MicroRNAs and their isomiRs function cooperatively to target common biological pathways.
MicroRNAs and their isomiRs function cooperatively to target common biological pathways.
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DOI：
10.1186/gb-2011-12-12-r126
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发表时间：
2011-12-30
期刊：
影响因子：
12.3
通讯作者：
Grimmond SM
中科院分区：
文献类型：
--
作者：
Cloonan N;Wani S;Xu Q;Gu J;Lea K;Heater S;Barbacioru C;Steptoe AL;Martin HC;Nourbakhsh E;Krishnan K;Gardiner B;Wang X;Nones K;Steen JA;Matigian NA;Wood DL;Kassahn KS;Waddell N;Shepherd J;Lee C;Ichikawa J;McKernan K;Bramlett K;Kuersten S;Grimmond SM
microRNA（miRNAs）的变体，称为isomiR，在深度测序研究中经常被报道;然而，这些变体的功能意义仍然存在争议。观察性研究表明，isomiR模式是非随机的，暗示这些分子可以被调节，因此是功能性的，尽管这些分子没有明确的生物学作用。为了评估isomiRs的生物学相关性，我们对10种成人组织进行了超深miRNA-seq，并创建了一个名为miRNA-MATE的分析管道来比对、注释和分析miRNAs及其isomiRs。我们发现isomiRs与典型的miRNA共享序列和表达特征，并且通常与典型的miRNA表达强烈相关。很大比例的isomiR可能来源于AGO 2切割，不依赖于Dicer。我们分离了多核糖体相关的mRNA，捕获了mRNA结合的miRNA，并发现isomiRs和典型的miRNA同样与翻译机制相关。最后，我们用编码isomiRs或其典型对应物的生物素化RNA双链体转染细胞，并直接测定其mRNA靶标。这些研究使我们能够通过实验确定全基因组mRNA靶点，这些实验表明，典型miRNA及其isomiRs抑制的功能mRNA网络存在大量重叠。总之，这些结果发现isomiRs是典型miRNA的生物学相关和功能合作伙伴，其协调作用于功能相关基因的靶向途径。这项工作揭示了miRNA转录组的复杂性，并有助于解释一个主要的miRNA悖论：当miRNA靶向的特异性仅由6至11个核苷酸介导时，生物过程的特异性调节如何发生。
Variants of microRNAs (miRNAs), called isomiRs, are commonly reported in deep-sequencing studies; however, the functional significance of these variants remains controversial. Observational studies show that isomiR patterns are non-random, hinting that these molecules could be regulated and therefore functional, although no conclusive biological role has been demonstrated for these molecules. To assess the biological relevance of isomiRs, we have performed ultra-deep miRNA-seq on ten adult human tissues, and created an analysis pipeline called miRNA-MATE to align, annotate, and analyze miRNAs and their isomiRs. We find that isomiRs share sequence and expression characteristics with canonical miRNAs, and are generally strongly correlated with canonical miRNA expression. A large proportion of isomiRs potentially derive from AGO2 cleavage independent of Dicer. We isolated polyribosome-associated mRNA, captured the mRNA-bound miRNAs, and found that isomiRs and canonical miRNAs are equally associated with translational machinery. Finally, we transfected cells with biotinylated RNA duplexes encoding isomiRs or their canonical counterparts and directly assayed their mRNA targets. These studies allow us to experimentally determine genome-wide mRNA targets, and these experiments showed substantial overlap in functional mRNA networks suppressed by both canonical miRNAs and their isomiRs. Together, these results find isomiRs to be biologically relevant and functionally cooperative partners of canonical miRNAs that act coordinately to target pathways of functionally related genes. This work exposes the complexity of the miRNA-transcriptome, and helps explain a major miRNA paradox: how specific regulation of biological processes can occur when the specificity of miRNA targeting is mediated by only 6 to 11 nucleotides.
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影响因子：
14.9
作者：
Ebhardt HA;Tsang HH;Dai DC;Liu Y;Bostan B;Fahlman RP
通讯作者：
Fahlman RP
影响因子：
48
作者：
Cloonan, Nicole;Forrest, Alistair R. R.;Grimmond, Sean M.
通讯作者：
Grimmond, Sean M.
影响因子：
64.5
作者：
Han, Jinju;Lee, Yoontae;Kim, V. Narry
通讯作者：
Kim, V. Narry
影响因子：
56.9
作者：
Giraldez, AJ;Mishima, Y;Schier, AF
通讯作者：
Schier, AF
DOI：
10.1126/science.1190809
发表时间：
2010-06-25
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Cifuentes D;Xue H;Taylor DW;Patnode H;Mishima Y;Cheloufi S;Ma E;Mane S;Hannon GJ;Lawson ND;Wolfe SA;Giraldez AJ
通讯作者：
Giraldez AJ