To validate our formaldehyde based RNA immunoprecipitation method we immunoprecipitated the RNA binding protein hnRNPH, which plays a role in mRNA splicing69 and identified the associated RNAs. Consistent with known interactions, we identified a strong enrichment for its binding to intronic regions of mRNA genes. We validated these observed results in mouse ES cells by performing UV-crosslinking experiments70–72 and identified nearly identical results. We identified a similar correlation between the UV and formaldehyde crosslinked samples as for biological replicates of UV crosslinked samples and formaldehyde crosslinked samples and highly comparable enrichments (data not shown).
