Tandemly repeated DNA families in the mouse genome

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Komissarov, Aleksey S ^a   Gavrilova, Ekaterina V ^a,b,c   Demin, Sergey J ^a   Ishov, Alexander M ^c   Podgornaya, Olga I ^a,b  

^a INSTITUTE OF CYTOLOGY   (Russian Federation)

^b ST PETERSBURG STATE UNIVERSITY   (Russian Federation)

^c UNIVERSITY OF FLORIDA COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOINFORMATICS; CHROMOSOME 13; CHROMOSOME 16; CHROMOSOME 17; CHROMOSOME 3; CHROMOSOME 4; CHROMOSOME 8; DNA BASE COMPOSITION; FLUORESCENCE IN SITU HYBRIDIZATION; GENOME ANALYSIS; GENOME SIZE; MOUSE; MULTIGENE FAMILY; NONHUMAN; POLYPLOIDY; SEQUENCE HOMOLOGY; TANDEM REPEAT; TRANSPOSON; X CHROMOSOME; Y CHROMOSOME; ANIMAL; BIOLOGY; CHEMISTRY; DNA PROBE; GENETICS; GENOME; KARYOTYPING; METABOLISM;

SATELLITE DNA;

ANIMALS; COMPUTATIONAL BIOLOGY; DNA PROBES; DNA, SATELLITE; GENOME; IN SITU HYBRIDIZATION, FLUORESCENCE; KARYOTYPING; MICE;

EID: 80054975995     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-531     Document Type: Article

References (84)

