Chromosome 2 (human)

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Chromosome 2 (human)
Human male karyotpe high resolution - Chromosome 2 cropped.png
Human chromosome 2 pair after G-banding. One is from mother, one is from father.
Human male karyotpe high resolution - Chromosome 2.png
Chromosome 2 pair in human male karyogram.
Features
Length (bp) 242,193,529 bp
Number of genes 2,787
Type Autosome
Centromere position Submetacentric [1]
Identifiers
RefSeq NC_000002
GenBank CM000664
Fusion of ancestral chromosomes left distinctive remnants of telomeres, and a vestigial centromere
Map of Chromosome 2
Ideogram of human chromosome 2. Mbp means mega base pair. See locus for other notation.

Chromosome 2 is one of the 23 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 [2] (the building material of DNA) and representing almost 8% of the total DNA in cells.

Identifying genes on each chromosome is an active area of genetic research. Because researchers use different approaches to predict the number of genes on each chromosome, the estimated number of genes varies. Chromosome 2 likely contains 1,491 genes, including those of the HOXD homeobox gene cluster.[3]

Evolution[edit]

Further information: Chimpanzee genome project

All members of Hominidae except humans, Neanderthals, and Denisovans have 24 pairs of chromosomes.[4] Humans have only 23 pairs of chromosomes. Human chromosome 2 is widely accepted by the evolutionary community[clarification needed] to be a result of an end-to-end fusion of two ancestral chromosomes.[5][6]

The evidence for this includes:

  • The correspondence of chromosome 2 to two ape chromosomes has near-identical DNA sequences, but they are found in two separate chromosomes. The same is true of the more distant gorilla and orangutan.[7][8]
  • The presence of a vestigial centromere. Normally a chromosome has just one centromere, but in chromosome 2 there are remnants of a second centromere.[9] Further analysis shows that both centromeres are active. Also, because highly variable alphoid DNA is also commonly found in non-centromeric regions of human chromosomes, their presence does not indicate the remnants of a degenerate centromere. Not only does the DNA sequence at the putative cryptic centromere site argue against fusion, but a comparison of the chimp and human chromosomes reveals that the centromere in human chromosome 2 is in a very different location than predicted by a fusion event as shown in part two of this study. This necessitates an implausible series of events, including the loss of both chimp centromeres when chromosomes 2A and 2B fused, and the rapid evolution of a new centromere to provide functionality to human chromosome 2.
  • The presence of vestigial telomeres. These are normally found only at the ends of a chromosome, but in chromosome 2 there are additional sequences in the middle.[10] In reality, the putative fusion site is but a vague shadow of what should be present given the model in question. One of the major problems with the fusion model is that, within the 10 to 30 kb window of DNA sequence surrounding the hypothetical fusion site, a glaring paucity of telomeric repeats exist that appear mostly as independent monomers, not tandem repeats. Based on the predicted model, thousands of intact motifs in tandem should exist. For the TTAGGG repeat to the left of the fusion site, less than 35 motifs exist, a normal human telomere would typically have 1667 to 2500. For the CCCTAA reverse complement sequence, to the right of the fusion site, less than 150 telomere motifs can be found. Another problem with these two motifs, that we document in our companion research paper, is that their occurrences are found scattered throughout both sides of the fusion site where they would not be expected. In other words, both the forward and reverse complement of the telomere motif populate both sides of the fusion site.

Genes[edit]

Among the genes located on chromosome 2 are these:

  • AGXT: alanine-glyoxylate aminotransferase (oxalosis I; hyperoxaluria I; glycolicaciduria; serine-pyruvate aminotransferase)
  • ALS2: amyotrophic lateral sclerosis 2 (juvenile)
  • COL3A1: collagen, type III, alpha 1 (Ehlers-Danlos syndrome type IV, autosomal dominant)
  • COL4A3: collagen, type IV, alpha 3 (Goodpasture antigen)
  • COL4A4: collagen, type IV, alpha 4
  • COL5A2: collagen, type V, alpha 2
  • CTLA4: cytotoxic T-Lymphocyte Antigen 4
  • HADHA: hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit
  • HADHB: hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit
  • NCL: Nucleolin
  • NR4A2: nuclear receptor subfamily 4, group A, member 2
  • OTOF: otoferlin
  • PAX3: paired box gene 3 (Waardenburg syndrome 1)
  • PAX8: paired box gene 8
  • PELI1: Ubiquitin ligase
  • SLC40A1: solute carrier family 40 (iron-regulated transporter), member 1
  • SSB: Sjogren syndrome antigen B
  • TPO: thyroid peroxidase
  • TTN: titin

Genes located on the short arm of this chromosome include

Genes located on the long arm of this chromosome include

  • ABCA12: ATP-binding cassette, sub-family A (ABC1), member 12
  • BMPR2: bone morphogenetic protein receptor, type II (serine/threonine kinase)
  • TBR1: T-box, brain, 1

Related diseases and traits[edit]

The following diseases and traits are related to genes located on chromosome 2:

References[edit]

  1. ^ "Table 2.3: Human chromosome groups". Human Molecular Genetics (2nd ed.). Garland Science. 1999. 
  2. ^ Hillier et al. (2005). "Generation and annotation of the DNAD sequences of human chromosomes 2 and 4". Nature 434 (7034): 724–31. Bibcode:2005Natur.434..724H. doi:10.1038/nature03466. PMID 15815621. 
  3. ^ Vega Homo sapiens genome browser: HoxD cluster on Chromosome 2
  4. ^ Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andrés AM, Eichler EE, Slatkin M, Reich D, Kelso J, Pääbo S; Kircher; Gansauge; Li; Racimo; Mallick; Schraiber; Jay; Prüfer; De Filippo; Sudmant; Alkan; Fu; Do; Rohland; Tandon; Siebauer; Green; Bryc; Briggs; Stenzel; Dabney; Shendure; Kitzman; Hammer; Shunkov; Derevianko; Patterson; Andrés et al. (October 2012). "A high-coverage genome sequence from an archaic Denisovan individual". Science 338 (6104): 222–6. Bibcode:2012Sci...338..222M. doi:10.1126/science.1224344. PMC 3617501. PMID 22936568. 
  5. ^ Human Chromosome 2 is a fusion of two ancestral chromosomes by Alec MacAndrew; accessed 18 May 2006.
  6. ^ Evidence of Common Ancestry: Human Chromosome 2 (video) 2007
  7. ^ Yunis and Prakash; Prakash, O (1982). "The origin of man: a chromosomal pictorial legacy". Science 215 (4539): 1525–30. Bibcode:1982Sci...215.1525Y. doi:10.1126/science.7063861. PMID 7063861. 
  8. ^ Human and Ape Chromosomes; accessed 8 September 2007.
  9. ^ Avarello et al. (1992). "Evidence for an ancestral alphoid domain on the long arm of human chromosome 2". Human Genetics 89 (2): 247–9. doi:10.1007/BF00217134. PMID 1587535. 
  10. ^ IJdo et al. (1991). "Origin of human chromosome 2: an ancestral telomere-telomere fusion". Proc. Natl. Acad. Sci. U.S.A. 88 (20): 9051–5. Bibcode:1991PNAS...88.9051I. doi:10.1073/pnas.88.20.9051. PMC 52649. PMID 1924367.