1
|
Graham T, Boissinot S. The genomic distribution of L1 elements: the role of insertion bias and natural selection. J Biomed Biotechnol 2006; 2006:75327. [PMID: 16877820 PMCID: PMC1510949 DOI: 10.1155/jbb/2006/75327] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2005] [Revised: 12/06/2005] [Accepted: 12/13/2005] [Indexed: 11/19/2022] Open
Abstract
LINE-1 (L1) retrotransposons constitute the most successful family of retroelements in mammals and account for as much as 20% of mammalian DNA. L1 elements can be found in all genomic regions but they are far more abundant in AT-rich, gene-poor, and low-recombining regions of the genome. In addition, the sex chromosomes and some genes seem disproportionately enriched in L1 elements. Insertion bias and selective processes can both account for this biased distribution of L1 elements. L1 elements do not appear to insert randomly in the genome and this insertion bias can at least partially explain the genomic distribution of L1. The contrasted distribution of L1 and Alu elements suggests that postinsertional processes play a major role in shaping L1 distribution. The most likely mechanism is the loss of recently integrated L1 elements that are deleterious (negative selection) either because of disruption of gene function or their ability to mediate ectopic recombination. By comparison, the retention of L1 elements because of some positive effect is limited to a small fraction of the genome. Understanding the respective importance of insertion bias and selection will require a better knowledge of insertion mechanisms and the dynamics of L1 inserts in populations.
Collapse
Affiliation(s)
- Todd Graham
- Department of Biology, Queens College, City University of New York, Flushing, NY 11367, USA
| | - Stephane Boissinot
- Department of Biology, Queens College, City University of New York, Flushing, NY 11367, USA
- Graduate School and University Center, City University of New York, New York, NY 10016, USA
| |
Collapse
|
2
|
Zingler N, Weichenrieder O, Schumann GG. APE-type non-LTR retrotransposons: determinants involved in target site recognition. Cytogenet Genome Res 2005; 110:250-68. [PMID: 16093679 DOI: 10.1159/000084959] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2003] [Accepted: 02/05/2004] [Indexed: 10/25/2022] Open
Abstract
Non-long terminal repeat (Non-LTR) retrotransposons represent a diverse and widely distributed group of transposable elements and an almost ubiquitous component of eukaryotic genomes that has a major impact on evolution. Their copy number can range from a few to several million and they often make up a significant fraction of the genomes. The members of the dominating subtype of non-LTR retrotransposons code for an endonuclease with homology to apurinic/apyrimidinic endonucleases (APE), and are thus termed APE-type non-LTR retrotransposons. In the last decade both the number of identified non-LTR retrotransposons and our knowledge of biology and evolution of APE-type non-LTR retrotransposons has increased tremendously.
Collapse
Affiliation(s)
- N Zingler
- Paul-Ehrlich-Institut, Langen, Germany
| | | | | |
Collapse
|
3
|
Chen JM, Stenson PD, Cooper DN, Férec C. A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease. Hum Genet 2005; 117:411-27. [PMID: 15983781 DOI: 10.1007/s00439-005-1321-0] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2005] [Accepted: 04/04/2005] [Indexed: 10/25/2022]
Abstract
Diverse long interspersed element-1 (LINE-1 or L1)-dependent mutational mechanisms have been extensively studied with respect to L1 and Alu elements engineered for retrotransposition in cultured cells and/or in genome-wide analyses. To what extent the in vitro studies can be held to accurately reflect in vivo events in the human genome, however, remains to be clarified. We have attempted to address this question by means of a systematic analysis of recent L1-mediated retrotranspositional events that have caused human genetic disease, with a view to providing a more complete picture of how L1-mediated retrotransposition impacts upon the architecture of the human genome. A total of 48 such mutations were identified, including those described as L1-mediated retrotransposons, as well as insertions reported to contain a poly(A) tail: 26 were L1 trans-driven Alu insertions, 15 were direct L1 insertions, four were L1 trans-driven SVA insertions, and three were associated with simple poly(A) insertions. The systematic study of these lesions, when combined with previous in vitro and genome-wide analyses, has strengthened several important conclusions regarding L1-mediated retrotransposition in humans: (a) approximately 25% of L1 insertions are associated with the 3' transduction of adjacent genomic sequences, (b) approximately 25% of the new L1 inserts are full-length, (c) poly(A) tail length correlates inversely with the age of the element, and (d) the length of target site duplication in vivo is rarely longer than 20 bp. Our analysis also suggests that some 10% of L1-mediated retrotranspositional events are associated with significant genomic deletions in humans. Finally, the identification of independent retrotranspositional events that have integrated at the same genomic locations provides new insight into the L1-mediated insertional process in humans.
