). In Turner syndrome, female sexual characteristics are present but underdeveloped. People with Turner syndrome often have a short stature, low hairline, abnormal eye features and bone development and a "caved-in" appearance to the chest. XYY syndrome. XYY boys are usually taller than their siblings. Like XXY boys and XXX girls, they are somewhat more likely to have learning difficulties. Triple-X syndrome (XXX). XXX girls tend to be tall and thin. They have a higher incidence of dyslexia. Small supernumerary marker chromosome. This means there is an extra, abnormal chromosome. Features depend on the origin of the extra genetic material. Cat-eye syndrome and isodicentric chromosome 15 syndrome (or Idic15) are both caused by a supernumerary marker chromosome, as is Pallister-Killian syndrome. Chromosomal mutations produce changes in whole chromosomes (more than one gene) or in the number of chromosomes present. Deletion - loss of part of a chromosome Duplication - extra copies of a part of a chromosome Inversion - reverse the direction of a part of a chromosome Translocation - part of a chromosome breaks off and attaches to another chromosome Most mutations are neutral - have little or no effect A detailed graphical display of all human chromosomes and the diseases annotated at the correct spot may be found at. Human chromosomes Human cells have 23 pairs of large linear nuclear chromosomes, giving a total of 46 per cell. In addition to these, human cells have many hundreds of copies of the mitochondrial genome. Sequencing of the human genome has provided a great deal of information about each of the chromosomes. Below is a table compiling statistics for the chromosomes, based on the Sanger Institute's human genome information in the Vertebrate Genome Annotation (VEGA) database. Number of genes is an estimate as it is in part based on gene predictions. Total chromosome length is an estimate as well, based on the estimated size of unsequenced heterochromatin regions. Chromosome Genes Total bases Sequenced bases 1 3,148 247,200,000 224,999,719 2 902 242,750,000 237,712,649 3 1,436 199,450,000 194,704,827 4 453 191,260,000 187,297,063 5 609 180,840,000 177,702,766 6 1,585 170,900,000 167,273,992 7 1,824 158,820,000 154,952,424 8 781 146,270,000 142,612,826 9 1,229 140,440,000 120,312,298 10 1,312 135,370,000 131,624,737 11 405 134,450,000 131,130,853 12 1,330 132,290,000 130,303,534 13 623 114,130,000 95,559,980 14 886 106,360,000 88,290,585 15 676 100,340,000 81,341,915 16 898 88,820,000 78,884,754 17 1,367 78,650,000 77,800,220 18 365 76,120,000 74,656,155 19 1,553 63,810,000 55,785,651 20 816 62,440,000 59,505,254 21 446 46,940,000 34,171,998 22 595 49,530,000 34,893,953 X (sex chromosome) 1,093 154,910,000 151,058,754 Y (sex chromosome) 125 57,740,000 22,429,293 See also Locus (explains gene location nomenclature) Sex-determination system XY sex-determination system X chromosome X-inactivation Y chromosome Y-chromosomal Adam Y-chromosomal Aaron Genetic genealogy Genealogical DNA test Genetic deletion List of number of chromosomes of various organisms External links Chromosome Abnormalities at AtlasGeneticsOncology What Can Our Chromosomes Tell Us?, from the University of Utah's Genetic Science Learning Center Try making a karyotype yourself, from the University of Utah's Genetic Science Learning Center Kimballs Chromosome pages Chromosome News from Genome News Network Eurochromnet, European network for Rare Chromosome Disorders on the Internet http://www.ensembl.org Ensembl project, presenting chromosomes, their genes and syntenic loci graphically via the web Genographic Project Home reference on Chromosomes from the U.S. National Library of Medicine References