Challenges inherent to the sequencing and quantification of short non‐coding RNAs and how to address them

The tRNA Val half: A strong endogenous Toll-like receptor 7 ligand with a 5′-terminal universal sequence signature

“…sncRNAs generally possess either a hydroxyl group (OH), a phosphate (P), or a 2′,3′-cyclic phosphate (cP) at their termini ( 26 ). To date, most sncRNA sequencing studies have relied on a standard small RNA-seq method in which 5′- and 3′-adaptors (AD) can be ligated only to the 5′-P and 3′-OH ends of RNAs; thus, current sncRNA analyses significantly underrepresent non-miRNA-sncRNAs lacking the 5′-P or 3′-OH ends ( 26 – 28 ). This notion is especially important when it comes to the sequencing analyses of ex-sncRNAs because many ex-sncRNAs lack 5′-P or 3′-OH ( 29 – 31 ).…”