1. Morris CA, Moazed D. Centromere assembly and propagation. Cell 2007, 128:647-50. 10.1016/j.cell.2007.02.002, 17320502.
2. Martienssen RA. Maintenance of heterochromatin by RNA interference of tandem repeats. Nature genetics 2003, 35:213-4. 10.1038/ng1252, 14593407.
3. Alleman M, Sidorenko L, McGinnis K, Seshadri V, Dorweiler JE, White J, Sikkink K, Chandler VL. An RNA-dependent RNA polymerase is required for paramutation in maize. Nature 2006, 442:295-8. 10.1038/nature04884, 16855589.
4. Enukashvily NI, Malashicheva AB, Waisertreiger IS-R. Satellite DNA spatial localization and transcriptional activity in mouse embryonic E-14 and IOUD2 stem cells. Cytogenetic and genome research 2009, 124:277-87. 10.1159/000218132, 19556780.
5. Ames D, Murphy N, Helentjaris T, Sun N, Chandler V. Comparative analyses of human single- and multilocus tandem repeats. Genetics 2008, 179:1693-704. 10.1534/genetics.108.087882, 2475761, 18562644.
6. Warburton PE, Hasson D, Guillem F, Lescale C, Jin X, Abrusan G. Analysis of the largest tandemly repeated DNA families in the human genome. BMC genomics 2008, 9:533. 10.1186/1471-2164-9-533, 2588610, 18992157.
7. Schueler MG, Higgins AW, Rudd MK, Gustashaw K, Willard HF. Genomic and genetic definition of a functional human centromere. Science 2001, 294:109-15. 10.1126/science.1065042, 11588252.
8. Rudd MK, Willard HF. Analysis of the centromeric regions of the human genome assembly. Trends in genetics 2004, 20:529-33. 10.1016/j.tig.2004.08.008, 15475110.
9. Choo KH. Centromere DNA dynamics: latent centromeres and neocentromere formation. American journal of human genetics 1997, 61:1225-33. 10.1086/301657, 1716064, 9399915.
10. Lee C, Wevrick R, Fisher RB, Ferguson-Smith MA, Lin CC. Human centromeric DNAs. Human genetics 1997, 100:291-304. 10.1007/s004390050508, 9272147.
11. Moyzis RK, Albright KL, Bartholdi MF, Cram LS, Deaven LL, Hildebrand CE, Joste NE, Longmire JL, Meyne J, Schwarzacher-Robinson T. Human chromosome-specific repetitive DNA sequences: novel markers for genetic analysis. Chromosoma 1987, 95:375-86. 10.1007/BF00333988, 3677921.
12. Prosser J, Frommer M, Paul C, Vincent PC. Sequence relationships of three human satellite DNAs. Journal of molecular biology 1986, 187:145-55. 10.1016/0022-2836(86)90224-X, 3701863.
13. Podgornaya O, Dey R, Lobov I, Enukashvili N. Human satellite 3 (HS3) binding protein from the nuclear matrix: isolation and binding properties. Biochimica et biophysica acta 2000, 1497:204-14. 10.1016/S0167-4889(00)00042-2, 10903425.
14. Kipling D, Ackford HE, Taylor BA, Cooke HJ. Mouse minor satellite DNA genetically maps to the centromere and is physically linked to the proximal telomere. Genomics 1991, 11:235-41. 10.1016/0888-7543(91)90128-2, 1685135.
15. Kalitsis P, Griffiths B, Choo KHA. Mouse telocentric sequences reveal a high rate of homogenization and possible role in Robertsonian translocation. Proc Natl Acad Sci 2006, 103:8786-91. 10.1073/pnas.0600250103, 1482656, 16731628.
16. Wong AK, Rattner JB. Sequence organization and cytological localization of the minor satellite of mouse. Nucleic acids research 1988, 16:11645-61. 10.1093/nar/16.24.11645, 339101, 3211746.
17. Guenatri M, Bailly D, Maison C, Almouzni G. Mouse centric and pericentric satellite repeats form distinct functional heterochromatin. The Journal of cell biology 2004, 166:493-505. 10.1083/jcb.200403109, 2172221, 15302854.
18. Broccoli D, Miller OJ, Miller DA. Relationship of mouse minor satellite DNA to centromere activity. Cytogenetics and cell genetics 1990, 54:182-6. 10.1159/000132989, 2265565.
19. Hörz W, Altenburger W. Nucleotide sequence of mouse satellite DNA. Nucleic acids research 1981, 9:683-96. 10.1093/nar/9.3.683, 327230, 6261227.
20. Pertile MD, Graham AN, Choo KHA, Kalitsis P. Rapid evolution of mouse Y centromere repeat DNA belies recent sequence stability. Genome research 2009, 19:2202-13. 10.1101/gr.092080.109, 2792177, 19737860.
21. Waterston RH, Lindblad-Toh K, Birney E, et al. Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420:520-62. 10.1038/nature01262, 12466850.
