Evolutionary genomic remodelling of the human 4q subtelomere (4q35.2)

BMC Evolutionary Biology

Volumn 7, Issue , 2007, Pages

  Bodega, Beatrice ^a   Cardone, Maria Francesca ^b   Müller, Stefan ^c   Neusser, Michaela ^c   Orzan, Francesca ^a   Rossi, Elena ^a   Battaglioli, Elena ^a   Marozzi, Anna ^a   Riva, Paola ^a   Rocchi, Mariano ^b   Meneveri, Raffaella ^d   Ginelli, Enrico ^a  

^a UNIVERSITY OF MILAN   (Italy)

^b UNIVERSITY OF BARI   (Italy)

^c UNIVERSITY OF MUNICH   (Germany)

^d UNIVERSITY OF MILANO BICOCCA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE DEACETYLASE; CHROMATIN; GENETIC MARKER;

ACETYLATION; ANIMAL CELL; APE; ARTICLE; CHIMPANZEE; CHROMATIN; CHROMATIN CONDENSATION; CONTROLLED STUDY; ENZYME INHIBITION; GENE; GENE EXPRESSION; GENE LOCUS; GENETIC TRANSCRIPTION; GENOMICS; GORILLA; NONHUMAN; NUCLEOTIDE SEQUENCE; TRANSCRIPTION REGULATION; ANIMAL; CHROMOSOME; CHROMOSOME 4; CHROMOSOME MAP; FACIOSCAPULOHUMERAL MUSCULAR DYSTROPHY; FLUORESCENCE IN SITU HYBRIDIZATION; GENE LIBRARY; GENETIC MARKER; GENETICS; HUMAN; MOLECULAR CLONING; MOLECULAR EVOLUTION; PAN TROGLODYTES; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SOUTHERN BLOTTING;

PAN;

ANIMALS; BLOTTING, SOUTHERN; CHROMATIN; CHROMOSOMES, HUMAN, PAIR 4; CHROMOSOMES, MAMMALIAN; CLONING, MOLECULAR; EVOLUTION, MOLECULAR; GENETIC MARKERS; GENOMIC LIBRARY; GORILLA GORILLA; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; MUSCULAR DYSTROPHY, FACIOSCAPULOHUMERAL; PAN TROGLODYTES; PHYSICAL CHROMOSOME MAPPING; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 33947575337     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-7-39     Document Type: Article

References (47)

