Bovine proteins containing poly-glutamine repeats are often polymorphic and enriched for components of transcriptional regulatory complexes

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Whan, Vicki ^a   Hobbs, Matthew ^b   McWilliam, Sean ^a   Lynn, David J ^c   Lutzow, Ylva S ^a   Khatkar, Mehar ^b   Barendse, William ^a   Raadsma, Herman ^b   Tellam, Ross L ^a  

^a CSIRO   (Australia)

^b UNIVERSITY OF SYDNEY   (Australia)

^c TEAGASC   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

POLYGLUTAMINE; MESSENGER RNA; PEPTIDE; PROTEIN;

ALTERNATIVE RNA SPLICING; ARTICLE; BRAIN; CAG REPEAT; CATTLE; CELL NUCLEUS; CONTROLLED STUDY; EPITHELIUM; GENE EXPRESSION; GENE REGULATORY NETWORK; GENETIC EPISTASIS; GENOME; NONHUMAN; PHENOTYPIC VARIATION; PROTEIN POLYMORPHISM; TESTIS; TRANSCRIPTION REGULATION; ALLELE; ANIMAL; CLUSTER ANALYSIS; EXON; GENE EXPRESSION REGULATION; GENE FREQUENCY; GENETIC POLYMORPHISM; GENETIC TRANSCRIPTION; GENETICS; HUMAN; METABOLISM; MOUSE; POLYMERASE CHAIN REACTION; RNA SPLICING; TRINUCLEOTIDE REPEAT;

BOS; BOVINAE; MAMMALIA;

ALLELES; ANIMALS; CATTLE; CLUSTER ANALYSIS; EXONS; GENE EXPRESSION REGULATION; GENE FREQUENCY; GENOME; HUMANS; MICE; PEPTIDES; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; PROTEINS; RNA SPLICING; RNA, MESSENGER; TRANSCRIPTION, GENETIC; TRINUCLEOTIDE REPEATS;

EID: 78549278120     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-654     Document Type: Article

References (58)

