Evolutionary aspects of the genomic organization of rat chromosome 10

Behboudi, Afrouz; Sjöstrand, Eleonor; Gómez-Fabre, Pedro M.; Sjöling, Åsa; Taïb, Ziad; Klinga-Levan, Karin; Ståhl, Fredrik; Levan, Göran

doi:10.1159/000063052

Cited by 4 publications

(4 citation statements)

References 20 publications

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“…From approximately the band 10q23 to its telomere, RNO10 corresponds to the entire HSA17, representing the longest region of conserved synteny between humans and rodents. 33 However, based on the comparison of the rat and the human draft DNA sequence, it is clear that the conservation with respect to gene order is not so great and that several intrachromosomal rearrangements have taken place in this region during the divergence between human and rat (Table VI). Starting from HSA17p telomere (PRH3AL, 0.06 Mb) till position of TP53 in the human DNA sequence (7.51 Mb), it is necessary to subdivide HSA17 into at least five segments (Table VI, segments A-E), which have been involved in different intrachromosomal rearrangements to generate the present RNO10 configuration.…”

Section: Ai In 12 Tumorsmentioning

confidence: 99%

Analysis of chromosome 10 aberrations in rat endometrial cancer—evidence for a tumor suppressor locus distal to Tp53

Nordlander

Karlsson

et al. 2007

Intl Journal of Cancer

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We have recently shown in the BDII rat model of human endometrial adenocarcinoma (EAC), rat chromosome 10 (RNO10) is frequently involved in chromosomal aberrations. In the present study, we investigated the association between RNO10 deletions, allelic imbalance (AI) at RNO10q24 and Tp53 mutation in 27 rat EAC tumors. We detected chromosomal breakage accompanied by loss of proximal and/or gain of distal parts of RNO10 in approximately 2/3 of the tumors. This finding is suggestive of a tumor suppressor activity encoded from the proximal RNO10. Given the fact that Tp53 is located at RNO10q24-q25, we then performed Tp53 mutation analysis. However, we could not find a strong correlation between AI/deletions at RNO10q24 and Tp53 mutation. Instead, the observed patterns for AI, chromosomal breaks and deletions suggest that major selection was directed against a region located close to, but distal of Tp53. In different human malignancies a similar situation of AI at chromosome band 17p13.3 (HSA17p13.3) unassociated with TP53 mutation has been observed. Although RNO10 is largely homologous to HSA17, the conservation with respect to gene order among them is not extensive. We utilized publicly available draft DNA sequences to study intrachromosomal rearrangement during the divergence between HSA17 and RNO10. By using reciprocal comparison of rat and human genome data, we could substantially narrow down the candidate tumor suppressor region in rat from 3 Mb to a chromosomal segment of about 0.5 Mb in size. These results provide scientific groundwork for identification of the putative tumor suppressor gene(s) at 17p13.3 in human tumors. ' 2006 Wiley-Liss, Inc.Key words: BDII; endometrial adenocarcinoma; RNO10; 17p13.3; allelic imbalance; Tp53 mutation; tumor suppressor gene Endometrial cancer is the most frequently diagnosed female genital tract malignancy in the western world. 1 Endometrial adenocarcinoma (EAC) is the prevalent subtype, accounting for approximately 75% of the reported cases. 2 It has been clearly demonstrated that an inherited genetic predisposition plays a critical role in the development of many cases of EAC, as the risk for a woman to develop EAC is tripled when there is an affected firstdegree relative. 3,4 Molecular genetic analysis of uterine tumor biopsies have revealed alterations in a number of chromosomal regions harboring transforming genes, including tumor suppressor genes (e.g. TP53, PTEN and hMLH1) and oncogenes (e.g. K-RAS and c-ERBB2/neu). 1,5-9 However, the molecular genetic events underlying endometrial cancer tumorigenesis are still poorly understood.Females of the inbred BDII rat strain are genetically prone to spontaneously occurring hormone-related endometrial carcinoma, providing a suitable experimental model system for genetic analysis of inherited EAC in humans. 10,11 Cytogenetic and comparative genome hybridization (CGH) analyses of the tumors pointed to common deletions in the proximal part of rat chromosome 10 (RNO10) in the tumor material. 12 According to Knudson's two-hit theo...

