Regulation of miRNA abundance by RNA binding protein TOUGH in
            <i>Arabidopsis</i>

Ren, Guodong; Xie, Meng; Dou, Yongchao; Zhang, Shuxin; Zhang, Chi; Yu, Bin

doi:10.1073/pnas.1204915109

Cited by 172 publications

(207 citation statements)

References 34 publications

Supporting

Mentioning

203

Contrasting

Order By: Relevance

“…TOUGH (TGH), another ssRNA-binding protein, is also a component of the plant microprocessor. TGH contributes to the interaction between pri-miRNA and HYL1 and may regulate DCL1 cleavage efficiency and/or recruitment of pri-miRNAs (29). A. thaliana encodes four additional dsRNA-binding proteins, DRB2-5, which are closely related to HYL1.…”

Section: Significancementioning

confidence: 99%

RNA-binding protein DUS16 plays an essential role in primary miRNA processing in the unicellular alga Chlamydomonas reinhardtii

Yamasaki

Onishi

Kim

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Canonical microRNAs (miRNAs) are embedded in duplexed stemloops in long precursor transcripts and are excised by sequential cleavage by DICER nuclease(s). In this miRNA biogenesis pathway, dsRNA-binding proteins play important roles in animals and plants by assisting DICER. However, these RNA-binding proteins are poorly characterized in unicellular organisms. Here we report that a unique RNA-binding protein, Dull slicer-16 (DUS16), plays an essential role in processing of primary-miRNA (pri-miRNA) transcripts in the unicellular green alga Chlamydomonas reinhardtii. In animals and plants, dsRNA-binding proteins involved in miRNA biogenesis harbor two or three dsRNA-binding domains (dsRBDs), whereas DUS16 contains one dsRBD and also an ssRNA-binding domain (RRM). The null mutant of DUS16 showed a drastic reduction in most miRNA species. Production of these miRNAs was complemented by expression of full-length DUS16, but the expression of RRM-or dsRBDtruncated DUS16 did not restore miRNA production. Furthermore, DUS16 is predominantly localized to the nucleus and associated with nascent (unspliced form) pri-miRNAs and the DICER-LIKE 3 protein. These results suggest that DUS16 recognizes pri-miRNA transcripts cotranscriptionally and promotes their processing into mature miRNAs as a component of a microprocessor complex. We propose that DUS16 is an essential factor for miRNA production in Chlamydomonas and, because DUS16 is functionally similar to the dsRNA-binding proteins involved in miRNA biogenesis in animals and land plants, our report provides insight into this mechanism in unicellular eukaryotes.Chlamydomonas | microRNA biogenesis | dsRNA-binding protein | small RNA-seq | mutagenesis

show abstract

Section: Significancementioning

confidence: 99%

RNA-binding protein DUS16 plays an essential role in primary miRNA processing in the unicellular alga Chlamydomonas reinhardtii

Yamasaki

Onishi

Kim

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…We next asked whether CDC5 could function after MIR transcription by examining the effect of cdc5-1 on the accumulation of miRNAs in an in vitro processing assay (13,35). In this in vitro processing assay, a portion of pri-miR162b that contains the predicted stem-loop of miR162b with 6-nt arms at each end (MIR162b; Fig.…”

Section: Cdc5 Ismentioning

confidence: 99%

“…We have previously used this assay to determine the association of TOUGH with the DCL1 complex (13). The protein partners were fused to the N-terminal fragment of Venus (nVenus) or C-terminal fragment of cyan fluorescent protein (cCFP) under the control of a Cauliflower mosaic virus 35S promoter and cointroduced into Nicotiana benthamiana.…”

Section: Cdc5 Ismentioning

confidence: 99%

“…After transcription, pri-miRNAs are processed by an RNase III enzyme called DICER-LIKE1 (DCL1) to miRNA precursors and then to mature miRNAs (9,10). The efficient processing of pri-miRNA requires SERRATE (SE; a zinc finger protein), TOUGH (an RNA-binding protein), and a dephosphorylated HYPONASTIC LEAVES1 (HYL1; a double-stranded RNA binding protein) that form a complex with DCL1 (11)(12)(13)(14)(15)(16)(17)(18). SE and HYL1 also promote the processing accuracy of pri-miRNAs (19).…”

mentioning

confidence: 99%

See 1 more Smart Citation

CDC5, a DNA binding protein, positively regulates posttranscriptional processing and/or transcription of primary microRNA transcripts

