Transcendent Elements: Whole-Genome Transposon Screens and Open Evolutionary Questions
- Bioinformatics Group, Department of Statistics, University of Oxford, Oxford OXI 3TG, United Kingdom
This extract was created in the absence of an abstract.
Transposable elements (TEs), or transposons, form a major fraction of the eukaryotic genome (Kidwell and Lisch 2001). Dismissed for some time as junk DNA, these repetitive sequences are now recognized for their diverse evolutionary roles. In this issue ofGenome Research, Bao and Eddy (2002) describe a software tool (RECON) for de novo annotation of transposons in genomic sequence, offering new possibilities for discovery to biologists interested in TE evolution as well as a practical tool for masking repetitive DNA from genomic annotation pipelines.
In this commentary, I begin by reviewing why transposons are relevant to studies of genome evolution. I then outline the advances of Bao and Eddy's method from previous work, highlighting certain exemplary features of the RECON method. Finally I describe some of the open questions of transposable element evolution that may be more easily addressed by large-scale bioinformatics and functional genomics approaches as RECON, and more tools like it, become available.
Why Care about Transposable Elements?
Transposable elements (Box ) are of interest to geneticists (as an experimental tool), genome annotators (typically as junk DNA to be screened out), and structural and evolutionary biologists (for many reasons). My own bias lies toward the latter two (structural and evolutionary) aspects, and I will only briefly outline the former two (experimental and annotative) aspects before moving onto molecular evolution.
Some Known Types of Transposable Elements
Transposable elements are DNA sequences that move or are copied from one genomic location to another (Feschotte et al. 2002). They can be classified according to their transposition intermediate, RNA (class I) or DNA (class II), and whether they code for genes that catalyze transposition (autonomous TEs) or require these genes to be provided, usually by other TEs in the host (nonautonomous TEs). The genes required for autonomy are different for class I and class II transposons. …
