TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates

TL;DR

This paper introduces TranspoGene and microTranspoGene databases that catalog transposed elements and TE-derived microRNAs across seven species, highlighting their influence on gene structure, expression, and evolution.

Contribution

The study provides comprehensive databases linking transposed elements to gene and transcript modifications in multiple species, facilitating research on TE impacts.

Findings

Cataloged TEs in seven species with detailed annotations

Linked TEs to gene structure, expression, and splicing changes

Identified TE-derived microRNAs in four species

Abstract

Transposed elements (TEs) are mobile genetic sequences. During the evolution of eukaryotes TEs were inserted into active protein-coding genes, affecting gene structure, expression and splicing patterns, and protein sequences. Genomic insertions of TEs also led to creation and expression of new functional non-coding RNAs such as micro- RNAs. We have constructed the TranspoGene database, which covers TEs located inside proteincoding genes of seven species: human, mouse, chicken, zebrafish, fruit fly, nematode and sea squirt. TEs were classified according to location within the gene: proximal promoter TEs, exonized TEs (insertion within an intron that led to exon creation), exonic TEs (insertion into an existing exon) or intronic TEs. TranspoGene contains information regarding specific type and family of the TEs, genomic and mRNA location, sequence, supporting transcript accession and alignment to the TE consensus sequence. The database also contains host gene specific data: gene name, genomic location, Swiss-Prot and RefSeq accessions, diseases associated with the gene and splicing pattern. In addition, we created microTranspoGene: a database of human, mouse, zebrafish and nematode TEderived microRNAs. The TranspoGene and micro- TranspoGene databases can be used by researchers interested in the effect of TE insertion on the eukaryotic transcriptome.