Impact of transposable elements on the evolution of mammalian gene regulation

@article{Medstrand2005ImpactOT,
  title={Impact of transposable elements on the evolution of mammalian gene regulation},
  author={Patrik Medstrand and Louie N. van de Lagemaat and Catherine A Dunn and Josette Ren{\'e}e Landry and Daniel Svenback and Dixie L. Mager},
  journal={Cytogenetic and Genome Research},
  year={2005},
  volume={110},
  pages={342 - 352}
}
Transposable elements (TEs) are present in all organisms and nearly half of the human and mouse genome is derived from ancient transpositions. This fact alone suggests that TEs have played a major role in genome organization and evolution. Studies undertaken over the last two decades or so clearly show that TEs of various kinds have played an important role in organism evolution. Here we review the impact TEs have on the evolution of gene regulation and gene function with an emphasis on humans… 

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References

SHOWING 1-10 OF 168 REFERENCES

Transposable elements and the evolution of eukaryotic complexity.

A number of specific scenarios are presented that implicate transposable elements in the evolution of the complex molecular and cellular machinery that are characteristic of the eukaryotic domain of life.

Retrotransposons and the evolution of mammalian gene expression

Two recently elucidated examples suggest transposable elements may have a significant impact in evolution of gene expression, and one shows that within the human amylase gene family, salivary specific expression has arisen due to inserted sequences, deriving perhaps from a conjunction of two retrotransposability elements.

Transposable elements are found in a large number of human protein-coding genes.

Cases of ancient mobile element DNA insertions that now affect gene regulation.

  • R. Britten
  • Biology
    Molecular phylogenetics and evolution
  • 1996
In many eukaryotes, segments of repetitive DNA (mobile elements) that have been inserted in the past in regions of many eUKaryote genes have been preserved by selection and now affect the transcriptional control of these specific genes.

PERSPECTIVE: TRANSPOSABLE ELEMENTS, PARASITIC DNA, AND GENOME EVOLUTION

It is argued that easy popular appellations such as “selfish DNA’ and “junk DNA” may be either inaccurate or misleading and that a more enlightened view of the transposable element-host relationship encompasses a continuum from extreme parasitism to mutualism.

Transposable elements as sources of variation in animals and plants.

  • M. G. KidwellD. Lisch
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1997
Here, TE-induced variation is viewed from three evolutionary perspectives that are not mutually exclusive and possible coadaptations between elements and their hosts that appear to have evolved to reduce the deleterious effects of new insertions on host fitness are described.

The role of selfish genetic elements in eukaryotic evolution

Diverse elements of eukaryotes, such as transposons, homing endonucleases, meiotic drive chromosomes and heritable microorganisms, are discussed and their potential importance in the evolution of genetic systems, adaptation, and the extinction and birth of species is discussed.

Interspersed repeats and other mementos of transposable elements in mammalian genomes.

  • A. Smit
  • Biology
    Current opinion in genetics & development
  • 1999
...