A map of nuclear matrix attachment regions within the breast cancer loss-of-heterozygosity region on human chromosome 16q22.1

Genomics

Volumn 89, Issue 3, 2007, Pages 354-361

  Shaposhnikov, Sergey A ^a,b   Akopov, Sergey B ^c   Chernov, Igor P ^c   Thomsen, Preben D ^d   Joergensen, Claus ^d   Collins, Andrew R ^a   Frengen, Eirik ^b,e   Nikolaev, Lev G ^c  

^a UNIVERSITY OF OSLO   (Norway)

^b UNIVERSITY OF OSLO   (Norway)

^c SHEMYAKIN OVCHINNIKOV INSTITUTE OF BIOORGANIC CHEMISTRY   (Russian Federation)

^d UNIVERSITY OF COPENHAGEN   (Denmark)

^e ULLEVÅL UNIVERSITY HOSPITAL   (Norway)

Author keywords

Functional genomics; Gene regulation; Nuclear matrix; Physical mapping; Scaffold matrix attachment regions

Indexed keywords

ARTICLE; BREAST CANCER; CHROMOSOME 16Q; CONTROLLED STUDY; DNA STRUCTURE; FEMALE; GENE CONTROL; GENE FUNCTION; GENE LOCUS; GENE MAPPING; HETEROZYGOSITY LOSS; HUMAN; HUMAN CELL; INTRON; MATRIX ATTACHMENT REGION; NONHUMAN; PRIORITY JOURNAL;

EUKARYOTA;

EID: 33846786710     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2006.11.003     Document Type: Article

References (46)

