Human X chromosome | |
---|---|
Features | |
Length (bp) | 154,259,566 bp (CHM13) |
No. of genes | 804 (CCDS) |
Type | Allosome |
Centromere position | Submetacentric [1] (61.0 Mbp) [2] |
Complete gene lists | |
CCDS | Gene list |
HGNC | Gene list |
UniProt | Gene list |
NCBI | Gene list |
External map viewers | |
Ensembl | Chromosome X |
Entrez | Chromosome X |
NCBI | Chromosome X |
UCSC | Chromosome X |
Full DNA sequences | |
RefSeq | NC_000023 (FASTA) |
GenBank | CM000685 (FASTA) |
The X chromosome is one of the two sex chromosomes in many organisms, including mammals, and is found in both males and females. It is a part of the XY sex-determination system and XO sex-determination system. The X chromosome was named for its unique properties by early researchers, which resulted in the naming of its counterpart Y chromosome, for the next letter in the alphabet, following its subsequent discovery. [3]
It was first noted that the X chromosome was special in 1890 by Hermann Henking in Leipzig. Henking was studying the testicles of Pyrrhocoris and noticed that one chromosome did not take part in meiosis. Chromosomes are so named because of their ability to take up staining (chroma in Greek means color). Although the X chromosome could be stained just as well as the others, Henking was unsure whether it was a different class of the object and consequently named it X element, [4] which later became X chromosome after it was established that it was indeed a chromosome. [5]
The idea that the X chromosome was named after its similarity to the letter "X" is mistaken. All chromosomes normally appear as an amorphous blob under the microscope and take on a well-defined shape only during mitosis. This shape is vaguely X-shaped for all chromosomes. It is entirely coincidental that the Y chromosome, during mitosis, has two very short branches which can look merged under the microscope and appear as the descender of a Y-shape. [6]
It was first suggested that the X chromosome was involved in sex determination by Clarence Erwin McClung in 1901. After comparing his work on locusts with Henking's and others, McClung noted that only half the sperm received an X chromosome. He called this chromosome an accessory chromosome, and insisted (correctly) that it was a proper chromosome, and theorized (incorrectly) that it was the male-determining chromosome. [4]
This section relies largely or entirely upon a single source .(August 2021) |
Luke Hutchison noticed that a number of possible ancestors on the X chromosome inheritance line at a given ancestral generation follows the Fibonacci sequence. [7] A male individual has an X chromosome, which he received from his mother, and a Y chromosome, which he received from his father. The male counts as the "origin" of his own X chromosome (), and at his parents' generation, his X chromosome came from a single parent (). The male's mother received one X chromosome from her mother (the son's maternal grandmother), and one from her father (the son's maternal grandfather), so two grandparents contributed to the male descendant's X chromosome (). The maternal grandfather received his X chromosome from his mother, and the maternal grandmother received X chromosomes from both of her parents, so three great-grandparents contributed to the male descendant's X chromosome (). Five great-great-grandparents contributed to the male descendant's X chromosome (), etc. (Note that this assumes that all ancestors of a given descendant are independent, but if any genealogy is traced far enough back in time, ancestors begin to appear on multiple lines of the genealogy, until eventually, a population founder appears on all lines of the genealogy.)
The X chromosome in humans spans more than 153 million base pairs (the building material of DNA). It represents about 800 protein-coding genes compared to the Y chromosome containing about 70 genes, out of 20,000–25,000 total genes in the human genome. Each person usually has one pair of sex chromosomes in each cell. Females typically have two X chromosomes, whereas males typically have one X and one Y chromosome. Both males and females retain one of their mother's X chromosomes, and females retain their second X chromosome from their father. Since the father retains his X chromosome from his mother, a human female has one X chromosome from her paternal grandmother (father's side), and one X chromosome from her mother. This inheritance pattern follows the Fibonacci numbers at a given ancestral depth.[ citation needed ]
Genetic disorders that are due to mutations in genes on the X chromosome are described as X linked. If the X chromosome has a genetic disease gene, it always causes illness in male patients, since men have only one X chromosome and therefore only one copy of each gene. Females, instead, require both X chromosomes to have the illness, and as a result could potentially only be a carrier of genetic illness, since their second X chromosome overrides the first. For example, hemophilia A and B and congenital red–green color blindness run in families this way.
