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GraphClust2: annotation and discovery of structured RNAs with scalable and accessible integrative clustering

View ORCID ProfileMilad Miladi, Eteri Sokhoyan, View ORCID ProfileTorsten Houwaart, Steffen Heyne, View ORCID ProfileFabrizio Costa, View ORCID ProfileBjörn Grüning, View ORCID ProfileRolf Backofen
doi: https://doi.org/10.1101/550335
Milad Miladi
1Bioinformatics Group, Department of Computer Science, University of Freiburg, Germany
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Eteri Sokhoyan
1Bioinformatics Group, Department of Computer Science, University of Freiburg, Germany
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Torsten Houwaart
2Institute of Medical Microbiology and Hospital Hygiene, University of Dusseldorf, Germany
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Steffen Heyne
3Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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Fabrizio Costa
4Department of Computer Science, University of Exeter, UK
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Björn Grüning
1Bioinformatics Group, Department of Computer Science, University of Freiburg, Germany
5ZBSA Centre for Biological Systems Analysis, University of Freiburg, Germany
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  • For correspondence: backofen@informatik.uni-freiburg.de gruening@informatik.uni-freiburg.de
Rolf Backofen
1Bioinformatics Group, Department of Computer Science, University of Freiburg, Germany
5ZBSA Centre for Biological Systems Analysis, University of Freiburg, Germany
6Center for Biological Signaling Studies (BIOSS), University of Freiburg, Germany
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  • For correspondence: backofen@informatik.uni-freiburg.de gruening@informatik.uni-freiburg.de
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Abstract

RNA plays essential roles in all known forms of life. Clustering RNA sequences with common sequence and structure is an essential step towards studying RNA function. With the advent of high-throughput sequencing (HTS) techniques, experimental and genomic data are expanding to complement the predictive methods. However, the existing methods do not effectively utilize and cope with the immense amount of data becoming available.

Hundreds of thousands of non-coding RNAs (ncRNAs) have been detected, however, the annotation of these ncRNAs is lacking behind. Here we present GraphClust2, a comprehensive approach for scalable clustering of RNAs based on sequence and structural similarities. GraphClust2 bridges the gap between HTS and structural RNA analysis, and provides an integrative solution by incorporating diverse experimental and genomic data in an accessible manner via the Galaxy framework. GraphClust2 can efficiently cluster and annotate large datasets of RNAs and supports structure probing data. We demonstrate that the annotation performance of clustering functional RNAs can be considerably improved. Furthermore, an off-the-shelf procedure is introduced for identifying locally conserved structure candidates in long RNAs. We suggest the presence and the sparsity of phylogenetically conserved local structures for a collection of long non-coding RNAs.

By clustering data from two CLIP experiments, we demonstrate the benefits of GraphClust2 for motif discovery under the presence of biological and methodological biases. Finally, we uncover prominent targets of doublestranded RNA binding protein Roquin-1, such as BCOR’s 3 UTR that contains multiple binding stem-loops which are evolutionary conserved.

Footnotes

  • Metatranscriptome large data clustering, Updated SLBP Figure 5, extended methods description, and some punctuation fixes.

  • 7.1 List of abbreviations

    ARI
    adjusted Rand index;
    CDE
    constitutive decay element;
    CLIP
    cross-linking immunoprecipitation;
    CM
    covariance model;
    DMS
    dimethyl sulfate;
    HPC
    high-performance computing;
    HTS
    high-throughput sequencing;
    lncRNA
    long non-coding RNA;
    MAF
    Multiz alignment format;
    mRNA
    messenger RNA;
    ncRNA
    non-coding RNA;
    RBP
    RNA binding protein;
    SCFG
    stochastic context-free grammar;
    SHAPE
    selective 2’-hydroxyl acylation analyzed by primer extension;
    SP
    Structure probing;
  • Copyright 
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    Posted October 16, 2019.
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    GraphClust2: annotation and discovery of structured RNAs with scalable and accessible integrative clustering
    Milad Miladi, Eteri Sokhoyan, Torsten Houwaart, Steffen Heyne, Fabrizio Costa, Björn Grüning, Rolf Backofen
    bioRxiv 550335; doi: https://doi.org/10.1101/550335
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    GraphClust2: annotation and discovery of structured RNAs with scalable and accessible integrative clustering
    Milad Miladi, Eteri Sokhoyan, Torsten Houwaart, Steffen Heyne, Fabrizio Costa, Björn Grüning, Rolf Backofen
    bioRxiv 550335; doi: https://doi.org/10.1101/550335

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