22. Mural RJ, Adams MD, Myers EW, et al. A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science 2002, 296:1661-71. 10.1126/science.1069193, 12040188.
23. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic acids research 1999, 27:573-80. 10.1093/nar/27.2.573, 148217, 9862982.
24. Abdurashitov MA, Chernukhin VA, Gonchar DA, Degtyarev SK. GlaI digestion of mouse gamma-satellite DNA: study of primary structure and ACGT sites methylation. BMC genomics 2009, 10:322. 10.1186/1471-2164-10-322, 2722675, 19607729.
25. Vissel B, Choo KH. Mouse major (gamma) satellite DNA is highly conserved and organized into extremely long tandem arrays: implications for recombination between nonhomologous chromosomes. Genomics 1989, 5:407-14. 10.1016/0888-7543(89)90003-7, 2613229.
26. Kidd JM, Sampas N, Antonacci F, Graves T, Fulton R, Hayden HS, Alkan C, Malig M, Ventura M, Giannuzzi G, Kallicki J, Anderson P, Tsalenko A, Yamada NA, Tsang P, Kaul R, Wilson RK, Bruhn L, Eichler EE. Characterization of missing human genome sequences and copy-number polymorphic insertions. Nature methods 2010, 7:365-71. 10.1038/nmeth.1451, 2875995, 20440878.
27. She X, Horvath JE, Jiang Z, Liu G, Furey TS, Christ L, Clark R, Graves T, Gulden CL, Alkan C, Bailey JA, Sahinalp C, Rocchi M, Haussler D, Wilson RK, Miller W, Schwartz S, Eichler EE. The structure and evolution of centromeric transition regions within the human genome. Nature 2004, 430:857-64. 10.1038/nature02806, 15318213.
28. Kipling D, Wilson HE, Mitchell AR, Taylor BA, Cooke HJ. Mouse centromere mapping using oligonucleotide probes that detect variants of the minor satellite. Chromosoma 1994, 103:46-55. 10.1007/BF00364725, 8013255.
29. Kuznetsova IS, Enukashvily NI, Noniashvili EM, Shatrova AN, Aksenov ND, Zenin VV, Dyban AP, Podgornaya OI. Evidence for the existence of satellite DNA-containing connection between metaphase chromosomes. Journal of cellular biochemistry 2007, 101:1046-61. 10.1002/jcb.21237, 17340617.
30. Kuznetsova IS, Voronin AP, Podgornaya OI. Telomere and TRF2/MTBP localization in respect to satellite DNA during the cell cycle of mouse cell line L929. Rejuvenation research 2006, 9:391-401. 10.1089/rej.2006.9.391, 16859480.
31. Kuznetsova I, Podgornaya O, Ferguson-Smith M. High-resolution organization of mouse centromeric and pericentromeric DNA. Cytogenetic and genome research 2006, 112:248-55. 10.1159/000089878, 16484780.
32. Broccoli D, Trevor KT, Miller OJ, Miller DA. Isolation of a variant family of mouse minor satellite DNA that hybridizes preferentially to chromosome 4. Genomics 1991, 10:68-74. 10.1016/0888-7543(91)90485-W, 2045111.
33. Richard G-F, Kerrest A, Dujon B. Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol Mol Biol Rev 2008, 72:686-727. 10.1128/MMBR.00011-08, 2593564, 19052325.
34. Enukashvily NI, Donev R, Waisertreiger IS-R, Podgornaya OI. Human chromosome 1 satellite 3 DNA is decondensed, demethylated and transcribed in senescent cells and in A431 epithelial carcinoma cells. Cytogenetic and genome research 2007, 118:42-54. 10.1159/000106440, 17901699.
35. Namekawa SH, Payer B, Huynh KD, Jaenisch R, Lee JT. Two-step imprinted X inactivation: repeat versus genic silencing in the mouse. Molecular and cellular biology 2010, 30:3187-205. 10.1128/MCB.00227-10, 2897575, 20404085.
36. Cooke HJ, Brown WR, Rappold GA. Hypervariable telomeric sequences from the human sex chromosomes are pseudoautosomal. Nature 1985, 317:687-92. 10.1038/317687a0, 2997619.
37. Cooke HJ, Brown WA, Rappold GA. Closely related sequences on human X and Y chromosomes outside the pairing region. Nature 1984, 311:259-61. 10.1038/311259a0, 6090928.
38. Giordano J, Ge Y, Gelfand Y, Abrusán G, Benson G, Warburton PE. Evolutionary history of mammalian transposons determined by genome-wide defragmentation. PLoS computational biology 2007, 3:e137. 10.1371/journal.pcbi.0030137, 1914374, 17630829.
39. Smit AF. Identification of a new, abundant superfamily of mammalian LTR-transposons. Nucleic acids research 1993, 21:1863-72. 10.1093/nar/21.8.1863, 309426, 8388099.
40. Stocking C, Kozak CA. Murine endogenous retroviruses. Cellular and molecular life sciences 2008, 65:3383-98. 10.1007/s00018-008-8497-0, 18818872.
