Abstract
The reversible N6-methyladenosine (m6A) modification of eukaryotic messenger RNAs (mRNAs) is a widespread regulatory mechanism that impacts every step in the mRNA life cycle. The effect of m6A on mRNA fate depends on the binding of "m6A reader" proteins - RNA binding proteins that specifically bind to RNAs containing m6A. Here, we describe an RNA pull-down method that can be used to identify novel m6A reader proteins starting from a known m6A-modified site in cellular or viral RNA. We further describe how a combination of immunoprecipitation-based sequencing methods can be used to identify m6A-modified sites bound by an m6A reader protein on a transcriptome-wide level. The discovery of new m6A reader proteins and their m6A-modified targets would provide further insight into the mechanisms and functions of m6A in the cell.