Chromosome 22

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Chromosome 22
Human male karyotpe high resolution - Chromosome 22 cropped.png
Human chromosome 22 pair after G-banding.
One is from mother, one is from father.
Human male karyotpe high resolution - Chromosome 22.png
Chromosome 22 pair
in human male karyogram.
Features
Length (bp) 50,818,468 bp
(GRCh38)[1]
No. of genes 417 (CCDS)[2]
Type Autosome
Centromere position Acrocentric[3]
(15.0 Mbp[4])
Complete gene lists
CCDS Gene list
HGNC Gene list
UniProt Gene list
NCBI Gene list
External map viewers
Ensembl Chromosome 22
Entrez Chromosome 22
NCBI Chromosome 22
UCSC Chromosome 22
Full DNA sequences
RefSeq NC_000022 (FASTA)
GenBank CM000684 (FASTA)

Chromosome 22 is one of the 23 pairs of chromosomes in human cells. Humans normally have two copies of chromosome 22 in each cell. Chromosome 22 is the second smallest human chromosome (chromosome 21 being smaller), spanning about 49 million DNA base pairs and representing between 1.5 and 2% of the total DNA in cells.

In 1999, researchers working on the Human Genome Project announced they had determined the sequence of base pairs that make up this chromosome. Chromosome 22 was the first human chromosome to be fully sequenced.[5]

Chromosome 22 was originally identified as the smallest chromosome. After extensive research, however, researchers concluded that chromosome 21 was smaller. The numbering of these chromosomes wasn't rearranged because of chromosome 21 being known by that designation as the chromosome that can lead to Down syndrome, or trisomy 21.[citation needed]

Genes[edit]

Number of genes[edit]

The following are some of the gene count estimates of human chromosome 22. 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.[6]

Estimated by Protein-coding genes Non-coding RNA genes Pseudogenes Source Release date
CCDS 417 - - [2] 2016-09-08
HGNC 424 148 288 [7] 2017-05-12
Ensembl 489 515 325 [8] 2017-03-29
UniProt 496 - - [9] 2018-02-28
NCBI 474 392 379 [10][11][12] 2017-05-19

Gene list[edit]

The following is a partial list of genes on human chromosome 22. For complete list, see the link in the infobox on the right.

Locus Gene Description Condition
22q11.1-q11.2 IGL@ Asymmetric crying facies (Cayler cardiofacial syndrome)
22q11.21 TBX1 T-box 1
22q11 RTN4R Reticulon 4 receptor Schizophrenia
22q11.21-q11.23 COMT catechol-O-methyltransferase gene
22q12.1-q13.1 NEFH neurofilament, heavy polypeptide 200kDa
22q12.1[13] CHEK2 CHK2 checkpoint homolog (S. pombe)
22q12.2 NF2 neurofibromin 2 bilateral acoustic neuroma
22q13 SOX10 SRY (sex determining region Y)-box 10
22q13.1 APOL1 Apolipoprotein L1
22q13.2 EP300 E1A binding protein p300
22q13.3 WNT7B Wingless-type MMTV integration site family, member 7B 22q13 deletion syndrome
22q13.3 SHANK3 SH3 and multiple ankyrin repeat domains 3 22q13 deletion syndrome
22q13.3 SULT4A1 sulfotransferase family 4A, member 1 22q13 deletion syndrome
22q13.3 PARVB parvin beta (cytoskeleton organization and cell adhesion) 22q13 deletion syndrome

Diseases and disorders[edit]

The following diseases are some of those related to genes on chromosome 22:

Chromosomal conditions[edit]

The following conditions are caused by changes in the structure or number of copies of chromosome 22:

