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IRIS:A method for predicting in vivo RNA secondary structures using PARIS data

Quantitative Biology 2020年第4期8卷 369-381页

作者： Jianyu Zhou Pan Li Wanwen Zeng Wenxiu Ma Zhipeng Lu Rui Jiang Qiangfeng Cliff Zhang Tao Jiang Bioinformatics Division BNRISTTsinghua UniversityBeijing 100084China Department of Computer Science and Technology Tsinghua UniversityBeijing 100084China MOE Key Laboratory of Bioinformatics Beijing Advanced Innovation Center for Structural BiologyCenter for Synthetic and Systems BiologyTsinghua-Peking Center for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing 100084China College of Software Nankai UniversityTianjin 300071China Department of Statistics University of CaliforniaRiversideCA 92521USA Department of Pharmacology and Pharmaceutical Sciences University of Southern CaliforniaCA 90089USA Department of Automation Tsinghua UniversityBeijing 100084China Department of Computer Science and Engineering University of CaliforniaRiversideCA 92521USA

Background:RNA secondary structures play a pivotal role in posttranscriptional regulation and the functions of non-coding RNAs,yet in vivo RNA secondary structures remain ***(Psoralen Analysis of RNA Interactions and structures)is a recently developed high-throughput sequencing-based approach that enables direct capture of RNA duplex structures in ***,the existence of incompatible,fuzzy pairing information obstructs the integration of PARIS data with the existing tools for reconstructing RNA secondary structure models at the single-base ***:We introduce IRIS,a method for predicting RNA secondary structure ensembles based on PARIS *** generates a large set of candidate RNA secondary structure models under the guidance of redistributed PARIS reads and then uses a Bayesian model to identify the optimal ensemble,according to both thermodynamic principles and PARIS ***:The predicted RNA structure ensembles by IRIS have been verified based on evolutionary conservation information and consistency with other experimental RNA structural *** is implemented in Python and freely available at http://***:IRIS capitalizes upon PARIS data to improve the prediction of in vivo RNA secondary structure *** expect that IRIS will enhance the application of the PARIS technology and shed more insight on in vivo RNA secondary structures.

关键词： RNA secondary structure PARIS data in vivo structure ensembles incompatible reads

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