Chromosome 21 (human)

From Wikipedia, the free encyclopedia
Jump to: navigation, search
Chromosome 21 (human)
Human male karyotpe high resolution - Chromosome 21 cropped.png
Human chromosome 21 pair after G-banding.
One is from mother, one is from father.
Human male karyotpe high resolution - Chromosome 21.png
Chromosome 21 pair
in human male karyogram.
Features
Length (bp) 46,709,983 bp
(GRCh38)[1]
No. of genes 215 (CCDS)[2]
Type Autosome
Centromere position Acrocentric[3]
(12.0 Mbp[4])
External map viewers
Ensembl Chromosome 21
Entrez Chromosome 21
NCBI Chromosome 21
UCSC Chromosome 21
Full DNA sequences
RefSeq NC_000021 (FASTA)
GenBank CM000683 (FASTA)

Chromosome 21 is one of the 23 pairs of chromosomes in humans. Chromosome 21 is the smallest human autosome, with 48 million nucleotides (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 that they had determined the sequence of base pairs that make up this chromosome. Chromosome 21 was the second human chromosome to be fully sequenced, after chromosome 22.

Genes[edit]

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.[5]

When simply saying "number of genes", in most cases, it refers only to "number of protein-coding genes".

Estimated by Protein-coding genes Non-coding RNA genes Pseudogenes Source Release date
CCDS 215 - - [2] 2016-09-08
HGNC 217 165 180 [6] 2017-05-12
Ensembl 234 404 183 [7] 2017-03-29
NCBI 256 356 207 [8][9][10] 2017-05-19

The following are some of the genes located on chromosome 21:

  • APP: amyloid beta (A4) precursor protein (peptidase nexin-II, Alzheimer disease)[11]
  • C21orf45: encoding protein Protein Mis18-alpha
  • C21orf55/DNAJC28: encoding protein DnaJ homolog subfamily C member 28
  • C21orf56: encoding protein Uncharacterized protein C21orf56
  • C21orf59: Chromosome 21 open reading frame 59
  • C21orf62: expressed in tissues of the brain and reproductive organs
  • C21orf66: encoding protein GC-rich sequence DNA-binding factor homolog
  • CBS: cystathionine-beta-synthase
  • CLDN14: claudin 14
  • CRYZL1: Crystallin zeta-like 1
  • CYYR1: Cysteine and tyrosine rich 1
  • DIP2A: Disco-interacting protein 2 homolog A
  • DOPEY2: Dopey family member 2
  • DSCR1: Down Syndrome critical region 1[12]
  • DYRK1A: dual specificity tyrosine-(Y)-phosphorylation regulated kinase 1A
  • FAM3B: Family with sequence similarity 3 member B
  • FRGCA: encoding protein FOXM1-regulated, gastric cancer associated
  • 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)
  • PCNT: centrosomal pericentrin
  • PDXK: encoding enzyme Pyridoxal kinase
  • PSMG1: Proteasome assembly chaperone 1
  • 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
  • S100B: calcium binding protein
  • SOD1: superoxide dismutase 1, soluble (amyotrophic lateral sclerosis 1 (adult))
  • TMEM1: encoding protein Trafficking protein particle complex subunit 10
  • TMPRSS3: transmembrane protease, serine 3
  • TTC3: Tetratricopeptide Repeat Domain 3

Diseases and disorders[edit]

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

Chromosomal conditions[edit]

Translocation Down's syndrome affecting Chromosome 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.[11] 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[edit]

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,[13] 550[14] and 850[4]). Band length in this diagram is based on the ideograms from ISCN (2013).[15] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process.[16]
G-bands of human chromosome 21 in resolution 850 bphs[17]
Chr. Arm[18] Band[19] ISCN
start[20]
ISCN
stop[20]
Basepair
start
Basepair
stop
Stain[21] Density
21 p 13 0 311 1 3,100,000 gvar
21 p 12 311 683 3,100,001 7,000,000 stalk
21 p 11.2 683 1056 7,000,001 10,900,000 gvar
21 p 11.1 1056 1274 10,900,001 12,000,000 acen
21 q 11.1 1274 1367 12,000,001 13,000,000 acen
21 q 11.2 1367 1584 13,000,001 15,000,000 gneg
21 q 21.1 1584 2019 15,000,001 22,600,000 gpos 100
21 q 21.2 2019 2144 22,600,001 25,500,000 gneg
21 q 21.3 2144 2330 25,500,001 30,200,000 gpos 75
21 q 22.11 2330 2485 30,200,001 34,400,000 gneg
21 q 22.12 2485 2610 34,400,001 36,400,000 gpos 50
21 q 22.13 2610 2703 36,400,001 38,300,000 gneg
21 q 22.2 2703 2858 38,300,001 41,200,000 gpos 50
21 q 22.3 2858 3200 41,200,001 46,709,983 gneg

References[edit]

