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Phase separation of SERRATE drives dicing body assembly and promotes miRNA processing in Arabidopsis

Abstract

MicroRNA (miRNA) production entails the step-wise processing of primary miRNAs (pri-miRNAs) into precursor miRNAs (pre-miRNAs) and miRNA/* duplexes by Dicing complexes containing DCL1, HYL1 and SE, which are localized in nuclear dicing bodies (D-bodies)1,2. Here, we show that D-bodies are phase-separated condensates. SE forms droplets and drives DCL1, HYL1 and pri/pre-miRNAs into the droplets in vitro, and mutation of SE abrogates the formation of D-bodies in vivo, which indicates that D-bodies arise through SE-mediated phase separation. Disruption of SE phase separation greatly reduces its activity in promoting miRNA processing both in vitro and in vivo. We further show that pre-miRNAs are processed into miRNA/* duplexes in the droplets and, after processing, miRNA/* duplexes are bound by HYL1 and released from the droplets. Our findings provide evidence that efficient miRNA processing depends on the SE-phase-separation-mediated formation of D-bodies and suggest a paradigm that the products made in phase-separated condensates can be shipped out for subsequent processes.

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Fig. 1: D-bodies are phase-separated condensates.
Fig. 2: Phase separation of SE drives D-body formation.
Fig. 3: Phase separation of SE promotes miRNA processing.
Fig. 4: D-bodies are miRNA processing centres.
Fig. 5: miRNA/* duplex release from D-bodies is facilitated by HYL1.

Data availability

All data supporting the findings of this study are available from the corresponding author upon reasonable request. Source data are provided with this paper.

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Acknowledgements

This work was supported by grants from the National Natural Science Foundation of China (grant number 31788103) and the National Key R&D Program of China (grants 2016YFA0500800 to Y.Q. and 2019YFA0508403 to P.L.). Y.Q. is a visiting investigator of the CAS Center for Excellence in Molecular Plant Sciences.

Author information

Authors and Affiliations

Authors

Contributions

The scientific concept was developed by Y.Q., D.X., M.C. and J.N., and L.W. executed the experiments. D.X., M.C., J.N., Y.L., X.F., P.L. and Y.Q. analysed the data. Y.L. and Y.Q. wrote the manuscript.

Corresponding author

Correspondence to Yijun Qi.

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Competing interests

The authors declare no competing interests.

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Peer review information Peer reviewer reports are available. Nature Cell Biology thanks Sascha Laubinger and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 D-bodies are sensitive to 1,6-hexanediol.

a, Representative images from four biological replicates showing D-bodies in Arabidopsis root tip cells from the pHYL1::HYL1-YFP and pDCL1::DCL1-YFP transgenic plants before and after treatment with 10% 1,6-hexanediol for 90 sec. Scale bar, 5 μm. b, Percentages of nuclei with D-bodies before and after treatment with 10% 1,6-hexanediol. Data are expressed as mean ± SD (n = 4 independent experiments). Statistical significance was determined using a two-tailed Student’s t-test. *P ≤ 0.05 (Ppre-treatment vs post-treatment for DCL1-YFP = 0.00018, Ppre-treatment vs post-treatment for HYL1-YFP = 0.00033). c, Protein levels of HYL1-YFP before and after treatment with 10% 1,6-hexanediol as determined by western blotting. Data are representative of 3 independent experiments. d, Protein levels of DCL1-YFP and HYL1-YFP transiently expressed in N. benthamiana leaf epidermal cells under the control of 35S promoter or their native promoters as determined by western blotting. Data are representative of 3 independent experiments. e, FRAP of HYL1-YFP and DCL1-YFP transiently expressed in N. benthamiana leaf epidermal cells under the control of their native promoters. Data are representative of 10 nuclei for each protein. White arrows indicate the nuclear bodies that are bleached. Scale bars, 2 μm. f, FRAP recovery curves of HYL1-YFP and DCL1-YFP transiently expressed in N. benthamiana leaf epidermal cells under the control of their native promoters. Data are expressed as mean ± SD (n = 10 foci analysed in 3 independent experiments). Uncropped blots for c and d and statistical source data for b and f are provided in Source Data Extended Data Fig. 1.

