I am now reading a paper about the purification and identification of mRNAs and its RNA binding proteins by using UV crosslinking and immunoprecipitation. I came upon this sentence which puzzled me
Up to 28% of all uridines present in 3' UTRs showed diagnostic T-C changes in the protein occupancy profiling sequence reads. This number is reasonably high, considering observations that typically only one of a few uridines in RNA binding sites when substituted by 4SU, crosslinks to proteins.
What I do not understand is why does 4-thiouracil (4SU) labelling in the cell show T-C changes. Would the uracil-adenine base pairing not be affected?
How does the 4SU labelling really work?