Widespread siRNA "off-target'' transcript silencing mediated by seed region sequence complementarity
Widespread siRNA "off-target'' transcript silencing mediated by seed region sequence complementarity
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DOI：
10.1261/rna.25706
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发表时间：
2006-07-01
期刊：
影响因子：
4.5
通讯作者：
Linsley, Peter S.
中科院分区：
文献类型：
--
作者：
Jackson, Aimee L.;Burchard, Julja;Linsley, Peter S.
转基因的siRNAs和miRNAs调控大量的转录本，这些转录本只与RNA双链的活性链具有有限的互补性。这一过程反映了miRNAs对靶的自然调控，但却是siRNA介导的沉默的意外结果(“非靶”)。在这里，我们证明了这种意外的脱靶沉默是普遍存在的，并且发生的方式使人想起miRNAs的靶沉默。在被siRNAs沉默的非预期转录本中，有很高比例的转录产物与siRNA的种子区存在3‘UTR序列互补。SiRNA种子区内的碱基错配减少了原始非靶标转录本的集合，但产生了与错配种子序列具有序列互补性的新的沉默转录本集合。可诱导的shRNA沉默了被相同序列的siRNA沉默的转录子集，表明意外的沉默是序列介导的，并且与递送方法无关。在所有情况下，非靶标转录本沉默伴随着相应蛋白质的丢失，并且发生的依赖于siRNA浓度，类似于靶转录本沉默。因此，siRNA或shRNA种子区的短序列互补性是沉默非预期转录本的关键。
Transfected siRNAs and miRNAs regulate numerous transcripts that have only limited complementarity to the active strand of the RNA duplex. This process reflects natural target regulation by miRNAs, but is an unintended ("off-target'') consequence of siRNA-mediated silencing. Here we demonstrate that this unintended off-target silencing is widespread, and occurs in a manner reminiscent of target silencing by miRNAs. A high proportion of unintended transcripts silenced by siRNAs showed 3' UTR sequence complementarity to the seed region of the siRNA. Base mismatches within the siRNA seed region reduced the set of original off-target transcripts but generated new sets of silenced transcripts with sequence complementarity to the mismatched seed sequence. An inducible shRNA silenced a subset of transcripts that were silenced by an siRNA of the same sequence, demonstrating that unintended silencing is sequence mediated and is independent of delivery method. In all cases, off-target transcript silencing was accompanied by loss of the corresponding protein and occurred with dependence on siRNA concentration similar to that of silencing of the target transcript. Thus, short stretches of sequence complementarity to the siRNA or shRNA seed region are key to the silencing of unintended transcripts.