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Open Access Highly Accessed Research article

A gene expression restriction network mediated by sense and antisense Alu sequences located on protein-coding messenger RNAs

Kung-Hao Liang1 and Chau-Ting Yeh12*

Author Affiliations

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

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BMC Genomics 2013, 14:325  doi:10.1186/1471-2164-14-325

Published: 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.

Antisense Alu; Gene expression restriction; Double-stranded Alu; Alu-carrying protein-coding RNA