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PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays

Li, Bo and Tambe, Akshay and Aviran, Sharon and Pachter, Lior (2017) PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays. Cell Systems, 4 (5). pp. 568-574. ISSN 2405-4712. PMCID PMC5758053. doi:10.1016/j.cels.2017.04.007.

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A number of sequencing-based transcriptase drop-off assays have recently been developed to probe post-transcriptional dynamics of RNA-protein interaction, RNA structure, and RNA modification. Although these assays survey a diverse set of epitranscriptomic marks, we use the term toeprinting assays since they share methodological similarities. Their interpretation is predicated on addressing a similar computational challenge: how to learn isoform-specific chemical modification profiles in the face of complex read multi-mapping. We introduce PROBer, a statistical model and associated software, that addresses this challenge for the analysis of toeprinting assays. PROBer takes sequencing data as input and outputs estimated transcript abundances and isoform-specific modification profiles. Results on both simulated and biological data demonstrate that PROBer significantly outperforms individual methods tailored for specific toeprinting assays. Since the space of toeprinting assays is ever expanding and these assays are likely to be performed and analyzed together, we believe PROBer's unified data analysis solution will be valuable to the RNA community.

Item Type:Article
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URLURL TypeDescription CentralArticle
Li, Bo0000-0002-8019-8891
Pachter, Lior0000-0002-9164-6231
Additional Information:© 2017 Elsevier Inc. Received 6 July 2016, Revised 19 December 2016, Accepted 13 April 2017, Available online 10 May 2017. We thank Yiliang Ding, Yin Tang, Joel McManus, and Thomas Carlile for discussions and clarifications on the StructureFold, Mod-seeker, and Pseudo-seq methods. We thank Yeon Lee, Julian König, Eric Van Nostrand, Gabriel Pratt, and Gene Yeo for discussions on the iCLIP and eCLIP protocols. This work is supported by NIH grants R01 HG006129 to L.P. and R00 HG006860 to S.A., and by the Center for RNA Systems Biology at UC Berkeley (NIH P50GM102706 grant) to B.L. A.T. was partially supported by NIH Molecular Biophysics Training grant (NIH GM08295).
Funding AgencyGrant Number
NIHR01 HG006129
NIHR00 HG006860
NIH Predoctoral FellowshipGM08295
Subject Keywords:post-transcriptional regulation; toeprinting by high-throughput sequencing; bioinformatics; RNA structure probing; post-transcriptional modification of RNA nucleotides; RNA-protein interactions
Issue or Number:5
PubMed Central ID:PMC5758053
Record Number:CaltechAUTHORS:20170510-142406445
Persistent URL:
Official Citation:Bo Li, Akshay Tambe, Sharon Aviran, Lior Pachter, PROBer Provides a General Toolkit for Analyzing Sequencing-Based Toeprinting Assays, Cell Systems, Volume 4, Issue 5, 24 May 2017, Pages 568-574.e7, ISSN 2405-4712,
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:77353
Deposited By: Tony Diaz
Deposited On:12 May 2017 22:35
Last Modified:28 Mar 2022 21:54

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