1 rnaCrosslinkOO

Please check out the publication if you interesting in this tool and the github.

2 The COMRADES experiment


The COMRADES experimental protocol for the prediction of RNA structure in vivo was first published in 2018 (Ziv et al., 2019) where they predicted the structure of the Zika virus. The protocol has subsequently been use to predict the structure of SARS-CoV-2 (Ziv et al., 2020). Have a look to get an understanding of the protocol:

  • COMRADES determines in vivo RNA structures and interactions. (2018). Omer Ziv, Marta Gabryelska, Aaron Lun, Luca Gebert. Jessica Sheu-Gruttadauria and Luke Meredith, Zhong-Yu Liu, Chun Kit Kwok, Cheng-Feng Qin, Ian MacRae, Ian Goodfellow , John Marioni, Grzegorz Kudla, Eric Miska. Nature Methods. Volume 15. https://doi.org/10.1038/s41592-018-0121-0

  • The Short- and Long-Range RNA-RNA Interactome of SARS-CoV-2. (2020). Omer Ziv, Jonathan Price, Lyudmila Shalamova, Tsveta Kamenova, Ian Goodfellow, Friedemann Weber, Eric A. Miska. Molecular Cell, Volume 80 https://doi.org/10.1016/j.molcel.2020.11.004

Figure from Ziv et al., 2020. Virus-inoculated cells are crosslinked using clickable psoralen. Viral RNA is pulled down from the cell lysate using an array of biotinylated DNA probes, following digestion of the DNA probes and fragmentation of the RNA. Biotin is attached to crosslinked RNA duplexes via click chemistry, enabling pulling down crosslinked RNA using streptavidin beads. Half of the RNA duplexes are proximity-ligated, following reversal of the crosslinking to enable sequencing. The other half serves as a control, in which crosslink reversal proceeds the proximity ligation
Figure from Ziv et al., 2020. Virus-inoculated cells are crosslinked using clickable psoralen. Viral RNA is pulled down from the cell lysate using an array of biotinylated DNA probes, following digestion of the DNA probes and fragmentation of the RNA. Biotin is attached to crosslinked RNA duplexes via click chemistry, enabling pulling down crosslinked RNA using streptavidin beads. Half of the RNA duplexes are proximity-ligated, following reversal of the crosslinking to enable sequencing. The other half serves as a control, in which crosslink reversal proceeds the proximity ligation

After sequencing, short reads are produced similar to a spliced / chimeric RNA read but where one half of the read corresponds to one half of a structural RNA duplex and the other half of the reads corresponds to the other half of the structural RNA duplex. This package has been designed to analyse this data. The short reads need to be prepared in a specific way to be inputted into this package.

There are other types of crosslinking data!