Retrotransposition and Structural Variation in the Human Genome

Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX 77030, USA.
Cell (Impact Factor: 33.12). 06/2010; 141(7):1110-2. DOI: 10.1016/j.cell.2010.06.014
Source: PubMed

ABSTRACT New assays are revealing that the diploid human genome contains extensive amounts of structural variation. Genome-wide approaches described in three papers in this issue (Beck et al., 2010; Huang et al., 2010; Iskow et al., 2010) paint a dynamic portrait of our genome, revealing a prominent role for repetitive sequences in shaping its structural variation.

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    ABSTRACT: Long interspersed nuclear elements-1 (LINE-1) are the most abundant and active retrotransposons in the mammalian genomes. Traditionally, the occurrence of LINE-1 sequences in the genome of mammals has been explained by the selfish DNA hypothesis. Nevertheless, recently, it has also been argued that these sequences could play important roles in these genomes, as in the regulation of gene expression, genome modelling and X-chromosome inactivation. The non-random chromosomal distribution is a striking feature of these retroelements that somehow reflects its functionality. In the present study, we have isolated and analysed a fraction of the open reading frame 2 (ORF2) LINE-1 sequence from three rodent species, Cricetus cricetus, Peromyscus eremicus and Praomys tullbergi. Physical mapping of the isolated sequences revealed an interspersed longitudinal AT pattern of distribution along all the chromosomes of the complement in the three genomes. A detailed analysis shows that these sequences are preferentially located in the euchromatic regions, although some signals could be detected in the heterochromatin. In addition, a coincidence between the location of imprinted gene regions (as Xist and Tsix gene regions) and the LINE-1 retroelements was also observed. According to these results, we propose an involvement of LINE-1 sequences in different genomic events as gene imprinting, X-chromosome inactivation and evolution of repetitive sequences located at the heterochromatic regions (e.g. satellite DNA sequences) of the rodents' genomes analysed.
    Journal of applied genetics 08/2014; 56(1). DOI:10.1007/s13353-014-0241-x · 1.90 Impact Factor
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    ABSTRACT: Transposable Elements (TEs) or transposons are low-complexity elements (e.g., LINEs, SINEs, SVAs, and HERVs) that make up to two-thirds of the human genome. There is mounting evidence that TEs play an essential role in genomic architecture and regulation related to both normal function and disease states. Recently, the identification of active TEs in several different human brain regions suggests that TEs play a role in normal brain development and adult physiology and quite possibly in psychiatric disorders. TEs have been implicated in hemophilia, neurofibromatosis, and cancer. With the advent of next-generation whole-genome sequencing approaches, our understanding of the relationship between TEs and psychiatric disorders will greatly improve. We will review the biology of TEs and early evidence for TE involvement in psychiatric disorders. © 2014 Wiley Periodicals, Inc.
    American Journal of Medical Genetics Part B Neuropsychiatric Genetics 04/2014; 165(3). DOI:10.1002/ajmg.b.32225 · 3.27 Impact Factor
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    ABSTRACT: Differences in the content and organization of DNA, collectively referred to as structural variation, have emerged as a major source of genetic and phenotypic diversity within and between species. In addition, structural variation provides an important substrate for evolutionary innovations. Here, we review recent progress in characterizing patterns of canine structural variation within and between breeds, and in correlating copy number variants (CNVs) with phenotypes. Because of the extensive phenotypic diversity that exists within and between breeds and the tantalizing examples of canine CNVs that influence traits such as skin wrinkling in Shar-Pei, dorsal hair ridge in Rhodesian and Thai Ridgebacks, and short limbs in many breeds such as Dachshunds and Corgis, we argue that domesticated dogs are uniquely poised to contribute novel insights into CNV biology. As new technologies continue to be developed and refined, the field of canine genomics is on the precipice of a deeper understanding of how structural variation and CNVs contribute to canine genetic diversity, phenotypic variation, and disease susceptibility.
    Mammalian Genome 12/2011; 23(1-2):144-63. DOI:10.1007/s00335-011-9369-8 · 2.88 Impact Factor