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Section: Ai In 12 Tumorsmentioning

confidence: 99%

Analysis of chromosome 10 aberrations in rat endometrial cancer—evidence for a tumor suppressor locus distal to Tp53

Nordlander

Karlsson

et al. 2007

Intl Journal of Cancer

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“…Recent analysis showed that chromosome 10 of the rat differs by several chromosome rearrangements from both the mouse and the human homologs [27], see also [28]. Here we report on the evaluation of the insertion/deletion pattern in a sample consisting of immune genes (with all intron sequences and with 5000nt of flanking sequence on each side) from human, mouse, and rat.…”

Section: An Applicationmentioning

confidence: 94%

“…Recent analysis showed that chromosome 10 of the rat differs by several chromosome rearrangements from both the mouse and the human homologues, see also ref . It is of interest whether this increased activity is associated with an elevated indel rate in the mouse.…”

Section: An Applicationmentioning

confidence: 99%

The Footprint Sorting Problem

Fried¹,

Hordijk²,

Prohaska³

et al. 2004

J. Chem. Inf. Comput. Sci.

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Phylogenetic footprints are short pieces of non-coding DNA sequence in the vicinity of a gene that are conserved between evolutionary distant species. A seemingly simple problem is to sort footprints in their order along the genomes. It is complicated by the fact that not all footprints are co-linear: they may cross each other. The problem thus becomes the identification of the crossing footprints, the sorting of the remaining co-linear cliques, and finally the insertion of the non-colinear ones at "reasonable" positions. We show that solving the footprint sorting problem requires the solution of the "Minimum Weight Vertex Feedback Set Problem", which is known to be NP-complete and APX-hard. Nevertheless good approximations can be obtained for datasets of interest. The remaining steps of the sorting process are straight forward: computation of the transitive closure of an acyclic graph, linear extension of the resulting partial order, and finally sorting w.r.t. the linear extension. Alternatively, the footprint sorting problem can be rephrased as a combinatorial optimization problem for which approximate solutions can be obtained by means of general purpose heuristics. Footprint sortings obtained with different methods can be compared using a version of multiple sequence alignment that allows the identification of unambiguously ordered sub-lists.

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“…It is shown that this human chromosome is represented by a single synteny in mouse (MMU11), rat (RNO10), cattle (BTA19), pig (SSC12), horse (ECA11), shrew ( h arm of chromosome hn ), and cat (chromosome E1) (Larkin et al, 2000(Larkin et al, , 2004Behboudi et al, 2002;Chowdhary et al, 2002;Waterston et al, 2002;Menotti-Raymond et al, 2003;Evertsvan der Wind et al, 2004). Zoo-FISH analysis of various mammalian genomes showed single chromosomes painted with HSA17 probe in ten orders of mammals.…”

Section: Introductionmentioning

confidence: 99%

Comparative mapping of cattle chromosome 19: cytogenetic localization of 19 BAC clones

Larkin

Astakhova

Prokhorovich

et al. 2006

Cytogenet Genome Res

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Here we present the results of fluorescent in situ hybridization (FISH) mapping of a set of cattle BAC clones preselected for assignment on cattle chromosome 19 (BTA19). The BAC clones were anchored to human chromosome 17 (HSA17) sequences by BLASTn similarity search of cattle BAC-ends against the human genome sequence (NCBI build 33). Five blocks of homologous synteny were defined in the comparative map of BTA19 and HSA17 built with FISH data and the human genome coordinates. The positions for four evolutionary breakpoints in the bovine and human chromosomes were identified. Comparison of the FISH comparative map with previously published comparative RH, physical, and cytogenetic maps of BTA19 did not reveal major conflicts and allowed for the extension of the boundaries of homology between BTA19 and HSA17. Comparative analysis of HSA17, BTA19, and mouse chromosome 11 (MMU11) demonstrates that most likely mice retain the ancestral organization of the synteny group, and both cattle and human chromosomes underwent several major internal rearrangements after the divergence of Primates, Rodentia, and Cetartiodactyla.

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Evolutionary aspects of the genomic organization of rat chromosome 10

Cited by 4 publications

References 20 publications

Analysis of chromosome 10 aberrations in rat endometrial cancer—evidence for a tumor suppressor locus distal to Tp53

Analysis of chromosome 10 aberrations in rat endometrial cancer—evidence for a tumor suppressor locus distal to Tp53

The Footprint Sorting Problem

Comparative mapping of cattle chromosome 19: cytogenetic localization of 19 BAC clones

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