Paired-end small RNA sequencing reveals a possible overestimation in the isomiR sequence repertoire previously reported from conventional single read data analysis

Abstract Background Next generation sequencing has allowed the discovery of miRNA isoforms, termed isomiRs. Some isomiRs are derived from imprecise processing pre-miRNA precursors, leading to length variants. Additional variability is introduced by non-templated addition bases at ends or editing internal bases, resulting in base differences relative template DNA sequence. We hypothesized that some component isomiR variation reported so far could be due systematic technical noise and not real. Results have developed XICRA pipeline analyze small RNA data level. exploited its ability use single merged reads compare results paired-end (PE) with those (SR) address whether detectable sequence canonical miRNAs found true biological variations result errors sequencing. detected non-negligible between SR PE which primarily affect putative internally edited isomiRs, a much smaller frequency terminal changing This relevant for identification datasets. Conclusions conclude potential artifacts and/or an overestimation abundance diversity isoforms. Efforts annotating isomiRnome should take this into account.