The X chromosome carries hundreds of genes but few, if any, of these have anything to do directly with sex determination. Early in embryonic development in females, one of the two X chromosomes is permanently inactivated in nearly all somatic cells (cells other than egg and sperm cells). This phenomenon is called X-inactivation or Lyonization, and creates a Barr body. If X-inactivation in the somatic cell meant a complete de-functionalizing of one of the X-chromosomes, it would ensure that females, like males, had only one functional copy of the X chromosome in each somatic cell. This was previously assumed to be the case. However, recent research suggests that the Barr body may be more biologically active than was previously supposed. [8]
The partial inactivation of the X-chromosome is due to repressive heterochromatin that compacts the DNA and prevents the expression of most genes. Heterochromatin compaction is regulated by Polycomb Repressive Complex 2 (PRC2). [9]
The following are some of the gene count estimates of human X chromosome. Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome varies (for technical details, see gene prediction). Among various projects, the collaborative consensus coding sequence project (CCDS) takes an extremely conservative strategy. So CCDS's gene number prediction represents a lower bound on the total number of human protein-coding genes. [10]
Estimated by | Protein-coding genes | Non-coding RNA genes | Pseudogenes | Source | Release date |
---|---|---|---|---|---|
CCDS | 804 | — | — | [11] | 2016-09-08 |
HGNC | 825 | 260 | 606 | [12] | 2017-05-12 |
Ensembl | 841 | 639 | 871 | [13] | 2017-03-29 |
UniProt | 839 | — | — | [14] | 2018-02-28 |
NCBI | 874 | 494 | 879 | [15] [16] [17] | 2017-05-19 |
The following is a partial list of genes on human chromosome X. For complete list, see the link in the infobox on the right.
It is theorized by Ross et al. 2005 and Ohno 1967 that the X chromosome is at least partially derived from the autosomal (non-sex-related) genome of other mammals, evidenced from interspecies genomic sequence alignments.
The X chromosome is notably larger and has a more active euchromatin region than its Y chromosome counterpart. Further comparison of the X and Y reveal regions of homology between the two. However, the corresponding region in the Y appears far shorter and lacks regions that are conserved in the X throughout primate species, implying a genetic degeneration for Y in that region. Because males have only one X chromosome, they are more likely to have an X chromosome-related disease.
It is estimated that about 10% of the genes encoded by the X chromosome are associated with a family of "CT" genes, so named because they encode for markers found in both tumor cells (in cancer patients) as well as in the human testis (in healthy patients). [18]
Sex linkage was first discovered in insects, e.g., T. H. Morgan's 1910 discovery of the pattern of inheritance of the white eyes mutation in Drosophila melanogaster . [23] Such discoveries helped to explain x-linked disorders in humans, e.g., haemophilia A and B, adrenoleukodystrophy, and red-green color blindness.
XX male syndrome is a rare disorder, where the SRY region of the Y chromosome has recombined to be located on one of the X chromosomes. As a result, the XX combination after fertilization has the same effect as a XY combination, resulting in a male. However, the other genes of the X chromosome cause feminization as well.
X-linked endothelial corneal dystrophy is an extremely rare disease of cornea associated with Xq25 region. Lisch epithelial corneal dystrophy is associated with Xp22.3.
Megalocornea 1 is associated with Xq21.3-q22[ medical citation needed ]
Adrenoleukodystrophy, a rare and fatal disorder that is carried by the mother on the x-cell. It affects only boys between the ages of 5 and 10 and destroys the protective cell surrounding the nerves, myelin, in the brain. The female carrier hardly shows any symptoms because females have a copy of the x-cell. This disorder causes a once healthy boy to lose all abilities to walk, talk, see, hear, and even swallow. Within 2 years after diagnosis, most boys with Adrenoleukodystrophy die.
