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In Silico Biology 5, 0037 (2005); ©2005, Bioinformation Systems e.V.  

Folded RNA from an intron of one gene might inhibit expression of a counteracting gene

Clark Jeffries1,2,3*, Michael Jarstfer2 and Diana O. Perkins1

1 Department of Psychiatry, University of North Carolina at Chapel Hill, USA
2 School of Pharmacy, University of North Carolina at Chapel Hill, USA
3 Renaissance Computing Institute, USA

* Corresponding author; E-mail:

Edited by E. Wingender; received April 27, 2005; revised June 15; accepted June 18, 2005; published July 03, 2005


Homeostatic maintenance of mRNA levels including prompt availability of mRNAs for translation in response to changing protein demands might be partly enabled by a system of combinatorial controls involving noncoding RNA blocking agents. This article proposes a specific version of that control mechanism, namely, a double-stranded RNA folding from transcription of an intron of one gene might and leading to an agent that inhibits mRNA of a counteracting gene. Thus transcription of the first gene would automatically repress translation of the second.

On the basis of a bioinformatics search, we suggest a possible example, namely, that pro-apoptosis gene PAR4 might inhibit anti-apoptosis gene XIAP. Part of an intron from PAR4 folds to form a large, stable hairpin, and reverse complement of the hairpin stem (with ~280 nucleotides) matches a sub-sequence of an exon in XIAP. This would be part of an efficient system to drive initiated apoptosis to its conclusion. Figuratively speaking, it replaces two control knobs with one.

Since repeats, some with many thousands of copies, occur throughout the genome with complex distributions, care must be taken before asserting that the presence of any repeat in any gene is significant. Our apoptosis example involves repeats, so experimental verification is needed and planned. However, if it is found that the noncoding RNA by-product of one gene folds into a hairpin that is processed into an agent that inhibits a counteracting gene, then the same type of control unit might be found extensively among counteracting families of genes of many types.

Keywords: counteracting genes, RNA hairpins, noncoding RNA, miRNA, Alu repeat