5′XP sRNA-seq: efficient identification of transcripts with and without 5′ phosphorylation reveals evolutionary conserved small RNA

Small RNA (sRNA) sequencing has been critical for our understanding of many cellular processes, including gene regulation. Nonetheless, the varying biochemical properties of sRNA, such as 5 ' nucleotide modifications, make many sRNA subspecies incompatible with common protocols for sRNA sequencing. Here we describe 5XP-seq that outlines a novel strategy that captures a more complete picture of sRNA. By tagging 5 ' P sRNA during library preparation, 5XP-seq combines an open approach that includes all types of 5MODIFIER LETTER PRIME-terminal modifications (5 ' X), with a selective approach for 5-phosphorylated sRNA (5 ' P). We show that 5XP-seq not only enriches phosphorylated miRNA and piRNA but successfully discriminates these sRNA from all other sRNA species. We further demonstrate the importance of this strategy by successful inter-species validation of sRNAs that would have otherwise failed, including human to insect translation of several tRNA (tRFs) and rRNA (rRFs) fragments. By combining 5 ' insensitive library strategies with 5 ' sensitive tagging, we have successfully tackled an intrinsic bias in modern sRNA sequencing that will help us reveal the true complexity and the evolutionary significance of the sRNA world.