High-resolution fish on DNA fibers for low-copy repeats genome architecture studies.

Molina, O., Blanco, J., Anton, E., Vidal, F. and Volpi, E.V. 2012. High-resolution fish on DNA fibers for low-copy repeats genome architecture studies. Genomics. 100 (6), pp. 380-386. https://doi.org/10.1016/j.ygeno.2012.08.007

TitleHigh-resolution fish on DNA fibers for low-copy repeats genome architecture studies.
TypeJournal article
AuthorsMolina, O., Blanco, J., Anton, E., Vidal, F. and Volpi, E.V.
Abstract

Low-copy repeats (LCRs) constitute 5% of the human genome. LCRs act as substrates for non-allelic homologous recombination (NAHR) leading to genomic structural variation. The aim of this study was to assess the potential of Fiber-FISH for LCRs direct visualization to support investigations of genome architecture within these challenging genomic regions. We describe a set of Fiber-FISH experiments designed for the study of the LCR22-2. This LCR is involved in recurrent reorganizations causing different genomic disorders. Four fosmid clones covering the entire length of the LCR22-2 and two single-copy BAC-clones, delimiting the LCR22-2 proximally and distally, were selected. The probes were hybridized in different multiple color combinations on DNA fibers from two karyotypically normal cell lines. We were able to identify three distinct structural haplotypes characterized by differences in copy-number and arrangement of the LCR22-2 genes and pseudogenes. Our results show that Multicolor Fiber-FISH is a viable methodological approach for the analysis of genome organization within complex LCR regions.

JournalGenomics
Journal citation100 (6), pp. 380-386
ISSN0888-7543
Year2012
PublisherElsevier
Digital Object Identifier (DOI)https://doi.org/10.1016/j.ygeno.2012.08.007
PubMed ID22954586
Web address (URL)http://europepmc.org/abstract/med/22954586
Publication dates
PublishedDec 2012

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Bendall, J.K., Rinze, R., Adlam, D., Tatham, A.L., de Bono, J., Wilson, N., Volpi, E. and Channon, K.M. 2007. Endothelial Nox2 overexpression potentiates vascular oxidative stress and hemodynamic response to angiotensin II: studies in endothelial-targeted Nox2 transgenic mice. Circulation Research. 100, pp. 1016-1025. https://doi.org/10.1161/01.res.0000263381.83835.7b

Replication profile of PCDH11X and PCDH11Y, a gene pair located in the non-pseudoautosomal homologous region Xq21.3/Yp11.2.
Wilson, N.D., Ross, L.J., Close, J., Mott, R., Crow, T.J. and Volpi, E.V. 2007. Replication profile of PCDH11X and PCDH11Y, a gene pair located in the non-pseudoautosomal homologous region Xq21.3/Yp11.2. Chromosome Research. 15, pp. 485-498. https://doi.org/10.1007/s10577-007-1153-y

Search for neuroblastoma loci: characterization of tumor cell lines that could facilitate their positional cloning.
Romani, M., Muresu, R., Volpi, E.V., Rozzo, C., Marchi, J.M. and Casciano, I. 2007. Search for neuroblastoma loci: characterization of tumor cell lines that could facilitate their positional cloning. Journal of Neuro-oncology . 31, pp. 41-47. https://doi.org/10.1023/a:1005725112688

PCDH11 is X/Y homologous in Homo sapiens but not in Gorilla gorilla and Pan troglodytes.
Wilson, N.D., Ross, L.J., Crow, T.J. and Volpi, E.V. 2006. PCDH11 is X/Y homologous in Homo sapiens but not in Gorilla gorilla and Pan troglodytes. Cytogenetic and Genome Research. 114, pp. 137-139. https://doi.org/10.1159/000093329

The leukocyte receptor complex in chicken is characterized by massive expansion and diversification of immunoglobulin-like Loci.
Laun, K., Coggill, P., Palmer, S., Sims, S., Ning, Z., Ragoussis, J., Volpi, E., Wilson, N., Beck, S., Ziegler, A. and Volz, A. 2006. The leukocyte receptor complex in chicken is characterized by massive expansion and diversification of immunoglobulin-like Loci. PLoS Genetics. 2 (5) e73. https://doi.org/10.1371/journal.pgen.0020073

An interstitial deletion-insertion involving chromosomes 2p25.3 and Xq27.1, near SOX3, causes X-linked recessive hypoparathyroidism.
Bowl, M.R., Nesbit, M.A., Harding, B., Levy, E., Jefferson, A., Volpi, E.V., Rizzoti, K., Lovell-Badge, R., Schlessinger, D., Whyte, M.P. and Thakker, R.V. 2005. An interstitial deletion-insertion involving chromosomes 2p25.3 and Xq27.1, near SOX3, causes X-linked recessive hypoparathyroidism. Journal of Clinical Investigation. 115 (10), pp. 2822-2831. https://doi.org/10.1172/jci24156

