Frequent Human Genomic DNA Transduction Driven by LINE-1 Retrotransposition

Pickeral, Oxana K.; Makałowski, Wojciech; Boguski, Mark S.; Boeke, Jef D.

doi:10.1101/gr.10.4.411

Cited by 261 publications

(226 citation statements)

References 18 publications

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“…Our observation of high clustering of LCR15 in discrete and large regions of the chromosome suggests that LCR15 duplicon could be considered as a`mobile' element in the evolution of this chromosome. Although other types of repeated sequences such as LINE elements show high mobility rates, 46 the mobility capacity of duplicons is unknown. The common presence of pseudogene sequences within LCR15 copies suggests a role for an open DNA/ chromatin structure.…”

Section: Discussionmentioning

confidence: 99%

Human chromosome 15q11-q14 regions of rearrangements contain clusters of LCR15 duplicons

et al. 2002

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Six breakpoint regions for rearrangements of human chromosome 15q11-q14 have been described. These rearrangements involve deletions found in approximately 70% of Prader-Willi or Angelman's syndrome patients (PWS, AS), duplications detected in some cases of autism, triplications and inverted duplications. HERC2-containing (HEct domain and RCc1 domain protein 2) segmental duplications or duplicons are present at two of these breakpoints (BP2 and BP3) mainly associated with deletions. We show here that clusters containing several copies of the human chromosome 15 low-copy repeat (LCR15) duplicon are located at each of the six described 15q11-q14 BPs. In addition, our results suggest the existence of breakpoints for large 15q11-q13 deletions in a proximal duplicon-containing clone. The study reveals that HERC2-containing duplicons (estimated on 50 ± 400 kb) and LCR15 duplicons (*15 kb on 15q11-q14) share the golgin-like protein (GLP) genomic sequence. Through the analysis of a human BAC library and public databases we have identified 36 LCR15 related sequences in the human genome, most (27) mapping to chromosome 15q and being transcribed. LCR15 analysis in non-human primates and age-sequence divergences support a recent origin of this family of segmental duplications through human speciation.

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Section: Discussionmentioning

confidence: 99%

Human chromosome 15q11-q14 regions of rearrangements contain clusters of LCR15 duplicons

et al. 2002

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“…Thus, sequences from the genome downstream of the LINE become incorporated into its transcript and are subsequently "retrotransduced" or inserted at a new genome location [182]. It has been demonstrated experimentally that LINE element retrotransduction of downstream sequences is a feasible mechanism of exon mobilization in protein evolution [183].…”

Section: Lines and Sinesmentioning

confidence: 99%

How life changes itself: The Read–Write (RW) genome

Shapiro

2013

Physics of Life Reviews

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The genome has traditionally been treated as a Read-Only Memory (ROM) subject to change by copying errors and accidents. In this review, I propose that we need to change that perspective and understand the genome as an intricately formatted Read-Write (RW) data storage system constantly subject to cellular modifications and inscriptions. Cells operate under changing conditions and are continually modifying themselves by genome inscriptions. These inscriptions occur over three distinct time-scales (cell reproduction, multicellular development and evolutionary change) and involve a variety of different processes at each time scale (forming nucleoprotein complexes, epigenetic formatting and changes in DNA sequence structure). Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences.

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“…2). Transduction by transposable elements generates genome diversity by exon shuffling (Moran et al 1999;Goodier et al 2000;Pickeral et al 2000;Beck et al 2010) or through gene family formation ) and at least two of the active human retrotransposon families, LINE-1 and SVA, are known to have participated in transduction events (Holmes et al 1994;Goodier et al 2000;Pickeral et al 2000;Ostertag et al 2003;Xing et al 2006). These events provide a means of rapid lineage-specific evolution.…”

Section: Human Applications: Variationmentioning

confidence: 99%

Reading TE leaves: New approaches to the identification of transposable element insertions

Ray¹,

Batzer²

2011

Genome Res.

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Transposable elements (TEs) are a tremendous source of genome instability and genetic variation. Of particular interest to investigators of human biology and human evolution are retrotransposon insertions that are recent and/or polymorphic in the human population. As a consequence, the ability to assay large numbers of polymorphic TEs in a given genome is valuable. Five recent manuscripts each propose methods to scan whole human genomes to identify, map, and, in some cases, genotype polymorphic retrotransposon insertions in multiple human genomes simultaneously. These technologies promise to revolutionize our ability to analyze human genomes for TE-based variation important to studies of human variability and human disease. Furthermore, the approaches hold promise for researchers interested in nonhuman genomic variability. Herein, we explore the methods reported in the manuscripts and discuss their applications to aspects of human biology and the biology of other organisms.

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Frequent Human Genomic DNA Transduction Driven by LINE-1 Retrotransposition

Cited by 261 publications

References 18 publications

Human chromosome 15q11-q14 regions of rearrangements contain clusters of LCR15 duplicons

Human chromosome 15q11-q14 regions of rearrangements contain clusters of LCR15 duplicons

How life changes itself: The Read–Write (RW) genome

Reading TE leaves: New approaches to the identification of transposable element insertions

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