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Wichman HA, Scott L, Howell EK, Martinez AR, Yang L, Baker RJ. Flying Around in the Genome: Characterization of LINE-1 in Chiroptera. SPECIAL PUBLICATIONS (TEXAS TECH UNIVERSITY. MUSEUM) 2019; 71:379-392. [PMID: 32095030 PMCID: PMC7039574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
L1s are transposable elements that move by a copy-and-paste mechanism that continuously increases their copy number in the genome, such that each genome has a record of the L1 history in that host lineage. They make up about 20% of the genomes of eutherian mammals and have played a major role in shaping genome evolution. Chiroptera has the lowest average genome size among mammalian orders and the only documented case of L1 extinction affecting an entire mammalian family. Herein, L1 activity and extinction are characterized in all families of the order Chiroptera using a method that enriches for the youngest lineages of L1s in the genome. In addition to the previously reported L1 extinction in Pteropodidae, L1 extinction was documented to occur in Mormoops blainvilli, but this event did not affect all species of Mormoopidae. Further, there was no evidence of concordance between the evolution of L1s and their chiropteran host. There were two L1 lineages present before the divergence of all extant bats. Both lineages are extinct in the Pteropodidae. One or the other L1 lineage is extinct in almost all bat families, but Taphozous melanopogon maintains active members of both. Most intriguingly, some families within the Rhinolophoidea retain one active L1 lineage whereas other families retain the other, creating a deep discontinuity between L1 phylogeny and chiropteran phylogeny. These results indicate that there have been numerous losses of active L1 lineages over the history of chiropteran evolution, but that all chiropteran families except Pteropodidae have retained L1 activity.
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Affiliation(s)
- Holly A Wichman
- Center for Modeling Complex Interactions & Department of Biological Sciences, University of Idaho, MS 1122, Moscow, ID 83844 -3051 USA
| | - LuAnn Scott
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051 USA
| | - Eric K Howell
- ÅF AB, Frösundaleden 2A, 169 99, Solna, Stockholm, Sweden
| | - Armando R Martinez
- Environmental Compliance Division, City of Nampa, 340 W. Railroad St. Nampa, ID 83687 USA
| | - Lei Yang
- Pacific Northwest Research Institute, 720 Broadway, Seattle, WA 98122 USA
| | - Robert J Baker
- Department of Biological Sciences and the Museum, Texas Tech University, Lubbock, TX 79409-3131 USA
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Sookdeo A, Hepp CM, Boissinot S. Contrasted patterns of evolution of the LINE-1 retrotransposon in perissodactyls: the history of a LINE-1 extinction. Mob DNA 2018; 9:12. [PMID: 29610583 PMCID: PMC5872511 DOI: 10.1186/s13100-018-0117-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/22/2018] [Indexed: 12/30/2022] Open
Abstract
Background LINE-1 (L1) is the dominant autonomously replicating non-LTR retrotransposon in mammals. Although our knowledge of L1 evolution across the tree of life has considerably improved in recent years, what we know of L1 evolution in mammals is biased and comes mostly from studies in primates (mostly human) and rodents (mostly mouse). It is unclear if patterns of evolution that are shared between those two groups apply to other mammalian orders. Here we performed a detailed study on the evolution of L1 in perissodactyls by making use of the complete genome of the domestic horse and of the white rhinoceros. This mammalian order offers an excellent model to study the extinction of L1 since the rhinoceros is one of the few mammalian species to have lost active L1. Results We found that multiple L1 lineages, carrying different 5’UTRs, have been simultaneously active during the evolution of perissodactyls. We also found that L1 has continuously amplified and diversified in horse. In rhinoceros, L1 was very prolific early on. Two successful families were simultaneously active until ~20my ago but became extinct suddenly at exactly the same time. Conclusions The general pattern of L1 evolution in perissodactyls is very similar to what was previously described in mouse and human, suggesting some commonalities in the way mammalian genomes interact with L1. We confirmed the extinction of L1 in rhinoceros and we discuss several possible mechanisms. Electronic supplementary material The online version of this article (10.1186/s13100-018-0117-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Akash Sookdeo
