Mammalian-wide interspersed repeats (MIRs) and their role in mammalian gene function and evolution

• Main Author: Croft, S. M.
• Published: Nottingham Trent University 2009
• Subjects: 572
• Online Access: http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.629132

Transposable elements (TEs) are ubiquitous components of plant and animal genomes and constitute more than ~45% of the human genome. Though originally considered as 'parasitic' or 'junk' DNA, TEs are now thought to have played a role in shaping genomes during evolution, contributing to genome plasticity and diversity. All classes of retrotransposons accumulate in the genome via a process termed retrotransposition, wherein the elements are reverse transcribed into RNA and inserted into the genome as DNA. Exaptation of these elements can provide additional or novel function for endogenous genes. Mammalian-wide interspersed repeats (MIRs) are short interspersed nuclear elements (SINEs), belonging to the non-autonomous class of retroelements and are found in all mammals. The recruitment of an MIR element by a gene may provide insight into mammalian evolution and gene function. The human genome was screened for genes that have exaptated MIR elements and the compiled dataset was analysed to determine any commonality which may suggest conserved function(s). Subsequently 1359 genes were identified that have exaptated MIR elements, constituting 5% of the total genes in the human genome. MIR elements may be multifunctional, as 1% of the total human genes contain MIRs that are spliced and/or are contributing to protein coding sequences. Subsequently sequence motifs were identified in the MIR consensus sequences which resemble canonical mammalian splice sites; therefore MIR elements recruited in the 5'-UTR and coding sequence may be a result of the exonisation of intronic elements. The MIR-containing transcripts are frequently expressed in neurological tissue, suggesting a role in neuronal function. Moreover a number of MIR-containing mRNA transcripts are known to be localised to the dendritic compartment of the neurone, and ciliated region of photoreceptors. Some of the localised mRNAs contain putative microRNA binding sites within the MIR sequence, and possible dsRNA structures were noted between MIR elements. It is proposed that exaptated MIR elements may be a source of cis-acting regulatory elements, involved in post-transcriptional control of gene expression, including localisation of mRNA to distinct intracellular compartments.