miRTCat：人类和小鼠 microRNA 靶位点的综合图谱，包括非经典起始凸起。

miRTCat: a comprehensive map of human and mouse microRNA target sites including non-canonical nucleation bulges.

机构信息

Samsung Biomedical Research Institute, Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University and Samsung Research Institute for Future Medicine, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul 135-710, Korea.

出版信息

Bioinformatics. 2013 Aug 1;29(15):1898-9. doi: 10.1093/bioinformatics/btt296. Epub 2013 May 24.

DOI:10.1093/bioinformatics/btt296

PMID:23709495

Abstract

SUMMARY

MicroRNAs (miRNAs) regulate various biological functions by binding hundreds of transcripts to impart post-transcriptional repression. Recently, by applying a transcriptome-wide experimental method for identifying miRNA target sites (Ago HITS-CLIP), a novel non-canonical target site, named 'nucleation bulge', was discovered as widespread, functional and evolutionally conserved. Although such non-canonical nucleation bulges have been proven to be predictive by using 'pivot pairing rule' and sequence conservation, this approach has not been applied yet. To facilitate the functional studies of non-canonical miRNA targets, we implement miRTCat: a comprehensive searchable map of miRNA target sites, including non-canonical nucleation bulges, not only mapped in experimentally verified miRNA-bound regions but also predicted in all 3'-untranslated regions (3'-UTRs) derived from human and mouse (∼15.6% as expected false-positive results).

AVAILABILITY

http://ion.skku.edu/mirtcat.

CONTACT

swchi@skku.edu

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

MicroRNAs（miRNAs）通过结合数百个转录本来施加转录后抑制，从而调节各种生物功能。最近，通过应用一种全转录组识别 miRNA 靶标位点的实验方法（Ago HITS-CLIP），发现了一种新的非规范靶标位点，称为“起始凸起”，该位点具有广泛、功能和进化保守性。尽管已经通过“枢轴配对规则”和序列保守性证明了这种非规范的起始凸起具有预测性，但尚未应用这种方法。为了促进非规范 miRNA 靶标的功能研究，我们实现了 miRTCat：一个包含非规范起始凸起的 miRNA 靶标位点的综合可搜索图谱，不仅在实验验证的 miRNA 结合区域中进行了映射，而且在源自人和小鼠的所有 3'-非翻译区（3'-UTRs）中进行了预测（预计约有 15.6%的假阳性结果）。