The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects
RNA interference (RNAi) is a powerful tool for post-transcriptional gene silencing. However, the siRNA guide strand may bind unintended off-target transcripts via partial sequence complementarity by a mechanism closely mirroring micro RNA (miRNA) silencing. To better understand these off-target effe...
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Published in | PLoS computational biology Vol. 11; no. 12; p. e1004656 |
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Main Authors | , , , , |
Format | Journal Article |
Language | English |
Published |
United States
Public Library of Science
01.12.2015
Public Library of Science (PLoS) |
Subjects | |
Online Access | Get full text |
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Summary: | RNA interference (RNAi) is a powerful tool for post-transcriptional gene silencing. However, the siRNA guide strand may bind unintended off-target transcripts via partial sequence complementarity by a mechanism closely mirroring micro RNA (miRNA) silencing. To better understand these off-target effects, we investigated the correlation between sequence features within various subsections of siRNA guide strands, and its corresponding target sequences, with off-target activities. Our results confirm previous reports that strength of base-pairing in the siRNA seed region is the primary factor determining the efficiency of off-target silencing. However, the degree of downregulation of off-target transcripts with shared seed sequence is not necessarily similar, suggesting that there are additional auxiliary factors that influence the silencing potential. Here, we demonstrate that both the melting temperature (Tm) in a subsection of siRNA non-seed region, and the GC contents of its corresponding target sequences, are negatively correlated with the efficiency of off-target effect. Analysis of experimentally validated miRNA targets demonstrated a similar trend, indicating a putative conserved mechanistic feature of seed region-dependent targeting mechanism. These observations may prove useful as parameters for off-target prediction algorithms and improve siRNA 'specificity' design rules. |
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Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Conceived and designed the experiments: PJK KUT. Performed the experiments: YN TT. Analyzed the data: PJK. Contributed reagents/materials/analysis tools: PJK KUT. Wrote the paper: PJK PAW KUT. PAW is a paid employee of GlaxoSmithKline (GSK) and PJK's EPSRC Industrial CASE doctoral studentships is co-sponsored by GSK. This does not alter our adherence to the PLOS policies on sharing data and materials. All other authors have declared that no competing interests exist. |
ISSN: | 1553-7358 1553-734X 1553-7358 |
DOI: | 10.1371/journal.pcbi.1004656 |