Chr. | Arm [28] | Band [29] | ISCN start [30] | ISCN stop [30] | Basepair start | Basepair stop | Stain [31] | Density |
---|---|---|---|---|---|---|---|---|
X | p | 22.33 | 0 | 323 | 1 | 4,400,000 | gneg | |
X | p | 22.32 | 323 | 504 | 4,400,001 | 6,100,000 | gpos | 50 |
X | p | 22.31 | 504 | 866 | 6,100,001 | 9,600,000 | gneg | |
X | p | 22.2 | 866 | 1034 | 9,600,001 | 17,400,000 | gpos | 50 |
X | p | 22.13 | 1034 | 1345 | 17,400,001 | 19,200,000 | gneg | |
X | p | 22.12 | 1345 | 1448 | 19,200,001 | 21,900,000 | gpos | 50 |
X | p | 22.11 | 1448 | 1577 | 21,900,001 | 24,900,000 | gneg | |
X | p | 21.3 | 1577 | 1784 | 24,900,001 | 29,300,000 | gpos | 100 |
X | p | 21.2 | 1784 | 1862 | 29,300,001 | 31,500,000 | gneg | |
X | p | 21.1 | 1862 | 2120 | 31,500,001 | 37,800,000 | gpos | 100 |
X | p | 11.4 | 2120 | 2430 | 37,800,001 | 42,500,000 | gneg | |
X | p | 11.3 | 2430 | 2624 | 42,500,001 | 47,600,000 | gpos | 75 |
X | p | 11.23 | 2624 | 2948 | 47,600,001 | 50,100,000 | gneg | |
X | p | 11.22 | 2948 | 3129 | 50,100,001 | 54,800,000 | gpos | 25 |
X | p | 11.21 | 3129 | 3206 | 54,800,001 | 58,100,000 | gneg | |
X | p | 11.1 | 3206 | 3297 | 58,100,001 | 61,000,000 | acen | |
X | q | 11.1 | 3297 | 3491 | 61,000,001 | 63,800,000 | acen | |
X | q | 11.2 | 3491 | 3620 | 63,800,001 | 65,400,000 | gneg | |
X | q | 12 | 3620 | 3827 | 65,400,001 | 68,500,000 | gpos | 50 |
X | q | 13.1 | 3827 | 4137 | 68,500,001 | 73,000,000 | gneg | |
X | q | 13.2 | 4137 | 4292 | 73,000,001 | 74,700,000 | gpos | 50 |
X | q | 13.3 | 4292 | 4447 | 74,700,001 | 76,800,000 | gneg | |
X | q | 21.1 | 4447 | 4732 | 76,800,001 | 85,400,000 | gpos | 100 |
X | q | 21.2 | 4732 | 4809 | 85,400,001 | 87,000,000 | gneg | |
X | q | 21.31 | 4809 | 5107 | 87,000,001 | 92,700,000 | gpos | 100 |
X | q | 21.32 | 5107 | 5184 | 92,700,001 | 94,300,000 | gneg | |
X | q | 21.33 | 5184 | 5430 | 94,300,001 | 99,100,000 | gpos | 75 |
X | q | 22.1 | 5430 | 5701 | 99,100,001 | 103,300,000 | gneg | |
X | q | 22.2 | 5701 | 5843 | 103,300,001 | 104,500,000 | gpos | 50 |
X | q | 22.3 | 5843 | 6050 | 104,500,001 | 109,400,000 | gneg | |
X | q | 23 | 6050 | 6322 | 109,400,001 | 117,400,000 | gpos | 75 |
X | q | 24 | 6322 | 6619 | 117,400,001 | 121,800,000 | gneg | |
X | q | 25 | 6619 | 7059 | 121,800,001 | 129,500,000 | gpos | 100 |
X | q | 26.1 | 7059 | 7253 | 129,500,001 | 131,300,000 | gneg | |
X | q | 26.2 | 7253 | 7395 | 131,300,001 | 134,500,000 | gpos | 25 |
X | q | 26.3 | 7395 | 7602 | 134,500,001 | 138,900,000 | gneg | |
X | q | 27.1 | 7602 | 7808 | 138,900,001 | 141,200,000 | gpos | 75 |
X | q | 27.2 | 7808 | 7886 | 141,200,001 | 143,000,000 | gneg | |
X | q | 27.3 | 7886 | 8145 | 143,000,001 | 148,000,000 | gpos | 100 |
X | q | 28 | 8145 | 8610 | 148,000,001 | 156,040,895 | gneg |
In July 2020 scientists reported the first complete and gap-less assembly of a human X chromosome. [32] [33]
Chromosome 21 is one of the 23 pairs of chromosomes in humans. Chromosome 21 is both the smallest human autosome and chromosome, with 46.7 million base pairs representing about 1.5 percent of the total DNA in cells. Most people have two copies of chromosome 21, while those with three copies of chromosome 21 have Down syndrome.
