With SHIFTR you can identify proteins directly bound to a specific region within any endogenous RNA. In addition to delivering region-resolution, SHIFTR requires orders of magnitude lower input material compared to the state-of-the-art, thus removing a critical bottleneck.

In brief, SHIFTR relies on the sequence-independent isolation of crosslinked RNA-protein complexes by organic phase separation as described in OOPS, XRNAX, or PTex.

Proteins bound to a specific RNA can be released from interphase extracts by selectively degrading the RNA of interest, for instance with RNase H + specific DNA probes. Loss of the RNA leads to a SHIFT of crosslinked proteins to the organic phase in the next extraction step.

SHIFTR works for RNAs of different length and abundance (snRNAs, lncRNAs, mRNAs) and is compatible with sequentially releasing interactomes for multiple target RNAs in a single experiment.

Using SHIFTR, we identify interactions of the 5′ and 3′-terminal regions of authentic SARS-CoV-2 RNAs produced during infection and accurately recover known and novel RNA interactors.