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    Identification of both copy number variation-type and constant-type core elements in a large segmental duplication region of the mouse genome

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    Authors
    Umemori, Juzoh
    Mori, Akihiro
    Ichiyanagi, Kenji
    Uno, Takeaki
    Koide, Tsuyoshi
    UMass Chan Affiliations
    Program in Gene Function and Expression
    Document Type
    Journal Article
    Publication Date
    2013-07-08
    Keywords
    Algorithms
    Animals
    Cluster Analysis
    DNA Copy Number Variations
    Gene Duplication
    Genomics
    Mice
    Nucleic Acid Hybridization
    Repetitive Sequences, Nucleic Acid
    Sequence Analysis, DNA
    Sequence Homology, Nucleic Acid
    Species Specificity
    Genomics
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    Abstract
    BACKGROUND: Copy number variation (CNV), an important source of diversity in genomic structure, is frequently found in clusters called CNV regions (CNVRs). CNVRs are strongly associated with segmental duplications (SDs), but the composition of these complex repetitive structures remains unclear. RESULTS: We conducted self-comparative-plot analysis of all mouse chromosomes using the high-speed and large-scale-homology search algorithm SHEAP. For eight chromosomes, we identified various types of large SD as tartan-checked patterns within the self-comparative plots. A complex arrangement of diagonal split lines in the self-comparative-plots indicated the presence of large homologous repetitive sequences. We focused on one SD on chromosome 13 (SD13M), and developed SHEPHERD, a stepwise ab initio method, to extract longer repetitive elements and to characterize repetitive structures in this region. Analysis using SHEPHERD showed the existence of 60 core elements, which were expected to be the basic units that form SDs within the repetitive structure of SD13M. The demonstration that sequences homologous to the core elements (>70% homology) covered approximately 90% of the SD13M region indicated that our method can characterize the repetitive structure of SD13M effectively. Core elements were composed largely of fragmented repeats of a previously identified type, such as long interspersed nuclear elements (LINEs), together with partial genic regions. Comparative genome hybridization array analysis showed that whereas 42 core elements were components of CNVR that varied among mouse strains, 8 did not vary among strains (constant type), and the status of the others could not be determined. The CNV-type core elements contained significantly larger proportions of long terminal repeat (LTR) types of retrotransposon than the constant-type core elements, which had no CNV. The higher divergence rates observed in the CNV-type core elements than in the constant type indicate that the CNV-type core elements have a longer evolutionary history than constant-type core elements in SD13M. CONCLUSIONS: Our methodology for the identification of repetitive core sequences simplifies characterization of the structures of large SDs and detailed analysis of CNV. The results of detailed structural and quantitative analyses in this study might help to elucidate the biological role of one of the SDs on chromosome 13.
    Source
    Umemori J, Mori A, Ichiyanagi K, Uno T, Koide T. Identification of both copy number variation-type and constant-type core elements in a large segmental duplication region of the mouse genome. BMC Genomics. 2013 Jul 8;14:455. doi: 10.1186/1471-2164-14-455. Link to article on publisher's site
    DOI
    10.1186/1471-2164-14-455
    Permanent Link to this Item
    http://hdl.handle.net/20.500.14038/30096
    PubMed ID
    23834397
    Related Resources
    Link to Article in PubMed
    Rights
    Copyright 2013 Umemori et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
    ae974a485f413a2113503eed53cd6c53
    10.1186/1471-2164-14-455
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