Unexpected complexity in the haplotypes of commonly used inbred strains of laboratory mice
Yalcin, B., Fullerton, J., Miller, S., Keays, D.A., Brady, S., Bhomra, A., Jefferson, A., Volpi, E., Copley, R.R., Flint, J. and Mott, R. 2004. Unexpected complexity in the haplotypes of commonly used inbred strains of laboratory mice. Proceedings of the National Academy of Sciences of the United States of America. https://doi.org/10.1073/pnas.0401189101

Mapping of three translocation breakpoints associated with orofacial clefting within 6p24 and identification of new transcripts within the region
Davies, S.J., Wise, C., Venkatesh, B., Mirza, G., Jefferson, A., Volpi, E.V. and Ragoussis, J. 2004. Mapping of three translocation breakpoints associated with orofacial clefting within 6p24 and identification of new transcripts within the region. Cytogenetic and Genome Research. 105, pp. 47-53. https://doi.org/10.1159/000078008

Cohesion, but not too close
Volpi, E.V., Sheer, D. and Uhlmann, F. 2001. Cohesion, but not too close. Current Biology. 11 (10), p. R378. https://doi.org/10.1016/s0960-9822(01)00212-3

Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei.
Volpi, E.V., Chevret, E., Jones, T., Vatcheva, R., Williamson, J., Beck, S., Campbell, R.D., Goldsworthy, M., Powis, S.H., Ragoussis, J., Trowsdale, J. and Sheer, D. 2000. Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei. Journal of Cell Science. 113 (Pt 9), pp. 1565-1576. https://doi.org/10.1242/jcs.113.9.1565

Mini review: form and function in the human interphase chromosome
Chevret, E., Volpi, E.V. and Sheer, D. 2000. Mini review: form and function in the human interphase chromosome. Cytogenetics and Cell Genetics. 90 (1-2), pp. 13-21. https://doi.org/10.1159/000015654

Nucleotide sequence and chromosomal mapping of the 5S rDNA repeat of the crustacean Proasellus coxalis.
Pelliccia, F., Barzotti, R., Volpi, E.V., Bucciarelli, E. and Rocchi, A. 1998. Nucleotide sequence and chromosomal mapping of the 5S rDNA repeat of the crustacean Proasellus coxalis. Genome. 41 (1), pp. 129-123. https://doi.org/10.1139/g97-110

Numerical abnormalities of chromosomes 1 and 10 in endometrial adenocarcinoma: fluorescence in situ hybridization analysis of 23 archival paraffin-embedded samples.
Muresu, R., Cossu, A., Scarpa, A.M., Volpi, E.V., Rocca, P.C., Pintus, A., Tibiletti, M.G., Tanda, F., Pirastu, M. and Massarelli, G. 1998. Numerical abnormalities of chromosomes 1 and 10 in endometrial adenocarcinoma: fluorescence in situ hybridization analysis of 23 archival paraffin-embedded samples. Cancer Genetics and Cytogenetics. 107 (1), pp. 37-42. https://doi.org/10.1016/s0165-4608(98)00059-4

An integrated physical and genetic map spanning chromosome band 10q24.
Gray, I.C., Fallowfield, J., Ford, S., Nobile, C., Volpi, E.V. and Spurr, N.K. 1997. An integrated physical and genetic map spanning chromosome band 10q24. Genomics. 43 (1), pp. 85-88. https://doi.org/10.1006/geno.1997.4809

Detailed physical analysis of a 1.5-megabase YAC contig containing the MXI1 and ADRA2A genes.
Manca, A., Volpi, E.V., Laficara, F., Muresu, R., Gray, I.C., Spurr, N.K. and Nobile, C. 1997. Detailed physical analysis of a 1.5-megabase YAC contig containing the MXI1 and ADRA2A genes. Genomics. 45 (2), pp. 407-411. https://doi.org/10.1006/geno.1997.4924

Taxonomic and biogeographic analysis of the Proasellus coxalis-group (Crustacea, Isopoda, Asellidae) in Sicily, with description of Proasellus montalentii n.sp.
Stoch, F., Valentino, F. and Volpi, E. 1996. Taxonomic and biogeographic analysis of the Proasellus coxalis-group (Crustacea, Isopoda, Asellidae) in Sicily, with description of Proasellus montalentii n.sp. Hydrobiologia. 317, pp. 247-258. https://doi.org/10.1007/bf00036474

More detailed characterization of some of the HL60 karyotypic features by fluorescence in situ hybridization.
Volpi, E.V., Vatcheva, R., Labella, T. and Gan, S.U. 1996. More detailed characterization of some of the HL60 karyotypic features by fluorescence in situ hybridization. Cancer Genetics and Cytogenetics. 87 (2), pp. 103-106. https://doi.org/10.1016/0165-4608(95)00214-6

Molecular and genetic studies on the region of translocation and duplication in the neuroblastoma cell line NGP at the 1p36.13-p36.32 chromosomal site
Casciano, I., Marchi, J.V.M., Muresu, R., Volpi, E.V., Rozzo, C., Opdenakker, G. and Romani, M. 1996. Molecular and genetic studies on the region of translocation and duplication in the neuroblastoma cell line NGP at the 1p36.13-p36.32 chromosomal site. Oncogene. 12 (10), pp. 2101-2108.

