Chromosome 21

Chromosome 21
Human chromosome 21 pair after G-banding.
One is from the mother, one is from the father.
Chromosome 21 pair
in human male karyogram.
Features
Length (bp)46,709,983 bp
(GRCh38)[1]
No. of genes215 (CCDS)[2]
TypeAutosome
Centromere positionAcrocentric[3]
(12.0 Mbp[4])
Complete gene lists
CCDSGene list
HGNCGene list
UniProtGene list
NCBIGene list
External map viewers
EnsemblChromosome 21
EntrezChromosome 21
NCBIChromosome 21
UCSCChromosome 21
Full DNA sequences
RefSeqNC_000021 (FASTA)
GenBankCM000683 (FASTA)

Chromosome 21 is one of the 23 pairs of chromosomes in humans. Chromosome 21 is both the smallest human autosome and chromosome,[5] with 48 million base pairs (the building material of DNA) 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, also called "trisomy 21".

Researchers working on the Human Genome Project announced in May 2000 that they had determined the sequence of base pairs that make up this chromosome.[6] Chromosome 21 was the second human chromosome to be fully sequenced, after chromosome 22.

Genes

Number of genes

The following are some of the gene count estimates of human chromosome 21. 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.[7]

Estimated by Protein-coding genes Non-coding RNA genes Pseudogenes Source Release date
CCDS215—— [2] 2016-09-08
HGNC217165180 [8] 2017-05-12
Ensembl234404183 [9] 2017-03-29
UniProt252—— [10] 2018-02-28
NCBI256356207 [11][12][13] 2017-05-19

Gene list

The following is a partial list of genes on human chromosome 21. For complete list, see the link in the infobox on the right.

  • ABCG1: encoding ATP-binding cassette sub-family G member 1
  • ADAMTS1
  • ADAMTS5: encoding enzyme a disintegrin and metalloproteinase with thrombospondin motifs 5
  • AGPAT3: encoding enzyme 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma
  • AIRE: encoding protein autoimmune regulator
  • APP: amyloid beta (A4) precursor protein (peptidase nexin-II, Alzheimer disease)[14]
  • ATP5PF: encoding enzyme subunit ATP synthase-coupling factor 6, mitochondrial
  • ATP5PO: encoding enzyme subunit ATP synthase subunit O, mitochondrial
  • B3GALT5: encoding enzyme beta-1,3-galactosyltransferase 5
  • C21orf62: expressed in tissues of the brain and reproductive organs
  • CBR1: encoding enzyme carbonyl reductase [NADPH] 1
  • CBR3: encoding enzyme carbonyl reductase [NADPH] 3
  • CBS: cystathionine-beta-synthase
  • CFAP298: encoding cilia- and flagella-associated protein 298
  • CLDN14: claudin 14
  • CRYZL1: Crystallin zeta-like 1
  • CYYR1: Cysteine and tyrosine rich 1
  • DIP2A: Disco-interacting protein 2 homolog A
  • DNAJC28: encoding protein DnaJ homolog subfamily C member 28
  • DOPEY2: Dopey family member 2
  • DSCR1: Down Syndrome critical region 1[15]
  • DYRK1A: dual specificity tyrosine-(Y)-phosphorylation regulated kinase 1A
  • ERG
  • ETS2
  • FAM3B: Family with sequence similarity 3 member B
  • FRGCA: encoding protein FOXM1-regulated, gastric cancer associated
  • GATD3A: encoding glutamine amidotransferase-like class 1 domain-containing protein 3A, mitochondrial
  • HLCS: holocarboxylase synthetase (biotin-(propionyl-Coenzyme A-carboxylase (ATP-hydrolysing)) ligase)
  • KCNE1: potassium voltage-gated channel, Isk-related family, member 1
  • KCNE2: potassium voltage-gated channel, Isk-related family, member 2
  • LAD: leukocyte adhesion deficiency (symbols are ITGB2, CD18, LCAMB)
  • MIS18A: encoding protein Protein Mis18-alpha
  • NRIP1
  • OLIG2
  • PAXBP1: encoding protein GC-rich sequence DNA-binding factor homolog
  • PCNT: centrosomal pericentrin
  • PDXK: encoding enzyme Pyridoxal kinase
  • PSMG1: Proteasome assembly chaperone 1
  • RNR4: RNA, ribosomal 45S cluster 4
  • RRP1: encoding protein Ribosomal RNA processing protein 1 homolog A
  • RRP1B: ribosomal RNA processing 1 homolog B
  • RWDD2B: encoding protein RWD domain-containing protein 2B
  • RUNX1
  • S100B: calcium binding protein
  • SOD1: superoxide dismutase 1, soluble (amyotrophic lateral sclerosis 1 (adult))
  • SPATC1L: encoding protein SPATC1L
  • TFF1, TFF2, TFF3
  • TIAM1
  • TMEM1: encoding protein Trafficking protein particle complex subunit 10
  • TMPRSS2
  • TMPRSS3: transmembrane protease, serine 3
  • TTC3: Tetratricopeptide Repeat Domain 3

Diseases and disorders

The following diseases and disorders are some of those related to genes on chromosome 21:

Chromosomal conditions

A karyotype of somebody affected with Down syndrome, depicting the presence of a full additional copy of chromosome 21. The presence of this extra copy is also referred to as Trisomy 21.

