Representing GC variation along eukaryotic chromosomes

Pačes, Jan; Zı́ka, Radek; Pačes, Václav; Pavlı́ček, Adam; Clay, Oliver; Bernardi, Giorgio

doi:10.1016/j.gene.2004.02.041

Cited by 37 publications

(36 citation statements)

References 34 publications

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“…S2 shows a size peak of isochores around 500 kb). The color-coded map shows 100-kb moving window plots using the program draw_chromosome_gc.pl (Pačes et al 2004) (http://genomat.img.cas.cz). The color code spans the spectrum of GC levels in five steps, indicated by broken horizontal lines, from ultramarine blue (GC-poorest L1 isochores) to scarlet red (GC-richest H3 isochores).…”

Section: Isochore Bordersmentioning

confidence: 99%

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An isochore map of human chromosomes

Costantini¹,

Clay²,

Auletta³

et al. 2006

Genome Res.

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300

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Isochores are large DNA segments (≫300 kb on average) that are characterized by an internal variation in GC well below the full variation seen in the mammalian genome. Precisely defining in terms of size and composition as well as mapping the isochores on human chromosomes have, however, remained largely unsolved problems. Here we used a very simple approach to segment the human chromosomes de novo, based on assessments of GC and its variation within and between adjacent regions. We obtain a complete coverage of the human genome (neglecting the remaining gaps) by ∼3200 isochores, which may be visualized as the ultimate chromosomal bands. Isochores visibly belong to five families characterized by different GC levels, as expected from previous investigations. Since we previously showed that isochores are tightly linked to basic biological properties such as gene density, replication timing, and recombination, the new level of detail provided by the isochore map will help the understanding of genome structure, function, and evolution.

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Section: Isochore Bordersmentioning

confidence: 99%

“…1; Pavliček et al 2002;Pačes et al 2004). The window size of 100 kb was motivated by the existence of a horizontal plateau in variance plots after ∼100 kb (see Results).…”

Section: Isochore Mappingmentioning

confidence: 99%

An isochore map of human chromosomes

Costantini¹,

Clay²,

Auletta³

et al. 2006

Genome Res.

Self Cite

210

300

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show abstract

“…15 The freely distributed program draw chromosomegc.pl (http://genomat.img.cas.cz) was used to analyze and plot the genome-wide GC content in windows of 100-kb size along the chromosomes as described by Paces and colleagues. 16 Sequence data were obtained from the Human Genome Assembly, National Center for Biotechnology Information build 34.…”

Section: Analysis Of Gc Content and Gc Heterogeneitymentioning

confidence: 99%

Amplification of Whole Tumor Genomes and Gene-by-Gene Mapping of Genomic Aberrations from Limited Sources of Fresh-Frozen and Paraffin-Embedded DNA