41. Mamaeva S. Atlas of chromosomes of human and animal cell lines 2002, 1-236. Moscow: Scentific World.
42. Ushiki T, Hoshi O. Atomic force microscopy for imaging human metaphase chromosomes. Chromosome Res 2008, 16:383-96. 10.1007/s10577-008-1241-7, 18461479.
43. Kireeva N, Lakonishok M, Kireev I, Hirano T, Belmont AS. Visualization of early chromosome condensation: a hierarchical folding, axial glue model of chromosome structure. The Journal of cell biology 2004, 166:775-85. 10.1083/jcb.200406049, 2172117, 15353545.
44. Alkan C, Cardone MF, Catacchio CR, Antonacci F, O'Brien SJ, Ryder OA, Purgato S, Zoli M, Della Valle G, Eichler EE, Ventura M. Genome-wide characterization of centromeric satellites from multiple mammalian genomes. Genome research 2010,
45. Alkan C, Ventura M, Archidiacono N, Rocchi M, Sahinalp SC, Eichler EE. Organization and evolution of primate centromeric DNA from whole-genome shotgun sequence data. PLoS computational biology 2007, 3:1807-18. 1994983, 17907796.
46. Mayer C, Leese F, Tollrian R. Genome-wide analysis of tandem repeats in Daphnia pulex - a comparative approach. BMC genomics 2010, 11:277. 10.1186/1471-2164-11-277, 3152781, 20433735.
47. Plohl M, Luchetti A, Mestrović N, Mantovani B. Satellite DNAs between selfishness and functionality: structure, genomics and evolution of tandem repeats in centromeric (hetero)chromatin. Gene 2008, 409:72-82. 10.1016/j.gene.2007.11.013, 18182173.
48. Podgornaya OI, Voronin AP, Enukashvily NI, Matveev IV, Lobov IB. Structure-specific DNA-binding proteins as the foundation for three-dimensional chromatin organization. International review of cytology 2003, 224:227-96.
49. Kobliakova I, Zatsepina O, Stefanova V, Polyakov V, Kireev I. The topology of early- and late-replicating chromatin in differentially decondensed chromosomes. Chromosome Res 2005, 13:169-81. 10.1007/s10577-005-0308-y, 15861306.
50. Yunis JJ, Yasmineh WG. Heterochromatin, satellite DNA, and cell function. Structural DNA of eucaryotes may support and protect genes and aid in speciation. Science 1971, 174:1200-9. 10.1126/science.174.4015.1200, 4943851.
51. Grewal SIS, Elgin SCR. Transcription and RNA interference in the formation of heterochromatin. Nature 2007, 447:399-406. 10.1038/nature05914, 2950806, 17522672.
52. Maison C, Bailly D, Peters AH, Quivy JP, Roche D, Taddei A, Lachner M, Jenuwein T, Almouzni G. Higher-order structure in pericentric heterochromatin involves a distinct pattern of histone modification and an RNA component. Nature genetics 2002, 30:329-34. 10.1038/ng843, 11850619.
53. Muchardt C, Guilleme M, Seeler JS, Trouche D, Dejean A, Yaniv M. Coordinated methyl and RNA binding is required for heterochromatin localization of mammalian HP1alpha. EMBO reports 2002, 3:975-81. 10.1093/embo-reports/kvf194, 1307621, 12231507.
54. Lu J, Gilbert DM. Proliferation-dependent and cell cycle regulated transcription of mouse pericentric heterochromatin. The Journal of cell biology 2007, 179:411-21. 10.1083/jcb.200706176, 2064789, 17984319.
55. Probst AV, Okamoto I, Casanova M, El Marjou F, Le Baccon P, Almouzni G. A strand-specific burst in transcription of pericentric satellites is required for chromocenter formation and early mouse development. Developmental cell 2010, 19:625-38. 10.1016/j.devcel.2010.09.002, 20951352.
56. Falconer E, Chavez EA, Henderson A, Poon SS, McKinney S, Brown L, Huntsman DG, Lansdorp PM. Identification of sister chromatids by DNA template strand sequences. Nature 2010, 463:93-7. 10.1038/nature08644, 20016487.
57. Biro PA, Carr-Brown A, Southern EM, Walker PM. Partial sequence analysis of mouse satellite DNA evidence for short range periodicities. Journal of molecular biology 1975, 94:71-86. 10.1016/0022-2836(75)90405-2, 806696.
58. Southern EM. Long range periodicities in mouse satellite DNA. Journal of molecular biology 1975, 94:51-69. 10.1016/0022-2836(75)90404-0, 1142436.
59. Hayashi T, Ohtsuka H, Kuwabara K, Mafune Y, Miyashita N, Moriwaki K, Takahashi Y, Kominami R. A variant family of mouse minor satellite located on the centromeric region of chromosome 2. Genomics 1993, 17:490-2. 10.1006/geno.1993.1352, 8406499.