Simple DNA repeats and sex chromosome differentiation in asellus aquaticus (Crustacea, isopoda)
Volpi, E.V., Pelliccia, F., Lanza, V., Barzotti, R. and Rocchi, A. 1995. Simple DNA repeats and sex chromosome differentiation in asellus aquaticus (Crustacea, isopoda). Heredity. 75, p. 267–272. https://doi.org/10.1038/hdy.1995.134

Cytogenetic and molecular studies on the neuroblastoma cell line NGP: identification of a reciprocal t(1;15) involving the "consensus region" 1p36.1.
Muresu, R., Casciano I., Volpi, E.V., Siniscalco, M. and Romani, M. 1995. Cytogenetic and molecular studies on the neuroblastoma cell line NGP: identification of a reciprocal t(1;15) involving the "consensus region" 1p36.1. Genes, Chromosomes & Cancer. 13 (1), pp. 66-71. https://doi.org/10.1002/gcc.2870130111

Subregional mapping of the human lymphocyte-specific protein tyrosine kinase gene (LCK) to 1p35-->p34.3 and its position relative to the 1p marker D1S57.
Volpi, E.V., Romani, M. and Siniscalco, M. 1994. Subregional mapping of the human lymphocyte-specific protein tyrosine kinase gene (LCK) to 1p35-->p34.3 and its position relative to the 1p marker D1S57. Cytogenetics and Cell Genetics. 67, pp. 187-189. https://doi.org/10.1159/000133819

Telomeric sequences of ase/lus aquaticus (Crust. isop.)
Pelliccia, F., Volpi, E.V., Lanza, V., Gaddini, L., Balding, A. and Rocchi, A. 1994. Telomeric sequences of ase/lus aquaticus (Crust. isop.). Heredity. 72, pp. 78-80. https://doi.org/10.1038/hdy.1994.9

Concurrent mapping of an adenovirus 5/SV40 integration site and the U1 snRNA cluster (RNU1) within 400 kb of the chromosome region 1p36.1.
Romani, M., Baldini, A., Volpi, E., Casciano, I., Nobile, C., Muresu, R. and Siniscalco, M. 1994. Concurrent mapping of an adenovirus 5/SV40 integration site and the U1 snRNA cluster (RNU1) within 400 kb of the chromosome region 1p36.1. Cytogenetics and Cell Genetics. 67, pp. 37-40. https://doi.org/10.1159/000133793

MULTIPRINS: a method for multicolour primed in situ labelling
Volpi, E. and Baldini, A. 1993. MULTIPRINS: a method for multicolour primed in situ labelling. Chromosome Research. 1, pp. 257-260. https://doi.org/10.1007/bf00710131

Morphological differentiation of a sex chromosome and ribosomal genes in asellus aquaticus (Crust. Isop.)
Volpi, E.V., Pelliccia, F., Lanza, V., Di Castro, M. and Rocchi, A. 1992. Morphological differentiation of a sex chromosome and ribosomal genes in asellus aquaticus (Crust. Isop.). Heredity. https://doi.org/10.1038/hdy.1992.153

GATA repeats in the genome of Asellus aquaticus (Crustacea, Isopoda).
Pelliccia, F., Di Castro, M., Lanza, V., Volpi, E.V. and Rocchi, A. 1991. GATA repeats in the genome of Asellus aquaticus (Crustacea, Isopoda). Chromosoma. 100, pp. 152-155. https://doi.org/10.1007/bf00337243

Light-dark cycle and mitotic index in Asellus aquaticus (L.) (Crustacea, Isopoda)
Valentino, F., Volpi, E.V., Antolini, R. and Migliore, L. 1990. Light-dark cycle and mitotic index in Asellus aquaticus (L.) (Crustacea, Isopoda). Genetica. 82, pp. 147-150. https://doi.org/10.1007/bf00124645

The genetic isolation between some populations of Proasellus coxalis
Volpi, E.V., Antolini, R. and Valentino, F. 1989. The genetic isolation between some populations of Proasellus coxalis. Journal of Zoological Systematics and Evolutionary Research. 27 (3), pp. 246-251. https://doi.org/10.1111/j.1439-0469.1989.tb00346.x

Characterization of the karyotype of proasellus meridianusby differential staining techniques
Di Castro, M., Lanza, V., Volpi, E.V. and Rocchi, A. 1989. Characterization of the karyotype of proasellus meridianusby differential staining techniques. Caryologia. 42 (3-4), pp. 235-242. https://doi.org/10.1080/00087114.1989.10796970

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