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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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2015-12-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004656&type=printable |
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| author | Piotr J Kamola Yuko Nakano Tomoko Takahashi Paul A Wilson Kumiko Ui-Tei |
| author_facet | Piotr J Kamola Yuko Nakano Tomoko Takahashi Paul A Wilson Kumiko Ui-Tei |
| author_sort | Piotr J Kamola |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-b8ff598165424ab9a4b15e47d523d88c |
| institution | DOAJ |
| issn | 1553-734X 1553-7358 |
| language | English |
| publishDate | 2015-12-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj-art-b8ff598165424ab9a4b15e47d523d88c2025-08-20T03:10:58ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582015-12-011112e100465610.1371/journal.pcbi.1004656The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects.Piotr J KamolaYuko NakanoTomoko TakahashiPaul A WilsonKumiko Ui-TeiRNA 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.https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004656&type=printable |
| spellingShingle | Piotr J Kamola Yuko Nakano Tomoko Takahashi Paul A Wilson Kumiko Ui-Tei The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects. PLoS Computational Biology |
| title | The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects. |
| title_full | The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects. |
| title_fullStr | The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects. |
| title_full_unstemmed | The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects. |
| title_short | The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects. |
| title_sort | sirna non seed region and its target sequences are auxiliary determinants of off target effects |
| url | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004656&type=printable |
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