Source data

Extended Data Fig. 2 SE phase separates into droplets in vitro.

a, Protein domain architectures of DCL1, HYL1 and SE and prediction of intrinsically disordered regions (IDRs) by PONDR (www.pondr.com). b, Schematic diagrams of DCL1, HYL1 and SE proteins with the indicated tags. c, Coomassie blue staining of DCL1, HYL1 and SE proteins with the indicated tags. Images are representative of 3 independent experiments. d, Images showing formation of droplets at different concentrations of BFP-SE, SE-BFP, mCherry-HYL1 and HYL1-mCherry. Scale bar, 5 μm. Data are representative of 3 independent experiments. e, Images showing formation of droplets at different concentrations of BFP-SE and NaCl. Scale bar, 5 μm. Data are representative of 3 independent experiments. Uncropped blots for c are provided in Source Data Extended Data Fig. 2.

Source data

Extended Data Fig. 3 The N-terminal IDR is required for phase separation of SE.

a, Schematic diagrams and Coomassie blue staining of BFP-tagged and MBP-tagged full-length SE protein, SE protein with the IDR1 domain deleted (SE∆IDR1) and BFP-tagged SE protein with the IDR1 domain replaced by the LCD of FUS (LCD-SE∆IDR1). Data are representative of 3 independent experiments. b, Electrophoretic Mobility Shift Assay (EMSA) results showing the binding of SE and SE∆IDR1 with pri-miR172b. Data are representative of 3 independent experiments. c, Pull-down results showing the interactions of SE and SE∆IDR1 with HYL1. Data are representative of 3 independent experiments. d, Pull-down results showing the interactions of SE and SE∆IDR1 with DCL1-GFP. Data are representative of 3 independent experiments. e, Images showing that BFP-SE_IDR1 forms droplets. Scale bar, 5 μm. Images are representative of 3 independent experiments. f, FRAP of BFP-SE_IDR1 droplets. Data are representative of 10 independent droplets. Scale bar, 0.5 μm. g, FRAP recovery curve of BFP-SE_IDR1 droplets. Data are expressed as mean ± SD (n = 10 droplets analysed in 3 independent experiments). Uncropped blots for a-d and statistical source data for g are provided in Source Data Extended Data Fig. 3.

Source data

Extended Data Fig. 4 Phase separation of SE drives D-body formation.

a, Images showing the incorporation of DCL1-GFP into BFP-SE droplets. Scale bar, 5 μm. b, Images showing the incorporation of mCherry-HYL1 into BFP-SE droplets. Scale bar, 5 μm. c, Images showing the incorporation of Cy5-internally-labeled pri-miR172b into BFP-SE droplets. Scale bar, 5 μm. d, Images showing the incorporation of Cy5-internally-labeled pre-miR172b into BFP-SE droplets. Scale bar, 5 μm. Data in a-d are representative of 3 independent experiments. e, Relative enrichment of BFP-SE, DCL1-GFP, mCherry-HYL1 and Cy5-pre-miR172b within BFP-SE droplets. f, Images showing the incorporation of DCL1-GFP, mCherry-HYL1 and Cy5-internally-labeled pri-miR172b into droplets formed by BFP-SE or BFP-LCD-SE∆IDR1. BFP-SE∆IDR1 is unable to form droplets and incorporate other proteins and RNAs. Scale bar, 5 μm. Data are representative of 3 independent experiments. g, Relative enrichment of BFP-SE, DCL1-GFP, mCherry-HYL1 and Cy5-pri-miR172b within BFP-SE droplets. h, Fluorescence images showing D-bodies in the root tip cells of wild-type (Col-0), se-1, se-1 complemented with mCherry-SE (se-1 SE), mCherry-SE∆IDR1 (se-1 SE∆IDR1) or mCherry-LCD-SE∆IDR1 (se-1 LCD-SE∆IDR1) plants, which all express HYL1-YFP under the control of the native HYL1 promoter. D-bodies are indicated by discrete punctate HYL1-YFP signals. Each image was generated by maximum intensity projection. Scale bars, 5 μm. Images are representative of 3 independent experiments. i, Percentages of nuclei containing D-bodies in different genotypes. Data are expressed as mean ± SD (n = 4 root tips analysed in 3 independent experiments. ~40 nuclei in each root tip were examined). Statistical source data for e, g and i are provided in Source Data Extended Data Fig. 4.

