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Deep Sequencing Analyses of DsiRNAs Reveal the Influence of 3′ Terminal Overhangs on Dicing Polarity, Strand Selectivity, and RNA Editing of siRNAs

Identifieur interne : 001301 ( Pmc/Checkpoint ); précédent : 001300; suivant : 001302

Deep Sequencing Analyses of DsiRNAs Reveal the Influence of 3′ Terminal Overhangs on Dicing Polarity, Strand Selectivity, and RNA Editing of siRNAs

Auteurs : Jiehua Zhou [États-Unis] ; Min-Sun Song [États-Unis] ; Ashley M. Jacobi [États-Unis] ; Mark A. Behlke [États-Unis] ; Xiwei Wu [États-Unis] ; John J. Rossi [États-Unis]

Source :

RBID : PMC:3384246

Abstract

25/27 Base duplex RNAs that are substrates for Dicer have been demonstrated to enhance RNA interference (RNAi) potency and efficacy. Since the target sites are not always equally susceptible to suppression by small interfering RNA (siRNA), not all 27-mer duplexes that are processed into the corresponding conventional siRNAs show increased potency. Thus random designing of Dicer-substrate siRNAs (DsiRNAs) may generate siRNAs with poor RNAi due to unpredictable Dicer processing. Previous studies have demonstrated that the 3-overhang affects dicing cleavage site and the orientation of Dicer entry. Moreover, an asymmetric 27-mer duplex having a 3 two-nucleotide overhang and 3-DNA residues on the blunt end has been rationally designed to obtain greater efficacy. This asymmetric structure directs dicing to predictably yield a single primary cleavage product. In the present study, we analyzed the in vitroand intracellular dicing patterns of chemically synthesized duplex RNAs with different 3-overhangs. Consistent with previous studies, we observed that Dicer preferentially processes these RNAs at a site 21–22 nucleotide (nt) from the two-base 3-overhangs. We also observed that the direction and ability of human Dicer to generate siRNAs can be partially or completely blocked by DNA residues at the 3-termimi. To examine the effects of various 3-end modifications on Dicer processing in cells, we employed Illumina Deep sequencing analyses to unravel the fates of the asymmetric 27-mer duplexes. To validate the strand selection process and knockdown capabilities we also conducted dual-luciferase psiCHECK reporter assays to monitor the RNAi potencies of both the “sense” (S) and “antisense” (AS) strands derived from these DsiRNAs. Consistent with our in vitro Dicer assays, the asymmetric duplexes were predictably processed into desired primary cleavage products of 21–22-mers in cells. We also observed the trimming of the 3 end, especially when DNA residues were incorporated into the overhangs and this trimming ultimately influenced the Dicer-cleavage site and RNAi potency. Moreover, the observation that the most efficacious strand was the most abundant revealed that the relative frequencies of each “S” or “AS” strand are highly correlated with the silencing activity and strand selectivity. Collectively, our data demonstrate that even though the only differences between a family of DsiRNAs was the 3 two-nuclotide overhang, dicing polarity and strand selectivity are distinct depending upon the sequence and chemical nature of this overhang. Thus, it is possible to predictably control dicing polarity and strand selectivity via simply changing the 3-end overhangs without altering the original duplex sequence. These optimal design features of 3-overhangs might provide a facile approach for rationally designing highly potent 25/27-mer DsiRNAs.


Url:
DOI: 10.1038/mtna.2012.6
PubMed: 23343928
PubMed Central: 3384246


Affiliations:


