Fake IDs? Widespread misannotation of DNA Transposons as a General Transcription Factor

Transposable elements (TEs) account for a large proportion of genomic content and are major determinants of genome structure and function in eukaryotes. The annotation of TEs is a critical part of our understanding of genomes, however, the accuracy of gene/TE annotation pipelines remains an issue as TEs are frequently underestimated or misannotated. In this paper, we report that the mammalian General Transcription Factor II-I Repeat Domain-Containing Protein 2 (GTF2IRD2) was used to erroneously annotate DNA transposons in a variety of non-mammalian species because the transcription factor contains a 3’ fused hAT transposase domain. The consequences of the misannotation of TEs as trans-regulatory elements such as transcription factors can lead to errors in phylogenetic trees based on orthologs and to significant wasted time for investigators interested in gene regulation. This study reiterates the importance of structural analysis and effective annotation methods that minimise transitive error propagation when characterising non-mammalian genomes.