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  • 1
    Electronic Resource
    Electronic Resource
    Ethical Issues in the Genetic Study of Deafness (1991)
    Oxford, UK : Blackwell Publishing Ltd
    Annals of the New York Academy of Sciences 630 (1991), S. 0 
    Details
    ISSN: 1749-6632
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Natural Sciences in General
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1749-6632.1991.tb19593.x
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  • 2
    Electronic Resource
    Electronic Resource
    Evidence for the Role of Recombination in the Regulatory Evolution of Saccharomyces cerevisiae Ty Elements (1998)
    Springer
    Journal of molecular evolution 47 (1998), S. 14-20 
    Details
    ISSN: 1432-1432
    Keywords: Key words:Saccharomyces cerevisiae— Ty — Retrotransposons — Regulatory evolution — Recombination
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. The recent completion of the sequencing of the Saccharomyces cerevisiae genome provides a unique opportunity to analyze the evolutionary relationships existing among the entire complement of retrotransposons residing within a single genome. In this article we report the results of such an analysis of two closely related families of yeast long terminal repeat (LTR) retrotransposons, Ty1 and Ty2. In our study, we analyzed the molecular variation existing among the 32 Ty1 and 13 Ty2 elements present within the S. cerevisiae genome recently sequenced within the context of the yeast genome project. Our results indicate that while the Ty1 family is most likely ancestral to Ty2 elements, both families of elements are relatively recent components of the S. cerevisiae genome. Our results also indicate that both families of elements have been subject to purifying selection within their protein coding regions. Finally, and perhaps most interestingly, our results indicate that a relatively recent recombination event has occurred between Ty2 and a subclass of Ty1 elements involving the LTR regulatory region. We discuss the possible biological significance of these findings and, in particular, how they contribute to a better overall understanding of LTR retrotransposon evolution.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006358
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  • 3
    Electronic Resource
    Electronic Resource
    The Role of Interelement Selection in Saccharomyces cerevisiae Ty Element Evolution (1999)
    Springer
    Journal of molecular evolution 49 (1999), S. 352-357 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Interelement selection —Saccharomyces cerevisiae— Ty elements — Retrotransposons
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Retrotransposons are mobile genetic elements that are ubiquitous components of eukaryotic genomes. The evolutionary success of retrotransposons is explained by their ability to replicate faster than the host genomes in which they reside. Elements with higher rates of genomic replication possess a selective advantage over less active elements. Retrotransposon populations, therefore, are shaped largely by selective forces acting at the genomic level between elements. To evaluate rigorously the effects of selective forces acting on retrotransposons, detailed information on the patterns of molecular variation within and between retrotransposon families is needed. The sequencing of the Saccharomyces cerevisiae genome, which includes the entire genomic complement of yeast retrotransposons, provides an unprecedented opportunity to access and analyze such data. In this study, we analyzed in detail the patterns of nucleotide variation within the open reading frames of two parental (Ty1 and Ty2) and one hybrid (Ty1/2) family of yeast retrotransposons. The pattern and distribution of nucleotide changes on the phylogenetic reconstructions of the three families of Ty elements reveal evidence of negative selection on both internal and external branches of the Ty phylogenies. These results indicate that most, if not all, Ty elements examined represent active or recently active retrotransposon lineages. We discuss the relevance of these findings with respect to the coevolutionary dynamic operating between genomic element populations and the host organisms in which they reside.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006558
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  • 4
    Electronic Resource
    Electronic Resource
    Interelement Selection in the Regulatory Region of the copia Retrotransposon (1998)
    Springer
    Journal of molecular evolution 47 (1998), S. 670-676 
    Details
    ISSN: 1432-1432
    Keywords: Key words:Drosophila—copia— Retrotransposons — Regulatory evolution — Selection
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. We report the results of an analysis of naturally occurring cis-regulatory variation within and between two families of the copia Drosophila long terminal repeat (LTR) retrotransposon. The copia 5′ LTR and adjacent untranslated leader region (ULR) consists of a number of well-characterized sequence motifs which play a role in regulating expression of the element. In order to understand the evolutionary forces which may be responsible for generating and maintaining copia regulatory sequence variation, we have quantified levels of naturally occurring copia LTR-ULR nucleotide variation and subjected the data to a series of tests of neutrality. Our analysis indicates that the copia LTR-ULR has been subject to negative purifying selection within families and positive adaptive selection between families. We discuss these findings with respect to the regulatory evolution of retrotransposons and the phenomenon of interelement selection.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006425
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  • 5
    Electronic Resource
    Electronic Resource
    A universal trend of amino acid gain and loss in protein evolution (2005)
    [s.l.] : Macmillian Magazines Ltd.