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PMC:3384246

Le document en format XML

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<p>25/27 Base duplex RNAs that are substrates for Dicer have been demonstrated to enhance RNA interference (RNAi) potency and efficacy. Since the target sites are not always equally susceptible to suppression by small interfering RNA (siRNA), not all 27-mer duplexes that are processed into the corresponding conventional siRNAs show increased potency. Thus random designing of Dicer-substrate siRNAs (DsiRNAs) may generate siRNAs with poor RNAi due to unpredictable Dicer processing. Previous studies have demonstrated that the 3
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-overhang affects dicing cleavage site and the orientation of Dicer entry. Moreover, an asymmetric 27-mer duplex having a 3
<bold></bold>
two-nucleotide overhang and 3
<bold></bold>
-DNA residues on the blunt end has been rationally designed to obtain greater efficacy. This asymmetric structure directs dicing to predictably yield a single primary cleavage product. In the present study, we analyzed the
<italic>in vitro</italic>
and intracellular dicing patterns of chemically synthesized duplex RNAs with different 3
<bold></bold>
-overhangs. Consistent with previous studies, we observed that Dicer preferentially processes these RNAs at a site 21–22 nucleotide (nt) from the two-base 3
<bold></bold>
-overhangs. We also observed that the direction and ability of human Dicer to generate siRNAs can be partially or completely blocked by DNA residues at the 3
<bold></bold>
-termimi. To examine the effects of various 3
<bold></bold>
-end modifications on Dicer processing in cells, we employed Illumina Deep sequencing analyses to unravel the fates of the asymmetric 27-mer duplexes. To validate the strand selection process and knockdown capabilities we also conducted dual-luciferase psiCHECK reporter assays to monitor the RNAi potencies of both the “sense” (S) and “antisense” (AS) strands derived from these DsiRNAs. Consistent with our
<italic>in vitro</italic>
Dicer assays, the asymmetric duplexes were predictably processed into desired primary cleavage products of 21–22-mers in cells. We also observed the trimming of the 3
<bold></bold>
end, especially when DNA residues were incorporated into the overhangs and this trimming ultimately influenced the Dicer-cleavage site and RNAi potency. Moreover, the observation that the most efficacious strand was the most abundant revealed that the relative frequencies of each “S” or “AS” strand are highly correlated with the silencing activity and strand selectivity. Collectively, our data demonstrate that even though the only differences between a family of DsiRNAs was the 3
<bold></bold>
two-nuclotide overhang, dicing polarity and strand selectivity are distinct depending upon the sequence and chemical nature of this overhang. Thus, it is possible to predictably control dicing polarity and strand selectivity
<italic>via</italic>
simply changing the 3
<bold></bold>
-end overhangs without altering the original duplex sequence. These optimal design features of 3
<bold></bold>
-overhangs might provide a facile approach for rationally designing highly potent 25/27-mer DsiRNAs.</p>
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</TEI>
<pmc article-type="research-article">
<pmc-dir>properties open_access</pmc-dir>
<front>
<journal-meta>
<journal-id journal-id-type="nlm-ta">Mol Ther Nucleic Acids</journal-id>
<journal-id journal-id-type="iso-abbrev">Mol Ther Nucleic Acids</journal-id>
<journal-title-group>
<journal-title>Molecular therapy. Nucleic acids</journal-title>
</journal-title-group>
<issn pub-type="epub">2162-2531</issn>
<publisher>
<publisher-name>Nature Publishing Group</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="pmid">23343928</article-id>
<article-id pub-id-type="pmc">3384246</article-id>
<article-id pub-id-type="pii">mtna20126</article-id>
<article-id pub-id-type="doi">10.1038/mtna.2012.6</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Original Article</subject>
</subj-group>
</article-categories>
<title-group>
<article-title>Deep Sequencing Analyses of DsiRNAs Reveal the Influence of 3′ Terminal Overhangs on Dicing Polarity, Strand Selectivity, and RNA Editing of siRNAs</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Zhou</surname>
<given-names>Jiehua</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Song</surname>
<given-names>Min-Sun</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Jacobi</surname>