Source data

Extended Data Fig. 5 Phase separation of SE promotes miRNA processing in vitro.

a, Time course of pre-miRNA processing with different concentrations (0–0.75 μM) of BFP-SE. DCL1-GFP, mCherry-HYL1 and Cy5-internally-labeled pre-miR172b were incubated with increasing concentrations of BFP-SE in the presence of Mg2+. Results from three replicates are shown. b, Time course of pre-miRNA processing with BFP-SE or BFP-SE variants. DCL1-GFP, mCherry-HYL1 and Cy5-internally-labeled pre-miR172b were incubated with 0.75 μM BFP-SE or BFP-SE variants in the presence of Mg2+. Results from three replicates are shown. Uncropped blots for a and b are provided in Source Data Extended Data Fig. 5.

Source data

Extended Data Fig. 6 Phase separation of SE promotes miRNA processing in vivo.

a, Phenotypes of 3-week-old Col-0, se-1, se-1 SE, se-1 SE∆IDR1 and se-1 LCD-SE∆IDR1. Scale bar, 1 cm. b, Accumulation of miRNAs in the indicated plants as determined by northern blot. The bands are quantified and their relative intensities are shown. U6 was probed as a loading control. Results from two additional replicates are shown. Uncropped blots for b are provided in Source Data Extended Data Fig. 6.

Source data

Extended Data Fig. 7 D-bodies are miRNA processing centers that can release miRNA/* duplexes.

a, Distribution of pre-miR172b, miR172b/*, BFP-SE, DCL1-GFP and mCherry-HYL1 in pelleted droplet (P) and supernatant (S) fractions before and upon pre-miRNA cleavage. Results from two additional replicates are shown. The relative amounts of the proteins in droplets are determined by densitometry values of the pellet fraction bands relative to that of the unfractionated sample (Total) bands. b, Pull-down results showing the interactions of SE-Flag with DCL1-GFP and HYL1 in the absence or presence of Mg2+. Results from two additional replicates are shown. c, Pull-down results showing the interactions of SE-Flag with DCL1-GFP and HYL1 in the absence or presence of DCL1-GFP. Results from two additional replicates are shown. d, Images showing the incorporation of mCherry-HYL1 into BFP-SE droplets in the presence of pre-miRNA or miRNA/*. Scale bar, 5 μm. Results from two additional replicates are shown. e, Pull-down results showing the interactions of SE-Flag with DCL1-GFP and HYL1 in the absence of RNA or in the presence of pre-miR172b or miR172b/*. Results from two additional replicates are shown. f, Distribution of pre-miR172b, miR172b/* duplex, DCL1, HYL1 and SE in pelleted droplet and supernatant fractions upon pre-miRNA cleavage in the absence or presence of HYL1. Results from two additional replicates are shown. The relative amounts of miR172b/* in the pelleted droplet (P) and supernatant (S) fractions are determined by densitometry values of the pellet and supernatant fraction bands relative to that of the unfractionated sample (Total) bands. g, EMSA results showing the interaction of HYL1 with miR172b/*. Data are representative of 3 independent experiments. h, Pull-down results showing the interaction of HYL1 with miR172b/*. Results from two additional replicates are shown. Uncropped blots for a-c and e-h are provided in Source Data Extended Data Fig. 7.

Source data

Supplementary information

Reporting Summary

Peer Review Information

Supplementary Table 1

Oligonucleotides used in this study.

Supplementary Video 1

FRAP of DCL1–YFP in a root tip cell from the pDCL1::DCL1–YFP transgenic plant. DCL1–YFP in a D-body was bleached. Recovery was recorded every second after bleaching. Scale bar, 5 μm.

Supplementary Video 2

Supplementary Video 2 FRAP of HYL1–YFP in a root tip cell from the pHYL1::HYL1–YFP transgenic plant. HYL1–YFP in a D-body was bleached. Recovery was recorded every second after bleaching. Scale bar, 5 μm.

Supplementary Video 3

D-body dissolution by 1,6-hexanediol treatment. A root tip from the pDCL1::DCL1–YFP transgenic plant was treated with 10% 1,6-hexanediol. D-body dissolution was recorded every second. Scale bar, 5 μm.

Supplementary Video 4

D-body dissolution by 1,6-hexanediol treatment. A root tip from the pHYL1::HYL1–YFP transgenic plant was treated with 10% 1,6-hexanediol. D-body dissolution was recorded every second. Scale bar, 5 μm.

