Determinants of targeting by endogenous and exogenous microRNAs and siRNAs
Determinants of targeting by endogenous and exogenous microRNAs and siRNAs
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DOI：
10.1261/rna.768207
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发表时间：
2007-11-01
期刊：
影响因子：
4.5
通讯作者：
Burge, Christopher B.
中科院分区：
文献类型：
--
作者：
Nielsen, Cydney B.;Shomron, Noam;Burge, Christopher B.
脊椎动物mRNA经常被microRNA（miRNA）靶向用于转录后抑制，通过涉及39个UTR种子匹配与miRNA的59末端处的碱基配对的机制。通过分析miRNA或siRNA过表达或抑制后的表达阵列数据，我们发现mRNA倍数变化成倍增加（即，对数相加）与种子匹配计数的关系，并且单个8聚体种子匹配介导的下调与两个7聚体种子匹配相当。我们鉴定了几种增强种子匹配相关mRNA抑制的靶向决定簇，包括与miRNA碱基1相对的腺苷和与miRNA碱基9相对的腺苷或尿苷的存在，而与siRNA/miRNA的互补性无关。种子匹配的50个碱基59和39中增加的序列保守性和种子匹配的增加的Au含量39各自独立地与增加的mRNA下调相关。所有这些决定簇在保守的miRNA种子匹配附近富集，支持它们在内源性miRNA靶向中的活性。总之，我们的研究结果能够改善siRNA脱靶预测，允许保守和非保守的miRNA靶标的综合排名，并表明内源性和外源性miRNA/siRNA的靶向涉及相似或相同的决定簇。
Vertebrate mRNAs are frequently targeted for post-transcriptional repression by microRNAs ( miRNAs) through mechanisms involving pairing of 39 UTR seed matches to bases at the 59 end of miRNAs. Through analysis of expression array data following miRNA or siRNA overexpression or inhibition, we found that mRNA fold change increases multiplicatively (i.e., log-additively) with seed match count and that a single 8 mer seed match mediates down-regulation comparable to two 7 mer seed matches. We identified several targeting determinants that enhance seed match- associated mRNA repression, including the presence of adenosine opposite miRNA base 1 and of adenosine or uridine opposite miRNA base 9, independent of complementarity to the siRNA/miRNA. Increased sequence conservation in the; 50 bases 59 and 39 of the seed match and increased AU content 39 of the seed match were each independently associated with increased mRNA down-regulation. All of these determinants are enriched in the vicinity of conserved miRNA seed matches, supporting their activity in endogenous miRNA targeting. Together, our results enable improved siRNA off-target prediction, allow integrated ranking of conserved and nonconserved miRNA targets, and show that targeting by endogenous and exogenous miRNAs/siRNAs involves similar or identical determinants.