Bidirectional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1

Zhu, Hongliang; Zhou, Yuyi; Castillo-González, Claudia; Lu, Amber; Ge, Chunxiao; Zhao, Ying; Liu, Duan; Li, Zhaohu; Axtell, Michael J.; Wang, Xiu Jie; Zhang, Xiuren

doi:10.1038/nsmb.2646

Cited by 135 publications

(147 citation statements)

References 44 publications

(62 reference statements)

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“…Loop-to-base processing occurs in specific cases, such as miR159 and miR319 (Bologna et al, 2009). A unique case of bidirectional processing was observed for miR166, where it seems to play a regulatory role (Zhu et al, 2013). Plants also have non-canonical miRNAs, such as mirtrons, which skip the first cleavage step by DCL1 (Meng and Shao, 2012).…”

Section: Rdr6mentioning

confidence: 99%

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

Pačes

Nič²,

Novotný³

et al. 2017

EFSA Supporting Publications

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This report is the outcome of an EFSA procurement aiming at investigating and summarising the state of knowledge on (I) the mode-of-action of dsRNA and miRNA pathways, (II) the potential for nontarget gene regulation by dsRNA-derived siRNAs or miRNAs, (III) the determination of siRNA pools in plant tissues and the importance of individual siRNAs for silencing. The report is based on a comprehensive and systematic literature search, starting with the identification and retrieval of~190,000 publications related to the research area and further filtered down with keywords to produce focused collections used for subsequent screening of titles and abstracts. The report is comprised of an (I) Introduction to the field of small RNAs, (II) a Data and Methodologies section containing strategies used for literature search and study selection, and (III) the Results of the literature review organized according to the three main procurement tasks. The outcome of the first task reviews dsRNA and miRNA pathways in mammals (including humans), birds, fish, arthropods, annelids, molluscs, nematodes, and plants. Eight taxon-dedicated chapters are based on~1,400 cumulative references chosen from~10,000 inspected titles and abstracts. We review conserved and divergent aspects of small RNA pathways and dsRNA responses in animals and plants including structure and function of key proteins as well as four basic mechanisms: genome-encoded posttranscriptional regulations (miRNA), degradation of RNAs by short interfering RNA pools generated from long dsRNA (RNAi), transcriptional silencing, and sequence-independent responses to dsRNA. The outcome of the second task focuses on base pairing between small RNAs and their target RNAs and predictability of biological effects of small RNAs in animals and plants. The outcome of the last task reviews methodology, siRNA pools, and movement of small RNAs in plants. Potential transfer of small RNAs between species and circulating miRNAs in mammals is described in the final chapter.

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Section: Rdr6mentioning

confidence: 99%

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

Pačes

Nič²,

Novotný³

et al. 2017

EFSA Supporting Publications

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“…In Arabidopsis thaliana, four DCLs display specialized functions by producing specific sRNA products (Bologna and Voinnet 2014). The precise processing of microRNAs (miRNAs) from imperfect, foldback endogenous transcripts is mostly dependent on DCL1, the activity of which is aided by the RNA-binding partner Hyponastic Leaves 1 (HYL1) and Serrate (Kurihara et al 2006;Dong et al 2008;Zhu et al 2013). The other three DCLs participate in the production of small interfering RNAs (siRNAs).…”

Section: Introductionmentioning

confidence: 99%

Biochemical and genetic functional dissection of the P38 viral suppressor of RNA silencing

Iki

Tschopp

Voinnet

2017

RNA

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Phytoviruses encode viral suppressors of RNA silencing (VSRs) to counteract the plant antiviral silencing response, which relies on virus-derived small interfering (si)RNAs processed by Dicer RNaseIII enzymes and subsequently loaded into ARGONAUTE (AGO) effector proteins. Here, a tobacco cell-free system was engineered to recapitulate the key steps of antiviral RNA silencing and, in particular, the most upstream double-stranded (ds)RNA processing reaction, not kinetically investigated thus far in the context of plant VSR studies. Comparative biochemical analyses of distinct VSRs in the reconstituted assay showed that in all cases tested, VSR interactions with siRNA duplexes inhibited the loading, but not the activity, of antiviral AGO1 and AGO2. Turnip crinkle virus P38 displayed the additional and unique property to bind both synthetic and RNA-dependent-RNA-polymerase-generated long dsRNAs, and inhibited the processing into siRNAs. Single amino acid substitutions in P38 could dissociate dsRNAprocessing from AGO-loading inhibition in vitro and in vivo, illustrating dual-inhibitory strategies discriminatively deployed within a single viral protein, which, we further show, are bona fide suppressor functions that evolved independently of the conserved coat protein function of P38.

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“…Plant miRNA precursor can be processed either base-to-loop or loop-to-base or bidirectional, depending on the secondary structures. In longer stems, the processing is sequential producing one or more miRNA/miRNA* duplex (Zhu et al, 2013;Cuperus et al, 2009;Bologna et al, 2009;Mateos et al, 2010;Werner et al, 2010;Song et al, 2010). Three independent research groups (Song et al, 2010;Werner et al, 2010;Mateos et al, 2010) using mutagenesis based structure-function approach on selected conserved miRNAs have shown that in base-to-loop processing, the first cut mediated by DCL1 and its partners is made ~15-nt upstream of a big bulge or ssRNA-dsRNA junction from the base.…”

Section: Structural Determinants Of Mirna Biogenesismentioning

confidence: 99%

Regulation of Plant miRNA Biogenesis

Anushree¹,

Shivaprasad

2017

Proceedings of the Indian National Science Academy

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Micro (mi)RNAs are small regulatory RNA molecules involved in post-transcriptional silencing of their target mRNAs. In plants, these miRNAs target mRNAs coding for transcription factors and key regulators, thus modulating plant development, defence, and metabolic processes. miRNAs mostly originate from MIR genes that are transcribed to long primary (pri)miRNA transcripts by Pol II. These pri-miRNA transcripts fold-back to give rise to specific stem-loop structures that are cleaved by Dicer-like (DCL) proteins to Pre-miRNA intermediates. Pre-miRNAs are precisely processed into mature miRNA/miRNA* duplex of 20-22-nt length by DCL1 with the help of few accessory proteins. It is not known why only one or rarely more than one miRNA results from these long dsRNA precursors. In this review, we discuss recent studies including our unpublished work on structural and sequence determinants of plant miRNAs that distinguish them from their precursor regions. These determinants play a major role in accurate and precise dicing of miRNAs from their precursors, thus contributing to abundance and stability of mature miRNAs.

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Bidirectional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1

Cited by 135 publications

References 44 publications

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

Literature review of baseline information to support the risk assessment of RNAi‐based GM plants

Biochemical and genetic functional dissection of the P38 viral suppressor of RNA silencing

Regulation of Plant miRNA Biogenesis

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