- 1Department of Biology, New York University, New York, NY USA
| | - Crystal M Hepp
- 2School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ USA
| | - Stéphane Boissinot
- 3New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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Ivancevic AM, Kortschak RD, Bertozzi T, Adelson DL. LINEs between Species: Evolutionary Dynamics of LINE-1 Retrotransposons across the Eukaryotic Tree of Life. Genome Biol Evol 2016; 8:3301-3322. [PMID: 27702814 PMCID: PMC5203782 DOI: 10.1093/gbe/evw243] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
LINE-1 (L1) retrotransposons are dynamic elements. They have the potential to cause great genomic change because of their ability to ‘jump’ around the genome and amplify themselves, resulting in the duplication and rearrangement of regulatory DNA. Active L1, in particular, are often thought of as tightly constrained, homologous and ubiquitous elements with well-characterized domain organization. For the past 30 years, model organisms have been used to define L1s as 6–8 kb sequences containing a 5′-UTR, two open reading frames working harmoniously in cis, and a 3′-UTR with a polyA tail. In this study, we demonstrate the remarkable and overlooked diversity of L1s via a comprehensive phylogenetic analysis of elements from over 500 species from widely divergent branches of the tree of life. The rapid and recent growth of L1 elements in mammalian species is juxtaposed against the diverse lineages found in other metazoans and plants. In fact, some of these previously unexplored mammalian species (e.g. snub-nosed monkey, minke whale) exhibit L1 retrotranspositional ‘hyperactivity’ far surpassing that of human or mouse. In contrast, non-mammalian L1s have become so varied that the current classification system seems to inadequately capture their structural characteristics. Our findings illustrate how both long-term inherited evolutionary patterns and random bursts of activity in individual species can significantly alter genomes, highlighting the importance of L1 dynamics in eukaryotes.
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Affiliation(s)
- Atma M Ivancevic
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - R Daniel Kortschak
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Terry Bertozzi
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia
| | - David L Adelson
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
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Yang L, Brunsfeld J, Scott L, Wichman H. Reviving the dead: history and reactivation of an extinct l1. PLoS Genet 2014; 10:e1004395. [PMID: 24968166 PMCID: PMC4072516 DOI: 10.1371/journal.pgen.1004395] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 04/07/2014] [Indexed: 11/18/2022] Open
Abstract
Although L1 sequences are present in the genomes of all placental mammals and marsupials examined to date, their activity was lost in the megabat family, Pteropodidae, ∼24 million years ago. To examine the characteristics of L1s prior to their extinction, we analyzed the evolutionary history of L1s in the genome of a megabat, Pteropus vampyrus, and found a pattern of periodic L1 expansion and quiescence. In contrast to the well-characterized L1s in human and mouse, megabat genomes have accommodated two or more simultaneously active L1 families throughout their evolutionary history, and major peaks of L1 deposition into the genome always involved multiple families. We compared the consensus sequences of the two major megabat L1 families at the time of their extinction to consensus L1s of a variety of mammalian species. Megabat L1s are comparable to the other mammalian L1s in terms of adenosine content and conserved amino acids in the open reading frames (ORFs). However, the intergenic region (IGR) of the reconstructed element from the more active family is dramatically longer than the IGR of well-characterized human and mouse L1s. We synthesized the reconstructed element from this L1 family and tested the ability of its components to support retrotransposition in a tissue culture assay. Both ORFs are capable of supporting retrotransposition, while the IGR is inhibitory to retrotransposition, especially when combined with either of the reconstructed ORFs. We dissected the inhibitory effect of the IGR by testing truncated and shuffled versions and found that length is a key factor, but not the only one affecting inhibition of retrotransposition. Although the IGR is inhibitory to retrotransposition, this inhibition does not account for the extinction of L1s in megabats. Overall, the evolution of the L1 sequence or the quiescence of L1 is unlikely the reason of L1 extinction.
