Variation in array size, monomer composition and expression of the macrosatellite DXZ4

PLoS ONE

Volumn 6, Issue 4, 2011, Pages

  Tremblay, Deanna C ^a   Moseley, Shawn ^a   Chadwick, Brian P ^a  

^a FLORIDA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOME PROTEIN; MONOMER; PROTEIN DZX4; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CHROMOSOMAL INSTABILITY; CHROMOSOME INACTIVATION; COPY NUMBER VARIATION; DNA BASE COMPOSITION; DNA MICROARRAY; FLUORESCENCE IN SITU HYBRIDIZATION; GENE EXPRESSION; GENE FREQUENCY; GENE SEQUENCE; HETEROCHROMATIN; HUMAN; HUMAN GENOME; MACROSATELLITE; MEIOSIS; MICROSATELLITE MARKER; MOLECULAR CLONING; NUCLEOTIDE SEQUENCE; POLYMORPHIC LOCUS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; TANDEM REPEAT; X CHROMOSOME; FEMALE; GENETICS; MALE; NUCLEOTIDE REPEAT; PHYLOGENY;

DNA COPY NUMBER VARIATIONS; FEMALE; GENOME, HUMAN; HUMANS; MALE; PHYLOGENY; REPETITIVE SEQUENCES, NUCLEIC ACID;

EID: 79955538818     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0018969     Document Type: Article

References (37)

1. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
2. 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.
3. Bruce HA, Sachs N, Rudnicki DD, Lin SG, Willour VL, et al. (2009) Long tandem repeats as a form of genomic copy number variation: structure and length polymorphism of a chromosome 5p repeat in control and schizophrenia populations. Psychiatr Genet 19: 64-71.
4. Chadwick BP, (2008) DXZ4 chromatin adopts an opposing conformation to that of the surrounding chromosome and acquires a novel inactive X-specific role involving CTCF and antisense transcripts. Genome Res 18: 1259-1269.
5. Giacalone J, Friedes J, Francke U, (1992) A novel GC-rich human macrosatellite VNTR in Xq24 is differentially methylated on active and inactive X chromosomes. Nat Genet 1: 137-143.
6. Okada T, Gondo Y, Goto J, Kanazawa I, Hadano S, et al. (2002) Unstable transmission of the RS447 human megasatellite tandem repetitive sequence that contains the USP17 deubiquitinating enzyme gene. Hum Genet 110: 302-313.
7. 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.
8. van Deutekom JC, Wijmenga C, van Tienhoven EA, Gruter AM, Hewitt JE, et al. (1993) FSHD associated DNA rearrangements are due to deletions of integral copies of a 3.2 kb tandemly repeated unit. Hum Mol Genet 2: 2037-2042.
9. Wijmenga C, Hewitt JE, Sandkuijl LA, Clark LN, Wright TJ, et al. (1992) Chromosome 4q DNA rearrangements associated with facioscapulohumeral muscular dystrophy. Nat Genet 2: 26-30.
10. Deidda G, Cacurri S, Grisanti P, Vigneti E, Piazzo N, et al. (1995) Physical mapping evidence for a duplicated region on chromosome 10qter showing high homology with the facioscapulohumeral muscular dystrophy locus on chromosome 4qter. Eur J Hum Genet 3: 155-167.
11. Winokur ST, Bengtsson U, Vargas JC, Wasmuth JJ, Altherr MR, et al. (1996) The evolutionary distribution and structural organization of the homeobox-containing repeat D4Z4 indicates a functional role for the ancestral copy in the FSHD region. Hum Mol Genet 5: 1567-1575.
12. Tawil R, (2008) Facioscapulohumeral muscular dystrophy. Neurotherapeutics 5: 601-606.
13. Payer B, Lee JT, (2008) X Chromosome Dosage Compensation: How Mammals Keep the Balance. Annu Rev Genet 42: 29.1-29.40.
14. Carrel L, Willard HF, (2005) X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature 434: 400-404.
15. Chadwick BP, (2007) Variation in Xi chromatin organization and correlation of the H3K27me3 chromatin territories to transcribed sequences by microarray analysis. Chromosoma 116: 147-157.
16. Chadwick BP, Willard HF, (2004) Multiple spatially distinct types of facultative heterochromatin on the human inactive X chromosome. Proc Natl Acad Sci U S A 101: 17450-17455.
17. Chadwick BP, Willard HF, (2002) Cell cycle-dependent localization of macroH2A in chromatin of the inactive X chromosome. J Cell Biol 157: 1113-1123.
18. Chadwick BP, Willard HF, (2003) Chromatin of the Barr body: histone and non-histone proteins associated with or excluded from the inactive X chromosome. Hum Mol Genet 12: 2167-2178.
19. Mohandas T, Sparkes RS, Shapiro LJ, (1981) Reactivation of an inactive human X chromosome: evidence for X inactivation by DNA methylation. Science 211: 393-396.
20. Pfeifer GP, Tanguay RL, Steigerwald SD, Riggs AD, (1990) In vivo footprint and methylation analysis by PCR-aided genomic sequencing: comparison of active and inactive X chromosomal DNA at the CpG island and promoter of human PGK-1. Genes Dev 4: 1277-1287.
21. Kim UJ, Birren BW, Slepak T, Mancino V, Boysen C, et al. (1996) Construction and characterization of a human bacterial artificial chromosome library. Genomics 34: 213-218.
22. Florijn RJ, Bonden LA, Vrolijk H, Wiegant J, Vaandrager JW, et al. (1995) High-resolution DNA Fiber-FISH for genomic DNA mapping and colour bar-coding of large genes. Hum Mol Genet 4: 831-836.
23. Beck CR, Collier P, Macfarlane C, Malig M, Kidd JM, et al. (2010) LINE-1 retrotransposition activity in human genomes. Cell 141: 1159-1170.
24. van Deutekom JC, Bakker E, Lemmers RJ, van der Wielen MJ, Bik E, et al. (1996) Evidence for subtelomeric exchange of 3.3 kb tandemly repeated units between chromosomes 4q35 and 10q26: implications for genetic counselling and etiology of FSHD1. Hum Mol Genet 5: 1997-2003.
25. Snider L, Asawachaicharn A, Tyler AE, Geng LN, Petek LM, et al. (2009) RNA Transcripts, miRNA-sized Fragments, and Proteins Produced from D4Z4 Units: New Candidates for the Pathophysiology of Facioscapulohumeral Dystrophy. Hum Mol Genet.
26. Dixit M, Ansseau E, Tassin A, Winokur S, Shi R, et al. (2007) DUX4, a candidate gene of facioscapulohumeral muscular dystrophy, encodes a transcriptional activator of PITX1. Proc Natl Acad Sci U S A 104: 18157-18162.
27. Lemmers RJ, van der Vliet PJ, Klooster R, Sacconi S, Camano P, et al. (2010) A Unifying Genetic Model for Facioscapulohumeral Muscular Dystrophy. Science.
28. Andreassen R, Olaisen B, (1998) De novo mutations and allelic diversity at minisatellite locus D7S22 investigated by allele-specific four-state MVR-PCR analysis. Hum Mol Genet 7: 2113-2120.
29. Vergnaud G, Mariat D, Apiou F, Aurias A, Lathrop M, et al. (1991) The use of synthetic tandem repeats to isolate new VNTR loci: cloning of a human hypermutable sequence. Genomics 11: 135-144.
30. Vergnaud G, Denoeud F, (2000) Minisatellites: mutability and genome architecture. Genome Res 10: 899-907.
31. Jeffreys AJ, Tamaki K, MacLeod A, Monckton DG, Neil DL, et al. (1994) Complex gene conversion events in germline mutation at human minisatellites. Nat Genet 6: 136-145.
32. Grafodatskaya D, Choufani S, Ferreira JC, Butcher DT, Lou Y, et al. (2010) EBV transformation and cell culturing destabilizes DNA methylation in human lymphoblastoid cell lines. Genomics 95: 73-83.
33. Saferali A, Grundberg E, Berlivet S, Beauchemin H, Morcos L, et al. (2010) Cell culture-induced aberrant methylation of the imprinted IG DMR in human lymphoblastoid cell lines. Epigenetics 5: 50-60.
34. Chen YT, Iseli C, Venditti CA, Old LJ, Simpson AJ, et al. (2006) Identification of a new cancer/testis gene family, CT47, among expressed multicopy genes on the human X chromosome. Genes Chromosomes Cancer 45: 392-400.
35. Gjerstorff MF, Ditzel HJ, (2008) An overview of the GAGE cancer/testis antigen family with the inclusion of newly identified members. Tissue Antigens 71: 187-192.
36. Sambrook J, Fritsch EF, Maniatis T, (1989) Molecular Cloning: A laboratory manual. Second edition Cold Spring Harbor, NY Cold Spring Harbor Laboratory Press.
37. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.