1. Harper PS. Trinucleotide repeat disorders. Journal of inherited metabolic disease 1997, 20(2):122-124. 10.1023/A:1005388218625, 9211184.
2. Huang H, Winter EE, Wang H, Weinstock KG, Xing H, Goodstadt L, Stenson PD, Cooper DN, Smith D, Alba MM, et al. Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes. Genome biology 2004, 5(7):R47. 10.1186/gb-2004-5-7-r47, 463309, 15239832.
3. La Spada AR, Taylor JP. Repeat expansion disease: progress and puzzles in disease pathogenesis. Nature reviews 2010, 11(4):247-258. 10.1038/nrg2748, 20177426.
4. Pearson CE, Nichol Edamura K, Cleary JD. Repeat instability: mechanisms of dynamic mutations. Nature reviews 2005, 6(10):729-742. 10.1038/nrg1689, 16205713.
5. A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes. The Huntington's Disease Collaborative Research Group. Cell 1993, 72(6):971-983. 10.1016/0092-8674(93)90585-E, 8458085.
6. Kieburtz K, MacDonald M, Shih C, Feigin A, Steinberg K, Bordwell K, Zimmerman C, Srinidhi J, Sotack J, Gusella J, et al. Trinucleotide repeat length and progression of illness in Huntington's disease. Journal of medical genetics 1994, 31(11):872-874. 10.1136/jmg.31.11.872, 1016662, 7853373.
7. Restituito S, Thompson RM, Eliet J, Raike RS, Riedl M, Charnet P, Gomez CM. The polyglutamine expansion in spinocerebellar ataxia type 6 causes a beta subunit-specific enhanced activation of P/Q-type calcium channels in Xenopus oocytes. J Neurosci 2000, 20(17):6394-6403.
8. Richards RI, Sutherland GR. Dynamic mutation: possible mechanisms and significance in human disease. Trends in biochemical sciences 1997, 22(11):432-436. 10.1016/S0968-0004(97)01108-0, 9397685.
9. Matsuyama Z, Wakamori M, Mori Y, Kawakami H, Nakamura S, Imoto K. Direct alteration of the P/Q-type Ca2+ channel property by polyglutamine expansion in spinocerebellar ataxia 6. J Neurosci 1999, 19(12):RC14.
10. Yue S, Serra HG, Zoghbi HY, Orr HT. The spinocerebellar ataxia type 1 protein, ataxin-1, has RNA-binding activity that is inversely affected by the length of its polyglutamine tract. Human molecular genetics 2001, 10(1):25-30. 10.1093/hmg/10.1.25, 11136710.
11. Butland SL, Devon RS, Huang Y, Mead CL, Meynert AM, Neal SJ, Lee SS, Wilkinson A, Yang GS, Yuen MM, et al. CAG-encoded polyglutamine length polymorphism in the human genome. BMC genomics 2007, 8:126. 10.1186/1471-2164-8-126, 1896166, 17519034.
12. Alba MM, Guigo R. Comparative analysis of amino acid repeats in rodents and humans. Genome research 2004, 14(4):549-554. 10.1101/gr.1925704, 383298, 15059995.
13. Mularoni L, Ledda A, Toll-Riera, Alba MM. Natural selection drives the accumulation of amino acvid tandem repeats in human proteins. Genome research 2010, 2877571, 20335526.
14. Caburet S, Cocquet J, Vaiman D, Veitia RA. Coding repeats and evolutionary "agility". Bioessays 2005, 27(6):581-587. 10.1002/bies.20248, 15892112.
15. Fondon JW, Garner HR. Molecular origins of rapid and continuous morphological evolution. Proceedings of the National Academy of Sciences of the United States of America 2004, 101(52):18058-18063. 10.1073/pnas.0408118101, 539791, 15596718.
16. Fondon JW, Garner HR. Detection of length-dependent effects of tandem repeat alleles by 3-D geometric decomposition of craniofacial variation. Development genes and evolution 2007, 217(1):79-85. 10.1007/s00427-006-0113-4, 17066275.
17. Andres AM, Lao O, Soldevila M, Calafell F, Bertranpetit J. Dynamics of CAG repeat loci revealed by the analysis of their variability. Human mutation 2003, 21(1):61-70. 10.1002/humu.10151, 12497632.
18. National Center for Biotechnology Information. , http://www.ncbi.nlm.nih.gov/
19. Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigo R, et al. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (New York, NY 2009, 324(5926):522-528.
20. Tellam RL, Lemay DG, Van Tassell CP, Lewin HA, Worley KC, Elsik CG. Unlocking the bovine genome. BMC genomics 2009, 10:193. 10.1186/1471-2164-10-193, 2680899, 19393070.
