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0  structures 26  species 0  interactions 961  sequences 17  architectures

Family: DUF1220 (PF06758)

Summary: Repeat of unknown function (DUF1220)

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DUF1220 Edit Wikipedia article

Domain of unknown function (DUF1220)
Identifiers
Symbol DUF1220
Pfam PF06758
InterPro IPR010630
PROSITE PS51316

DUF1220 is a protein domain of unknown function that shows a striking human lineage-specific (HLS) increase in copy number and may be important to human brain evolution.[1] The copy number of DUF1220 domains increases generally as a function of a species evolutionary proximity to humans. DUF1220 copy number is highest in human (over 270, with some person-to-person variations).[2] and shows the largest HLS increase in copy number (an additional 160 copies) of any protein coding region in the human genome. DUF1220 copy number is reduced in African great apes (estimated 125 copies in chimpanzees), further reduced in orangutan (92) and Old World monkeys (35), single- or low-copy in non-primate mammals and absent in non-mammals.[2] DUF1220 domains are approximately 65 amino acids in length and are encoded by a two-exon doublet. In the human genome DUF1220 sequences are located primarily on chromosome 1 in region 1q21.1-q21.2, with several copies also found at 1p36, 1p13.3, and 1p12. Sequences encoding DUF1220 domains show signs of positive selection, especially in primates, and are expressed in several human tissues including brain, where their expression is restricted to neurons.[1]

DUF1220 history[edit]

The gene showing a human-specific increase in DUF1220 copy number was first identified as the result of a genome-wide array CGH study of lineage-specific copy number differences between human and great ape species.[3] The study found 134 genes that showed human lineage-specific increases in copy number, one of which, MGC8902 (also known as NBPF15, cDNA IMAGE:843276), encoded 6 DUF1220 domains.[1] DUF1220 protein domains are found almost exclusively in the NBPF gene family (which includes the MGC8902 gene), which was independently identified as a result of the first member of this family being disrupted in an individual with neuroblastoma.[4] It was recently found that the exceptional increase in human DUF1220 copy number was the results of intragenic domain hyper-amplification primarily involving the three-domain unit called the HLS DUF1220 triplet.[2] Hyper-amplification of the triplet resulted in the addition of ~149 copies of DUF1220 specifically to the human lieage since its divergence from the Pan species, chimpanzee and bonobo, approximately 6 million years ago.[2] The ancestral DUF1220 domain is not part of the NBPF family but rather is found as a single copy within the PDE4DIP (Myomegalin) gene. PDE4DIP encodes a centrosomal protein and is a homolog of CDK5RAP2, a gene that lacks DUF1220 sequences and, when mutated, has been implicated in microcephaly.[5][6]

Links with disease and evolutionary adaptation[edit]

An increasingly large number of disease-associated copy number variations (CNVs) have been reported in the 1q21.1 region and these CNVs either encompass or directly flank DUF1220 domain sequences.[7] Two independent reports [8][9] have linked reciprocal 1q21.1 deletions and duplications in this region with microcephaly and macrocephaly, respectively, raising the possibility that DUF1220 copy number may be involved in influencing human brain size. More recently, Dumas et al.[10] used targeted 1q21 array CGH to follow up on this possibility and implicated DUF1220 copy number loss in 1q21-associated microcephaly. Of all 1q21 sequences tested, DUF1220 sequences were the only ones to show consistent correlation between copy number and brain size in both disease (micro/macrocephaly) and non-disease populations. In addition, in primates there is a significant correlation of DUF1220 copy number with brain size as well as with brain cortical neuron number.[10] For the above reasons and because DUF1220 sequences at 1q21.1 have undergone a dramatic and evolutionarily rapid increase in copy number in humans, a model has been developed that proposes that:

1) increasing DUF1220 domain dosage is the primary driving force behind the evolutionary expansion of the primate (and human) brain,

2) the instability of the 1q21.1 region has facilitated the rapid increase in DUF1220 copy number in humans, and

3) the evolutionary advantage of rapidly increasing DUF1220 copy number in the human genome has resulted in favoring retention of the high genomic instability of the 1q21.1 region, which, in turn, has precipitated a spectrum of recurrent human brain and developmental disorders.

From this perspective, the large number of disease-associated 1q21.1 CNVs may be the price the human species paid, and continues to pay, for the adaptive benefit of having large numbers of DUF1220 copies in its genome.[7]

These observations suggest that the 1q21.1 genome instability problems DUF1220 sequences are thought to promote may be one of the triggers of 1q21.1 duplication syndrome and 1q21.1 deletion syndrome.[7]


References[edit]

