The transcript repeat element: The human Alu sequence as a component of gene networks influencing cancer

Paula Moolhuijzen, Jerzy K. Kulski, David S. Dunn, David Schibeci, Roberto Barrero, Takashi Gojobori, Matthew Bellgard*

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

15 Scopus citations


A small percentage (3%) of the 1.3 million copies of Alu sequences in the human genome is expressed individually or as part of various gene transcripts with potential regulatory and pathophysiological importance. In order to better understand the role of repetitive elements within transcripts, this review focuses on Alu-containing transcripts of normal and cancerous tissue in a transcriptome-wide survey of the H-Invitational human transcript database on 106,825 tissue-derived transcripts expressed at 29,979 loci. The Alu elements in transcripts of cancerous tissues are significantly underrepresented in comparison to those in normal tissues. In this review, we propose a model for Alu-mediated siRNA down-regulation of Alu-containing transcripts in cancer tissues. In cancer or other rapidly dividing tissues, hypomethylation of repeat element regions triggers the expression of transposon elements including Alu, which can potentially form double-stranded RNA molecules for use as templates to generate Alu-derived siRNAs (Alu-siRNAs). The generated Alu-siRNAs target endogenous messenger RNAs harbouring sequence similarity to Alu elements. This model correlates with the observation that there is substantial under-representation of Alu-containing mRNAs in cancer cells. This new perspective of gene regulation in disease conditions can provide a basis for starting to account for changes in complex gene network in cancer.

Original languageEnglish (US)
Pages (from-to)307-319
Number of pages13
JournalFunctional and Integrative Genomics
Issue number3
StatePublished - Aug 2010
Externally publishedYes

Bibliographical note

Funding Information:
Acknowledgments We wish to acknowledge Professor Rudi Appels for his guidance in compiling this review. The H-Inv human transcript data was analysed mostly by Paula Moolhuijzen as part of her studies for a Ph.D. The Australian Research Council (ARC) grant number DP0559547 provided financial support. The authors are grateful to Mr. Adam Hunter (CCG) and Chisato Yamasaki (Integrated Database Group, Japan Biological Information Research Centre, JBIRC) for facilitating access to a broad range of databases.


  • Bioinformatics
  • Comparative genomics
  • Disease
  • Gene control

ASJC Scopus subject areas

  • Genetics


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