Chromosome 1 is the designation for the largest human chromosome. Humans have two copies of chromosome 1, as they do with all of the autosomes, which are the non-sex chromosomes. Chromosome 1 spans about 249 million nucleotide base pairs, which are the basic units of information for DNA. It represents about 8% of the total DNA in human cells.
Chromosome 6 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 6 spans nearly 171 million base pairs and represents between 5.5 and 6% of the total DNA in cells. It contains the major histocompatibility complex, which contains over 100 genes related to the immune response, and plays a vital role in organ transplantation.
Chromosome 13 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 13 spans about 113 million base pairs and represents between 3.5 and 4% of the total DNA in cells.
Chromosome 2 is one of the twenty-three pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 2 is the second-largest human chromosome, spanning more than 242 million base pairs and representing almost eight percent of the total DNA in human cells.
Chromosome 3 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 3 spans more than 198 million base pairs and represents about 6.5 percent of the total DNA in cells.
Chromosome 4 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 4 spans more than 190 million base pairs and represents between 6 and 6.5 percent of the total DNA in cells.
Chromosome 5 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 5 spans about 182 million base pairs and represents almost 6% of the total DNA in cells. Chromosome 5 is the 5th largest human chromosome, yet has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of non-coding and syntenic conservation with non-mammalian vertebrates, suggesting they are functionally constrained.
Chromosome 7 is one of the 23 pairs of chromosomes in humans, who normally have two copies of this chromosome. Chromosome 7 spans about 160 million base pairs and represents between 5 and 5.5 percent of the total DNA in cells.
Chromosome 8 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 8 spans about 146 million base pairs and represents between 4.5 and 5.0% of the total DNA in cells.
Chromosome 9 is one of the 23 pairs of chromosomes in humans. Humans normally have two copies of this chromosome, as they normally do with all chromosomes. Chromosome 9 spans about 138 million base pairs of nucleic acids and represents between 4.0 and 4.5% of the total DNA in cells.
Chromosome 10 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 10 spans about 134 million base pairs and represents between 4 and 4.5 percent of the total DNA in cells.
Chromosome 11 is one of the 23 pairs of chromosomes in humans. Humans normally have two copies of this chromosome. Chromosome 11 spans about 135 million base pairs and represents between 4 and 4.5 percent of the total DNA in cells. The shorter arm is termed 11p while the longer arm is 11q. At about 21.5 genes per megabase, chromosome 11 is one of the most gene-rich, and disease-rich, chromosomes in the human genome.
Chromosome 14 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 14 spans about 107 million base pairs and represents between 3 and 3.5% of the total DNA in cells.
Chromosome 15 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 15 spans about 99.7 million base pairs and represents between 3% and 3.5% of the total DNA in cells. Chromosome 15 is an acrocentric chromosome, with a very small short arm, which contains few protein coding genes among its 19 million base pairs. It has a larger long arm that is gene rich, spanning about 83 million base pairs.
Chromosome 16 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 16 spans about 90 million base pairs and represents just under 3% of the total DNA in cells.
Chromosome 17 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 17 spans more than 84 million base pairs and represents between 2.5 and 3% of the total DNA in cells.
Chromosome 18 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 18 spans about 80 million base pairs and represents about 2.5 percent of the total DNA in cells.
Chromosome 19 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 19 spans more than 61.7 million base pairs, the building material of DNA. It is considered the most gene-rich chromosome containing roughly 1,500 genes, despite accounting for only 2 percent of the human genome.
Chromosome 20 is one of the 23 pairs of chromosomes in humans. Chromosome 20 spans around 66 million base pairs and represents between 2 and 2.5 percent of the total DNA in cells. Chromosome 20 was fully sequenced in 2001 and was reported to contain over 59 million base pairs. Since then, due to sequencing improvements and fixes, the length of chromosome 20 has been updated to just over 66 million base pairs.