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Affiliation(s)
- Lei Yang
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
| | - John Brunsfeld
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - LuAnn Scott
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Holly Wichman
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America
- * E-mail:
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Sookdeo A, Hepp CM, McClure MA, Boissinot S. Revisiting the evolution of mouse LINE-1 in the genomic era. Mob DNA 2013; 4:3. [PMID: 23286374 PMCID: PMC3600994 DOI: 10.1186/1759-8753-4-3] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 10/25/2012] [Indexed: 11/10/2022] Open
Abstract
Background LINE-1 (L1) is the dominant category of transposable elements in placental mammals. L1 has significantly affected the size and structure of all mammalian genomes and understanding the nature of the interactions between L1 and its mammalian host remains a question of crucial importance in comparative genomics. For this reason, much attention has been dedicated to the evolution of L1. Among the most studied elements is the mouse L1 which has been the subject of a number of studies in the 1980s and 1990s. These seminal studies, performed in the pre-genomic era when only a limited number of L1 sequences were available, have significantly improved our understanding of L1 evolution. Yet, no comprehensive study on the evolution of L1 in mouse has been performed since the completion of this genome sequence. Results Using the Genome Parsing Suite we performed the first evolutionary analysis of mouse L1 over the entire length of the element. This analysis indicates that the mouse L1 has recruited novel 5’UTR sequences more frequently than previously thought and that the simultaneous activity of non-homologous promoters seems to be one of the conditions for the co-existence of multiple L1 families or lineages. In addition the exchange of genetic information between L1 families is not limited to the 5’UTR as evidence of inter-family recombination was observed in ORF1, ORF2, and the 3’UTR. In contrast to the human L1, there was little evidence of rapid amino-acid replacement in the coiled-coil of ORF1, although this region is structurally unstable. We propose that the structural instability of the coiled-coil domain might be adaptive and that structural changes in this region are selectively equivalent to the rapid evolution at the amino-acid level reported in the human lineage. Conclusions The pattern of evolution of L1 in mouse shows some similarity with human suggesting that the nature of the interactions between L1 and its host might be similar in these two species. Yet, some notable differences, particularly in the evolution of ORF1, suggest that the molecular mechanisms involved in host-L1 interactions might be different in these two species.
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Affiliation(s)
- Akash Sookdeo
- Department of Biology, Queens College, the City University of New York, 65-30 Kissena Boulevard, Flushing, NY 11367-1597, USA.
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Platt II RN, Ray DA. A non-LTR retroelement extinction in Spermophilus tridecemlineatus. Gene 2012; 500:47-53. [DOI: 10.1016/j.gene.2012.03.051] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/08/2012] [Accepted: 03/09/2012] [Indexed: 10/28/2022]
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Cantrell MA, Carstens BC, Wichman HA. X chromosome inactivation and Xist evolution in a rodent lacking LINE-1 activity. PLoS One 2009; 4:e6252. [PMID: 19603076 PMCID: PMC2705805 DOI: 10.1371/journal.pone.0006252] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Accepted: 05/28/2009] [Indexed: 02/05/2023] Open
Abstract
Dosage compensation in eutherian mammals occurs by inactivation of one X chromosome in females. Silencing of that X chromosome is initiated by Xist, a large non-coding RNA, whose coating of the chromosome extends in cis from the X inactivation center. LINE-1 (L1) retrotransposons have been implicated as possible players for propagation of the Xist signal, but it has remained unclear whether they are essential components. We previously identified a group of South American rodents in which L1 retrotransposition ceased over 8 million years ago and have now determined that at least one species of these rodents, Oryzomys palustris, still retains X inactivation. We have also isolated and analyzed the majority of the Xist RNA from O. palustris and a sister species retaining L1 activity, Sigmodon hispidus, to determine if evolution in these sequences has left signatures that might suggest a critical role for L1 elements in Xist function. Comparison of rates of Xist evolution in the two species fails to support L1 involvement, although other explanations are possible. Similarly, comparison of known repeats and potential RNA secondary structures reveals no major differences with the exception of a new repeat in O. palustris that has potential to form new secondary structures.
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Affiliation(s)
- Michael A. Cantrell
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Bryan C. Carstens
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Holly A. Wichman
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
- * E-mail:
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Cantrell MA, Scott L, Brown CJ, Martinez AR, Wichman HA. Loss of LINE-1 activity in the megabats. Genetics 2008; 178:393-404. [PMID: 18202382 PMCID: PMC2206088 DOI: 10.1534/genetics.107.080275] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Accepted: 11/02/2007] [Indexed: 11/18/2022] Open
Abstract
LINE-1 (L1) retrotransposons are the most abundant type of mammalian retroelement. They have profound effects on genome plasticity and have been proposed to fulfill essential host functions, yet it remains unclear where they lie on the spectrum from parasitism to mutualism. Their ubiquity makes it difficult to determine the extent of their effects on genome evolution and gene expression because of the relative dearth of animal models lacking L1 activity. We have isolated L1 sequences from 11 megabat species by a method that enriches for recently inserted L1s and have done a bioinformatic examination of L1 sequences from a 12th species whose genome was recently shotgun sequenced. An L1 extinction event appears to have occurred at least 24 million years ago (MYA) in an ancestor of the megabats. The ancestor was unusual in having maintained two highly divergent long-term L1 lineages with different levels of activity, which appear, on an evolutionary scale, to have simultaneously lost that activity. These megabat species can serve as new animal models to ask what effect loss of L1 activity has on mammalian genome evolution and gene expression.
