Direct Visualization of the Highly Polymorphic RNU2 Locus in Proximity to the BRCA1 Gene

PLoS ONE

Volumn 8, Issue 10, 2013, Pages

  Tessereau, Chloé ^a,b   Buisson, Monique ^a   Monnet, Nastasia ^a   Imbert, Marine ^a   Barjhoux, Laure ^a   Schluth Bolard, Caroline ^a   Sanlaville, Damien ^a   Conseiller, Emmanuel ^b   Ceppi, Maurizio ^b   Sinilnikova, Olga M ^a,c   Mazoyer, Sylvie ^a  

^a UNIVERSITÉ LYON 1   (France)

^b Genomic Vision   (France)

^c HOSPICES CIVILS DE LYON   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BRCA1 PROTEIN; SMALL NUCLEAR RIBONUCLEOPROTEIN;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CHROMOSOME 17Q; CONTROLLED STUDY; DNA POLYMORPHISM; FLUORESCENCE IN SITU HYBRIDIZATION; GEL ELECTROPHORESIS; GENE LOCATION; GENE LOCUS; GENE SEQUENCE; HETEROZYGOSITY; HUMAN; HUMAN CELL; HUMAN GENOME; LONG TERMINAL REPEAT; LYMPHOBLASTOID CELL LINE; METAPHASE; MICROSATELLITE MARKER; NUCLEOTIDE SEQUENCE; PULSED FIELD GEL ELECTROPHORESIS; RNU2 GENE; TUMOR GENE; TUMOR SUPPRESSOR GENE; VARIABLE NUMBER OF TANDEM REPEAT;

ALLELES; BREAST NEOPLASMS; CHROMOSOMES, HUMAN, PAIR 17; FEMALE; GENE EXPRESSION; GENES, BRCA1; GENETIC LOCI; HETEROZYGOTE; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; MICROSATELLITE REPEATS; PHYSICAL CHROMOSOME MAPPING; RNA, SMALL NUCLEAR;

EID: 84885404619     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0076054     Document Type: Article

References (36)