<given-names>Ashley M</given-names>
</name>
<xref ref-type="aff" rid="aff2">2</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Behlke</surname>
<given-names>Mark A</given-names>
</name>
<xref ref-type="aff" rid="aff2">2</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Wu</surname>
<given-names>Xiwei</given-names>
</name>
<xref ref-type="aff" rid="aff3">3</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Rossi</surname>
<given-names>John J</given-names>
</name>
<xref ref-type="aff" rid="aff1">1</xref>
<xref ref-type="aff" rid="aff4">4</xref>
</contrib>
<aff id="aff1">
<label>1</label>
<institution>Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope</institution>
, Duarte, California,
<country>USA</country>
</aff>
<aff id="aff2">
<label>2</label>
<institution>Integrated DNA Technologies, Inc.</institution>
Coralville, Iowa,
<country>USA</country>
</aff>
<aff id="aff3">
<label>3</label>
<institution>Department of Molecular Medicine, Beckman Research Institute of City of Hope</institution>
, Duarte, California,
<country>USA</country>
</aff>
<aff id="aff4">
<label>4</label>
<institution>Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope</institution>
, Duarte, California,
<country>USA</country>
</aff>
</contrib-group>
<author-notes>
<corresp id="caf1">
<label>*</label>
Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, California 91010, USA. E-mail address:
<email>jrossi@coh.org</email>
</corresp>
</author-notes>
<pub-date pub-type="ppub">
<month>04</month>
<year>2012</year>
</pub-date>
<pub-date pub-type="epub">
<day>03</day>
<month>04</month>
<year>2012</year>
</pub-date>
<pub-date pub-type="pmc-release">
<day>1</day>
<month>4</month>
<year>2012</year>
</pub-date>
<volume>1</volume>
<issue>4</issue>
<fpage>e17</fpage>
<lpage></lpage>
<history>
<date date-type="received">
<day>23</day>
<month>01</month>
<year>2012</year>
</date>
<date date-type="rev-recd">
<day>18</day>
<month>02</month>
<year>2012</year>
</date>
<date date-type="accepted">
<day>03</day>
<month>04</month>
<year>2012</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright © 2012 American Society of Gene & Cell Therapy</copyright-statement>
<copyright-year>2012</copyright-year>
<copyright-holder>American Society of Gene & Cell Therapy</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by-nc-nd/3.0/">
<pmc-comment>author-paid</pmc-comment>
<license-p>
<italic>Molecular Therapy-Nucleic Acids</italic>
is an open-access journal published by Nature Publishing Group. This work is licensed under the Creative Commons Attribution-NonCommercial-No Derivative Works 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/3.0/</license-p>
</license>
</permissions>
<abstract>
<p>25/27 Base duplex RNAs that are substrates for Dicer have been demonstrated to enhance RNA interference (RNAi) potency and efficacy. Since the target sites are not always equally susceptible to suppression by small interfering RNA (siRNA), not all 27-mer duplexes that are processed into the corresponding conventional siRNAs show increased potency. Thus random designing of Dicer-substrate siRNAs (DsiRNAs) may generate siRNAs with poor RNAi due to unpredictable Dicer processing. Previous studies have demonstrated that the 3
<bold></bold>
-overhang affects dicing cleavage site and the orientation of Dicer entry. Moreover, an asymmetric 27-mer duplex having a 3
<bold></bold>
two-nucleotide overhang and 3
<bold></bold>
-DNA residues on the blunt end has been rationally designed to obtain greater efficacy. This asymmetric structure directs dicing to predictably yield a single primary cleavage product. In the present study, we analyzed the
<italic>in vitro</italic>
and intracellular dicing patterns of chemically synthesized duplex RNAs with different 3
<bold></bold>
-overhangs. Consistent with previous studies, we observed that Dicer preferentially processes these RNAs at a site 21–22 nucleotide (nt) from the two-base 3
<bold></bold>
-overhangs. We also observed that the direction and ability of human Dicer to generate siRNAs can be partially or completely blocked by DNA residues at the 3
<bold></bold>
-termimi. To examine the effects of various 3
<bold></bold>
-end modifications on Dicer processing in cells, we employed Illumina Deep sequencing analyses to unravel the fates of the asymmetric 27-mer duplexes. To validate the strand selection process and knockdown capabilities we also conducted dual-luciferase psiCHECK reporter assays to monitor the RNAi potencies of both the “sense” (S) and “antisense” (AS) strands derived from these DsiRNAs. Consistent with our
