MicroRNA modules prefer to bind weak and unconventional target sites.
MicroRNA modules prefer to bind weak and unconventional target sites.
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DOI：
10.1093/bioinformatics/btu833
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发表时间：
2015-05-01
期刊：
影响因子：
--
通讯作者：
Hu H
中科院分区：
文献类型：
--
作者：
Ding J;Li X;Hu H
动机：MicroRNA (miRNA) 在基因调控中发挥着关键作用。尽管众所周知多个miRNA可以作为miRNA模块来协同调节共同的靶标mRNA，但对miRNA模块的理解仍处于起步阶段。结果：我们利用最近生成的高通量实验数据来研究 miRNA 模块。我们预测了 181 个 miRNA 模块和 306 个潜在 miRNA 模块。我们观察到，这些预测模块的靶位点总体上比那些未结合 miRNA 模块的靶位点更弱。我们还发现预测模块中的 miRNA 更喜欢结合非常规目标位点而不是经典位点。令人惊讶的是，与之前的研究相反，我们发现来自相同 miRNA 模块的大多数相邻 miRNA 靶位点不在 10-130 个核苷酸的范围内。有趣的是，当 miRNA 模块结合非常规而非规范位点时，同一模块中 miRNA 结合的靶位点距离更短。我们的研究为 miRNA 结合和 miRNA 靶位点提供了新的线索，这可能会增进我们对 miRNA 调控的理解。可用性和实施：软件 miRModule 可以在 http://hulab.ucf.edu/research/projects/miRNA/miRModule 免费下载。补充信息：补充数据可在生物信息学在线获取。联系方式：haihu@cs.ucf.edu 或 xiaoman@mail.ucf.edu。
Motivation: MicroRNAs (miRNAs) play critical roles in gene regulation. Although it is well known that multiple miRNAs may work as miRNA modules to synergistically regulate common target mRNAs, the understanding of miRNA modules is still in its infancy. Results: We employed the recently generated high throughput experimental data to study miRNA modules. We predicted 181 miRNA modules and 306 potential miRNA modules. We observed that the target sites of these predicted modules were in general weaker compared with those not bound by miRNA modules. We also discovered that miRNAs in predicted modules preferred to bind unconventional target sites rather than canonical sites. Surprisingly, contrary to a previous study, we found that most adjacent miRNA target sites from the same miRNA modules were not within the range of 10–130 nucleotides. Interestingly, the distance of target sites bound by miRNAs in the same modules was shorter when miRNA modules bound unconventional instead of canonical sites. Our study shed new light on miRNA binding and miRNA target sites, which will likely advance our understanding of miRNA regulation. Availability and implementation: The software miRModule can be freely downloaded at http://hulab.ucf.edu/research/projects/miRNA/miRModule. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: haihu@cs.ucf.edu or xiaoman@mail.ucf.edu.
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DOI：
10.1093/bioinformatics/btr206
发表时间：
2011-07-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Zhang S;Li Q;Liu J;Zhou XJ
通讯作者：
Zhou XJ
影响因子：
14.9
作者：
Saetrom P;Heale BS;Snøve O Jr;Aagaard L;Alluin J;Rossi JJ
通讯作者：
Rossi JJ
影响因子：
14.9
作者：
Xu J;Li CX;Li YS;Lv JY;Ma Y;Shao TT;Xu LD;Wang YY;Du L;Zhang YP;Jiang W;Li CQ;Xiao Y;Li X
通讯作者：
Li X
影响因子：
64.5
作者：
Hafner M;Landthaler M;Burger L;Khorshid M;Hausser J;Berninger P;Rothballer A;Ascano M Jr;Jungkamp AC;Munschauer M;Ulrich A;Wardle GS;Dewell S;Zavolan M;Tuschl T
通讯作者：
Tuschl T
影响因子：
4.4
作者：
Wang Y;Li X;Hu H
通讯作者：
Hu H