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LINE-1 Retrotransposition: Impact on Genome Stability and Diversity and Human Disease

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LINE-1 Retrotransposition: Impact on Genome Stability and Diversity and Human Disease Journal of Biomedicine and Biotechnology LINE-1 Retrotransposition: Impact on Genome Stability and Diversity and Human Disease Guest Editors: Nina Luning Prak and Abdelali Haoudi Journal of Biomedicine and Biotechnology LINE-1 Retrotransposition: Impact on Genome Stability and Diversity and Human Disease Journal of Biomedicine and Biotechnology LINE-1 Retrotransposition: Impact on Genome Stability and Diversity and Human Disease Guest Editors: Nina Luning Prak and Abdelali Haoudi Copyright © 2006 Hindawi Publishing Corporation. All rights reserved. This is a special issue published in volume 2006 of “Journal of Biomedicine and Biotechnology.” All articles are open access articles distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Founding Managing Editor Abdelali Haoudi, Eastern Virginia Medical School, USA Editors-in-Chief H. N. Ananthaswamy, USA Marc Fellous, France Peter M. Gresshoff, Australia Associate Editors Halima Bensmail, USA Vladimir Larionov, USA Wolfgang A. Schulz, Germany Marìa A. Blasco, Spain George Perry, USA O. John Semmes, USA Shyam K. Dube, USA Steffen B. Petersen, Denmark James L. Sherley, USA Mauro Giacca, Italy Nina Luning Prak, USA Mark A. Smith, USA James Huff, USA Annie J. Sasco, France Lisa Wiesmuller, Germany Editors Claude Bagnis, France Shahid Jameel, India Allal Ouhtit, USA Mohamed Boutjdir, USA Celina Janion, Poland Kanury V. S. Rao, India Douglas Bristol, USA Pierre Lehn, France Gerald G. Schumann, Germany Ronald E. Cannon, USA Nan Liu, USA Pierre Tambourin, France V. Singh Chauhan, India Yan Luo, USA Michel Tibayrenc, France Jean Dausset, France John Macgregor, France Leila Zahed, Lebanon John W. Drake, USA James M. Mason, USA Steven L. Zeichner, USA Hatem El Shanti, USA Ali Ouaissi, France Contents LINE-1 Retrotransposition: Impact on Genome Stability and Diversity and Human Disease, Nina Luning Prak and Abdelali Haoudi Volume 2006 (2006), Article ID 37049, 2 pages The ORF1 Protein Encoded by LINE-1: Structure and Function During L1 Retrotransposition, Sandra L. Martin Volume 2006 (2006), Article ID 45621, 6 pages Do LINEs Have a Role in X-Chromosome Inactivation?, Mary F. Lyon Volume 2006 (2006), Article ID 59746, 6 pages LINE-1 Endonuclease-Dependent Retrotranspositional Events Causing Human Genetic Disease: Mutation Detection Bias and Multiple Mechanisms of Target Gene Disruption, Jian-Min Chen, Claude Férec, and David N. Cooper Volume 2006 (2006), Article ID 56182, 9 pages L1 Antisense Promoter Drives Tissue-Specific Transcription of Human Genes, Kert Mätlik, Kaja Redik, and Mart Speek Volume 2006 (2006), Article ID 71753, 16 pages Links Between Repeated Sequences, Sachiko Matsutani Volume 2006 (2006), Article ID 13569, 3 pages The Genomic Distribution of L1 Elements: The Role of Insertion Bias and Natural Selection, Todd Graham and Stephane Boissinot Volume 2006 (2006), Article ID 75327, 5 pages L1 Retrotransposons in Human Cancers, Wolfgang A. Schulz Volume 2006 (2006), Article ID 83672, 12 pages LINE-1 Hypomethylation in a Choline-Deficiency-Induced Liver Cancer in Rats: Dependence on Feeding Period, Kiyoshi Asada, Yashige Kotake, Rumiko Asada, Deborah Saunders, Robert H. Broyles, Rheal A. Towner, Hiroshi Fukui, and Robert A. Floyd Volume 2006 (2006), Article ID 17142, 6 pages DNA Damage and L1 Retrotransposition, Evan A. Farkash and Eline T. Luning Prak Volume 2006 (2006), Article ID 37285, 8 pages Do Small RNAs Interfere With LINE-1?, Harris S. Soifer Volume 2006 (2006), Article ID 29049, 8 pages The Potential Regulation of L1 Mobility by RNA Interference, Shane R. Horman, Petr Svoboda, and Eline T. Luning Prak Volume 2006 (2006), Article ID 32713, 8 pages Hindawi Publishing Corporation Journal of Biomedicine and Biotechnology Volume 2006, Article ID 37049, Pages 1–2 DOI 10.1155/JBB/2006/37049 Editorial LINE-1 Retrotransposition: Impact on Genome Stability and Diversity and Human Disease Nina Luning Prak and Abdelali Haoudi Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23501, USA Received 6 February 2006; Accepted 6 February 2006 Copyright © 2006 N. L. Prak and A. Haoudi. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. When we started thinking about devoting an issue of the cleic acid binding, and nucleic acid chaperone activity. In her Journal of Biomedicine and Biotechnology to LINE-1s, we were paper, Mary F Lyon discusses the possible role of L1s in X- not sure it would fly. LINE-1s are long interspersed elements chromosome inactivation (XCI). Lyon presents evidence and that account for 17% of the mass of the human genome (1), a possible mechanism for the accumulation of L1s on the hu- but far fewer than 17% of geneticists work on them! Nev- man X-chromosome in such a manner that they could fulfill ertheless, L1s have received considerable press lately, includ- the potential function as booster elements in XCI. Whether ing a number of high-profile stories featuring retrotranspo- L1s are part of the mechanism of XCI or a result of it re- sition in L1 transgenic mice, functional studies of L1, and mains enigmatic. Shifting gears from L1 biology to L1 ef- the potential contributions of L1s to the transcriptome (2– fects on the genome, Jian-Min Chen et al point to the chal- 13). Based on these exciting developments in the L1 field and lenges of detecting of autosomal L1-mediated insertions in the collective enthusiasm and expertise of the contributors to their review article. In addition, Chen et al discuss the man- this edition, we are pleased to present this special L1 issue. ner in which target genes are disrupted by L1-mediated retro- The LINE-1 element (long interspersed element, L1) is an transpositional events and comment that these are likely to autonomous retrotransposon that propagates in the genome depend upon several different factors such as the type of via retrotransposition. During retrotransposition, L1 DNA insertion (ie, L1 direct, L1 trans-driven Alu,orL1trans- is transcribed to RNA and processed. The processed RNA driven SVA), the precise locations of the inserted sequences is reverse-transcribed by the L1-encoded reverse transcrip- within the target gene regions, the length of the inserted tase and the cDNA copy is inserted into a new chromoso- sequences, and possibly also their orientation. In their re- mal location. Over 500,000 L1 copies reside in the human search article, Kert Matl¨ık et al identify and characterize 49 genome, but L1 retrotransposition can also mobilize Alu ele- chimeric L1 mRNAs, continuing the theme of L1 effects on ments (short interspersed elements) and contribute to pro- genes. These chimeric transcripts are due to L1 sense or anti- cessed pseudogene formation (1, 14–16). Much have been sense promoter activity arising from within or nearby exist- learned in recent years about L1 structure, function, and con- ing genes. In 45 out of the 49 cases, the chimeric transcript tribution to the genome, but much more remain to be under- is in the same transcriptional orientation as the neighbor- stood, particularly how L1 insertions influence the expres- ing/surrounding gene. In addition, Matl¨ık et al show that the sion and function of neighboring genes and how L1 mobility L1 antisense promoter (ASP) can give rise to a chimeric tran- is kept in check. script whose coding region is identical to the ORF of mRNA This L1 issue is organized into two parts. The first part of several genes such as: KIAA1797, CLCN5,andSLCO1A2. consists of six papers describing L1 biology (two papers) and Finally and most provocatively, they provide evidence that the interactions of L1s with the genome (four papers). In the L1 ASP can alter the tissue-specific pattern of transcrip- a minireview, Sandra L Martin describes the structure and tion of some genes. Their study provides another dimension function of the L1 ORF1 protein during L1 retrotransposi- to the ways in which L1 can influence gene expression. In a tion. Her minireview article includes an update on recent minireview article, Sachiko Matsutani discusses the links be- studies describing L1 ORF1 protein-protein interactions, nu- tween LINE-1 and SINE (Alu) elements and how L1-encoded 2 Journal of Biomedicine and Biotechnology proteins contribute to the mobilization of other mobile el- could be targeted by RNAi, with an emphasis on different ements including Alu andprocessedpseudogenesandeven forms of double-stranded and hairpin RNA. Horman et al cellular genes. In their minireview article, Todd Graham and also point out that the conventional cell-culture-based L1 Stephane Boissinot discuss factors affecting how L1s are dis- retrotransposition assay (which relies on the expression of an tributed in the genome. L1 elements do not appear to be antisense marker cassette) may induce RNAi. randomly distributed in the genome. Graham and Boissinot We thank the contributors for their thought-provoking discuss factors that could skew the distribution of L1s in manuscripts and hope that readers will enjoy this special is- the genome, including L1 insertion bias and selection (ei- sue of the Journal of Biomedicine and Biotechnology on L1s. ther negative or positive) after insertion. The notion of neg- ative selection arising when an L1 insertion has especially Nina Luning Prak deleterious consequences (including increased recombina- Abdelali Haoudi tion, altered transcription of neighboring genes, and contin- ued retrotransposition) provides a bridge to the second sec- tion of the issue, which deals with the regulation of L1s. Nina Luning Prak is an Assistant Profes- The regulation of L1s can occur on many levels. L1 reg- sor at the Department of Pathology and ulation can occur before the element has a chance to get Laboratory Medicine at the University of going (pre- or posttranscriptional silencing, inefficient full- Pennsylvania Health System.
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