  • 22q11.2 deletion syndrome: Most people with 22q11.2 deletion syndrome are missing about 3 million base pairs on one copy of chromosome 22 in each cell. The deletion occurs near the middle of the chromosome at a location designated as q11.2. This region contains about 30 genes, but many of these genes have not been well characterized. A small percentage of affected individuals have shorter deletions in the same region.
    The loss of one particular gene, TBX1, is thought to be responsible for many of the characteristic features of 22q11.2 deletion syndrome, such as heart defects, an opening in the roof of the mouth (a cleft palate), distinctive facial features, and low calcium levels. A loss of this gene does not appear to cause learning disabilities, however. Other genes in the deleted region are also likely to contribute to the signs and symptoms of 22q11.2 deletion syndrome.
  • 22q11.2 distal deletion syndrome
  • 22q13 deletion syndrome
  • Other chromosomal conditions: Other changes in the number or structure of chromosome 22 can have a variety of effects, including mental retardation, delayed development, physical abnormalities, and other medical problems. These changes include an extra piece of chromosome 22 in each cell (partial trisomy), a missing segment of the chromosome in each cell (partial monosomy), and a circular structure called ring chromosome 22 that is caused by the breakage and reattachment of both ends of the chromosome.
  • Cat-eye syndrome is a rare disorder most often caused by a chromosomal change called an inverted duplicated 22. A small extra chromosome is made up of genetic material from chromosome 22 that has been abnormally duplicated (copied). The extra genetic material causes the characteristic signs and symptoms of cat-eye syndrome, including an eye abnormality called ocular iris coloboma (a gap or split in the colored part of the eye), small skin tags or pits in front of the ear, heart defects, kidney problems, and, in some cases, delayed development.
  • A rearrangement (translocation) of genetic material between chromosomes 9 and 22 is associated with several types of blood cancer (leukemia). This chromosomal abnormality, which is commonly called the Philadelphia chromosome, is found only in cancer cells. The Philadelphia chromosome has been identified in most cases of a slowly progressing form of blood cancer called chronic myeloid leukemia, or CML. It also has been found in some cases of more rapidly progressing blood cancers (acute leukemias). The presence of the Philadelphia chromosome can help predict how the cancer will progress and provides a target for molecular therapies.
  • Emanuel Syndrome is a translocation of chromosomes 11 and 22. Originally known as Supernumerary der(22) Syndrome, it occurs when an individual has an extra chromosome composed of pieces of the 11th and 22nd chromosomes.
  • the 22q11 locus contains the subgenes for immunoglobulin light chain lambda: the immunoglobulin lambda light chain locus contains protein-coding genes that can be lost with its rearrangement.[15] This is based on a physiological mechanism and is not pathogenetic for leukemias or lymphomas.[15] However, the rearrangement of several lambda variable subgenes can activate expression of an overlapping miRNA gene, which has consequences for gene expression regulation.[16]

Cytogenetic band[edit]

G-banding ideograms of human chromosome 22
G-banding ideogram of human chromosome 22 in resolution 850 bphs. Band length in this diagram is proportional to base-pair length. This type of ideogram is generally used in genome browsers (e.g. Ensembl, UCSC Genome Browser).
G-banding patterns of human chromosome 22 in three different resolutions (400,[17] 550[18] and 850[4]). Band length in this diagram is based on the ideograms from ISCN (2013).[19] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process.[20]
G-bands of human chromosome 22 in resolution 850 bphs[21]
Chr. Arm[22] Band[23] ISCN
start[24]
ISCN
stop[24]
Basepair
start
Basepair
stop
Stain[25] Density
22 p 13 0 260 1 4,300,000 gvar
22 p 12 260 576 4,300,001 9,400,000 stalk
22 p 11.2 576 836 9,400,001 13,700,000 gvar
22 p 11.1 836 1015 13,700,001 15,000,000 acen
22 q 11.1 1015 1234 15,000,001 17,400,000 acen
22 q 11.21 1234 1563 17,400,001 21,700,000 gneg
22 q 11.22 1563 1700 21,700,001 23,100,000 gpos 25
22 q 11.23 1700 1878 23,100,001 25,500,000 gneg
22 q 12.1 1878 2029 25,500,001 29,200,000 gpos 50
22 q 12.2 2029 2194 29,200,001 31,800,000 gneg
22 q 12.3 2194 2413 31,800,001 37,200,000 gpos 50
22 q 13.1 2413 2687 37,200,001 40,600,000 gneg
22 q 13.2 2687 2852 40,600,001 43,800,000 gpos 50
22 q 13.31 2852 3181 43,800,001 48,100,000 gneg
22 q 13.32 3181 3290 48,100,001 49,100,000 gpos 50
22 q 13.33 3290 3400 49,100,001 50,818,468 gneg

References[edit]

