The m 7G cap is important for processing, stability, transport and translation ( 4).

In eukaryotes, the most common, or canonical, 5′-end modification of mRNAs is the N 7-methylguanosine (m 7G) cap, which is converted from the nascent 5′ triphosphate by three enzymatic reactions ( 3).

RNA modifications at the 5′ end play a particularly significant role in the ‘epitranscriptomic’ pathway because the 5′ end regulates most aspects of the life cycle of RNA, from biogenesis to decay ( 3–8). Recent advances in RNA sequencing techniques have uncovered novel RNA modifications and revealed their modes of regulation and impact on cellular processes and disease ( 1, 2). RNA modifications have emerged as key regulators of RNA function and metabolism. We have developed FAD-capQ to detect and quantify FAD-capped RNAs and determined that FAD caps are present on short RNAs (with less than ∼200 nucleotides) in human cells and that these RNAs are stabilized in the absence of DXO. The flavin of FAD and the pantetheine group of CoA contact the same region at the bottom of the active site tunnel, which undergoes conformational changes to accommodate the different cap moieties. FAD and CoA are accommodated in the DXO/Rai1 active site by adopting folded conformations. The crystal structures of mammalian DXO with 3′-FADP or CoA and fission yeast Rai1 with 3′-FADP provide elegant insight to these activities. Here, we report that these enzymes can also remove FAD and dephospho-CoA (dpCoA) non-canonical caps from RNA, and we have named these activities deFADding and deCoAping. In eukaryotes, the DXO/Rai1 enzymes can eliminate most of the incomplete and non-canonical NAD caps through their decapping, deNADding and pyrophosphohydrolase activities.

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