Collapse
Affiliation(s)
- Jian-Min Chen
- INSERM U613-Génétique Moléculaire et Génétique Epidémiologique, Etablissement Français du Sang-Bretagne, Université de Bretagne Occidentale, Centre Hospitalier Universitaire, Brest, 29220, France.
| | | | | | | |
Collapse
|
4
|
Boissinot S, Entezam A, Young L, Munson PJ, Furano AV. The insertional history of an active family of L1 retrotransposons in humans. Genome Res 2004; 14:1221-31. [PMID: 15197167 PMCID: PMC442137 DOI: 10.1101/gr.2326704] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
As humans contain a currently active L1 (LINE-1) non-LTR retrotransposon family (Ta-1), the human genome database likely provides only a partial picture of Ta-1-generated diversity. We used a non-biased method to clone Ta-1 retrotransposon-containing loci from representatives of four ethnic populations. We obtained 277 distinct Ta-1 loci and identified an additional 67 loci in the human genome database. This collection represents approximately 90% of the Ta-1 population in the individuals examined and is thus more representative of the insertional history of Ta-1 than the human genome database, which lacked approximately 40% of our cloned Ta-1 elements. As both polymorphic and fixed Ta-1 elements are as abundant in the GC-poor genomic regions as in ancestral L1 elements, the enrichment of L1 elements in GC-poor areas is likely due to insertional bias rather than selection. Although the chromosomal distribution of Ta-1 inserts is generally a function of chromosomal length and gene density, chromosome 4 significantly deviates from this pattern and has been much more hospitable to Ta-1 insertions than any other chromosome. Also, the intra-chromosomal distribution of Ta-1 elements is not uniform. Ta-1 elements tend to cluster, and the maximal gaps between Ta-1 inserts are larger than would be expected from a model of uniform random insertion.
Collapse
Affiliation(s)
- Stéphane Boissinot
- Section on Genomic Structure and Function, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, USA
| | | | | | | | | |
Collapse
|
5
|
Boissinot S, Roos C, Furano AV. Different rates of LINE-1 (L1) retrotransposon amplification and evolution in New World monkeys. J Mol Evol 2004; 58:122-30. [PMID: 14743320 DOI: 10.1007/s00239-003-2539-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2003] [Accepted: 08/08/2003] [Indexed: 10/26/2022]
Abstract
LINE-1 (L1) elements constitute the major family of retrotransposons in mammalian genomes. Here we report the first investigation of L1 evolution in New World monkeys (NWM). Two regions of the second open-reading frame were analyzed by two methods in three NWM species, the squirrel monkey (Saimiri sciureus), the tamarin (Saguinus oedipus), and the spider monkey (Ateles paniscus). Since these three species diverged, L1 has amplified in the Saimiri and Saguinus lineages but L1 activity seems to have been strongly reduced in the Ateles lineage. In addition, the active L1 lineage has evolved rapidly in Saimiri and Saguinus, generating species-specific subfamilies. In contrast, we found no evidence for a species-specific subfamily in Ateles, a result consistent with the low L1 activity in this species for the last approximately 25 My.
Collapse
Affiliation(s)
- Stéphane Boissinot
- Section on Genomic Structure and Function, Laboratory of Molecular and Cellular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0830, USA
| | | | | |
Collapse
|
6
|
Mathews LM, Chi SY, Greenberg N, Ovchinnikov I, Swergold GD. Large differences between LINE-1 amplification rates in the human and chimpanzee lineages. Am J Hum Genet 2003; 72:739-48. [PMID: 12574987 PMCID: PMC1180250 DOI: 10.1086/368275] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2002] [Accepted: 12/09/2002] [Indexed: 11/03/2022] Open
Abstract
The genomic evolution and causes of phenotypic variation among humans and great apes remain largely unknown, although the phylogenetic relationships among them have been extensively explored. Previous studies that focus on differences at the amino acid and nucleotide sequence levels have revealed a high degree of similarity between humans and chimpanzees, suggesting that other types of genomic change may have contributed to the relatively large phenotypic differences between them. For example, the activity of long interspersed element 1 (LINE-1) retrotransposons may impose significant changes on genomic structure and function and, consequently, on phenotype. Here we investigate the relative rates of LINE-1 amplification in the lineages leading to humans, bonobos (Pan paniscus), and chimpanzees (P. troglodytes). Our data indicate that LINE-1 insertions have accumulated at significantly greater rates in bonobos and chimpanzees than in humans, provide insights into the timing of major LINE-1 amplification events during great ape evolution, and identify a Pan-specific LINE-1 subfamily.