1. Genomic analysis of human chromosome 10q and 4q telomeres suggests a common origin. M van Geel MC Dickson AF Beck DJ Bolland RR Frants SM van der Maarel PJ de Jong JE Hewitt, Genomics 2002 79 210 217 10.1006/geno.2002.6690 11829491
2. Genetic linkage map of facioscapulohumeral muscular dystrophy and five polymorphic loci on chromosome 4q35-qter. C Wijmenga LA Sandkuijl P Moerer N van der Boorn SE Bodrug PN Ray OF Brouwer JC Murray GJ van Ommen GW Padberg, Am J Hum Genet 1992 51 411 415 1642239
3. Analysis of the tandem repeat locus D4Z4 associated with facioscapulohumeral muscular dystrophy. JE Hewitt R Lyle LN Clark EM Valleley TJ Wright C Wijmenga JC van Deutekom F Francis PT Sharpe M Hofker, Hum Mol Genet 1994 3 1287 1295 10.1093/hmg/3.8.1287 7987304
4. Human genome dispersal and evolution of 4q35 duplications and interspersed LSau repeats. L Ballarati I Piccini L Carbone N Archidiacono A Rollier A Marozzi R Meneveri E Ginelli, Gene 2002 296 21 27 10.1016/S0378- 1119(02)00858-2 12383499
5. FSHD associated DNA rearrangements are due to deletions of integral copies of a 3.2 kb tandemly repeated unit. JC van Deutekom C Wijmenga EA van Tienhoven AM Gruter JE Hewitt GW Padberg GJ van Ommen MH Hofker RR Frants, Hum Mol Genet 1993 2 2037 2042 10.1093/hmg/2.12.2037 8111371
6. Hypomethylation of D4Z4 in 4q-linked and non-4q-linked facioscapulohumeral muscular dystrophy. PG van Overveld RJ Lemmers LA Sandkuijl L Enthoven ST Winokur F Bakels GW Padberg GJ van Ommen RR Frants SM van der Maarel, Nat Genet 2003 35 315 317 10.1038/ng1262 14634647
7. Variable hypomethylation of D4Z4 in facioscapulohumeral muscular dystrophy. PG van Overveld L Enthoven E Ricci M Rossi L Felicetti M Jeanpierre ST Winokur RR Frants GW Padberg SM van der Maarel, Ann Neurol 2005 58 569 576 10.1002/ana.20625 16178028
8. Perturbations of chromatin structure in human genetic disease: recent advances. WA Bickmore SM van der Maarel, Hum Mol Genet 2003 12 Spec No 2 R207 13 10.1093/hmg/ddg260 12915455
9. Facioscapulohumeral muscular dystrophy in mice overexpressing FRG1. D Gabellini G D'Antona M Moggio A Prelle C Zecca R Adami B Angeletti P Ciscato MA Pellegrino R Bottinelli MR Green R Tupler, Nature 2006 439 973 977 16341202
10. Inappropriate gene activation in FSHD: a repressor complex binds a chromosomal repeat deleted in dystrophic muscle. D Gabellini MR Green R Tupler, Cell 2002 110 339 348 10.1016/S0092-8674(02)00826-7 12176321
11. FRG2, an FSHD candidate gene, is transcriptionally upregulated in differentiating primary myoblast cultures of FSHD patients. T Rijkers G Deidda S van Koningsbruggen M van Geel RJ Lemmers JC van Deutekom D Figlewicz JE Hewitt GW Padberg RR Frants SM van der Maarel, J Med Genet 2004 41 826 836 10.1136/jmg.2004.019364 15520407
12. Facioscapulohumeral muscular dystrophy. SM van der Maarel RR Frants GW Padberg, Biochim Biophys Acta 2007 1772 186 94 16837171
13. Testing the position-effect variegation hypothesis for facioscapulohumeral muscular dystrophy by analysis of histone modification and gene expression in subtelomeric 4q. G Jiang F Yang PG van Overveld V Vedanarayanan S van der Maarel M Ehrlich, Hum Mol Genet 2003 12 2909 2921 10.1093/hmg/ddg323 14506132
14. The 4q subtelomere harboring the FSHD locus is specifically anchored with peripheral heterochromatin unlike most human telomeres. R Tam KP Smith JB Lawrence, J Cell Biol 2004 167 269 279 10.1083/jcb.200403128 15504910
15. Localization of 4q35.2 to the nuclear periphery: is FSHD a nuclear envelope disease? PS Masny U Bengtsson SA Chung JH Martin B van Engelen SM van der Maarel ST Winokur, Hum Mol Genet 2004 13 1857 1871 10.1093/hmg/ddh205 15238509
16. Nuclear envelope dystrophies show a transcriptional fingerprint suggesting disruption of Rb-MyoD pathways in muscle regeneration. M Bakay Z Wang G Melcon L Schiltz J Xuan P Zhao V Sartorelli J Seo E Pegoraro C Angelini B Shneiderman D Escolar YW Chen ST Winokur LM Pachman C Fan R Mandler Y Nevo E Gordon Y Zhu Y Dong Y Wang EP Hoffman, Brain 2006 129 996 1013 10.1093/brain/awl023 16478798
