Response to the Comment on “DpCoA tagSeq: Barcoding dpCoA-Capped RNA for Direct Nanopore Sequencing via Maleimide-Thiol Reaction”

If the 5’ cap fits (wear it) – Non-canonical RNA capping

“… Nudt12 28 , Nudt13, Nudt16, DXO 76 U1 snRNA binding to target 101 , correlation with aging in mice 82 FAD Bacteria Unknown LC-MS 112 RNA polymerase 67 RNase AM 117 Unknown Yeast Unknown LC-MS 112 RNA polymerase (?) Rai1 113 , RNase AM 114 Unknown Mammalian cells Viral transcripts (HCV 117 , DENV-2 112 ) LC-MS 112 , sequencing 117 Viral RNA polymerase 117 DXO, Nudt2 28 , Nudt16 28 , XrnI 114 (Plant AtNudt23 used for sequencing 117 ) Evasion from innate immune recognition 117 CoA Bacteria Unknown LC-MS 70 , mercury affinity electrophoresis 104 RNA polymerase 69 and phosphopantetheine adenylyltransferase 111 NudC 105 , NudL 106 Unknown Mice livers mRNAs 108–110 ...…”

“…This led to the development of dpCoA tagSeq, which uses a maleimide-modified RNA to “tag” the dpCoA-RNA at the 5' end with a barcode sequence. Using the dpCoA tagSeq method, the authors identified more than 40 genes that code for RNAs that are subject to dpCoA modification in mouse livers [ 108 ]. It is important to note, however, that the vast majority of the identified sequences in this study were the results of false positives coming from chimeric reads between the sequences of highly abundant transcripts and the spike-in dpCoA-RNA added to the sample [ 109 ].…”