  1. ^ a b c Popesco MC, Maclaren EJ, Hopkins J, Dumas L, Cox M, Meltesen L, McGavran L, Wyckoff GJ, Sikela JM (2006). "Human lineage-specific amplification, selection, and neuronal expression of DUF1220 domains". Science 313 (5791): 1304–7. doi:10.1126/science.1127980. PMID 16946073. 
  2. ^ a b c d O'Bleness MS, Dickens CM, Dumas LJ, Kehrer-Sawatzki H, Wyckoff GJ, Sikela JM (2012). "Evolutionary History and Genome Organization of DUF1220 Protein Domains". G3 2: 977–86. doi:10.1534/g3.112.003061. PMID 22973535. 
  3. ^ Fortna A, Kim Y, MacLaren E, Marshall K, Hahn G, Meltesen L, Brenton M, Hink R, Burgers S, Hernandez-Boussard T, Karimpour-Fard A, Glueck D, McGavran L, Berry R, Pollack J, Sikela JM (2004). "Lineage-specific gene duplication and loss in human and great ape evolution". PLoS Biol 2: 937–954. doi:10.1371/journal.pbio.0020207. PMC 449870. PMID 15252450. 
  4. ^ Vandepoele K, Van Roy N, Staes K, Speleman F, van Roy F (2005). "A novel gene family NBPF: intricate structure generated by gene duplications during primate evolution". Mol. Biol. Evol. 22 (11): 2265–74. doi:10.1093/molbev/msi222. PMID 16079250. 
  5. ^ Bond J, Woods,CG (2006). "Cytoskeletal genes regulating brain size". Current Opinion in Cell Biology 18 (1): 95–101. doi:10.1016/j.ceb.2005.11.004. PMID 16337370. 
  6. ^ Dumas L, Kim YH, Karimpour-Fard A, Cox M, Hopkins J, Pollack JR, Sikela JM (2007). "Gene copy number variation spanning 60 million years of human and primate evolution". Genome Research 17 (9): 1266–1277. doi:10.1101/gr.6557307. PMID 17666543. 
  7. ^ a b c Dumas L, Sikela JM (2009). "DUF1220 domains, cognitive disease and human brain evolution". Cold Spring Harb. Symp. Quant. Biol. Evolution: The Molecular Landscape 74: 375–382. doi:10.1101/sqb.2009.74.025. PMC 2902282. PMID 19850849. 
  8. ^ Brunetti-Pierri N et al. (2008). "Recurrent reciprocal 1q21.1 deletions and duplications associated with microcephaly or macrocephaly and developmental and behavioral abnormalities.". Nat. Genet. 40 (12): 1466–1471. doi:10.1038/ng.279. PMC 2680128. PMID 19029900. 
  9. ^ Mefford HC et al. (2008). "Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes.". N. Engl. J. Med. 359: 1685–1699. doi:10.1056/NEJMoa0805384. PMC 2703742. PMID 18784092. 
  10. ^ a b Dumas L, O'Bleness MS, Davis JM, Dickens CM, AndersonN, Keeney JG, Jackson J, Sikela M, Raznahan A, Giedd J, Rapoport J, Nagamani SSC, Erez A, Brunetti-Pierri N, Sugalski R, Lupski JR, Fingerlin T, CHeung SW, Sikela JM (2012). "DUF1220 Domain Copy Number Implicated in Human Brain Size Pathology and Evolution". American Journal of Human Genetics 91: 444–454. doi:10.1016/j.ajhg.2012.07.016. 

Further reading[edit]

This article incorporates text from the public domain Pfam and InterPro IPR010630

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

"DUF" families are annotated with the Domain of unknown function Wikipedia article. This is a general article, with no specific information about individual Pfam DUFs. If you have information about this particular DUF, please let us know using the "Add annotation" button below.

Repeat of unknown function (DUF1220) Provide feedback

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Literature references

  1. Dumas L, Sikela JM;, Cold Spring Harb Symp Quant Biol. 2009; [Epub ahead of print]: DUF1220 Domains, Cognitive Disease, and Human Brain Evolution. PUBMED:19850849 EPMC:19850849


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR010630

This entry represents a highly conserved domain of unknown function which is around 65 residues long. It is primarily found in primate neuroblastoma breakpoint family proteins (NBPF) where it occurs as a repeat. Humans display elevated copy numbers of sequences encoding this domain when compared to other primates, and dramatically elevated copy numbers when compared to mouse/rat lineages. Increased copy number variations at human chromosome location 1q21.1, where most DUF1220-encoding sequences map, have been associated with several cognitive function disorders such as autistic spectrum disorder and schizophrenia [PUBMED:19850849]. This domain also occurs in myomegalin and Pde4dip proteins, as well as in other uncharacterised proteins.

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  Seed
(15)
Full
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Representative proteomes NCBI
(961)
Meta
(0)
RP15
(156)
RP35
(156)
RP55
(156)
RP75
(206)
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Seed source: Pfam-B_6292 (release 10.0)
Previous IDs: none
Type: Domain
Author: Moxon SJ
Number in seed: 15
Number in full: 961
Average length of the domain: 64.40 aa
Average identity of full alignment: 48 %
Average coverage of the sequence by the domain: 40.55 %

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HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.3 20.3
Trusted cut-off 20.6 20.3
Noise cut-off 20.1 20.2
Model length: 67
Family (HMM) version: 8
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