<italic>in vitro</italic>
Dicer assays, the asymmetric duplexes were predictably processed into desired primary cleavage products of 21–22-mers in cells. We also observed the trimming of the 3
<bold></bold>
end, especially when DNA residues were incorporated into the overhangs and this trimming ultimately influenced the Dicer-cleavage site and RNAi potency. Moreover, the observation that the most efficacious strand was the most abundant revealed that the relative frequencies of each “S” or “AS” strand are highly correlated with the silencing activity and strand selectivity. Collectively, our data demonstrate that even though the only differences between a family of DsiRNAs was the 3
<bold></bold>
two-nuclotide overhang, dicing polarity and strand selectivity are distinct depending upon the sequence and chemical nature of this overhang. Thus, it is possible to predictably control dicing polarity and strand selectivity
<italic>via</italic>
simply changing the 3
<bold></bold>
-end overhangs without altering the original duplex sequence. These optimal design features of 3
<bold></bold>
-overhangs might provide a facile approach for rationally designing highly potent 25/27-mer DsiRNAs.</p>
</abstract>
<kwd-group>
<kwd>RNA interference</kwd>
<kwd>Dicer-substrate siRNA (DsiRNA)</kwd>
<kwd>Deep sequencing</kwd>
<kwd>3′-overhang</kwd>
<kwd>Dicing polarity</kwd>
</kwd-group>
</article-meta>
</front>
<floats-group>
<fig id="fig1">
<label>Figure 1</label>
<caption>
<p>
<bold>
<italic>In vitro</italic>
Dicer processing of (a) 5</bold>
<bold>P</bold>
<sup>
<bold>32</bold>
</sup>
<bold>-end labeled sense or antisense (b) duplexes.</bold>
Two types of experimental approaches are displayed as method A and B, respectively. The dicing patterns are named by the direction of Dicer entering the duplex as left to right (L-R) and right to left (R-L).</p>
</caption>
<graphic xlink:href="mtna20126f1"></graphic>
</fig>
<fig id="fig2">
<label>Figure 2</label>
<caption>
<p>
<bold>
<italic>In vitro</italic>
Dicer cleavage of 5</bold>
<bold>P</bold>
<sup>
<bold>32</bold>
</sup>
<bold>-end labeled sense or antisense strands.</bold>
Group I duplexes. The cleavage fragments that result from dicing L-R and R-L were visualized autoradiographically following denaturing gel electrophoresis of the Dicer-cleavage products: (a) sense and (b) antisense. The two experimental approaches (method A and B) are defined in the legend to Figure 1.</p>
</caption>
<graphic xlink:href="mtna20126f2"></graphic>
</fig>
<fig id="fig3">
<label>Figure 3</label>
<caption>
<p>
<bold>Silencing of
<italic>Homo sapiens</italic>
transportin 3 (
<italic>TNPO3</italic>
) by group I duplex Dicer-substrate small interfering RNAs (DsiRNAs)</bold>
. HEK 293 cells were transfected with 50 or 10 nmol/l of the experimental anti-
<italic>TNPO3</italic>
duplex DsiRNAs.
<italic>TNPO3</italic>
mRNA levels were detected by quantitative real-time reverse transcription (qRT-PCR). The data are normalized with GAPDH mRNA levels and represent the average of three replicate assays.</p>
</caption>
<graphic xlink:href="mtna20126f3"></graphic>
</fig>
<fig id="fig4">
<label>Figure 4</label>
<caption>
<p>
<bold>
<italic>In vitro</italic>
Dicer cleavage of 5</bold>
<bold>P</bold>
<sup>
<bold>32</bold>
</sup>
<bold>-end labeled sense or antisense strands</bold>
. Group II asymmetric duplex Dicer-substrate small interfering RNAs (DsiRNAs) and RNA interference (RNAi) potency. The cleavage fragments that result from dicing L-R and R-L were visualized by autoradiography of the P
<sup>32</sup>
5′ end-labeled strands: (
<bold>a</bold>
) sense and (
<bold>b</bold>
) antisense. Two experimental approaches (method A and B) and the dicing pattern are defined the legend to Figure 1. (
<bold>c</bold>
) Silencing of
<italic>Homo sapiens</italic>
transportin 3 (
<italic>TNPO3</italic>
) triggered by group II duplex RNAs. HEK 293 cells were transfected with 50 or 10 nmol/l of the experimental anti-
<italic>TNPO3</italic>
duplex DsiRNAs. TNPO3 mRNA level were detected by quantitative real-time reverse transcription (qRT-PCR). The data were normalized with GAPDH mRNA and represent the average of three replicate assays.</p>
</caption>
<graphic xlink:href="mtna20126f4"></graphic>
</fig>
<fig id="fig5">
<label>Figure 5</label>
<caption>
<p>
<bold>Illumina Deep sequence analyses of asymmetric 27-mer
<italic>Homo sapiens</italic>
transportin 3 (
<italic>TNPO3</italic>
) Dicer-substrate siRNAs (group II).</bold>
