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Glukhova, Liubov; Zoubak, Sergei V.; Rynditch, A. V.; Miller, G. G.; Titova, Irina V.; Vorobyeva, N. V.; Lazurkevitch, Z. V.; Graphodatskii, Alexander S.; Кущ, А А; Bernardi, Giorgio

doi:10.1023/a:1009243115039

Cited by 11 publications

(1 citation statement)

References 20 publications

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“…One might, however, argue that, since all the retroviral sequences mentioned so far are GC-rich [31], integration into GC-rich isochores could depend upon the requirement for a compositional match between the retroviral sequence and the isochores of the host genome without being related to chromatin “openness”. Integration into GC-rich isochores was also found, however, for exogenous Mouse Mammary Tumor Virus (MMTV; [32]) and Human Immunodeficiency Virus (HIV-I; [6], [33]–[36]) which are GC-poor. This obviously favors the idea of an integration into open chromatin structures.…”

Section: Discussionmentioning

confidence: 99%

Mapping Insertions, Deletions and SNPs on Venter's Chromosomes

Costantini

Bernardi

2009

PLoS ONE

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BackgroundThe very recent availability of fully sequenced individual human genomes is a major revolution in biology which is certainly going to provide new insights into genetic diseases and genomic rearrangements.ResultsWe mapped the insertions, deletions and SNPs (single nucleotide polymorphisms) that are present in Craig Venter's genome, more precisely on chromosomes 17 to 22, and compared them with the human reference genome hg17. Our results show that insertions and deletions are almost absent in L1 and generally scarce in L2 isochore families (GC-poor L1+L2 isochores represent slightly over half of the human genome), whereas they increase in GC-rich isochores, largely paralleling the densities of genes, retroviral integrations and Alu sequences. The distributions of insertions/deletions are in striking contrast with those of SNPs which exhibit almost the same density across all isochore families with, however, a trend for lower concentrations in gene-rich regions.ConclusionsOur study strongly suggests that the distribution of insertions/deletions is due to the structure of chromatin which is mostly open in gene-rich, GC-rich isochores, and largely closed in gene-poor, GC-poor isochores. The different distributions of insertions/deletions and SNPs are clearly related to the two different responsible mechanisms, namely recombination and point mutations.

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Section: Discussionmentioning

confidence: 99%

Mapping Insertions, Deletions and SNPs on Venter's Chromosomes

Costantini

Bernardi

2009

PLoS ONE

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Retroviruses and Associated Diseases in Humans

Dezzutti

Heneine

Boneva

et al. 2010

Topley &Amp; Wilson's Microbiology and Microbial Infections

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Jumping translocations are common in solid tumor cell lines and result in recurrent fusions of whole chromosome arms

Padilla‐Nash

Heselmeyer‐Haddad

Wangsa

et al. 2001

Genes Chromosom. Cancer

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Jumping translocations (JTs) and segmental jumping translocations (SJTs) are unbalanced translocations involving a donor chromosome arm or chromosome segment that has fused to multiple recipient chromosomes. In leukemia, where JTs have been predominantly observed, the donor segment (usually 1q) preferentially fuses to the telomere regions of recipient chromosomes. In this study, spectral karyotyping (SKY) and FISH analysis revealed 188 JTs and SJTs in 10 cell lines derived from carcinomas of the bladder, prostate, breast, cervix, and pancreas. Multiple JTs and SJTs were detected in each cell line and contributed to recurrent unbalanced whole-arm translocations involving chromosome arms 5p, 14q, 15q, 20q, and 21q. Sixty percent (113/188) of JT breakpoints occurred within centromere or pericentromeric regions of the recipient chromosomes, whereas only 12% of the breakpoints were located in the telomere regions. JT breakpoints of both donor and recipient chromosomes coincided with numerous fragile sites as well as viral integration sites for human DNA viruses. The JTs within each tumor cell line promoted clonal progression, leading to the acquisition of extra copies of the donated chromosome segments that often contained oncogenes (MYC, ABL, HER2/NEU, etc.), consequently resulting in tumor-specific genomic imbalances. Published 2001 Wiley-Liss, Inc.

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Cited by 11 publications

References 20 publications

Mapping Insertions, Deletions and SNPs on Venter's Chromosomes

Mapping Insertions, Deletions and SNPs on Venter's Chromosomes

Retroviruses and Associated Diseases in Humans

Jumping translocations are common in solid tumor cell lines and result in recurrent fusions of whole chromosome arms

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