A gene expression restriction network mediated by sense and antisense Alu sequences located on protein-coding messenger RNAs
1 Liver Research Center, Chang Gung Memorial Hospital, Taipei, Taiwan
2 Molecular Medicine Research Center, Chang Gung University School of Medicine, 199 Tung Hwa North Road, Taipei 10507, Taiwan
BMC Genomics 2013, 14:325 doi:10.1186/1471-2164-14-325Published: 11 May 2013
Alus are primate-specific retrotransposons which account for 10.6% of the human genome. A large number of protein-coding mRNAs are encoded with sense or antisense Alus in the un-translated regions.
We postulated that mRNAs carrying Alus in the two opposite directions can generate double stranded RNAs, capable of regulating the levels of other Alu-carrying mRNAs post-transcriptionally. A gene expression profiling assay showed that the levels of antisense and sense Alus-carrying mRNAs were suppressed in a reversible manner by over-expression of exogenous sense and antisense Alus derived from mRNAs (Family-wise error rate P= 0.0483 and P < 0.0001 respectively). Screening through human mRNAs on the NCBI-RefSeq database, it was found that sense and antisense Alu-carrying transcripts were enriched in distinct cellular functions. Antisense Alu-carrying genes were particularly enriched in neurological and developmental processes, while sense Alu-carrying genes were enriched in immunological functions.
Taken together, we proposed a novel Alu-mediated regulation network capable of stabilizing Alu-carrying mRNA levels in different cell types and restricting the activated expression levels of protein-coding, Alu-carrying mRNAs.