17. The evolutionary distribution and structural organization of the homeobox-containing repeat D4Z4 indicates a functional role for the ancestral copy in the FSHD region. ST Winokur U Bengtsson JC Vargas JJ Wasmuth MR Altherr B Weiffenbach SJ Jacobsen, Hum Mol Genet 1996 5 1567 1575 10.1093/hmg/5.10.1567 8894690
18. The boundary of macaque rDNA is constituted by low-copy sequences conserved during evolution. B Bodega MF Cardone M Rocchi R Meneveri A Marozzi E Ginelli, Genomics 2006 88 564 571 10.1016/j.ygeno.2006.05.001 16765020
19. Recent amplification of the human FRG1 gene during primate evolution. PK Grewal M van Geel RR Frants P de Jong JE Hewitt, Gene 1999 227 79 88 10.1016/S0378-1119(98)00587-3 9931447
20. Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication. EV Linardopoulou EM Williams Y Fan C Friedman JM Young BJ Trask, Nature 2005 437 94 100 16136133 10.1038/nature04029
21. Human BLAT Search. http://www.genome.ucsc.edu/cgi-bin/hgBlat
22. The D4Z4 repeat-mediated pathogenesis of facioscapulohumeral muscular dystrophy. SM van der Maarel RR Frants, Am J Hum Genet 2005 76 375 386 15674778 10.1086/428361
23. The use of telomere probes to investigate submicroscopic rearrangements associated with mental retardation. J Flint S Knight, Curr Opin Genet Dev 2003 13 310 316 10.1016/S0959-437X(03)00049-2 12787795
24. Analysis of the organisation and localisation of the FSHD-associated tandem array in primates: implications for the origin and evolution of the 3.3 kb repeat family. LN Clark U Koehler DC Ward J Wienberg JE Hewitt, Chromosoma 1996 105 180 189 8781186
25. Genomic views of chromatin. DJ Huebert BE Bernstein, Curr Opin Genet Dev 2005 15 476 481 10.1016/j.gde.2005.08.001 16099159
26. The DNA sequence of the human X chromosome. MT Ross DV Grafham AJ Coffey S Scherer K McLay D Muzny M Platzer GR Howell C Burrows CP Bird A Frankish FL Lovell KL Howe JL Ashurst RS Fulton R Sudbrak G Wen MC Jones ME Hurles TD Andrews CE Scott S Searle J Ramser A Whittaker R Deadman NP Carter SE Hunt R Chen A Cree P Gunaratne P Havlak A Hodgson ML Metzker S Richards G Scott D Steffen E Sodergren DA Wheeler KC Worley R Ainscough KD Ambrose MA Ansari-Lari S Aradhya RI Ashwell AK Babbage CL Bagguley A Ballabio R Banerjee GE Barker KF Barlow IP Barrett KN Bates DM Beare H Beasley O Beasley A Beck G Bethel K Blechschmidt N Brady S Bray-Allen AM Bridgeman AJ Brown MJ Brown D Bonnin EA Bruford C Buhay P Burch D Burford J Burgess W Burrill J Burton JM Bye C Carder L Carrel J Chako JC Chapman D Chavez E Chen G Chen Y Chen Z Chen C Chinault A Ciccodicola SY Clark G Clarke CM Clee S Clegg K Clerc-Blankenburg K Clifford V Cobley CG Cole JS Conquer N Corby RE Connor R David J Davies C Davis J Davis O Delgado D Deshazo P Dhami Y Ding H Dinh S Dodsworth H Draper S Dugan-Rocha A Dunham M Dunn KJ Durbin I Dutta T Eades M Ellwood A Emery-Cohen H Errington KL Evans L Faulkner F Francis J Frankland AE Fraser P Galgoczy J Gilbert R Gill G Glockner SG Gregory S Gribble C Griffiths R Grocock Y Gu R Gwilliam C Hamilton EA Hart A Hawes PD Heath K Heitmann S Hennig J Hernandez B Hinzmann S Ho M Hoffs PJ Howden EJ Huckle J Hume PJ Hunt AR Hunt J Isherwood L Jacob D Johnson S Jones PJ de Jong SS Joseph S Keenan S Kelly JK Kershaw Z Khan P Kioschis S Klages AJ Knights A Kosiura C Kovar-Smith GK Laird C Langford S Lawlor M Leversha L Lewis W Liu C Lloyd DM Lloyd H Loulseged JE Loveland JD Lovell R Lozado J Lu R Lyne J Ma M Maheshwari LH Matthews J McDowall S McLaren A McMurray P Meidl T Meitinger S Milne G Miner SL Mistry M Morgan S Morris I Muller JC Mullikin N Nguyen G Nordsiek G Nyakatura CN O'Dell G Okwuonu S Palmer R Pandian D Parker J Parrish S Pasternak D Patel AV Pearce DM Pearson SE Pelan L Perez KM Porter Y Ramsey K Reichwald S Rhodes KA Ridler D Schlessinger MG Schueler HK Sehra C Shaw-Smith H Shen EM Sheridan R Shownkeen CD Skuce ML Smith EC Sotheran HE Steingruber