60. Gosden JR, Mtichell AR, Buckland RA, Clayton RP, Evans HJ. The location of four human satellite DNAs on human chromosomes. Cytogenetics and cell genetics 1975, 14:338-9. 10.1159/000130376, 1192810.
61. Therkelsen AJ, Nielsen A, Kølvraa S. Localisation of the classical DNA satellites on human chromosomes as determined by primed in situ labelling (PRINS). Human genetics 1997, 100:322-6. 10.1007/s004390050510, 9272149.
62. Higgins MJ, Wang HS, Shtromas I, Haliotis T, Roder JC, Holden JJ, White BN. Organization of a repetitive human 1.8 kb KpnI sequence localized in the heterochromatin of chromosome 15. Chromosoma 1985, 93:77-86. 10.1007/BF01259449, 2998709.
63. Cooke HJ, Hindley J. Cloning of human satellite III DNA: different components are on different chromosomes. Nucleic acids research 1979, 6:3177-97. 10.1093/nar/6.10.3177, 327928, 573470.
64. Palomeque T, Lorite P. Satellite DNA in insects: a review. Heredity 2008, 100:564-73. 10.1038/hdy.2008.24, 18414505.
65. Beridze T. Satellite DNA 1986, 149. Springer-Verlag.
66. Vinogradov AE. Noncoding DNA, isochores and gene expression: nucleosome formation potential. Nucleic acids research 2005, 33:559-63. 10.1093/nar/gki184, 548339, 15673716.
67. Vinogradov AE. DNA helix: the importance of being GC-rich. Nucleic acids research 2003, 31:1838-44. 10.1093/nar/gkg296, 152811, 12654999.
68. Mahtani MM, Willard HF. Pulsed-field gel analysis of alpha-satellite DNA at the human X chromosome centromere: high-frequency polymorphisms and array size estimate. Genomics 1990, 7:607-13. 10.1016/0888-7543(90)90206-A, 1974881.
69. Paar V, Pavin N, Rosandic M, Gluncic M, Basar I, Pezer R, Zinic SD. ColorHOR--novel graphical algorithm for fast scan of alpha satellite higher-order repeats and HOR annotation for GenBank sequence of human genome. Bioinformatics 2005, 21:846-852. 10.1093/bioinformatics/bti072, 15509609.
70. Warburton PE, Haaf T, Gosden J, Lawson D, Willard HF. Characterization of a chromosome-specific chimpanzee alpha satellite subset: evolutionary relationship to subsets on human chromosomes. Genomics 1996, 33:220-8. 10.1006/geno.1996.0187, 8660971.
71. Alexandrov I, Kazakov A, Tumeneva I, Shepelev V, Yurov Y. Alpha-satellite DNA of primates: old and new families. Chromosoma 2001, 110:253-266. 10.1007/s004120100146, 11534817.
72. Parris GE. Scope of medical implications of the Master Development Program hypothesis. Medical hypotheses 2010, 74:953. 10.1016/j.mehy.2009.12.001, 20031335.
73. GenBank ftp site. , ftp://ftp.ncbi.nih.gov/genbank/wgs
74. Mouse genome assembly build 37.1. , ftp://ftp.ncbi.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.1/Assembled_chromosomes/
75. MGSC genome assembly release 3. , ftp://ftp.ncbi.nih.gov/genomes/M_musculus/ARCHIVE/MGSCv3_Release3/Assembled_Chromosomes/
76. Mouse ideograms. , ftp://ftp.ncbi.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.1/mapview/ideogram.gz
77. Repbase collection version 15.7. , http://www.girinst.org/server/archive/RepBase15.07/
78. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC bioinformatics 2009, 10:421. 10.1186/1471-2105-10-421, 2803857, 20003500.
79. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenetic and genome research 2005, 110:462-7. 10.1159/000084979, 16093699.
80. Blake JA, Bult CJ, Eppig JT, Kadin JA, Richardson JE. The Mouse Genome Database genotypes::phenotypes. Nucleic acids research 2009, 37:D712-9. 10.1093/nar/gkn886, 2686566, 18981050.
81. Quinlan AR, Clark RA, Sokolova S, Leibowitz ML, Zhang Y, Hurles ME, Mell JC, Hall IM. Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome. Genome research 2010,
82. Ford EH, Hamerton JL. A study of the mitotic chromosomes of mice if the strong a line. Exp Cell Res 1963, 32:320-6. 10.1016/0014-4827(63)90106-X, 14080673.
83. Tagarro I, Fernández-Peralta AM, González-Aguilera JJ. Chromosomal localization of human satellites 2 and 3 by a FISH method using oligonucleotides as probes. Human genetics 1994, 93:383-8.
84. Demin S, Pleskach N, Svetlova M, Solovjeva L. High-Resolution Mapping of Interstitial Telomeric Repeats in Syrian Hamster Metaphase Chromosomes. Cytogenetic and genome research 2011, 132:151-5. 10.1159/000321676, 21063079.