Analysis of Orthologous Retrovirus-Like Elements in the White-Footed Mouse, Peromyscus leucopus

Sawby, Ryan; Wichman, Holly A.

doi:10.1007/pl00006123

Cited by 9 publications

(8 citation statements)

References 32 publications

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“…If a mutation occurs in one of the LTRs, the 5' and 3' LTRs will no longer be identical. Over evolutionary time, as the 5' and 3' LTRs within a single element gradually diverge, the degree of sequence diver-gence between them can provide an estimate of the time that has elapsed since the element inserted (Jordan & McDonald 1998, 1999bSan Miguel et al 1998;Sawby & Wichman 1997;Stavenhagen & Robins 1988;Voytas & Boeke 1992). Third, an element can be excised from the genome owing to recombination between its 5' and 3' LTRs.…”

Section: Introductionmentioning

confidence: 99%

“…Previous studies have attempted to estimate the rates of Ty element transposition and excision in the laboratory (Curcio & Gar¢nkel 1991;Winston et al 1984). Furthermore, previous studies of LTRs have used sequence divergence within elements to estimate the age of elements in the genome (Jordan & McDonald 1998, 1999bSanMiguel et al 1998;Sawby & Wichman 1997;Stavenhagen & Robins 1988;Voytas & Boeke 1992). However, until now it has not been possible to determine the e¡ective rates at which these processes of transposition and excision have operated in nature over evolutionary time.…”

Section: Introductionmentioning

confidence: 99%

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Genomic demography: a life-history analysis of transposable element evolution

Promislow

Jordan

McDonald

1999

Proc. R. Soc. Lond. B

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Retrotransposons are ubiquitous mobile genetic elements that have played a signi¢cant role in shaping eukaryotic genome evolution. The genome of the yeast Saccharomyces cerevisiae harbours ¢ve families of retrotransposons, Ty1^Ty5. With the publication of the S. cerevisiae genome sequence, for the ¢rst time a full genomic complement of retrotransposon sequences is available. Analysis of these sequences promises to yield insight into the nature of host^transposon coevolution. Evolutionary change in Ty elements depends on their replication and excision rates, which have been determined in the laboratory. Rates measured in the laboratory may di¡er from those that have operated over evolutionary time. Based on an analysis of sequence data for the Ty1, Ty2 and hybrid Ty1/2 families, we develop a novel`genomic demography' model to estimate long-term transposition and excision rates and to estimate how long ago these elements entered the yeast genome. We ¢nd that rates of excision and transposition have averaged 7.2^8.7 Â10 À8 per generation over evolutionary time. Two separate models provide upper-and lowerbound estimates for the age of the system, suggesting that the ¢rst elements entered the genome between approximately 50 million and 250 million generations ago.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genomic demography: a life-history analysis of transposable element evolution

Promislow

Jordan

McDonald

1999

Proc. R. Soc. Lond. B

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“…Thus, any change between LTR of a single element will have occurred after the insertion of the element. On this basis, Sawby and Wichman (1997) showed that the time elapsed since individual elements transposed can be estimated from the nucleotide differences between the 5) and the 3) LTR of a retrotransposon. The average percent identity between the 5) and 3) LTRs of individual Ty1 and Ty2 elements is greater than 99 % for both families, whereas the percent identity among all LTRs of either group is significantly lower (around 91 and 97 % for Ty1 and Ty2 LTRs, respectively), suggesting that Ty1 and Ty2 have probably retrotransposed recently (Jordan and McDonald, 1998).…”

