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A novel web-based TinT application and the chronology of the Primate Alu retroposon activity

Gennady Churakov1*, Norbert Grundmann2, Andrej Kuritzin3, Jürgen Brosius1, Wojciech Makałowski2 and Jürgen Schmitz1

Author Affiliations

1 Institute of Experimental Pathology, ZMBE, University of Münster, Von-Esmarch-Str. 56, 48149 Münster, Germany

2 Institute of Bioinformatics, Faculty of Medicine, University of Münster, Niels Stensen Str. 14, 48149 Münster, Germany

3 Department of Physics and Mathematics, Saint Petersburg State Institute of Technology, 26 Moskovsky av., St.-Petersburg 198013, Russia

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BMC Evolutionary Biology 2010, 10:376  doi:10.1186/1471-2148-10-376

Published: 2 December 2010

Abstract

Background

DNA sequences afford access to the evolutionary pathways of life. Particularly mobile elements that constantly co-evolve in genomes encrypt recent and ancient information of their host's history. In mammals there is an extraordinarily abundant activity of mobile elements that occurs in a dynamic succession of active families, subfamilies, types, and subtypes of retroposed elements. The high frequency of retroposons in mammals implies that, by chance, such elements also insert into each other. While inactive elements are no longer able to retropose, active elements retropose by chance into other active and inactive elements. Thousands of such directional, element-in-element insertions are found in present-day genomes. To help analyze these events, we developed a computational algorithm (Transpositions in Transpositions, or TinT) that examines the different frequencies of nested transpositions and reconstructs the chronological order of retroposon activities.

Results

By examining the different frequencies of such nested transpositions, the TinT application reconstructs the chronological order of retroposon activities. We use such activity patterns as a comparative tool to (1) delineate the historical rise and fall of retroposons and their relations to each other, (2) understand the retroposon-induced complexity of recent genomes, and (3) find selective informative homoplasy-free markers of phylogeny. The efficiency of the new application is demonstrated by applying it to dimeric Alu Short INterspersed Elements (SINE) to derive a complete chronology of such elements in primates.

Conclusion

The user-friendly, web-based TinT interface presented here affords an easy, automated screening for nested transpositions from genome assemblies or trace data, assembles them in a frequency-matrix, and schematically displays their chronological activity history.