Zhang

Xie

Ren

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

131

158

View full text Add to dashboard Cite

CDC5 is a MYB-related protein that exists in plants, animals, and fungi. In Arabidopsis, CDC5 regulates both growth and immunity through unknown mechanisms. Here, we show that CDC5 from Arabidopsis positively regulates the accumulation of microRNAs (miRNAs), which control many biological processes including development and adaptations to environments in plants. CDC5 interacts with both the promoters of genes encoding miRNAs (MIR) and the DNA-dependent RNA polymerase II. As a consequence, lack of CDC5 reduces the occupancy of polymerase II at MIR promoters, as well as MIR promoter activities. In addition, CDC5 is associated with the DICER-LIKE1 complex, which generates miRNAs from their primary transcripts and is required for efficient miRNA production. These results suggest that CDC5 may have dual roles in miRNA biogenesis: functioning as a positive transcription factor of MIR and/or acting as a component of the DICER-LIKE1 complex to enhance primary miRNA processing.M icroRNAs (miRNAs) and small interfering RNAs (siRNAs) are ∼22-nucleotide (nt) noncoding RNAs that regulate various biological processes including development, metabolism, and immunity in plants and animals (1-3). miRNAs are generated from primary miRNA transcripts (pri-miRNAs) containing stem-loop structure, whereas siRNAs are derived from long, perfect, doublestranded RNAs (dsRNAs) (1-3). They are associated with members of the Argonaute protein family to repress gene expression at posttranscriptional and/or transcriptional levels (1-3). In addition to miRNAs, plants encode two major classes of siRNAs: siRNAs derived from repeated DNAs (ra-siRNAs) and transacting siRNAs (ta-siRNAs) (4-6).Studies in Arabidopsis have established the framework of miRNA biogenesis in plants (1-3). In Arabidopsis, pri-miRNAs are primarily transcribed by DNA-dependent RNA polymerase II (Pol II), with assistance from the mediator complex and the transcription factor Negative on TATA less2 (NOT2) (7,8). After transcription, pri-miRNAs are processed by an RNase III enzyme called DICER-LIKE1 (DCL1) to miRNA precursors and then to mature miRNAs (9, 10). The efficient processing of pri-miRNA requires SERRATE (SE; a zinc finger protein), TOUGH (an RNA-binding protein), and a dephosphorylated HYPONASTIC LEAVES1 (HYL1; a double-stranded RNA binding protein) that form a complex with DCL1 (11-18). SE and HYL1 also promote the processing accuracy of pri-miRNAs (19). Four other proteins, DAWDLE (DDL; an RNA binding protein), Cap-binding protein 20, Cap-binding protein 80, and NOT2, which are associated with the DCL1 complex (8,(20)(21)(22), also function in miRNA biogenesis. Recent studies also reveal that the correct localization of DCL1 requires NOT2 and MODIFIER OF SNC1, 2 (an RNA binding protein) (8,23). In addition, the accumulation of a subset of miRNAs requires a proline-rich protein named SICKLE (24).The cell division cycle 5 (CDC5) protein is a conserved protein in animals, plants, and fungi (25). It was first isolated from Schizosaccharomyces pombe as a cell cycle regulat...

show abstract

“…27 Recently it has been shown that the efficiency of primiRNA recruitment to DCL1-HYL1-SE complex is also improved by a RNA binding protein TOUGH (TGH). 28 Other proteins required for proper plant miRNA biogenesis are DDL, STA1, SICLE (SIC), NOT2, and RACK1. [29][30][31][32][33] Mutations in the splicing factor STA1 gene have been shown to interfere with both premRNA and pri-miRNA splicing that leads to the accumulation of pri-miRNAs and concurrently to the downregulation of miRNA expression.…”

mentioning

confidence: 99%