Collapse
Affiliation(s)
- Lauren M Mathews
- Division of Molecular Medicine, Department of Medicine, Columbia University, New York, NY 10032, USA
| | | | | | | | | |
Collapse
|
7
|
von Sternberg R. On the roles of repetitive DNA elements in the context of a unified genomic-epigenetic system. Ann N Y Acad Sci 2002; 981:154-88. [PMID: 12547679 DOI: 10.1111/j.1749-6632.2002.tb04917.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Repetitive DNA sequences comprise a substantial portion of most eukaryotic and some prokaryotic chromosomes. Despite nearly forty years of research, the functions of various sequence families as a whole and their monomer units remain largely unknown. The inability to map specific functional roles onto many repetitive DNA elements (REs), coupled with the taxon-specificity of sequence families, have led many to speculate that these genomic components are "selfish" replicators generating genomic "junk." The purpose of this paper is to critically examine the selfishness, evolutionary effects, and functionality of REs. First, a brief overview of the range of ideas pertaining to RE function is presented. Second, the argument is presented that the selfish DNA "hypothesis" is actually a narrative scheme, that it serves to protect neo-Darwinian assumptions from criticism, and that this story is untestable and therefore not a hypothesis. Third, attempts to synthesize the selfish DNA concept with complex systems models of the genome and RE functionality are critiqued. Fourth, the supposed connection between RE-induced mutations and macroevolutionary events are stated to be at variance with empirical evidence and theoretical considerations. Hypotheses that base phylogenetic transitions in repetitive sequence changes thus remain speculative. Fifth and finally, the case is made for viewing REs as integrally functional components of chromosomes, genomes, and cells. It is argued throughout that a new conceptual framework is needed for understanding the roles of repetitive DNA in genomic/epigenetic systems, and that neo-Darwinian "narratives" have been the primary obstacle to elucidating the effects of these enigmatic components of chromosomes.
Collapse
Affiliation(s)
- Richard von Sternberg
- Department of Systematic Biology, NHB-163, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.
| |
Collapse
|
8
|
Furano AV. The biological properties and evolutionary dynamics of mammalian LINE-1 retrotransposons. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2000; 64:255-94. [PMID: 10697412 DOI: 10.1016/s0079-6603(00)64007-2] [Citation(s) in RCA: 145] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Mammalian LINE-1 (L1) elements belong to the superfamily of autonomously replicating retrotransposable elements that lack the long terminal repeated (LTR) sequences typical of retroviruses and retroviral-like retrotransposons. The non-LTR superfamily is very ancient and L1-like elements are ubiquitous in nature, having been found in plants, fungi, invertebrates, and various vertebrate classes from fish to mammals. L1 elements have been replicating and evolving in mammals for at least the past 100 million years and now constitute 20% or more of some mammalian genomes. Therefore, L1 elements presumably have had a profound, perhaps defining, effect on the evolution, structure, and function of mammalian genomes. L1 elements contain regulatory signals and encode two proteins: one is an RNA-binding protein and the second one presumably functions as an integrase-replicase, because it has both endonuclease and reverse transcriptase activities. This work reviews the structure and biological properties of L1 elements, including their regulation, replication, evolution, and interaction with their mammalian hosts. Although each of these processes is incompletely understood, what is known indicates that they represent challenging and fascinating biological phenomena, the resolution of which will be essential for fully understanding the biology of mammals.
Collapse
Affiliation(s)
- A V Furano
- Section on Genomic Structure and Function, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| |
Collapse
|
9
|
DeBerardinis RJ, Kazazian HH. Analysis of the promoter from an expanding mouse retrotransposon subfamily. Genomics 1999; 56:317-23. [PMID: 10087199 DOI: 10.1006/geno.1998.5729] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The mouse genome contains several subfamilies of the retrotransposon L1. One subfamily, TF, contains 4000-5000 full-length members and is expanding due to retrotransposition of a large number of active elements. Here we studied the TF 5' untranslated region (UTR), which contains promoter activity required for subfamily expression. Using reporter assays, we show that promoter activity is derived from TF-specific monomer sequences and is proportional to the number of monomers in the 5' UTR. These data suggest that nearly all full-length TF elements in the mouse genome are currently competent for expression. We aligned the sequences of 53 monomers to generate a consensus TF monomer and determined that most TF elements are truncated near a potential binding site for a transcription initiation factor. We also determined that much of the sequence variation among TF monomers results from transition mutations at CpG dinucleotides, suggesting that genomic TF 5' UTRs are methylated at CpGs.
Collapse
Affiliation(s)
- R J DeBerardinis
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | | |
Collapse
|