The following conditions are caused by changes in the structure or number of copies of chromosome 21:

  • Cancers: Rearrangements (translocations) of genetic material between chromosome 21 and other chromosomes have been associated with several types of cancer. For example, acute lymphoblastic leukemia (a type of blood cancer most often diagnosed in childhood) has been associated with a translocation between chromosomes 12 and 21. Another form of leukemia, acute myeloid leukemia, has been associated with a translocation between chromosomes 8 and 21.
  • In a small percentage of cases, Down syndrome is caused by a rearrangement of chromosomal material between chromosome 21 and another chromosome. As a result, a person has the usual two copies of chromosome 21, plus extra material from chromosome 21 attached to another chromosome. These cases are called translocation Down syndrome. Researchers believe that extra copies of genes on chromosome 21 disrupt the course of normal development, causing the characteristic features of Down syndrome and the increased risk of medical problems associated with this disorder.
  • Other changes in the number or structure of chromosome 21 can have a variety of effects, including intellectual disability, delayed development, and characteristic facial features. In some cases, the signs and symptoms are similar to those of Down syndrome. Changes to chromosome 21 include a missing segment of the chromosome in each cell (partial monosomy 21) and a circular structure called ring chromosome 21. A ring chromosome occurs when both ends of a broken chromosome are reunited.
  • Duplication in Amyloid precursor protein (APP) locus (duplicated segment varies in length but includes APP) on Chromosome 21 was found to cause early onset familial Alzheimer's disease in a French family set (Rovelet-Lecrux et al.) and a Dutch family set.[14] Compared to Alzheimer's caused by missense mutations in APP, the frequency of the Alzheimer's caused by APP duplications is significant. All patients that have an extra copy of APP gene due to the locus duplication show Alzheimer's with severe cerebral amyloid angiopathy.

Cytogenetic band

G-banding ideograms of human chromosome 21
G-banding ideogram of human chromosome 21 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 21 in three different resolutions (400,[16] 550[17] and 850[4]). Band length in this diagram is based on the ideograms from ISCN (2013).[18] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process.[19]
G-bands of human chromosome 21 in resolution 850 bphs[4]
Chr. Arm[20] Band[21] ISCN
start[22]		 ISCN
stop[22]		 Basepair
start		 Basepair
stop		 Stain[23] Density
21p 13031113,100,000 gvar
21p 123116833,100,0017,000,000 stalk
21p 11.268310567,000,00110,900,000 gvar
21p 11.11056127410,900,00112,000,000 acen
21q 11.11274136712,000,00113,000,000 acen
21q 11.21367158413,000,00115,000,000 gneg
21q 21.11584201915,000,00122,600,000 gpos100
21q 21.22019214422,600,00125,500,000 gneg
21q 21.32144233025,500,00130,200,000 gpos75
21q 22.112330248530,200,00134,400,000 gneg
21q 22.122485261034,400,00136,400,000 gpos50
21q 22.132610270336,400,00138,300,000 gneg
21q 22.22703285838,300,00141,200,000 gpos50
21q 22.32858320041,200,00146,709,983 gneg

References

  1. ↑ "Human Genome Assembly GRCh38 - Genome Reference Consortium". National Center for Biotechnology Information. 2013-12-24. Retrieved 2017-03-04.
  2. 1 2 "Search results - 21[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. 1 2 3 Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  5. ↑ "Chromosome 21".
  6. ↑ Hattori, M.; Fujiyama, A.; Taylor, T. D.; Watanabe, H.; Yada, T.; Park, H.-S.; Toyoda, A.; Ishii, K.; Totoki, Y.; Choi, D.-K.; Soeda, E.; Ohki, M.; Takagi, T.; Sakaki, Y.; Taudien, S.; Blechschmidt, K.; Polley, A.; Menzel, U.; Delabar, J.; Kumpf, K.; Lehmann, R.; Patterson, D.; Reichwald, K.; Rump, A.; Schillhabel, M.; Schudy, A.; Zimmermann, W.; Rosenthal, A.; Kudoh, J.; et al. (2000). "The DNA sequence of human chromosome 21". Nature. 405 (6784): 311–319. Bibcode:2000Natur.405..311H. doi:10.1038/35012518. PMID 10830953.
  7. ↑ 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 2898077. PMID 20441615.
  8. ↑ "Statistics & Downloads for chromosome 21". HUGO Gene Nomenclature Committee. 2017-05-12. Retrieved 2017-05-19.
  9. ↑ "Chromosome 21: Chromosome summary - Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19.
  10. ↑ "Human chromosome 21: entries, gene names and cross-references to MIM". UniProt. 2018-02-28. Retrieved 2018-03-16.
  11. ↑ "Search results - 21[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
  12. ↑ "Search results - 21[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.
  13. ↑ "Search results - 21[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
  14. 1 2 3 Sleegers K, Brouwers N, Gijselinck I, Theuns J, Goossens D, Wauters J, Del-Favero J, Cruts M, van Duijn CM, Van Broeckhoven C (2006). "APP duplication is sufficient to cause early onset Alzheimer's dementia with cerebral amyloid angiopathy". Brain. 129 (Pt 11): 2977–83. doi:10.1093/brain/awl203. PMID 16921174.
  15. ↑ Gardiner K, Davisson M (2000). "The sequence of human chromosome 21 and implications for research into Down syndrome". Genome Biol. 1 (2): REVIEWS0002. doi:10.1186/gb-2000-1-2-reviews0002. PMC 138845. PMID 11178230.
  16. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
  17. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.
  18. ↑ 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.
  19. ↑ Sethakulvichai, W.; Manitpornsut, S.; Wiboonrat, M.; Lilakiatsakun, W.; Assawamakin, A.; Tongsima, S. (2012). "Estimation of band level resolutions of human chromosome images". In Computer Science and Software Engineering (JCSSE), 2012 International Joint Conference on: 276–282. doi:10.1109/JCSSE.2012.6261965. ISBN 978-1-4673-1921-8. S2CID 16666470.
  20. ↑ "p": Short arm; "q": Long arm.
  21. ↑ For cytogenetic banding nomenclature, see article locus.
  22. 1 2 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.
  23. ↑ 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.
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