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Affiliation(s)
- Michael A Cantrell
- Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844-3051, USA
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9
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Scott LA, Kuroiwa A, Matsuda Y, Wichman HA. X accumulation of LINE-1 retrotransposons in Tokudaia osimensis, a spiny rat with the karyotype XO. Cytogenet Genome Res 2006; 112:261-9. [PMID: 16484782 DOI: 10.1159/000089880] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2005] [Accepted: 07/25/2005] [Indexed: 01/02/2023] Open
Abstract
The observation that LINE-1 transposable elements are enriched on the X in comparison to the autosomes led to the hypothesis that LINE-1s play a role in X chromosome inactivation. If this hypothesis is correct, loss of LINE-1 activity would be expected to result in species extinction or in an alternate pathway of dosage compensation. One such alternative pathway would be to evolve a karyotype that does not require dosage compensation between the sexes. Two of the three extant species of the Ryukyu spiny rat Tokudaia have such a karyotype; both males and females are XO. We asked whether this karyotype arose due to loss of LINE-1 activity and thus the loss of a putative component in the X inactivation pathway. Although XO Tokudaia has no need for dosage compensation, LINE-1s have been recently active in Tokudaia osimensis and show higher density on the lone X than on the autosomes.
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Affiliation(s)
- L A Scott
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051, USA
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Grahn RA, Rinehart TA, Cantrell MA, Wichman HA. Extinction of LINE-1 activity coincident with a major mammalian radiation in rodents. Cytogenet Genome Res 2005; 110:407-15. [PMID: 16093693 DOI: 10.1159/000084973] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2004] [Accepted: 04/07/2004] [Indexed: 11/19/2022] Open
Abstract
LINE-1 transposable elements (L1s) are ubiquitous in mammals and are thought to have remained active since before the mammalian radiation. Only one L1 extinction event, in South American rodents in the genus Oryzomys, has been convincingly demonstrated. Here we examine the phylogenetic limits and evolutionary tempo of that extinction event by characterizing L1s in related rodents. Fourteen genera from five tribes within the Sigmodontinae subfamily were examined. Only the Sigmodontini, the most basal tribe in this group, demonstrate recent L1 activity. The Oryzomyini, Akodontini, Phyllotini, and Thomasomyini contain only L1s that appear to have inserted long ago; their L1s lack open reading frames, have mutations at conserved amino acid residues, and show numerous private mutations. They also lack restriction site-defined L1 subfamilies specific to any species, genus or tribe examined, and fail to form monophyletic species, genus or tribal L1 clusters. We determine here that this L1 extinction event occurred roughly 8.8 million years ago, near the divergence of Sigmodon from the remaining Sigmodontinae species. These species appear to be ideal model organisms for studying the impact of L1 inactivity on mammalian genomes.
