Abstract
Cold acclimation is critical for the survival of plants in temperate regions under low temperatures, and C-REPEAT BINDING FACTORs (CBFs) are well established as key transcriptional factors that regulate this adaptive process by controlling the expression of cold-responsive genes. Here we demonstrate that CBFs are involved in modulating alternative splicing during cold acclimation through their interaction with subunits of the spliceosome complex. Under cold stress, CBF proteins accumulate and directly interact with SKI-INTERACTING PROTEIN (SKIP), a key component of the spliceosome, which positively regulates acquired freezing tolerance. This interaction facilitates the formation of SKIP nuclear condensates, which enhances the association between SKIP and specific cold-responsive transcripts, thereby increasing their splicing efficiency. Our findings uncover a regulatory role of CBFs in alternative splicing and highlight their pivotal involvement in the full development of cold acclimation, bridging transcriptional and post-transcriptional regulatory mechanisms.
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Data availability
All data supporting the findings of this study are available in the main text or the supplementary tables. The biological materials used in this study are available from the corresponding author upon reasonable request. The sequencing data (RNA-seq) for gene expression and AS analysis have been deposited in the publicly available repository Sequence Read Archive under accession code PRJNA990533. The structures of the CBF2 and SKIP proteins can be found in the AlphaFold Protein Structure Database (https://alphafold.com/). Major genes mentioned in this study can be found in the TAIR database (https://www.arabidopsis.org/) under the following accession numbers: AT1G77180 (SKIP), AT3G13200 (CWC15), AT1G13030 (COILIN), AT1G49590 (ZOP1), AT1G04510 (MAC3A), AT3G50670 (U1-70K), AT4G03430 (STA1), AT1G16610 (SR45), AT1G08890 (ESL3.05), AT1G51430, AT5G28770 (BZIP63), AT4G25490 (CBF1), AT4G25470 (CBF2), AT4G25480 (CBF3), AT5G53010, AT5G06520 (SWAP), AT4G01400 (MISF74), AT5G63370 (CDKG1), AT1G25682 (CWC16A), AT1G08115 (U1A snRNA), AT3G56705 (U2.6 snRNA), AT1G61275 (U12 snRNA), AT5G40395 (U6ACAT snRNA) and AT5G42300 (UBL5). Source data are provided with this paper.
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Acknowledgements
We thank L. Ma for providing skip-1, skip-1 proSKIP::SKIPNSNW–GFP, and skip-1 proSKIP::SKIP–GFP seeds; and X. Fang, Y. Miao, J. Li and J. Hua for helpful suggestions and discussions. This work was supported by the National Natural Science Foundation of China (grant nos 32230005, 32022008 and 31921001), and the Pinduoduo–China Agricultural University Research Fund (PC2023B01001).
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Y. Shi conceived and supervised the project. D.F., S.Y. and Y. Shi designed the experiments. D.F. and Y. Shi carried out most of the experiments with assistance from Y. Song, S.W., Y.P., Y.M., Z.L., X.Z., W.S., Z.S. and Z.G. D.F., Y. Shi and S.Y. analysed the data and wrote the paper.
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Extended data
Extended Data Fig. 1 CBFs associate with spliceosome-associated proteins.
a, A list of spliceosome-associated proteins identified as CBF2-interacting proteins. b, BiFC assays showing SKIP/CBF2 co-expressed with SR45–mCherry in the nuclei of N. benthamiana leaf cells. nYFP-GUS and cYFP-GUS serve as controls. Scale bars, 10 μm. c, Co-IP assays showing the interactions between SKIP and CBFs in Arabidopsis protoplasts.