  1. ^ "Human Genome AssemblGenome Reference Consortium". National Center for Biotechnology Information. 2013-12-24. Retrieved 2017-03-04. 
  2. ^ a b "Search results - 22[CHR] AND "Homo sapiens"[Organism] AND ("has ccds"[Properties] AND alive[prop]) - Gene". NCBI. CCDS Release 20 for Homo sapiens. 2016-09-08. Retrieved 2017-05-28. 
  3. ^ Tom Strachan; Andrew Read (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN 978-1-136-84407-2. 
  4. ^ a b Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  5. ^ Mayor, Susan (1999). "First human chromosome is sequenced". BMJ. BMJ Group. 319 (7223): 1453. doi:10.1136/bmj.319.7223.1453a. PMC 1117192Freely accessible. PMID 10582915. 
  6. ^ Pertea M, Salzberg SL (2010). "Between a chicken and a grape: estimating the number of human genes". Genome Biol. 11 (5): 206. doi:10.1186/gb-2010-11-5-206. PMC 2898077Freely accessible. PMID 20441615. 
  7. ^ "Statistics & Downloads for chromosome 22". HUGO Gene Nomenclature Committee. 2017-05-12. Retrieved 2017-05-19. 
  8. ^ "Chromosome 22: Chromosome summary - Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19. 
  9. ^ "Human chromosome 22: entries, gene names and cross-references to MIM". UniProt. 2018-02-28. Retrieved 2018-03-16. 
  10. ^ "Search results - 22[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20. 
  11. ^ "Search results - 22[CHR] AND "Homo sapiens"[Organism] AND ( ("genetype miscrna"[Properties] OR "genetype ncrna"[Properties] OR "genetype rrna"[Properties] OR "genetype trna"[Properties] OR "genetype scrna"[Properties] OR "genetype snrna"[Properties] OR "genetype snorna"[Properties]) NOT "genetype protein coding"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20. 
  12. ^ "Search results - 22[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20. 
  13. ^ Beck, Megan; Peterson, Jess F.; McConnell, Juliann; McGuire, Marianne; Asato, Miya; Losee, Joseph E.; Surti, Urvashi; Madan-Khetarpal, Suneeta; Rajkovic, Aleksandar; Yatsenko, Svetlana A. (May 2015). "Craniofacial abnormalities and developmental delay in two families with overlapping 22q12.1 microdeletions involving the gene". American Journal of Medical Genetics Part A. 167 (5): 1047–1053. doi:10.1002/ajmg.a.36839. PMID 25810350. 
  14. ^ Liu H, Abecasis GR, Heath SC, Knowles A, Demars S, Chen YJ, Roos JL, Rapoport JL, Gogos JA, Karayiorgou M (December 2002). "Genetic variation in the 22q11 locus and susceptibility to schizophrenia". Proc. Natl. Acad. Sci. U.S.A. 99 (26): 16859–64. doi:10.1073/pnas.232186099. PMC 139234Freely accessible. PMID 12477929. 
  15. ^ a b Mraz, M.; Stano Kozubik, K.; Plevova, K.; Musilova, K.; Tichy, B.; Borsky, M.; Kuglik, P.; Doubek, M.; Brychtova, Y.; Mayer, J.; Pospisilova, S. (2013). "The origin of deletion 22q11 in chronic lymphocytic leukemia is related to the rearrangement of immunoglobulin lambda light chain locus". Leukemia Research. 37 (7): 802–808. doi:10.1016/j.leukres.2013.03.018. PMID 23608880. 
  16. ^ Mraz, M.; Dolezalova, D.; Plevova, K.; Stano Kozubik, K.; Mayerova, V.; Cerna, K.; Musilova, K.; Tichy, B.; Pavlova, S.; Borsky, M.; Verner, J.; Doubek, M.; Brychtova, Y.; Trbusek, M.; Hampl, A.; Mayer, J.; Pospisilova, S. (2012). "MicroRNA-650 expression is influenced by immunoglobulin gene rearrangement and affects the biology of chronic lymphocytic leukemia". Blood. 119 (9): 2110–2113. doi:10.1182/blood-2011-11-394874. PMID 22234685. 
  17. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
  18. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.
  19. ^ International Standing Committee on Human Cytogenetic Nomenclature (2013). ISCN 2013: An International System for Human Cytogenetic Nomenclature (2013). Karger Medical and Scientific Publishers. ISBN 978-3-318-02253-7. 
  20. ^ Sethakulvichai, W.; Manitpornsut, S.; Wiboonrat, M.; Lilakiatsakun, W.; Assawamakin, A.; Tongsima, S. (2012). "Estimation of band level resolutions of human chromosome images" (PDF). In Computer Science and Software Engineering (JCSSE), 2012 International Joint Conference on: 276–282. doi:10.1109/JCSSE.2012.6261965. 
  21. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  22. ^ "p": Short arm; "q": Long arm.
  23. ^ For cytogenetic banding nomenclature, see article locus.
  24. ^ a b These values (ISCN start/stop) are based on the length of bands/ideograms from the ISCN book, An International System for Human Cytogenetic Nomenclature (2013). Arbitrary unit.
  25. ^ gpos: Region which is positively stained by G banding, generally AT-rich and gene poor; gneg: Region which is negatively stained by G banding, generally CG-rich and gene rich; acen Centromere. var: Variable region; stalk: Stalk.

Further reading[edit]

External links[edit]

  • National Institutes of Health. "Chromosome 22". Genetics Home Reference. Retrieved 2017-05-06. 
  • "Chromosome 22". Human Genome Project Information Archive 1990–2003. Retrieved 2017-05-06.