Bredel

Juric

et al. 2005

The Journal of Molecular Diagnostics

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Sufficient quantity of genomic DNA can be a bottleneck in genome-wide analysis of clinical tissue samples. DNA polymerase Phi29 can be used for the random-primed amplification of whole genomes, although the amplification may introduce bias in gene dosage. We have performed a detailed investigation of this technique in archival fresh-frozen and formalin-fixed/paraffinembedded tumor DNA by using cDNA microarray-based comparative genomic hybridization. Phi29 amplified DNA from matched pairs of fresh-frozen and formalinfixed/paraffin-embedded tumor samples with similar efficiency. The distortion in gene dosage representation in the amplified DNA was nonrandom and reproducibly involved distinct genomic loci. Regional amplification efficiency was significantly linked to regional GC content of the template genome. The biased gene representation in amplified tumor DNA could be effectively normalized by using amplified reference DNA. Our data suggest that genome-wide gene dosage alterations in clinical tumor samples can be reliably assessed from a few hundred tumor cells. Therefore, this amplification method should lend itself to high-throughput genetic analyses of limited sources of tumor, such as fineneedle biopsies, laser-microdissected tissue, and small paraffin-embedded specimens. The availability of a simple and reliable method for the amplification of entire genomes from limited sources of DNA would lend itself to high-throughput genetic analyses in virtually all areas of translational research. High-throughput genomic profiling, for example cDNA microarray-based comparative genomic hybridization (array-CGH), 1 requires g quantities of genomic DNA. A particular challenge for translation of array-CGH methodology to clinical application is to link it to a robust up-front technology that allows reliable and unbiased amplification of limited sources of DNA, for example from fine-needle biopsies. Much effort has been invested in developing methods for whole genome amplification, for example polymerase chain reaction-based methods. [2][3][4] In particular, the pitfalls of substantial variation in the extent of amplification occurring between different markers, incomplete representation, and inadequate average DNA size have limited the use of most existing amplification methods, making them particularly unsuitable for genomic applications. 2-4Bacteriophage Phi29 DNA polymerase random-primed DNA amplification 5-7 is based on an isothermal strand displacement amplification reaction in which random hexamer primers anneal to the genomic template at multiple sites and Phi29 initiates replication at these sites on the denatured linear DNA. As synthesis proceeds, strand displacement of complementary DNA generates new single-stranded DNA available to be primed by additional primers. The subsequent strand displacement replication of this DNA leads to the formation of double-stranded DNA. The presence of an associated proofreading activity of Phi29 ensures a high sequence accuracy of the amplified DNA, indicating its suitability f...

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“…The presence of fragile sites or a loss in chromatin methylation may also render a region more susceptible to DNA damage. The GC content of the regions associated with chromosomal breakage in our resistant cell lines was analyzed using the GC content maps available at http://genomat.img.cas.cz (Paces et al, 2004). While breakages tend to occur in regions of GC content 40% or greater they do not occur at the most GC-rich areas of the genome.…”

Section: Discussionmentioning

confidence: 99%

Similar chromosomal changes in cisplatin and oxaliplatin‐resistant sublines of the H69 SCLC cell line are not associated with platinum resistance

Stordal

Peters

Davey

2006

Genes Chromosomes & Cancer

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Small cell lung cancer (SCLC) initially responds well to DNA damaging drugs such as cisplatin, however this is transitory as resistance normally develops. To investigate whether changes in chromosomal copy number caused by platinum drug treatment contributes to platinum resistance, we have analyzed H69 SCLC cells and two low-level platinum-resistant sublines, H69CIS200 and H69OX400, derived by cisplatin and oxaliplatin treatment, respectively. Affymetrix 10K SNP array showed that cisplatin and oxaliplatin have independently caused similar changes including loss of segments 6q21-qter and 13pter-13q.14.11 and duplication of chromosome 21. Interestingly, despite using equally cytotoxic doses of drug in the development of the cell lines, oxaliplatin caused three times more chromosomal changes than cisplatin. The resistant cell lines lose their resistant phenotype after 3 months of drug-free culture. The revertant cell lines, denoted H69CIS200-S and H69OX400-S, were also analyzed by Affymetrix array to determine if chromosomal changes associated with resistance remain after the resistant phenotype is lost. In the H69OX400-S many of the changes observed in the resistant cells were absent suggesting that they contributed to the resistant phenotype including: loss of 1q23.3-qter, 10q11.23, and 19q13.12-q13.2 and duplication of segments 6p21.2-p12.3, 16q12.1-16q13, 16q21-q23.1, and 19q12. However, out of the similar changes induced by cisplatin and oxaliplatin, both the loss of 6q21-qter and gain of 21 were still present in the H69CIS200-S and H69OX400-S cells. This suggests that cisplatin and oxaliplatin induced similar changes due to inherent vulnerabilities in the H69 cells rather than changes associated with platinum resistance.

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Representing GC variation along eukaryotic chromosomes

Cited by 37 publications

References 34 publications

An isochore map of human chromosomes

An isochore map of human chromosomes

Amplification of Whole Tumor Genomes and Gene-by-Gene Mapping of Genomic Aberrations from Limited Sources of Fresh-Frozen and Paraffin-Embedded DNA

Similar chromosomal changes in cisplatin and oxaliplatin‐resistant sublines of the H69 SCLC cell line are not associated with platinum resistance

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