Rat–Mouse and Rat–Human Comparative Maps Based on Gene Homology and High-Resolution Zoo-FISH

Nilsson, Samuel; Helou, Khalil; Walentinsson, Anna; Szpirer, Claude; Nerman, Olle; Ståhl, Fredrik

doi:10.1006/geno.2001.6550

Cited by 59 publications

(49 citation statements)

References 17 publications

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“…The HSA 8 and HSA 19 association was found in different rodent species (that is, Castor fiber, P. capensis), but this involved different non-homologous fragments of HSA 8 so it cannot be considered ancestral for the group. The absence of HSA 1/10 was previously proposed as a signature for a clade comprising Anomaluromorpha+Myomorpha+Castorimorpha but this association was subsequently detected in karyotypes of M. musculus and R. norvegicus (Ensembl Mouse web site (http://www.ensembl.org); Nilsson et al, 2001). HSA 1/10 was not present in the Cavia karyotype.…”

Section: Overview Of Karyotype Evolution In Rodentsmentioning

confidence: 96%

Chromosomal evolution in Rodentia

et al. 2011

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Rodentia is the most species-rich mammalian order and includes several important laboratory model species. The amount of new information on karyotypic and phylogenetic relations within and among rodent taxa is rapidly increasing, but a synthesis of these data is currently lacking. Here, we have integrated information drawn from conventional banding studies, recent comparative painting investigations and molecular phylogenetic reconstructions of different rodent taxa. This permitted a revision of several ancestral karyotypic reconstructions, and a more accurate depiction of rodent chromosomal evolution.

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Section: Overview Of Karyotype Evolution In Rodentsmentioning

confidence: 96%

Chromosomal evolution in Rodentia

et al. 2011

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“…To amplify the hairpin mir-155 sequence in the rat genome, we first reasoned that, if 86%-94% of rat genes have orthologs in mice (Nilsson et al 2001;Hancock 2004), the region encompassing rat miRNA-155 could be quite conserved as well. Therefore, we designed a couple of primers (#1 and #2 in Supplemental Table S1) that are able to amplify a region surrounding the mouse mir-155 (Fig.…”

Section: Rat Total Rna Contains the Mature Mir-155-5pmentioning

confidence: 99%

Rat mir-155 generated from the lncRNA Bic is ‘hidden’ in the alternate genomic assembly and reveals the existence of novel mammalian miRNAs and clusters

Uva

Sacco

Cornò

et al. 2013

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MicroRNAs (miRNAs) are a class of small noncoding RNAs acting as post-transcriptional gene expression regulators in many physiological and pathological conditions. During the last few years, many novel mammalian miRNAs have been predicted experimentally with bioinformatics approaches and validated by next-generation sequencing. Although these strategies have prompted the discovery of several miRNAs, the total number of these genes still seems larger. Here, by exploiting the species conservation of human, mouse, and rat hairpin miRNAs, we discovered a novel rat microRNA, mir-155. We found that mature miR-155 is overexpressed in rat spleen myeloid cells treated with LPS, similarly to humans and mice. Rat mir-155 is annotated only on the alternate genome, suggesting the presence of other "hidden" miRNAs on this assembly. Therefore, we comprehensively extended the homology search also to mice and humans, finally validating 34 novel mammalian miRNAs (two in humans, five in mice, and up to 27 in rats). Surprisingly, 15 of these novel miRNAs (one for mice and 14 for rats) were found only on the alternate and not on the reference genomic assembly. To date, our findings indicate that the choice of genomic assembly, when mapping small RNA reads, is an important option that should be carefully considered, at least for these animal models. Finally, the discovery of these novel mammalian miRNA genes may contribute to a better understanding of already acquired experimental data, thereby paving the way to still unexplored investigations and to unraveling the function of miRNAs in disease models.

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“…in the case of a chinese hamster and mouse, when DNa probes from each mouse chromosome were hybridized to a chinese hamster chromosomes, DNa probes from mouse chromosomes 3, 4, 9, 14, 18, 19, and X each painted a single region on each chinese hamster chromosome, whilst mouse DNa probes from other chromosomes delineated multiple discrete chromosomal regions [13]. Similarly, conserved segments with locally strong signals on each chromosome between the rat and mouse, rat and human, or mouse and human have been reported by chromosome painting methods (Zoo-FiSH) [7]. Therefore, the result of this experiment also suggests that the several conserved regions in both species may be localized on mouse chromosomes, since overall slight and locally strong signals of gerbil genomic DNa probes were found in mouse chromosomes.…”

Section: Discussionmentioning

confidence: 99%

Use of Genomic <i>In Situ</i> Hybridization to Identify Chromosomes in Gerbil-Mouse Heterohybridomas

et al. 2013

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Heterohybridomas, created to secrete monoclonal antibodies, are generally unstable over long-term culture because of chromosome elimination during culture. To evaluate the karyotype of heterohybridomas, we used simultaneous genomic in situ hybridization (GISH), which can distinguish unambiguously between parental genomes in allopolyploid species. Using GISH, we discriminated gerbil and mouse chromosomes in heterohybridomas with high sensitivity. The GISH technique will allow evaluation of the stability and crossability of heterohybridomas made from the fusion of mouse cells with those of related species.

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Rat–Mouse and Rat–Human Comparative Maps Based on Gene Homology and High-Resolution Zoo-FISH

Cited by 59 publications

References 17 publications

Chromosomal evolution in Rodentia

Chromosomal evolution in Rodentia

Rat mir-155 generated from the lncRNA Bic is ‘hidden’ in the alternate genomic assembly and reveals the existence of novel mammalian miRNAs and clusters

Use of Genomic <i>In Situ</i> Hybridization to Identify Chromosomes in Gerbil-Mouse Heterohybridomas

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