Section: Ty Retrotransposons Diversity and Evolutionmentioning

confidence: 99%

Happy together: the life and times of Ty retrotransposons and their hosts

Lesage¹,

Todeschini²

2005

Cytogenet Genome Res

116

125

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The aim of this review is to describe the level of intimacy between Ty retrotransposons (Ty1–Ty5) and their host the yeast Saccharomyces cerevisiae. The effects of Ty location in the genome and of host proteins on the expression and mobility of Ty elements are highlighted. After a brief overview of Ty diversity and evolution, we describe the factors that dictate Ty target-site preference and the impact of targeting on Ty and adjacent gene expression. Studies on Ty3 and Ty5 have been especially informative in unraveling the role of host factors (Pol III machinery and silencing proteins, respectively) and integrase in controlling the specificity of integration. In contrast, not much is known regarding Ty1, Ty2 and Ty4, except that their insertion depends on the transcriptional competence of the adjacent Pol III gene and might be influenced by some chromatin components. This review also brings together recent findings on the regulation of Ty1 retrotransposition. A large number of host proteins (over 30) involved in a wide range of cellular processes controls either directly or indirectly Ty1 mobility, primarily at post-transcriptional steps. We focus on several genes for which more detailed analyses have permitted the elaboration of regulatory models. In addition, this review describes new data revealing that repression of Ty1 mobility also involves two forms of copy number control that act at both the trancriptional and post-transcriptional levels. Since S. cerevisiae lacks the conserved pathways for copy number control via transcriptional and post-transcriptional gene silencing found in other eukaryotes, Ty1 copy number control must be via another mechanism whose features are outlined. Ty1 response to stress also implicates activation at both transcriptional and postranscriptional steps of Ty1. Finally, we provide several insights in the role of Ty elements in chromosome evolution and yeast adaptation and discuss the factors that might limit Ty ectopic recombination.

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“…Additionally, evidence for recent activity of mys elements has been illustrated in the genus Peromyscus (Lee et al 1996;Sawby and Wichman 1997), and seemingly to be highly active in the lineage leading to the P. maniculatus/P. leucopus clade based on the rapid generation of different subfamilies (Lee et al 1996) with continued activity supported by the presence or absence of elements in orthologous loci of individual P. leucopus mice (Sawby and Wichman 1997). We therefore investigated mys elements in more detail, which yielded several surprising results.…”

Section: Discussionmentioning

confidence: 98%

“…The overarching objective of this investigation was to further explore the origins, expansion, and evolution of the novel mys family and potential subfamilies of LTR-retroelements of the understudied Cricetidae family of rodents (Wichman et al 1985), as the P. leucopus mys-1 element has been the only isolated full-length member with two nearly intact ORFs. Additionally, evidence for recent activity of mys elements has been illustrated in the genus Peromyscus (Lee et al 1996;Sawby and Wichman 1997), and seemingly to be highly active in the lineage leading to the P. maniculatus/P. leucopus clade based on the rapid generation of different subfamilies (Lee et al 1996) with continued activity supported by the presence or absence of elements in orthologous loci of individual P. leucopus mice (Sawby and Wichman 1997).…”

Section: Discussionmentioning

confidence: 99%

The discovery of multiple active mys-related LTR-retroelements within the Neotominae subfamily of cricetid rodents

Kass

Beatty

Smith

et al. 2022

Preprint

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Retrotransposon families in the rodent family Cricetidae have been understudied in contrast to Muridae, both taxa classified within the superfamily Muroidea. Therefore, we pursued advancing our knowledge of the unique mys-1 LTR-retroelement identified in Peromyscus leucopus by utilizing intra-ORF PCR, quantitative dot bots, DNA and protein library screens, the generation of molecular phylogenies, and analyses of orthologous LTR-retroelement loci. This led to the discovery of three additional related families of LTR-retroelements. These include a 2900 bp full-length element of mys-related sequences (mysRS), an 8,000 bp element containing the mys ORF1 sequence (mORF1) with ERV-related sequences downstream in the reverse orientation, as well as an 1800 bp element primarily consisting of mys ORF2 (mORF2) related sequences flanked by LTRs. Our data revealed a very limited number of full-length mys elements among genera of the Neotominae subfamily of cricetid rodents. Additionally, although we estimated roughly 5,000–10,000 genomic copies of the mysRS element among Neotominae, most exist as partial copies. The mORF1 elements are also limited to the genomes of the Neotominae subfamily of cricetid rodents, whereas mORF2 appears limited to the Peromyscus genus. Molecular phylogenies demonstrating concerted evolution, along with an assessment of orthologous loci in Peromyscus for the presence or absence of elements, are consistent with recent activity of these novel LTR-retroelement families. Together with known activity of various families of non-LTR retroelements in Peromyscus species, we propose that retrotransposons have been continually contributing to the dynamics of Peromyscus genomes and are plausibly associated with the evolution of the over 50 identified species.

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Analysis of Orthologous Retrovirus-Like Elements in the White-Footed Mouse, Peromyscus leucopus

Cited by 9 publications

References 32 publications

Genomic demography: a life-history analysis of transposable element evolution

Genomic demography: a life-history analysis of transposable element evolution

Happy together: the life and times of Ty retrotransposons and their hosts

The discovery of multiple active mys-related LTR-retroelements within the Neotominae subfamily of cricetid rodents

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