1. Eichler EE, Nickerson DA, Altshuler D, Bowcock AM, Brooks LD, et al. (2007) Completing the map of human genetic variation. Nature 447: 161-165.
2. Feuk L, Carson AR, Scherer SW, (2006) Structural variation in the human genome. Nat Rev Genet 7: 85-97.
3. Freeman JL, Perry GH, Feuk L, Redon R, McCarroll SA, et al. (2006) Copy number variation: new insights in genome diversity. Genome Res 16: 949-961.
4. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, et al. (2006) Global variation in copy number in the human genome. Nature 444: 444-454.
5. McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, et al. (2008) Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet 40: 1166-1174.
6. Warburton PE, Hasson D, Guillem F, Lescale C, Jin X, et al. (2008) Analysis of the largest tandemly repeated DNA families in the human genome. BMC Genomics 9: 533.
7. Abyzov A, Urban AE, Snyder M, Gerstein M, (2011) CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res 21: 974-984.
8. Van Arsdell SW, Weiner AM, (1984) Human genes for U2 small nuclear RNA are tandemly repeated. Mol Cell Biol 4: 492-499.
9. Westin G, Zabielski J, Hammarstrom K, Monstein HJ, Bark C, et al. (1984) Clustered genes for human U2 RNA. Proc Natl Acad Sci U S A 81: 3811-3815.
10. Hammarstrom K, Santesson B, Westin G, Pettersson U, (1985) The gene cluster for human U2 RNA is located on chromosome 17q21. Exp Cell Res 159: 473-478.
11. Lindgren V, Ares M Jr, Weiner AM, Francke U, (1985) Human genes for U2 small nuclear RNA map to a major adenovirus 12 modification site on chromosome 17. Nature 314: 115-116.
12. Abel KJ, Boehnke M, Prahalad M, Ho P, Flejter WL, et al. (1993) A radiation hybrid map of the BRCA1 region of chromosome 17q12-q21. Genomics 17: 632-641.
13. Albertsen HM, Smith SA, Mazoyer S, Fujimoto E, Stevens J, et al. (1994) A physical map and candidate genes in the BRCA1 region on chromosome 17q12-21. Nat Genet 7: 472-479.
14. Black DM, Nicolai H, Borrow J, Solomon E, (1993) A somatic cell hybrid map of the long arm of human chromosome 17, containing the familial breast cancer locus (BRCA1). Am J Hum Genet 52: 702-710.
15. Flejter WL, Barcroft CL, Guo SW, Lynch ED, Boehnke M, et al. (1993) Multicolor FISH mapping with Alu-PCR-amplified YAC clone DNA determines the order of markers in the BRCA1 region on chromosome 17q12-q21. Genomics 17: 624-631.
16. Liu X, Barker DF, (1999) Evidence for effective suppression of recombination in the chromosome 17q21 segment spanning RNU2-BRCA1. Am J Hum Genet 64: 1427-1439.
17. Neuhausen SL, Swensen J, Miki Y, Liu Q, Tavtigian S, et al. (1994) A P1-based physical map of the region from D17S776 to D17S78 containing the breast cancer susceptibility gene BRCA1. Hum Mol Genet 3: 1919-1926.
18. Pavelitz T, Rusche L, Matera AG, Scharf JM, Weiner AM, (1995) Concerted evolution of the tandem array encoding primate U2 snRNA occurs in situ, without changing the cytological context of the RNU2 locus. EMBO J 14: 169-177.
19. Pavelitz T, Liao D, Weiner AM, (1999) Concerted evolution of the tandem array encoding primate U2 snRNA (the RNU2 locus) is accompanied by dramatic remodeling of the junctions with flanking chromosomal sequences. EMBO J 18: 3783-3792.
20. Liao D, Pavelitz T, Kidd JR, Kidd KK, Weiner AM, (1997) Concerted evolution of the tandemly repeated genes encoding human U2 snRNA (the RNU2 locus) involves rapid intrachromosomal homogenization and rare interchromosomal gene conversion. EMBO J 16: 588-598.
21. Schaap M, Lemmers RJ, Maassen R, van der Vliet PJ, Hoogerheide LF, et al. (2013) Genome-wide analysis of macrosatellite repeat copy number variation in worldwide populations: evidence for differences and commonalities in size distributions and size restrictions. BMC Genomics 14: 143.
22. Sinilnikova OM, Mazoyer S, Bonnardel C, Lynch HT, Narod SA, et al. (2006) BRCA1 and BRCA2 mutations in breast and ovarian cancer syndrome: reflection on the Creighton University historical series of high risk families. Fam Cancer 5: 15-20.
23. Cheeseman K, Rouleau E, Vannier A, Thomas A, Briaux A, et al. (2012) A diagnostic genetic test for the physical mapping of germline rearrangements in the susceptibility breast cancer genes BRCA1 and BRCA2. Hum Mutat 33: 998-1009.
24. Michalet X, Ekong R, Fougerousse F, Rousseaux S, Schurra C, et al. (1997) Dynamic molecular combing: stretching the whole human genome for high-resolution studies. Science 277: 1518-1523.
25. Schluth-Bolard C, Delobel B, Sanlaville D, Boute O, Cuisset JM, et al. (2009) Cryptic genomic imbalances in de novo and inherited apparently balanced chromosomal rearrangements: array CGH study of 47 unrelated cases. Eur J Med Genet 52: 291-296.
26. Bailey AD, Li Z, Pavelitz T, Weiner AM, (1995) Adenovirus type 12-induced fragility of the human RNU2 locus requires U2 small nuclear RNA transcriptional regulatory elements. Mol Cell Biol 15: 6246-6255.
27. Yu A, Fan HY, Liao D, Bailey AD, Weiner AM, (2000) Activation of p53 or loss of the Cockayne syndrome group B repair protein causes metaphase fragility of human U1, U2, and 5S genes. Mol Cell 5: 801-810.
28. International Human Genome Sequencing Consortium, (2004) Finishing the euchromatic sequence of the human genome. Nature 431: 931-945.
29. Eichler EE, Clark RA, She X, (2004) An assessment of the sequence gaps: unfinished business in a finished human genome. Nat Rev Genet 5: 345-354.
30. Phillippy AM, Schatz MC, Pop M, (2008) Genome assembly forensics: finding the elusive mis-assembly. Genome Biol 9: R55.
31. Tremblay DC, Alexander G Jr, Moseley S, Chadwick BP, (2010) Expression, tandem repeat copy number variation and stability of four macrosatellite arrays in the human genome. BMC Genomics 11: 632.
32. Wahl MC, Will CL, Luhrmann R, (2009) The spliceosome: design principles of a dynamic RNP machine. Cell 136: 701-718.
33. Jia Y, Mu JC, Ackerman SL, (2012) Mutation of a U2 snRNA gene causes global disruption of alternative splicing and neurodegeneration. Cell 148: 296-308.
34. Padgett RA, (2012) New connections between splicing and human disease. Trends Genet 28: 147-154.
35. Henrichsen CN, Vinckenbosch N, Zollner S, Chaignat E, Pradervand S, et al. (2009) Segmental copy number variation shapes tissue transcriptomes. Nat Genet 41: 424-429.
36. Merla G, Howald C, Henrichsen CN, Lyle R, Wyss C, et al. (2006) Submicroscopic deletion in patients with Williams-Beuren syndrome influences expression levels of the nonhemizygous flanking genes. Am J Hum Genet 79: 332-341.