rnaCrosslinkOO – an object-oriented R package for the analysis of RNA structural data generated by RNA crosslinking experiments

RNA molecules stand as pivotal players, orchestrating a myriad of essential functions such as gene expression regulation, RNA processing, and localization. However, much like a tangled web, the structures of RNA molecules remain enigmatic, holding key insights into their functionality and potential implications for disease diagnosis and treatment.

To untangle this web of RNA structures and unlock their secrets, researchers have long sought sophisticated tools capable of analyzing complex in vivo RNA structural data. rnaCrosslinkOO (RNA Crosslink Object-Oriented) is a groundbreaking software package developed by researchers’ at the University of Cambridge and designed to revolutionize the analysis of RNA structures derived from the COMRADES (Crosslinking of Matched RNA and Deep Sequencing) method.

rnaCrosslinkOO

rnaCrosslinkOO. Main steps of the algorithm are shown in a,b, and c and optional analysis steps are shown in d-i. (a) Input for rnaCrosslinkOO and the main slots of the rnaCrosslinkDataSet object displayed with grey boxes with the functions used to access the slots in green. sampleTable—A table with the following column names; file (file path for sample), group (a code for the sample group), sample (a numeric value showing which replicates belong to which group), sampleName (a unique sample identifier). inputFiles, matrixList—The inputFiles slot contains the duplexes in their original input format (Supplementary Table S3) and the matrixList contains the data as contact matrices. clusterGRangesList, ClusterTableList—These two slots are related to the clustering of the duplexes and contain a GRanges object and data frame of the cluster coordinates. viennaStructures, dgs, clusterTableFolded, and interactionTable—These slots relate to the folding of the RNA. The viennaStructures and dgs slots contain the vienna format structures and the free energy value for the predicted structures for each sample. The interactionTable contains the constraints identified from folding each of the clusters and the clusterTableFolded slot contains the predicted fold for each cluster. (a–i) Schematics and examples of steps in the rnaCrosslinkOO package, further detail for each step can be found in the main text.

Main steps of the algorithm are shown in a,b, and c and optional analysis steps are shown in d-i. (a) Input for rnaCrosslinkOO and the main slots of the rnaCrosslinkDataSet object displayed with grey boxes with the functions used to access the slots in green. sampleTable—A table with the following column names; file (file path for sample), group (a code for the sample group), sample (a numeric value showing which replicates belong to which group), sampleName (a unique sample identifier). inputFiles, matrixList—The inputFiles slot contains the duplexes in their original input format and the matrixList contains the data as contact matrices. clusterGRangesList, ClusterTableList—These two slots are related to the clustering of the duplexes and contain a GRanges object and data frame of the cluster coordinates. viennaStructures, dgs, clusterTableFolded, and interactionTable—These slots relate to the folding of the RNA. The viennaStructures and dgs slots contain the vienna format structures and the free energy value for the predicted structures for each sample. The interactionTable contains the constraints identified from folding each of the clusters and the clusterTableFolded slot contains the predicted fold for each cluster. (a–i) Schematics and examples of steps in the rnaCrosslinkOO package, further detail for each step can be found in the main text.

rnaCrosslinkOO offers a comprehensive pipeline, guiding researchers from the raw sequencing reads to the identification and comparison of intricate RNA structural features. This innovative toolset includes a multitude of functionalities, including read processing and alignment, clustering of duplexes, data exploration, folding, and comparisons of RNA structures.

One of the standout features of rnaCrosslinkOO is its ability to facilitate comparisons between different experimental conditions, shedding light on how RNA structures vary under different biological contexts. Moreover, the software enables the identification of inter-RNA interactions, providing valuable insights into the complex networks formed by RNA molecules within the cell.

Furthermore, rnaCrosslinkOO goes beyond mere structural analysis by incorporating reactivity data, enhancing the accuracy of RNA structure prediction. By leveraging this additional information, researchers can gain a deeper understanding of RNA dynamics and function, paving the way for more targeted approaches to disease diagnosis and treatment.

rnaCrosslinkOO represents a significant leap forward in the field of RNA research, offering a powerful toolkit for unraveling the mysteries of RNA structures and their implications for cellular function and disease. With its user-friendly interface and comprehensive analytical capabilities, this software holds the promise of transforming our understanding of RNA biology and accelerating the development of novel therapeutic interventions.

Availability – rnaCrosslinkOO is freely available to noncommercial users and implemented in R, with the source code and documentation accessible at https://CRAN.R-project.org/package=rnaCrosslinkOO.

Price JL, Ziv O, Pinckert ML, Lim A, Miska EA. (2024) rnaCrosslinkOO: an object-oriented R package for the analysis of RNA structural data generated by RNA crosslinking experiments. Bioinformatics 40(4):btae193. [article]

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