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

Published online 5 November 2007 Nucleic Acids Research, 2008, Vol. 36, Database issue D47–D52 doi:10.1093/nar/gkm949 TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates Asaf Levy, Noa Sela and Gil Ast* Department of Molecular Genetics and Biochemistry, Tel-Aviv University Medical School, Tel Aviv 69978, Israel Received September 6, 2007; Revised October 14, 2007; Accepted October 15, 2007 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 inser- tions 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 protein- coding 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 infor- mation regarding specific type and family of the TEs, genomic and mRNA location, sequence, supporting transcript accession and alignment to the TE con- sensus 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 TE- derived microRNAs. The TranspoGene and micro- TranspoGene databases can be used by researchers interested in the effect of TE insertion on the eukaryotic transcriptome. Publicly available query interfaces to TranspoGene and micro- TranspoGene are available at http://transpogene. tau.ac.il/ and http://microtranspogene.tau.ac.il, respectively. The entire database can be down- loaded as flat files. INTRODUCTION Transposed elements (TEs) are mobile genetic sequences that constitute 45%, 38%, 15–22%, 12%, and 9% of the human, mouse, fruit fly, nematode and chicken genomes, respectively (1–4). TEs are distinguished by their mode of propagation: short interspersed repeat elements (SINE), long interspersed repeat elements (LINE) and retrovirus- like elements with long-terminal repeats (LTR) are propagated by reverse transcription of an RNA inter- mediate. In contrast, DNA transposons move through a direct ‘cut-and-paste’ mechanism (5). TEs have shaped the eukaryotic genome and transcrip- tome in several ways. Mammalian evolution was notably affected by TEs through their contribution to genetic diversity, genomic expansion, genomic content and genomic rearrangements (5,6). Although introns comprise only 24% of the human genome, 60% of all TEs are located in introns (7). L1 elements can significantly decrease mammalian gene expression when inserted within introns, due to inadequate transcriptional elonga- tion (8). Intronic TEs from all human and mouse TE families can gain mutations leading to creation of an additional exon in a process known as ‘exonization’. The most prominent TE involved in exonization process is the primate-specific Alu (7,9,10). TEs can also insert into exons, a phenomenon that is common mainly in the 50 and 30 untranslated region (UTR) exons, at least in human and mouse (7). TE insertion elongates the UTR and can serve as new cis-acting element such as microRNA-binding site (11). TE insertion can directly affect gene expression when the TE is incorporated into a gene promoter. The TE sequence may provide transcription factor binding sites previously not present in the promoter (12). About 25% of human promoter regions contain TE-derived sequences, including many experimentally characterized cis-regulatory elements (13). For example, some func- tional binding sites of the transcriptional repressor REST The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors. *To whom correspondence should be addressed. Tel: +972 3 640 6893; Fax: +972 3 640 9900; Email: gilast@post.tau.ac.il
2007 The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. originated from duplication and insertion of RE1- containing L2 and Alu retrotransposons (14). Not only protein-coding genes are affected by TE insertion. A recent work by Borchert et al. (15) demonstrated that several human microRNAs are transcribed by RNA polymerase III through promoters and/or terminators derived from the Alu retrotransposon. TEs can also control eukaryotic genes epigeneti

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