Abstract
Transposable elements, as major components of most eukaryotic organisms' genomes, define their structural organization and plasticity. They supply host genomes with functional elements, for example, binding sites of the pleiotropic master transcription factor p53 were identified in LINE1, Alu and LTR repeats in the human genome. Similarly, in this report we reveal the role of zebrafish (Danio rerio) EnSpmN6_DR non-autonomous DNA transposon in shaping the repertoire of the p53 target genes. The multiple copies of EnSpmN6_DR and their embedded p53 responsive elements drive in several instances p53-dependent transcriptional modulation of the adjacent gene, whose human orthologs were frequently previously annotated as p53 targets. These transposons define predominantly a set of target genes whose human orthologs contribute to neuronal morphogenesis, axonogenesis, synaptic transmission and the regulation of programmed cell death. Consistent with these biological functions the orthologs of the EnSpmN6_DR-colonized loci are enriched for genes expressed in the amygdala, the hippocampus and the brain cortex. Our data pinpoint a remarkable example of convergent evolution: the exaptation of lineage-specific transposons to shape p53-regulated neuronal morphogenesis-related pathways in both a hominid and a teleost fish.
Highlights
Transposable elements (TEs) represent the largest genomic component of most eukaryotic organisms
We used the 27 and 40 ESTs deposited in dbEST overlapping trim8a and trim8b, respectively, to assemble putative transcripts that corresponded to the Zv9 models of these genes
The trim8a model (Zv9) spans 2081 bp and five exons encoding a 368 residues protein (ENSDARG00000090512), while the trim8b putative transcript is 3589 bp and six exons long (ENSDART00000085888; Zv7, Zv8 and Zv9 assemblies). It encodes a 564 residues protein (ENSDARP00000080323). To validate these models we amplified by RT-polymerase chain reaction (PCR) the open reading frames (ORF) of the trim8a and trim8b predicted cDNAs using total RNA from zebrafish embryos, cloned them in a pcDNA3-HA vector and sequenced them for confirmation
Summary
Transposable elements (TEs) represent the largest genomic component of most eukaryotic organisms Their contribution to genome size reaches up to two third in vertebrate [1,2,3] invertebrate [4], and plant genomes [5,6]. The third example might stem from a predisposition of pogo-like transposases to encode centromeric proteins Members of this family of transposons were tamed in mammalian and fission yeast genomes to encode centromereassociated protein B (CENP-B) and CENP-B-like proteins, respectively [18]. These examples of convergent evolution illustrate well previous findings of the ENCODE consortium that many functional elements are seemingly unconstrained constituting a ‘‘warehouse’’ for natural selection
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