Transposable elements encoding functional proteins: pitfalls in unprocessed genomic data?

Pavlı́ček, Adam; Clay, Oliver; Bernardi, Giorgio

doi:10.1016/s0014-5793(02)02992-7

Cited by 12 publications

(9 citation statements)

References 23 publications

(35 reference statements)

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“…Taken together, these protein coding probability data are consistent with previous studies that have suggested caution is warranted when extrapolating genome sequence analyses to infer TE-CDS exaptation events [ 13 , 16 , 35 , 36 ]. In particular, the notion that non-autonomous TEs that do not encode any protein, including SINEs such as the Alu family of elements, can emerge as protein coding sequences after being incorporated into exons has been directly challenged [ 13 ]. On the other hand, Alus are frequently incorporated into mRNAs as exons [ 37 - 40 ], and there are a number of specific cases of Alu-derived CDS that have been proposed to provide novel CDS to primate genes [ 41 , 42 ].…”

Section: Resultssupporting

confidence: 89%

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Evaluating the protein coding potential of exonized transposable element sequences

et al. 2007

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Background: Transposable element (TE) sequences, once thought to be merely selfish or parasitic members of the genomic community, have been shown to contribute a wide variety of functional sequences to their host genomes. Analysis of complete genome sequences have turned up numerous cases where TE sequences have been incorporated as exons into mRNAs, and it is widely assumed that such 'exonized' TEs encode protein sequences. However, the extent to which TE-derived sequences actually encode proteins is unknown and a matter of some controversy. We have tried to address this outstanding issue from two perspectives: i-by evaluating ascertainment biases related to the search methods used to uncover TE-derived protein coding sequences (CDS) and ii-through a probabilistic codon-frequency based analysis of the protein coding potential of TE-derived exons.

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Section: Resultssupporting

confidence: 89%

“…This approach was first taken by Pavlicek et al . who surveyed a dataset of 781 non-redundant human proteins with 3D structures for the presence of TE-derived coding sequences [ 13 ]. They were not able to find a single reliable case of a TE-derived protein coding sequence in these data.…”

Section: Introductionmentioning

confidence: 99%

Evaluating the protein coding potential of exonized transposable element sequences

et al. 2007

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“…As noted by Claverie and Makalowski (1994) and Pavlicek et al (2002) many of the TE-containing protein-coding genes may be artifacts. Our analysis supports this clam and provides a reliable method for validation of functional TE insertions using comparative methods.…”

Section: Another Artifact?mentioning

confidence: 86%

mNSC1 shows no evidence of protein-coding capacity

Wilson

Goetting-Minesky

Nekrutenko

2006

Gene

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“…Pavlicek and colleagues took another look at the findings of Nekrutenko and Li and pointed out several caveats that should be taken into consideration when trying to determine the extent of CDSs derived from TEs [43]. First of all, they found that, of the set of genes identified by Nekrutenko and Li as TEderived, 30% were annotated as hypothetical and 63% were annotated as predicted.…”

Section: Genome Wide Analysesmentioning

confidence: 99%

Exaptation of Protein Coding Sequences from Transposable Elements

Bowen

Jordan²

2007

Genome Dynamics

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The activity of transposable elements (TEs) has had a profound impact on the evolution of eukaryotic genomes. Once thought to be purely selfish genomic entities, TEs are now recognized to occupy a continuum of relationships, ranging from parasitic to mutualistic, with their host genomes. One of the many ways that TEs contribute to the function and evolution of the genomes in which they reside is through the donation of host protein coding sequences (CDSs). In this chapter, we will describe several notable examples of eukaryotic host CDSs that are derived from TEs. Despite the existence of a number of such well-established cases, the overall extent and significance of this phenomenon remains a matter of controversy. Genome-scale computational analyses have yielded vastly different estimates for the fraction of host CDSs that are derived from TEs. We explain how these seemingly contradictory findings are the result of specific ascertainment biases introduced by the different methods used to detect TE-related sequences. In light of this problem, we propose a comprehensive and systematic framework for definitively characterizing the contribution of TEs to eukaryotic CDSs.

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Transposable elements encoding functional proteins: pitfalls in unprocessed genomic data?

Cited by 12 publications

References 23 publications

Evaluating the protein coding potential of exonized transposable element sequences

Evaluating the protein coding potential of exonized transposable element sequences

mNSC1 shows no evidence of protein-coding capacity

Exaptation of Protein Coding Sequences from Transposable Elements

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