21. Karlin S. Statistical significance of sequence patterns in proteins. Current opinion in structural biology 1995, 5(3):360-371. 10.1016/0959-440X(95)80098-0, 7583634.
22. UCSC Genome Bioinformatics. , http://genome.ucsc.edu/
23. Sando L, Pearson R, Gray C, Parker P, Hawken R, Thomson PC, Meadows JR, Kongsuwan K, Smith S, Tellam RL. Bovine Muc1 is a highly polymorphic gene encoding an extensively glycosylated mucin that binds bacteria. Journal of dairy science 2009, 92(10):5276-5291. 10.3168/jds.2009-2216, 19762846.
24. Buchanan G, Yang M, Cheong A, Harris JM, Irvine RA, Lambert PF, Moore NL, Raynor M, Neufing PJ, Coetzee GA, et al. Structural and functional consequences of glutamine tract variation in the androgen receptor. Human molecular genetics 2004, 13(16):1677-1692. 10.1093/hmg/ddh181, 15198988.
25. Rousset F, Raymond M. Testing heterozygote excess and deficiency. Genetics 1995, 140(4):1413-1419. 1206704, 7498780.
26. Dennis G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome biology 2003, 4(5):P3. 10.1186/gb-2003-4-5-p3, 12734009.
27. Huang DW, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Research 2009, 37(1):1-13. 10.1093/nar/gkn923, 2615629, 19033363.
28. InnateDB. , http://www.innatedb.ca/
29. Lynn DJ, Winsor GL, Chan C, Richard N, Laird MR, Barsky A, Gardy JL, Roche FM, Chan TH, Shah N, et al. InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Molecular systems biology 2008, 4:218. 10.1038/msb.2008.55, 2564732, 18766178.
30. Boutell JM, Thomas P, Neal JW, Weston VJ, Duce J, Harper PS, Jones AL. Aberrant interactions of transcriptional repressor proteins with the Huntington's disease gene product, huntingtin. Human molecular genetics 1999, 8(9):1647-1655. 10.1093/hmg/8.9.1647, 10441327.
31. Steffan JS, Kazantsev A, Spasic-Boskovic O, Greenwald M, Zhu YZ, Gohler H, Wanker EE, Bates GP, Housman DE, Thompson LM. The Huntington's disease protein interacts with p53 and CREB-binding protein and represses transcription. Proceedings of the National Academy of Sciences of the United States of America 2000, 97(12):6763-6768. 10.1073/pnas.100110097, 18731, 10823891.
32. Hooft van Huijsduijnen RA, Bollekens J, Dorn A, Benoist C, Mathis D. Properties of a CCAAT box-binding protein. Nucleic Acids Res 1987, 15(18):7265-7282. 10.1093/nar/15.18.7265, 306247, 3477778.
33. de Silvio A, Imbriano C, Mantovani R. Dissection of the NF-Y transcriptional activation potential. Nucleic Acids Res 1999, 27(13):2578-2584. 10.1093/nar/27.13.2578, 148464, 10373572.
34. Li XY, Hooft van Huijsduijnen R, Mantovani R, Benoist C, Mathis D. Intron-exon organization of the NF-Y genes. Tissue-specific splicing modifies an activation domain. The Journal of biological chemistry 1992, 267(13):8984-8990.
35. Harada N, Mitani T, Higashimura Y, Yamaji R, Okamoto K, Nakano Y, Inui H. Involvement of three glutamine tracts in human androgen receptor transactivation. The Journal of steroid biochemistry and molecular biology 2010, 118(1-2):77-84. 10.1016/j.jsbmb.2009.10.003, 19833203.
36. Jodice C, Giovannone B, Calabresi V, Bellocchi M, Terrenato L, Novelletto A. Population variation analysis at nine loci containing expressed trinucleotide repeats. Annals of human genetics 1997, 61(Pt 5):425-438.
37. Mularoni L, Guigo R, Alba MM. Mutation patterns of amino acid tandem repeats in the human proteome. Genome biology 2006, 7(4):R33. 10.1186/gb-2006-7-4-r33, 1557989, 16640792.
38. Sobczak K, Krzyzosiak WJ. Patterns of CAG repeat interruptions in SCA1 and SCA2 genes in relation to repeat instability. Human mutation 2004, 24(3):236-247. 10.1002/humu.20075, 15300851.
39. Wren JD, Forgacs E, Fondon JW, Pertsemlidis A, Cheng SY, Gallardo T, Williams RS, Shohet RV, Minna JD, Garner HR. Repeat polymorphisms within gene regions: phenotypic and evolutionary implications. American journal of human genetics 2000, 67(2):345-356. 10.1086/303013, 1287183, 10889045.