Extended Data Fig. 2 SKIP positively regulates acquired freezing tolerance and forms nuclear condensates in vivo.
a-c, Freezing tolerance of the skip-1, skip-1 proSKIP::SKIP-GFP and Col-0 under cold-acclimated (CA) conditions. Representative plant images of seedlings (a), survival rates (b), and ion leakage rates (c) are shown. In (b) and (c), data are means ± s.d. (n = 3 biologically independent experiments); means were compared by one-way ANOVA with Tukey’s multiple comparison tests. d, Subcellular localization of SKIP-GFP in the nuclei of N. benthamiana leaf cells under normal conditions. proSKIP::SKIP-GFP and pSuper::SKIP-GFP were transiently expressed in N. benthamiana leaf cells with different concentrations of Agrobacterium solution. e,f, Subcellular localization of SKIP-GFP under the indicated conditions in 7-d-old skip-1 proSKIP::SKIP-GFP seedlings. White arrows indicate representative condensates in the stele cells in the root elongation zone after cold treatment. Representative images (e), and quantification of cells with condensates (f) are shown. g,h, skip-1 proSKIP::SKIP-GFP seedlings grown at 22 °C for 7 days were treated at 4 °C for 6 h, and then shifted to 22 °C for recovery. Representative images of the stele cells in the root elongation zone (h), and quantification of cells with condensates (g) are shown. In (f) and (g), data are means ± s.d. (n = 3 root elongation zone analyzed in three independent experiments; ~30 nuclei in each root were examined). ND, not detected. Scale bars are indicated in figures.
Extended Data Fig. 3 SKIP is highly disordered and possesses liquid-like properties in vivo.
a, Prediction of disorder regions of SKIP by PONDR (VLXT). The scores are assigned between 0 and 1, and a score above 0.5 indicates disorder. b, Structure of SKIP protein predicted by AlphaFold. c,d, Cold-induced SKIP condensates are sensitive to 1,6-hexanediol. Representative images in the stele cells in the root elongation zone of cold-treated Arabidopsis with or without 10% 1,6-hexanediol for 90 s (c), and quantification of cells with condensates (d) are shown. In (d), data are means ± s.d. from three biologically independent experiments; statistical significance was determined using a two-tailed t-test. e,f, Time course of FRAP of SKIP nuclear condensates in the nuclei of N. benthamiana leaf cells under normal conditions (e), and in the nuclei of skip-1 proSKIP::SKIP-GFP root cells under cold conditions (f). Time 0 indicates the time of the photobleaching pulse. Data are means ± s.d. (n = 7 independent experiments), and representative images are shown. (g) Quantification of cells with condensates in Fig. 3a. Data are means ± s.d. (n = 3 root elongation zones analyzed in three independent experiments; ~30 nuclei in each root were examined). ND, not detected.
Extended Data Fig. 4 In vitro phase separation and in vivo protein levels of SKIP with or without cold treatment.
a,b, In vitro phase separation of recombinant His-GFP-SKIP and His-SKIP incubated at 22 °C for 10 min. Representative images (a), and coomassie blue staining of indicated proteins (b) are shown. His-GFP serves as a control. c, In vitro phase separation of recombinant His-GFP-SKIP incubated at 22 °C for 10 min at different concentrations. d, In vitro phase separation of recombinant His-GFP-SKIP incubated at 22 °C and 4 °C for 1 h. His-GFP serves as a control. e, Detection of the SKIP protein level in two-week-old Col-0 and skip-1 using anti-SKIP antibody. f, Detection of the SKIP protein level in two-week-old Col-0 with or without 4 °C treatment. Nuclear proteins were extracted, and H3 was used as a loading control.
Extended Data Fig. 5 CBFs co-localize with SKIP in nuclear condensates.
a, Subcellular localization of CBF3-GFP under cold conditions in 7-d-old pSuper::CBF3-GFP transgenic Arabidopsis plants. Red arrows indicate the nucleolus, and yellow arrows indicate the nuclear condensates. b, Live imaging of pSuper::CBFs-mCherry co-expressed with proSKIP::SKIP-GFP in the nuclei of N. benthamiana leaf cells. c, Fluorescence profiles of SKIP-GFP and CBFs-mCherry over the white line shown in (b). d, Immunoblot analysis of SKIP-GFP abundance in 7-d-old proSKIP::SKIP-GFP and cbfs-1 proSKIP::SKIP-GFP seedlings incubated at 22 °C or 4 °C for 6 h. Nuclear proteins were extracted, and H3 was used as a loading control.