    Nature 433 (2005), S. 633-638 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Amino acid composition of proteins varies substantially between taxa and, thus, can evolve. For example, proteins from organisms with (G + C)-rich (or (A + T)-rich) genomes contain more (or fewer) amino acids encoded by (G + C)-rich codons. However, no universal trends in ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nature03306
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  • 6
    Electronic Resource
    Electronic Resource
    Comparative genomics and evolutionary dynamics of Saccharomyces cerevisiae Ty elements (1999)
    Springer
    Genetica 107 (1999), S. 3-13 
    Details
    ISSN: 1573-6857
    Keywords: genomics ; molecular evolution ; retrotransposons ; selection ; Ty elements
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The availability of the complete genome sequence of cerevisiae provides the unique opportunity to study an entire genomic complement of retrotransposons from an evolutionary perspective. There are five families of yeast retrotransposons, Ty1-Ty5. We have conducted a series of comparative sequence analyses within and among S. cerevisiae Ty families in an effort to document the evolutionary forces that have shaped element variation. Our results indicate that within families Ty elements vary little in terms of both size and sequence. Furthermore, intra-element 5′–3′long terminal repeat (LTR) sequence comparisons indicate that almost all Ty elements in the genome have recently transposed. For each family, solo LTR sequences generated by intra-element recombination far outnumber full length insertions. Taken together, these results suggest a rapid genomic turnover of S. cerevisiae Ty elements. The closely related Ty1 and Ty2 are the most numerous elements in the genome. Phylogenetic analysis of full length insertions reveals that reverse transcriptase mediated recombination between Ty1 and Ty2 elements has generated a number of hybrid Ty1/2 elements. These hybrid Ty1/2 elements have similar genomic structures with chimeric LTRs and chimeric TYB (pol) genes. Analysis of the levels of nonsynonymous (Ka) and synonymous (Ks) nucleotide variation indicates that Ty1 and Ty2 coding regions have been subject to strong negative (purifying) selection. Distribution of Ka and Ks on Ty1, Ty2 and Ty1/2 phylogenies reveals evidence of negative selection on both internal and external branches. This pattern of variation suggests that the majority of full length Ty1, Ty2 and Ty1/2 insertions represent active or recently active element lineages and is consistent with a high level of genomic turnover. The evolutionary dynamics of S. cerevisae Ty elements uncovered by our analyses are discussed with respect to selection among elements and the interaction between the elements and their host genome.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1004022704701
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  • 7
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    MIR retrotransposon sequences provide insulators to the human genome (2015)
    National Academy of Sciences
    Details
    Publication Date: 2015-07-27
    Description: Insulators are regulatory elements that help to organize eukaryotic chromatin via enhancer-blocking and chromatin barrier activity. Although there are several examples of transposable element (TE)-derived insulators, the contribution of TEs to human insulators has not been systematically explored. Mammalian-wide interspersed repeats (MIRs) are a conserved family of TEs that have substantial regulatory capacity and share sequence characteristics with tRNA-related insulators. We sought to evaluate whether MIRs can serve as insulators in the human genome. We applied a bioinformatic screen using genome sequence and functional genomic data from CD4+ T cells to identify a set of 1,178 predicted MIR insulators genome-wide. These predicted MIR insulators were computationally tested to serve as chromatin barriers and regulators of gene expression in CD4+ T cells. The activity of predicted MIR insulators was experimentally validated using in vitro and in vivo enhancer-blocking assays. MIR insulators are enriched around genes of the T-cell receptor pathway and reside at T-cell–specific boundaries of repressive and active chromatin. A total of 58% of the MIR insulators predicted here show evidence of T-cell–specific chromatin barrier and gene regulatory activity. MIR insulators appear to be CCCTC-binding factor (CTCF) independent and show a distinct local chromatin environment with marked peaks for RNA Pol III and a number of histone modifications, suggesting that MIR insulators recruit transcriptional complexes and chromatin modifying enzymes in situ to help establish chromatin and regulatory domains in the human genome. The provisioning of insulators by MIRs across the human genome suggests a specific mechanism by which TE sequences can be used to modulate gene regulatory networks.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 8
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    Human cis natural antisense transcripts initiated by transposable elements (2008)
    Cell Press
    Details
    Publication Date: 2008-02-01
    Print ISSN: 0168-9525
    Electronic ISSN: 1362-4555
    Topics: Biology
    Published by Cell Press
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  • 9
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    Effect of the Transposable Element Environment of Human Genes on Gene Length and Expression (2011)
    Oxford University Press
    Details
    Publication Date: 2011-01-01
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    The Phenotypic Consequences of Genetic Divergence between Admixed Latin American Populations: Antioquia and Chocó, Colombia (2020)
    Oxford University Press
    Details
    Publication Date: 2020-07-18
    Description: Genome-wide association studies have uncovered thousands of genetic variants that are associated with a wide variety of human traits. Knowledge of how trait-associated variants are distributed within and between populations can provide insight into the genetic basis of group-specific phenotypic differences, particularly for health-related traits. We analyzed the genetic divergence levels for 1) individual trait-associated variants and 2) collections of variants that function together to encode polygenic traits, between two neighboring populations in Colombia that have distinct demographic profiles: Antioquia (Mestizo) and Chocó (Afro-Colombian). Genetic ancestry analysis showed 62% European, 32% Native American, and 6% African ancestry for Antioquia compared with 76% African, 10% European, and 14% Native American ancestry for Chocó, consistent with demography and previous results. Ancestry differences can confound cross-population comparison of polygenic risk scores (PRS); however, we did not find any systematic bias in PRS distributions for the two populations studied here, and population-specific differences in PRS were, for the most part, small and symmetrically distributed around zero. Both genetic differentiation at individual trait-associated single nucleotide polymorphisms and population-specific PRS differences between Antioquia and Chocó largely reflected anthropometric phenotypic differences that can be readily observed between the populations along with reported disease prevalence differences. Cases where population-specific differences in genetic risk did not align with observed trait (disease) prevalence point to the importance of environmental contributions to phenotypic variance, for both infectious and complex, common disease. The results reported here are distributed via a web-based platform for searching trait-associated variants and PRS divergence levels at http://map.chocogen.com (last accessed August 12, 2020).
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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