In plants, processing of precursor miRNAs (pre-miRNAs) by DCL1 produces mature miRNAs, which are loaded into AGOs to regulate their target RNAs mainly through two modes. The first mode, also known as the predominant way is that miRNAs cleave their targets (blue arrows), whereas the second mode involves miRNA-mediated translational regulation (grey arrows) (Rhoades et al. Cell,2002; Voinnet Cell,2009; Axtell, Annu Rev Plant Biol. 2013; Rogers et al. Plant Cell,2013).
The concept of conserved miRNAs target orthologous genes across species was first reported by Dr David Bartel’s lab. The conservation filter used in TargetScan (Lewis et al. Cell, 2003) has proved to be a robust way for searching animal miRNA targets. Such conservation strategy was later used in plant miRNA target prediction (Chorostecki et al. Bioinformatics, 2014). We previously developed the TarHunter pipeline that is able to automate identifying conserved miRNA targets in plants (Ma et al. Bioinformatics,2018).
Search NowDegradome sequencing or parallel analysis of RNA ends sequencing (PARE-seq) is a classic high-throughput method for identifying miRNA targets in plants (German et al. Nat Biotechnol,2008; Addo-Quaye et al. Curr Biol,2008). miRNA cleaved target RNAs have a 5’ phosphate that enables ligation to adaptor and subsequent deep sequencing. CleaveLand is a commonly used tool for degradome/PARE-seq analysis (Addo-Quaye et al. Bioinformatics,2009).
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In plants, a small set of miRNAs, particularly 22-nt in length, cleave target RNAs and trigger phased siRNAs (phasiRNAs) biogenesis (Allen et al. Cell, 2005; Liu et al. Plant Cell, 2020). In Arabidopsis, phasiRNAs are generally 21-nt, while in many monocot species, phasiRNAs have two classes: 21-nt and 24-nt.
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