Supplementary Video 5

FRAP of YFP–SE in a root tip cell from the 35S::YFP–SE transgenic plant. YFP–SE in a nuclear body was bleached. Recovery was recorded every second after bleaching. Scale bar, 5 μm.

Supplementary Video 6

FRAP of DCL1–YFP transiently expressed in a N. benthamiana leaf epidermal cell under the control of the 35S promoter. DCL1–YFP in a nuclear body was bleached. Recovery was recorded every second after bleaching. Scale bar, 5 μm

Supplementary Video 7

FRAP of HYL1–YFP transiently expressed in a N. benthamiana leaf epidermal cell under the control of the 35S promoter. HYL1–YFP in a nuclear body was bleached. Recovery was recorded every second after bleaching. Scale bar, 5 μm.

Supplementary Video 8

FRAP of YFP–SE transiently expressed in a N. benthamiana leaf epidermal cell under the control of the 35S promoter. YFP–SE in a nuclear body was bleached. Recovery was recorded every second after bleaching. Scale bar, 5 μm.

Supplementary Video 9

FRAP of DCL1–YFP transiently expressed in a N. benthamiana leaf epidermal cell under the control of the native DCL1 promoter. DCL1–YFP in a nuclear body was bleached. Recovery was recorded every second after bleaching. Scale bar, 5 μm.

Supplementary Video 10

FRAP of HYL1–YFP transiently expressed in a N. benthamiana leaf epidermal cell under the control of the native HYL1 promoter. HYL1–YFP in a nuclear body was bleached. Recovery was recorded every second after bleaching. Scale bar, 5 μm.

Supplementary Video 11

Fusion of two YFP–SE nuclear bodies in a N. benthamiana leaf epidermal cell. Fusion of two nuclear bodies was recorded every second. Scale bar, 2 μm.

Supplementary Video 12

upplementary Video 12 FRAP of a BFP–SE droplet formed in vitro. A region within the BFP–SE droplet was bleached, and recovery was recorded every second for the indicated time. Scale bar, 2 μm.

Supplementary Video 13

Fusion of two BFP–SE droplets formed in vitro. Fusion of two droplets was recorded every second. Scale bar, 5 μm.

Supplementary Video 14

FRAP of a BFP–SE_IDR1 droplet formed in vitro. A region within the BFP–SE_IDR1 droplet was bleached, and recovery was recorded every second for the indicated time. Scale bar, 2 μm.

Source data

Source Data Fig. 1

Statistical source data of Fig. 1.

Source Data Fig. 2

Statistical source data of Fig. 2.

Source Data Fig. 2

Unprocessed western blots of Fig. 2.

Source Data Fig. 3

Statistical source data of Fig. 3.

Source Data Fig. 3

Unprocessed gels and blots of Fig. 3.

Source Data Fig. 4

Statistical source data of Fig. 4.

Source Data Fig. 4

Unprocessed gels and blots of Fig. 4.

Source Data Fig. 5

Statistical source data of Fig. 5.

Source Data Fig. 5

Unprocessed gels and blots of Fig. 5.

Source Data Extended Data Fig. 1

Statistical source data of Extended Data Fig. 1.

Source Data Extended Data Fig. 1

Unprocessed western blots of Extended Data Fig. 1.

Source Data Extended Data Fig. 2

Unprocessed gels of Extended Data Fig. 2.

Source Data Extended Data Fig. 3

Statistical source data of Extended Data Fig. 3.

Source Data Extended Data Fig. 3

Unprocessed gels and western blots of Extended Data Fig. 3.

Source Data Extended Data Fig. 4

Statistical source data of Extended Data Fig. 4.

Source Data Extended Data Fig. 5

Unprocessed gels of Extended Data Fig. 5.

Source Data Extended Data Fig. 6

Unprocessed northern blots of Extended Data Fig. 6.

Source Data Extended Data Fig. 7

Unprocessed gels and western blots of Extended Data Fig. 7.

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Xie, D., Chen, M., Niu, J. et al. Phase separation of SERRATE drives dicing body assembly and promotes miRNA processing in Arabidopsis. Nat Cell Biol 23, 32–39 (2021). https://doi.org/10.1038/s41556-020-00606-5

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