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Affiliation(s)
- R A Grahn
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051, USA
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Papusheva E, Gruhl MC, Berezikov E, Groudieva T, Scherbik SV, Martin J, Blinov A, Bergtrom G. The Evolution of SINEs and LINEs in the genus Chironomus (Diptera). J Mol Evol 2004; 58:269-79. [PMID: 15045482 DOI: 10.1007/s00239-003-2549-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2002] [Accepted: 08/15/2003] [Indexed: 11/25/2022]
Abstract
Genomic DNA amplification from 51 species of the family Chironomidae shows that most contain relatives of NLRCth1 LINE and CTRT1 SINE retrotransposons first found in Chironomus thummi. More than 300 cloned PCR products were sequenced. The amplified region of the reverse transcriptase gene in the LINEs is intact and highly conserved, suggesting active elements. The SINEs are less conserved, consistent with minimal/no selection after transposition. A mitochondrial gene phylogeny resolves the Chironomus genus into six lineages (Guryev et al. 2001). LINE and SINE phylogenies resolve five of these lineages, indicating their monophyletic origin and vertical inheritance. However, both the LINE and the SINE tree topologies differ from the species phylogeny, resolving the elements into "clusters I-IV" and "cluster V" families. The data suggest a descent of all LINE and SINE subfamilies from two major families. Based on the species phylogeny, a few LINEs and a larger number of SINEs are cladisitically misplaced. Most misbranch with LINEs or SINEs from species with the same families of elements. From sequence comparisons, cladistically misplaced LINEs and several misplaced SINEs arose by convergent base substitutions. More diverged SINEs result from early transposition and some are derived from multiple source SINEs in the same species. SINEs from two species (C. dorsalis, C. pallidivittatus), expected to belong to the clusters I-IV family, branch instead with cluster V family SINEs; apparently both families predate separation of cluster V from clusters I-IV species. Correlation of the distribution of active SINEs and LINEs, as well as similar 3' sequence motifs in CTRT1 and NLRCth1, suggests coevolving retrotransposon pairs in which CTRT1 transposition depends on enzymes active during NLRCth1 LINE mobility.
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Abstract
Recently, a rapidly amplifying family of mouse LINE-1 (L1) has been identified and named T(F). The evolutionary context surrounding the derivation of the T(F) family was examined through phylogenetic analysis of sequences in the 3' portion of the repeat. The Mus musculus domesticus T(F) family was found to be the terminal subfamily of the previously identified L1Md4 lineage. The L1Md4 lineage joins the other prototypical mouse LINE-1 lineage (the L1MdA2 lineage) approximately 1 MYA at about the time of the common ancestor of M. m. domesticus, Mus spicilegus, and Mus spretus. However, the T(F) family from M. m. domesticus was found to join to the previously reported M. spretus Ms475 and Ms7024 LINE-1 families at just 0.5 MYA, indicating horizontal transfer. The T(F) family from M. m. domesticus was then found to be even more recently related to LINE-1's from another species, M. spicilegus. A separate spretus A2 lineage was found through a directed search of a PCR library. This lineage, in contrast to the spretus T(F) lineage, does join domesticus at about 1 MYA, as would be expected in the absence of horizontal transfer. A third major family was also found that splits off from the L1Md4 lineage shortly after its departure from the L1MdA2 lineage. The new family, named the Z family, was found to contain the de novo LINE-1 inserts causing the beige and med mutations. Whether the split with the Z family was before or after the recombination that introduced the F-type promoters and defined the inception of T(F) as a lineage is unclear. In enumerating copies of the various LINE-1 families, we found that T(F) 3' ends were not much more numerous than the reported number of 5' ends, suggesting that T(F) may not be subjected to the 90% truncation pattern typical of LINE-1 as a whole.
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Affiliation(s)
- S C Hardies
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, USA.
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Casavant NC, Scott L, Cantrell MA, Wiggins LE, Baker RJ, Wichman HA. The end of the LINE?: lack of recent L1 activity in a group of South American rodents. Genetics 2000; 154:1809-17. [PMID: 10747071 PMCID: PMC1461046 DOI: 10.1093/genetics/154.4.1809] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
L1s (LINE-1: Long Interspersed Nuclear Element 1) are present in all mammals examined to date. They occur in both placental mammals and marsupials and thus are thought to have been present in the genome prior to the mammalian radiation. This unusual conservation of a transposable element family for over 100 million years has led to speculation that these elements provide an advantage to the genomes they inhabit. We have recently identified a group of South American rodents, including rice rats (Oryzomys), in which L1s appear to be quiescent or extinct. Several observations support this conclusion. First, genomic Southern blot analysis fails to reveal genus-specific bands in Oryzomys. Second, we were unable to find recently inserted elements. Procedures to enrich for young elements did not yield any with an intact open reading frame for reverse transcriptase; all elements isolated had numerous insertions, deletions, and stop codons. Phylogenetic analysis failed to yield species-specific clusters among the L1 elements isolated, and all Oryzomys sequences had numerous private mutations. Finally, in situ hybridization of L1 to Oryzomys chromosomes failed to reveal the characteristic L1 distribution in Oryzomys with either a homologous or heterologous probe. Thus, Oryzomys is a viable candidate for L1 extinction from a mammalian host.
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Affiliation(s)
- N C Casavant
- Department of Biological Sciences, University of Idaho, Moscow 83844, USA
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