40. Ellegren H. Mismatch repair and mutational bias in microsatellite DNA. Trends Genet 2002, 18(11):552. 10.1016/S0168-9525(02)02804-4, 12414181.
41. Schlotterer C, Tautz D. Slippage synthesis of simple sequence DNA. Nucleic Acids Res 1992, 20(2):211-215. 10.1093/nar/20.2.211, 310356, 1741246.
42. Madsen LB, Thomsen B, Solvsten CA, Bendixen C, Fredholm M, Jorgensen AL, Nielsen AL. Identification of the porcine homologous of human disease causing trinucleotide repeat sequences. Neurogenetics 2007, 8(3):207-218. 10.1007/s10048-007-0088-y, 17516099.
43. Huntley MA, Golding GB. Selection and slippage creating serine homopolymers. Molecular biology and evolution 2006, 23(11):2017-2025. 10.1093/molbev/msl073, 16877497.
44. Lovell SC. Are non-functional, unfolded proteins ('junk proteins') common in the genome?. FEBS letters 2003, 554(3):237-239. 10.1016/S0014-5793(03)01223-7, 14623072.
45. Brown L, Paraso M, Arkell R, Brown S. In vitro analysis of partial loss-of-function ZIC2 mutations in holoprosencephaly: alanine tract expansion modulates DNA binding and transactivation. Human molecular genetics 2005, 14(3):411-420. 10.1093/hmg/ddi037, 15590697.
46. Galant R, Carroll SB. Evolution of a transcriptional repression domain in an insect Hox protein. Nature 2002, 415(6874):910-913. 10.1038/nature717, 11859369.
47. Gerber HP, Seipel K, Georgiev O, Hofferer M, Hug M, Rusconi S, Schaffner W. Transcriptional activation modulated by homopolymeric glutamine and proline stretches. Science (New York, NY 1994, 263(5148):808-811.
48. Haerty W, Golding GB. Genome-wide evidence for selection acting on single amino acid repeats. Genome research 2010, 20(6):755-760. 10.1101/gr.101246.109, 2877572, 20056893.
49. Janody F, Sturny R, Schaeffer V, Azou Y, Dostatni N. Two distinct domains of Bicoid mediate its transcriptional downregulation by the Torso pathway. Development (Cambridge, England) 2001, 128(12):2281-2290.
50. Lanz RB, Wieland S, Hug M, Rusconi S. A transcriptional repressor obtained by alternative translation of a trinucleotide repeat. Nucleic Acids Res 1995, 23(1):138-145. 10.1093/nar/23.1.138, 306641, 7532856.
51. Yu F, Sabeti PC, Hardenbol P, Fu Q, Fry B, Lu X, Ghose S, Vega R, Perez A, Pasternak S, et al. Positive selection of a pre-expansion CAG repeat of the human SCA2 gene. PLoS genetics 2005, 1(3):e41. 10.1371/journal.pgen.0010041, 1239938, 16205789.
52. Soding J, Lupas AN. More than the sum of their parts: on the evolution of proteins from peptides. Bioessays 2003, 25(9):837-846. 10.1002/bies.10321, 12938173.
53. Online Mendelian Inheritance in Man. , http://www.nslij-genetics.org/search_omim.html
54. Sasaki M, Kaneuchi M, Sakuragi N, Fujimoto S, Carroll PR, Dahiya R. The polyglycine and polyglutamine repeats in the androgen receptor gene in Japanese and Caucasian populations. Biochemical and biophysical research communications 2003, 312(4):1244-1247. 10.1016/j.bbrc.2003.11.075, 14652007.
55. Muhlenbein N, Hofmann S, Rothbauer U, Bauer MF. Organization and function of the small Tim complexes acting along the import pathway of metabolite carriers into mammalian mitochondria. The Journal of biological chemistry 2004, 279(14):13540-13546. 10.1074/jbc.M312485200, 14726512.
56. Goers ES, Purcell J, Voelker RB, Gates DP, Berglund JA. MBNL1 binds GC motifs embedded in pyrimidines to regulate alternative splicing. Nucleic Acids Res 2010, 38:2467-2484. 10.1093/nar/gkp1209, 2853123, 20071745.
57. Vuocolo T, Byrne K, White J, McWilliam S, Reverter A, Cockett NE, Tellam RL. Identification of a gene network contributing to hypertrophy in callipyge skeletal muscle. Physiological genomics 2007, 28(3):253-272. 10.1152/physiolgenomics.00121.2006, 17077277.
58. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research 2003, 13(11):2498-2504. 10.1101/gr.1239303, 403769, 14597658.