HEK 293 cells were transfected with 10 nmol/l of the asymmetric group II RNA duplexes. Forty hours post-transfection the total RNAs were isolated and prepared for Illumina Deep sequencing. The data collection and alignment are described in Materials and Methods section. (
<bold>a</bold>
) The total reads and abundance of sense and antisense strands from each duplex. (
<bold>b</bold>
) The strand distribution was calculated as the ratio of the abundance of antisense to sense. The ratio of antisense (AS) to sense (S) is ranked by the 3′ overhang GG > GC, AA > CC, UU ≫ tt. (
<bold>c</bold>
) The dicing pattern L-R and R-L are as previously described. The L-R pattern generates the desired siRNA species for target knockdown. Total reads from the top 10 antisense strands and the abundance of L-R cleavage products from the antisense strand. (
<bold>d</bold>
) Two types of RNA editing: trimming of the 3′ end and post-transcriptional addition of nucleotides at the 3′ or 5′ ends.</p>
</caption>
<graphic xlink:href="mtna20126f5"></graphic>
</fig>
<fig id="fig6">
<label>Figure 6</label>
<caption>
<p>
<bold>IC
<sub>50</sub>
values and strand selectivity of asymmetric 27-mer
<italic>Homo sapiens</italic>
transportin 3 (
<italic>TNPO3</italic>
) Dicer-substrate siRNAs (group II).</bold>
(
<bold>a</bold>
) IC
<sub>50</sub>
values of the asymmetric 27-mer duplexes were determined using the psiCHECK assays as described Materials and Methods section. When the antisense or sense was used as “guide” strand, the target knockdown efficiency is listed as the IC
<sub>50</sub>
. (
<bold>b</bold>
) The strand selectivity was calculated as the ratio of IC
<sub>50</sub>
values of the sense to antisense targets.</p>
</caption>
<graphic xlink:href="mtna20126f6"></graphic>
</fig>
<fig id="fig7">
<label>Figure 7</label>
<caption>
<p>
<bold>Illumina Deep sequence analyses of asymmetric 27-mer heterogeneous nuclear ribonucleoprotein H (
<italic>hnRNP H1</italic>
) Dicer-substrate small interfering RNA (siRNAs).</bold>
The data collection and alignment were as described above. (
<bold>a</bold>
) Total reads of the top 10 sense and antisense strands from each duplex. (
<bold>b</bold>
) The strand distribution was calculated as the ratio of the abundance of antisense to sense. Ratio of antisense (AS) to sense (S) is ranked by the 3′ overhang GG > AA in site 324 Dicer-substrate small interfering RNAs (DsiRNAs) and GG > CC in site 325 DsiRNAs. (
<bold>c</bold>
) The dicing pattern L-R and R-L are as previously described. The L-R model generates the desired siRNA species for target knockdown. The total reads of the top 10 antisense strands and the abundance of L-R cleavage products are presented.</p>
</caption>
<graphic xlink:href="mtna20126f7"></graphic>
</fig>
<table-wrap id="tbl1">
<label>Table 1</label>
<caption>
<title>The 21-mer siRNAs and 27-mer Dicer-substrate siRNAs targeting
<italic>TNPO3</italic>
and the target sequences are listed</title>
</caption>
<graphic xlink:href="mtna20126t1"></graphic>
</table-wrap>
<table-wrap id="tbl2">
<label>Table 2</label>
<caption>
<title>Illumina Deep sequence analyses and IC
<sub>50</sub>
values of asymmetric 27-mer
<italic>TNPO3</italic>
Dicer-substrate siRNAs (group II)</title>
</caption>
<graphic xlink:href="mtna20126t2"></graphic>
</table-wrap>
<table-wrap id="tbl3">
<label>Table 3</label>
<caption>
<title>Deep sequence analyses and IC
<sub>50</sub>
values of the
<italic>hnRNP H1</italic>
25/27-mer Dicer-substrate siRNAs</title>
</caption>
<graphic xlink:href="mtna20126t3"></graphic>
</table-wrap>
</floats-group>
</pmc>
<affiliations>
<list>
<country>
<li>États-Unis</li>
</country>
</list>
<tree>
<country name="États-Unis">
<noRegion>
<name sortKey="Zhou, Jiehua" sort="Zhou, Jiehua" uniqKey="Zhou J" first="Jiehua" last="Zhou">Jiehua Zhou</name>
</noRegion>
<name sortKey="Behlke, Mark A" sort="Behlke, Mark A" uniqKey="Behlke M" first="Mark A" last="Behlke">Mark A. Behlke</name>
<name sortKey="Jacobi, Ashley M" sort="Jacobi, Ashley M" uniqKey="Jacobi A" first="Ashley M" last="Jacobi">Ashley M. Jacobi</name>
<name sortKey="Rossi, John J" sort="Rossi, John J" uniqKey="Rossi J" first="John J" last="Rossi">John J. Rossi</name>
<name sortKey="Rossi, John J" sort="Rossi, John J" uniqKey="Rossi J" first="John J" last="Rossi">John J. Rossi</name>
<name sortKey="Song, Min Sun" sort="Song, Min Sun" uniqKey="Song M" first="Min-Sun" last="Song">Min-Sun Song</name>
<name sortKey="Wu, Xiwei" sort="Wu, Xiwei" uniqKey="Wu X" first="Xiwei" last="Wu">Xiwei Wu</name>
</country>
</tree>
</affiliations>
</record>

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