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Nucleic Acids Research 2004 32(15):4609-4617; doi:10.1093/nar/gkh790
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Published online 27 August 2004

Nucleic Acids Research, Vol. 32 No. 15 © Oxford University Press 2004; all rights reserved

Relative gene-silencing efficiencies of small interfering RNAs targeting sense and antisense transcripts from the same genetic locus

Xiuyuan Hu*, Sharlene Hipolito, Rebecca Lynn, Violet Abraham, Silvester Ramos and Flossie Wong-Staal

Immusol Incorporation, 10790 Roselle Street, San Diego, CA 92121, USA

* To whom correspondence should be addressed. Tel: +1 858 824 1100; Fax: +1 858 824 1112; Email: hu{at}immusol.com

Received June 18, 2004; Revised and Accepted August 8, 2004

Short interfering RNAs (siRNAs) directed against different regions of genes display marked variation in their potency in mediating mRNA degradation. Various factors have been proposed to affect the efficacy of siRNA. We explored some of the factors by evaluating in cultured human cells 28 randomly selected siRNAs targeting the GPR39 and MGC29643transcripts derived from the same genetic locus but transcribed in opposite directions. Twenty of the 24 siRNAs targeting the overlapping regions of the transcripts simultaneously reduced the levels of both transcripts. Single nucleotide changes in either of the siRNA strands significantly reduced the gene-silencing efficiency of the siRNA on targeted sense transcript without affecting the antisense transcript. Overall, we observed a greater gene-silencing efficiency on the MGC29643transcript than on the GPR39 transcript in HeLa cells. Since MGC29643transcript is more abundant than the GPR39 transcript [0.24 versus 0.008% relative to 100% for glyceraldehyde-3-phosphate dehydrogenase (GAPDH)], the results suggest that the abundance of the mRNA affects the efficiency of silencing. Two additional observations supported this hypothesis. First, GAPDH whose intracellular level is the highest of the three was the most efficiently silenced. Second, a reversal of gene-silencing efficiency was observed in U-138 MG cells in which the relative abundance of the GPR39 and MGC29643transcripts is also reversed. Our study suggests that low-abundant transcripts are less susceptible to siRNA-mediated degradation than medium- and high-abundant transcripts.


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