1. Berezney R., Mortillaro M.J., Ma H., Wei X., and Samarabandu J. The nuclear matrix: a structural milieu for genomic function. Int. Rev. Cytol. 162A (1995) 1-65
2. Hancock R. Topological organization of interphase DNA: the nuclear matrix and other skeletal structures. Biol. Cell 46 (1982) 105-122
3. Pardoll D.M., Vogelstein B., and Coffey D.S. A fixed site of DNA replication in eukaryotic cells. Cell 19 (1980) 527-536
4. Ciejek E.M., Tsai M.J., and O'Malley B.W. Actively transcribed genes are associated with the nuclear matrix. Nature 306 (1983) 607-609
5. Cook P.R. The nucleoskeleton and the topology of transcription. Eur. J. Biochem. 185 (1989) 487-501
6. Cook P.R. The nucleoskeleton and the topology of replication. Cell 66 (1991) 627-635
7. Cockerill P.N., and Garrard W.T. Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites. Cell 44 (1986) 273-282
8. Boulikas T. Chromatin domains and prediction of MAR sequences. Int. Rev. Cytol. 162A (1995) 279-388
9. Mirkovitch J., Mirault M.E., and Laemmli U.K. Organization of the higher-order chromatin loop: specific DNA attachment sites on nuclear scaffold. Cell 39 (1984) 223-232
10. Izaurralde E., Mirkovitch J., and Laemmli U.K. Interaction of DNA with nuclear scaffolds in vitro. J. Mol. Biol. 200 (1988) 111-125
11. Bode J., Stengert-Iber M., Kay V., Schlake T., and Dietz-Pfeilstetter A. Scaffold/matrix-attached regions: topological switches with multiple regulatory functions. Crit. Rev. Eukaryotic Gene Expression 6 (1996) 115-138
12. Geyer P.K. The role of insulator elements in defining domains of gene expression. Curr. Opin. Genet. Dev. 7 (1997) 242-248
13. Chernov I.P., Akopov S.B., and Nikolaev L.G. Structure and function of nuclear matrix associated regions (S/MARs). Bioorg. Khim. 30 (2004) 3-14
14. Razin S.V. DNA interactions with the nuclear matrix and spatial organization of replication and transcription. Bioessays 6 (1987) 19-23
15. Jackson D.A., Dolle A., Robertson G., and Cook P.R. The attachments of chromatin loops to the nucleoskeleton. Cell. Biol. Int. Rep. 16 (1992) 687-696
16. Nikolaev L.G., Tsevegiyn T., Akopov S.B., Ashworth L.K., and Sverdlov E.D. Construction of a chromosome specific library of human MARs and mapping of matrix attachment regions on human chromosome 19. Nucleic Acids Res. 24 (1996) 1330-1336
17. Chernov I.P., Akopov S.B., Nikolaev L.G., and Sverdlov E.D. Identification and mapping of nuclear matrix-attachment regions in a one megabase locus of human chromosome 19q13.12: long-range correlation of S/MARs and gene positions. J. Cell. Biochem. 84 (2002) 590-600
18. Cleton-Jansen A.M., Moerland E.W., Kuipers-Dijkshoorn N.J., Callen D.F., Sutherland G.R., Hansen B., Devilee P., and Cornelisse C.J. At least two different regions are involved in allelic imbalance on chromosome arm 16q in breast cancer. Genes Chromosomes Cancer 9 (1994) 101-107
19. Tsuda H., Callen D.F., Fukutomi T., Nakamura Y., and Hirohashi S. Allele loss on chromosome 16q24.2-qter occurs frequently in breast cancers irrespectively of differences in phenotype and extent of spread. Cancer Res. 54 (1994) 513-517
20. Dorion-Bonnet F., Mautalen S., Hostein I., and Longy M. Allelic imbalance study of 16q in human primary breast carcinomas using microsatellite markers. Genes Chromosomes Cancer 14 (1995) 171-181
21. Frengen E., Rocca-Serra P., Shaposhnikov S., Taine L., Thorsen J., Bepoldin C., Krekling M., Lafon D., Aas K.K., El Moneim A.A., et al. High-resolution integrated map encompassing the breast cancer loss of heterozygosity region on human chromosome 16q22.1. Genomics 70 (2000) 273-285
22. Sambrook J., and Russell D.W. Molecular Cloning: A Laboratory Manual. 3rd ed. (2001), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
23. Ioannou P.A., Amemiya C.T., Garnes J., Kroisel P.M., Shizuya H., Chen C., Batzer M.A., and de Jong P.J. A new bacteriophage P1-derived vector for the propagation of large human DNA fragments. Nat. Genet. 6 (1994) 84-89
24. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
25. Kent W.J. BLAT-the BLAST-like alignment tool. Genome Res. 12 (2002) 656-664
26. Kent W.J., Sugnet C.W., Furey T.S., Roskin K.M., Pringle T.H., Zahler A.M., and Haussler D. The human genome browser at UCSC. Genome Res. 12 (2002) 996-1006
27. Singh G.B., Kramer J.A., and Krawetz S.A. Mathematical model to predict regions of chromatin attachment to the nuclear matrix. Nucleic Acids Res. 25 (1997) 1419-1425
28. van Drunen C.M., Sewalt R.G., Oosterling R.W., Weisbeek P.J., Smeekens S.C., and van Driel R. A bipartite sequence element associated with matrix/scaffold attachment regions. Nucleic Acids Res. 27 (1999) 2924-2930
29. Frisch M., Frech K., Klingenhoff A., Cartharius K., Liebich I., and Werner T. In silico prediction of scaffold/matrix attachment regions in large genomic sequences. Genome Res. 12 (2002) 349-354
30. Iarovaia O.V., Akopov S.B., Nikolaev L.G., Sverdlov E.D., and Razin S.V. Induction of transcription within chromosomal DNA loops flanked by MAR elements causes an association of loop DNA with the nuclear matrix. Nucleic Acids Res. 33 (2005) 4157-4163
31. Boulikas T., and Kong C.F. Multitude of inverted repeats characterizes a class of anchorage sites of chromatin loops to the nuclear matrix. J. Cell Biochem. 53 (1993) 1-12
32. Jackson D.A., Dickinson P., and Cook P.R. Attachment of DNA to the nucleoskeleton of HeLa cells examined using physiological conditions. Nucleic Acids Res. 18 (1990) 4385-4393
33. Jack R.S., and Eggert H. The elusive nuclear matrix. Eur. J. Biochem. 209 (1992) 503-509
34. Iarovaia O.V., and Razin S.V. Comparison of positions of attachment sites of DNA loops to nuclear matrix, MAR-elements, and autonomously replicating sequences in the elongated region of Drosophila melanogaster X-chromosome. Mol. Biol. (Moscow) 30 (1996) 1184-1192
35. Heng H.H., Tsui L.C., and Moens P.B. Organization of heterologous DNA inserts on the mouse meiotic chromosome core. Chromosoma 103 (1994) 401-407
36. Heng H.H., Goetze S., Ye C.J., Liu G., Stevens J.B., Bremer S.W., Wykes S.M., Bode J., and Krawetz S.A. Chromatin loops are selectively anchored using scaffold/matrix-attachment regions. J. Cell Sci. 117 (2004) 999-1008
37. Marais G., Nouvellet P., Keightley P.D., and Charlesworth B. Intron size and exon evolution in Drosophila. Genetics 170 (2005) 481-485
38. Mlynarova L., Jansen R.C., Conner A.J., Stiekema W.J., and Nap J.P. The MAR-mediated reduction in position effect can be uncoupled from copy number-dependent expression in transgenic plants. Plant Cell 7 (1995) 599-609
39. Schubeler D., Mielke C., Maass K., and Bode J. Scaffold/matrix-attached regions act upon transcription in a context-dependent manner. Biochemistry 35 (1996) 11160-11169
40. Jackson D.A., Dickinson P., and Cook P.R. The size of chromatin loops in HeLa cells. EMBO J. 9 (1990) 567-571
41. Gerdes M.G., Carter K.C., Moen Jr. P.T., and Lawrence J.B. Dynamic changes in the higher-level chromatin organization of specific sequences revealed by in situ hybridization to nuclear halos. J. Cell Biol. 126 (1994) 289-304
42. Heng H.H., Krawetz S.A., Lu W., Bremer S., Liu G., and Ye C.J. Re-defining the chromatin loop domain. Cytogenet. Cell Genet. 93 (2001) 155-161
43. Phi-Van L., and Stratling W.H. Dissection of the ability of the chicken lysozyme gene 5′ matrix attachment region to stimulate transgene expression and to dampen position effects. Biochemistry 35 (1996) 10735-10742
44. Cleton-Jansen A.M., Callen D.F., Seshadri R., Goldup S., McCallum B., Crawford J., Powell J.A., Settasatian C., van Beerendonk H., Moerland E.W., et al. Loss of heterozygosity mapping at chromosome arm 16q in 712 breast tumors reveals factors that influence delineation of candidate regions. Cancer Res. 61 (2001) 1171-1177
45. Rakha E.A., Armour J.A., Pinder S.E., Paish C.E., and Ellis I.O. High-resolution analysis of 16q22.1 in breast carcinoma using DNA amplifiable probes (multiplex amplifiable probe hybridization technique) and immunohistochemistry. Int. J. Cancer 114 (2005) 720-729
46. Cleton-Jansen A.M. E-cadherin and loss of heterozygosity at chromosome 16 in breast carcinogenesis: different genetic pathways in ductal and lobular breast cancer?. Breast Cancer Res. 4 (2002) 5-8