Tracking microRNA Processing Signals by Degradome Sequencing Data Analysis.

Dongliang Yu,Weishan Shao,Xiaoxia Ma,Hidetaka Ito,Yijun Meng,Min Xu,Huizhong Wang

doi:10.3389/fgene.2018.00546

Dongliang Yu, Weishan Shao + Show 5 more

Open Access

https://doi.org/10.3389/fgene.2018.00546

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Abstract

Degradome sequencing (degradome-seq) was widely used for cleavage site mapping on the microRNA (miRNA) targets. Here, the application value of degradome-seq data in tracking the miRNA processing intermediates was reported. By adopting the parameter “signal/noise” ratio, prominent degradome signals on the miRNA precursors were extracted. For the 15 species analyzed, the processing of many miRNA precursors were supported by the degradome-seq data. We found that the supporting ratio of the “high-confidence” miRNAs annotated in miRBase was much higher than that of the “low-confidence.” For a specific species, the percentage of the miRNAs with degradome-supported processing signals was elevated by the increment of degradome sampling diversity. More interestingly, the tissue- or cell line-specific processing patterns of the miRNA precursors partially contributed to the accumulation patterns of the mature miRNAs. In this study, we also provided examples to show the value of the degradome-seq data in miRNA annotation. Based on the distribution of the processing signals, a renewed model was proposed that the stems of the miRNA precursors were diced through a “single-stranded cropping” mode, and “loop-to-base” processing was much more prevalent than previously thought. Together, our results revealed the remarkable capacity of degradome-seq in tracking miRNA processing signals.

Highlights

Degradome sequencing (Addo-Quaye et al, 2008), referred to as parallel analysis of RNA ends (PARE) (German et al, 2008) or genome-wide mapping of uncapped and cleaved transcripts (GMUCT) (Willmann et al, 2014), is an efficient strategy developed for transcriptomewide detection of the uncapped 5 ends of the polyadenylated RNAs
After pre-treatment, the degradome signatures were mapped onto the miRNA precursors obtained from miRBase (Kozomara and Griffiths-Jones, 2014), and the perfectly mapped signatures were retained
The processing of a mature miRNA was regarded to be supported by degradome-seq data, if a prominent degradome signal could be identified at its 5 end or 3 end + 1 nt

Summary

Introduction

Degradome sequencing (Addo-Quaye et al, 2008), referred to as PARE (German et al, 2008) or GMUCT (Willmann et al, 2014), is an efficient strategy developed for transcriptomewide detection of the uncapped 5 ends of the polyadenylated RNAs. The first cropping by Drosha takes place in the nucleus, while the second cropping by Dicer occurred in the cytoplasm (Carthew and Sontheimer, 2009) It is well-known that most of the miRNA genes are transcribed by RNA polymerase II in both animals (Lee et al, 2004) and plants (Xie et al, 2005), resulting in the polyadenylated primary transcripts. In this regard, it was proposed that the processing intermediates of the miRNA precursors could be detected by degradome-seq (Meng et al, 2010)

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