  1. ^ "Human Genome Assembly GRCh38 - Genome Reference Consortium". National Center for Biotechnology Information. 2013-12-24. Retrieved 2017-03-04. 
  2. ^ a b "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. ^ 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. ^ Pertea M, Salzberg SL (2010). "Between a chicken and a grape: estimating the number of human genes.". Genome Biol. 11 (5): 206. PMC 2898077Freely accessible. PMID 20441615. doi:10.1186/gb-2010-11-5-206. 
  6. ^ "Statistics & Downloads for chromosome 21". HUGO Gene Nomenclature Committee. 2017-05-12. Retrieved 2017-05-19. 
  7. ^ "Chromosome 21: Chromosome summary - Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19. 
  8. ^ "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. 
  9. ^ "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. 
  10. ^ "Search results - 21[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20. 
  11. ^ a b c 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. PMID 16921174. doi:10.1093/brain/awl203. 
  12. ^ Gardiner K, Davisson M (2000). "The sequence of human chromosome 21 and implications for research into Down syndrome". Genome Biol. 1 (2): REVIEWS0002. PMC 138845Freely accessible. PMID 11178230. doi:10.1186/gb-2000-1-2-reviews0002. 
  13. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
  14. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.
  15. ^ 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. 
  16. ^ 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. ISBN 978-1-4673-1921-8. doi:10.1109/JCSSE.2012.6261965. 
  17. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  18. ^ "p": Short arm; "q": Long arm.
  19. ^ For cytogenetic banding nomenclature, see article locus.
  20. ^ 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.
  21. ^ 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.
  • Antonarakis SE, Lyle R, Dermitzakis ET, Reymond A, Deutsch S (2004). "Chromosome 21 and down syndrome: from genomics to pathophysiology". Nat Rev Genet. 5 (10): 725–38. PMID 15510164. doi:10.1038/nrg1448. 
  • Antonarakis SE, Lyle R, Deutsch S, Reymond A (2002). "Chromosome 21: a small land of fascinating disorders with unknown pathophysiology". Int J Dev Biol. 46 (1): 89–96. PMID 11902692. 
  • Antonarakis SE (2001). "Chromosome 21: from sequence to applications". Curr Opin Genet Dev. 11 (3): 241–6. PMID 11377958. doi:10.1016/S0959-437X(00)00185-4. 
  • Gilbert F (1997). "Disease genes and chromosomes: disease maps of the human genome. Chromosome 21". Genet Test. 1 (4): 301–6. PMID 10464663. doi:10.1089/gte.1997.1.301. 
  • Hattori M, Fujiyama A, Taylor TD, Watanabe H, Yada T, Park HS, Toyoda A, Ishii K, Totoki Y, Choi DK, Groner Y, 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, Schibuya K, Kawasaki K, Asakawa S, Shintani A, Sasaki T, Nagamine K, Mitsuyama S, Antonarakis SE, Minoshima S, Shimizu N, Nordsiek G, Hornischer K, Brant P, Scharfe M, Schon O, Desario A, Reichelt J, Kauer G, Blocker H, Ramser J, Beck A, Klages S, Hennig S, Riesselmann L, Dagand E, Haaf T, Wehrmeyer S, Borzym K, Gardiner K, Nizetic D, Francis F, Lehrach H, Reinhardt R, Yaspo ML (2000). "The DNA sequence of human chromosome 21". Nature. 405 (6784): 311–9. PMID 10830953. doi:10.1038/35012518. 
  • Sawinska M, Ladon D (2004). "Mechanism, detection and clinical significance of the reciprocal translocation t(12;21)(p12;q22) in the children suffering from acute lymphoblastic leukaemia". Leuk Res. 28 (1): 35–42. PMID 14630078. doi:10.1016/S0145-2126(03)00160-7. 
  • Rovelet-Lecrux A, Hannequin D, Raux G, Le Meur N, Laquerriere A, Vital A, Dumanchin C, Feuillette S, Brice A, Vercelletto M, Dubas F, Frebourg T, Campion D (2005). "APP locus duplication causes autosomal dominant early-onset Alzheimer disease with cerebral amyloid angiopathy". Nature Genetics. 38 (1): 24–6. PMID 16369530. doi:10.1038/ng1718. 
  • Anita Rauch; Christian T. Thiel; Detlev Schindler; Ursula Wick; Yanick J. Crow; Arif B. Ekici; Anthonie J. van Essen; Timm O. Goecke; Lihadh Al-Gazali; Krystyna H. Chrzanowska; Christiane Zweier; Han G. Brunner; Kristin Becker; Cynthia J. Curry; Bruno Dallapiccola; Koenraad Devriendt; Arnd Dörfler; Esther Kinning; André Megarbane; Peter Meinecke; Robert K. Semple; Stephanie Spranger; Annick Toutain; Richard C. Trembath; Egbert Voss; Louise Wilson; Raoul Hennekam; Francis de Zegher; Helmut-Günther Dörr; André Reis (2008). "Mutations in the Pericentrin (PCNT) Gene Cause Primordial Dwarfism". Science Online: 7. 

External links[edit]

  • National Institutes of Health. "Chromosome 21". Genetics Home Reference. Retrieved 2017-05-06. 
  • "Chromosome 21". Human Genome Project Information Archive 1990–2003. Retrieved 2017-05-06.