CA Steward R Storey RM Swann D Swarbreck PE Tabor S Taudien T Taylor B Teague K Thomas A Thorpe K Timms A Tracey S Trevanion AC Tromans M d'Urso D Verduzco D Villasana L Waldron M Wall Q Wang J Warren GL Warry X Wei A West SL Whitehead MN Whiteley JE Wilkinson DL Willey G Williams L Williams A Williamson H Williamson L Wilming RL Woodmansey PW Wray J Yen J Zhang J Zhou H Zoghbi S Zorilla D Buck R Reinhardt A Poustka A Rosenthal H Lehrach A Meindl PJ Minx LW Hillier HF Willard RK Wilson RH Waterston CM Rice M Vaudin A Coulson DL Nelson G Weinstock JE Sulston R Durbin T Hubbard RA Gibbs S Beck J Rogers DR Bentley, Nature 2005 434 325 337 10.1038/nature03440 15772651
27. Three-dimensional maps of all chromosomes in human male fibroblast nuclei and prometaphase rosettes. A Bolzer G Kreth I Solovei D Koehler K Saracoglu C Fauth S Muller R Eils C Cremer MR Speicher T Cremer, PLoS Biol 2005 3 e157 15839726 10.1371/journal.pbio.0030157
28. Local gene density predicts the spatial position of genetic loci in the interphase nucleus. AE Murmann J Gao M Encinosa M Gautier ME Peter R Eils P Lichter JD Rowley, Exp Cell Res 2005 311 14 26 10.1016/j.yexcr.2005.07.020 16202404
29. NCBI Map Viewer. http://www.ncbi.nlm.nih.gov/mapview/
30. Gene order and dynamic domains. ST Kosak M Groudine, Science 2004 306 644 647 10.1126/science.1103864 15499009
31. Insulators: exploiting transcriptional and epigenetic mechanisms. M Gaszner G Felsenfeld, Nat Rev Genet 2006 7 703 713 10.1038/nrg1925 16909129
32. Dynamic interactions of nuclear lamina proteins with chromatin and transcriptional machinery. A Mattout-Drubezki Y Gruenbaum, Cell Mol Life Sci 2003 60 2053 2063 10.1007/s00018-003-3038-3 14618255
33. BACPAC Resources Center. http://bacpac.chori.org/
34. RepeatMasker Web Server. http://www.repeatmasker.org/cgi-bin/ WEBRepeatMasker
35. Molecular organization and chromosomal location of human GC-rich heterochromatic blocks. R Meneveri A Agresti A Marozzi S Saccone M Rocchi N Archidiacono G Corneo G Della Valle E Ginelli, Gene 1993 123 227 234 10.1016/0378-1119(93)90128-P 8428662
36. Identification of a human clustered G + C-rich DNA family of repeats (Sau3A family). R Meneveri A Agresti G Della Valle D Talarico AG Siccardi E Ginelli, J Mol Biol 1985 186 483 489 10.1016/0022-2836(85)90123-8 4093977
37. YAC mapping by FISH using Alu-PCR-generated probes. M Breen B Arveiler I Murray JR Gosden DJ Porteous, Genomics 1992 13 726 730 10.1016/0888-7543(92) 90148-L 1639400
38. NCBI. http://www.ncbi.nlm.nih.gov/
39. Primate Cytogenetics. http://www.biologia.uniba.it/primates/cell_lines. html
40. FISH with locus-specific probes on stretched chromosomes: a useful tool for genome organization studies. A Bentivegna M Venturin C Gervasini L Corrado L Larizza P Riva, Chromosome Res 2001 9 167 170 10.1023/A:1009287104812 11321371
41. Spatial preservation of nuclear chromatin architecture during three-dimensional fluorescence in situ hybridization (3D-FISH). I Solovei A Cavallo L Schermelleh F Jaunin C Scasselati D Cmarko C Cremer S Fakan T Cremer, Exp Cell Res 2002 276 10 23 10.1006/excr.2002.5513 11978004
42. ImageJ. http://rsb.info.nih.gov/ij
43. Non-random radial higher-order chromatin arrangements in nuclei of diploid human cells. M Cremer J von Hase T Volm A Brero G Kreth J Walter C Fischer I Solovei C Cremer T Cremer, Chromosome Res 2001 9 541 567 10.1023/A:1012495201697 11721953
44. Panels of somatic cell hybrids specific for chimpanzee, gorilla, orangutan, and baboon. R Marzella C Carrozzo P Chiarappa V Miolla M Rocchi, Cytogenet Genome Res 2005 108 223 228 10.1159/000080820 15545734
45. Selection of reference genes for gene expression studies in human neutrophils by real-time PCR. X Zhang L Ding AJ Sandford, BMC Mol Biol 2005 6 4 15720708 10.1186/1471-2199-6-4
46. Analysis of one-step and two-step real-time RT-PCR using SuperScript III. MJ Wacker MP Godard, J Biomol Tech 2005 16 266 271 16461951
47. UCSC Genome Browser. http://www.genome.ucsc.edu/