Extended Data Fig. 6 CBFs contain IDRs and promote SKIP condensation.
a, The proportion of cells with different numbers of SKIP nuclear condensates in Fig. 3h. b,c, In vitro phase separation of recombinant His-CBF-mCherry (10 μM) incubated at 22 °C for 10 min. Representative images (b), and coomassie blue staining of indicated proteins (c) are shown. His-GFP-SKIP serves as a positive control. d, Prediction of IDRs of CBFs by PONDR (VLXT). The scores are assigned between 0 and 1.0, and a score above 0.5 indicates disorder. e, The proportion of cells with different numbers of SKIP nuclear condensates in Fig. 3m.
Extended Data Fig. 7 Differentially expressed analysis of RNA-seq.
a, Principal component analysis of gene expression of two-week-old Col-0, cbfs-1, and skip-1 Arabidopsis seedlings under normal (22 °C) and cold conditions (4 °C for 6 h). b, Volcano plot of differentially expressed genes between cold-treated and non-treated WT (Col-0) plants. c,d, Volcano plot of differentially expressed genes between Col-0 and mutant (skip-1, cbfs-1) plants with or without cold treatment at 4 °C. In (b-d), the R package DESeq2 was used to analyze the differential expression of transcriptomes. And the differential expression analysis employs a two-tailed Wald test to assess the statistical significance of the log2 fold changes between different comparisons. e, Venn diagrams showing the number of up-regulated genes in Col-0 that were down-regulated in cbfs-1 and skip-1 compared to Col-0 under cold stress, and down-regulated genes in Col-0 that were up-regulated in cbfs-1 and skip-1 compared to Col-0 under cold stress. f, The ratio of CRDE genes regulated by CBFs and SKIP. g, Heat map representation and gene ontology analysis of CBFs- or SKIP-activated cold response genes under cold stress. Representatively enriched GO terms were determined by using AgriGO v.2.0. The P values are from Fisher’s exact test. h, Heat map representation of cold-activated genes that were regulated by CBFs but not by SKIP (71 genes in Extended Data Fig. 7e, up-regulated) under cold conditions. In (g) and (h), the z-score scale represents mean-subtracted regularized TPMs.
Extended Data Fig. 8 AS analysis of RNA-seq, and freezing tolerance of esl3.05 under cold-acclimated conditions.
a, Gene ontology analysis of 1,102 CBFs and SKIP co-regulated CRDS genes. The P values are from Fisher’s exact test. b, Heat map representation of AS events with decreased splicing efficiency for Col-0 after cold treatment and AS patterns in skip-1 and cbfs-1 compared to Col-0 in the same AS sites (222 AS events corresponding to 195 genes). Inclusion level differences were used to quantify the splicing efficiency. c, An RNA motif identified by MEME analysis using introns (entire introns plus 50 bp of 5′- and 3′-flanking exon sequences) with increased splicing efficiency in Supplementary Table 7. d, Integrative Genomics Viewer genome browser view showing the detected RNA-seq signals in the indicated conditions. Differentially spliced AS events were detected in the fifth intron (I5) of AT5G28770, the third intron (I3) of AT1G51430, the eleventh exon (E11), and the 3′SS in exon 24 (E24). Black arrows indicate the positions of designed primers. e, Characterization of esl3.05 T-DNA insertion mutants. f, RT-PCR analysis of ESL3.05 and EF1α expression in WT, esl3.05-1, and esl3.05-2 mutants. g-i, Freezing tolerance of the esl3.05 mutants under cold-acclimated conditions. Representative plant images (g), survival rates (h), and ion leakage rates (i) are shown. In (h) and (i), the values are the means ± s.d. (n = 3 independent experiments). Means were compared by two-tailed Student’s t-tests.
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Fu, D., Song, Y., Wu, S. et al. Regulation of alternative splicing by CBF-mediated protein condensation in plant response to cold stress. Nat. Plants 11, 505–517 (2025). https://doi.org/10.1038/s41477-025-01933-x
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DOI: https://doi.org/10.1038/s41477-025-01933-x
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