Supplementary Table 1. RIDome compared to other RNA-centric methods for the identification of RNA-protein interactions
Points of strength
vs in vitro
RNA affinity capture methods 1-4
vs in vivo
purification of endogenous RNPs 5-8
RIDome identifies the RNA-binding domains directly involved in the interaction
The ORF cDNA clone is immediately available after selection for downstream
validation purposes
A main challenge of MS-based studies is that proteins, unlike DNA or RNA, cannot
be amplified. This puts a practical constraint on the minimum material required for
purification schemes. Less expressed RBPs require more starting and the more likely
background from abundant nonspecific RNPs is to interfere with the real signal;
in RIDome, the relative abundancy of RNA-binding proteins in the library is
normalized, thus each RBP should be equally represented
The ORF library virtually represents the whole RBPome
RNA-protein crosslinking not required
Points of weakness
vs in vitro
vs in vivo
RNA affinity capture methods 1-4
purification of endogenous RNPs 5-8
RIDome is not suitable to detect interactions when post-translational modifications
are involved
RIDome cannot be employed to study RNA-protein interactions at specific cell
conditions (e.g. ageing, stress, differentiation)
Filtered ORF libraries are not commercially available
RIDome probes interactions in vitro, and
therefore validation of the results in cells
is required to establish the in vivo
relevance of the interaction.
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