Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Microarray-based global mapping of integration sites of retrotransposon, intracisternal A-particle, in mouse genome

ABSTRACT: Mammalian genomes have evolutionary harbored numerous mobile elements, a part of which are still active and evoke genomic instability. Their movement and positional diversity occasionally result in phenotypic changes and variation by causing altered expression and disruption of neighboring genes in the host genome. Here, we describe a novel microarray-based method by which dispersed genomic locations of a type of retrotransposons in mammalian genome can be identified at a time. By this method, we mapped the DNA elements for a mouse retrotransposon, intracisternal A-particle (IAP), within genomes of C3H/He and C57BL/6J inbred mouse strains; consequently we detected hundreds of probable IAP cDNA-integrating genomic regions. Among 147 putative insertions located nearby the promoter regions, 91 were considered to be present discriminatively in the genome either of C3H/He or C57BL/6J mice, suggesting the existence of considerable strain differences. In addition, by comparing genomic DNAs from a radiation-induced myeloid leukemia and its reference normal tissue, we detected 3 genomic regions around which an IAP element was integrated. These results demonstrate for the first time the successful genome-wide survey of a type of retrotransposon in mammalian genome. Keywords: retrotransposon mapping Genomic DNA fragments containing sequences that flank a mouse retrotransposon are purified and hybridized to the microarray. Experiments are comparisions between signal intensities obtained from Cy3-labeled purified DNA fragments (test) and Cy5-labeled whole genomic DNA fragments (reference).

ORGANISM(S): Mus musculus

SUBMITTER: Takashi Takabatake

PROVIDER: E-GEOD-9572 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Microarray-based global mapping of integration sites for the retrotransposon, intracisternal A-particle, in the mouse genome.

Takabatake Takashi T Ishihara Hiroshi H Ohmachi Yasushi Y Tanaka Izumi I Nakamura Masako M MM Fujikawa Katsuyoshi K Hirouchi Tokuhisa T Kakinuma Shizuko S Shimada Yoshiya Y Oghiso Yoichi Y Tanaka Kimio K

Nucleic acids research 20080501 10

Mammalian genomes contain numerous evolutionary harbored mobile elements, a part of which are still active and may cause genomic instability. Their movement and positional diversity occasionally result in phenotypic changes and variation by causing altered expression or disruption of neighboring host genes. Here, we describe a novel microarray-based method by which dispersed genomic locations of a type of retrotransposon in a mammalian genome can be identified. Using this method, we mapped the D ...[more]

PMID: 18450814

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Project description:Background. The bacterial foodborne pathogen Campylobacter jejuni is a common cause of acute gastroenteritis and is also associated with the postinfectious neuropathies, Guillain-BarrÃ© and Miller Fisher syndromes. This study described the use of multilocus sequence typing and DNA microarrays to examine the genetic content of a collection of South African C. jejuni strains, recovered from patients with enteritis, Guillain-BarrÃ© or Miller Fisher syndromes. Methodology/Principal Findings. The comparative genomic analysis by using multilocus sequence typing and DNA microarrays demonstrated that the South African strains with Penner heat-stable (HS) serotype HS:41 were clearly distinct from the other South African strains. Further analysis of the DNA microarray data demonstrated that the serotype HS:41 strains from South African GBS and enteritis patients are highly similar in gene content. Interestingly, the South African HS:41 strains were distinct in gene content when compared to serotype HS:41 strains from other geographical locations due to the presence of genomic islands, referred to as Campylobacter jejuni integrated elements. Only the genomic integrated element CJIE1, a Campylobacter Mu-like prophage, was present in the South African HS:41 strains whereas absent in the closely-related HS:41 strains from Mexico. A more distantly-related HS:41 strain from Canada possessed both genomic integrated elements CJIE1 and CJIE2. Conclusion/Significance. These findings demonstrated that these C. jejuni integrated elements may contribute to the differentiation of closely-related C. jejuni strains. In addition, the presence of bacteriophage-related genes in CJIE1 may probably contribute to increasing the genomic diversity of these C. jejuni strains. This comparative genomic analysis of the foodborne pathogen C. jejuni provides fundamental information that potentially could lead to improved methods for analyzing the epidemiology of disease outbreaks and their sources. The genomic diversity of 33 South African, 2 Mexican and 1 Canadian Campylobacter jejuni strains from humans were examined by microarray-based comparative genomic indexing (CGI) analysis. The CGI analysis allowed the assessment of CDS content for each C. jejuni strain relative to the C. jejuni DNA microarray, which comprises ORFs from strains NCTC 11168, RM1221. ORFs were spotted in duplicate. Genomic DNA from strains NCTC 11168/RM1221 were used as a reference DNA and competitively hybridized with genomic DNA from each of the other C. jejuni strains. Two or three replicates for each strain were performed. Data normalization was performed as in Parker et al. J Clin Microbiol 2006, 44(11):4125-4135.

Dataset Information

Microarray-based global mapping of integration sites of retrotransposon, intracisternal A-particle, in mouse genome

Publications

Microarray-based global mapping of integration sites for the retrotransposon, intracisternal A-particle, in the mouse genome.

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