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Maternal transmission of the epigenetic ‘memory of winter cold’ in Arabidopsis

Abstract

Some plants can ‘remember’ past environmental experience to become adapted to a given environment. For instance, after experiencing prolonged low-temperature exposure in winter (winter cold), vernalization-responsive plants remember past cold experience when temperature rises in spring, to acquire competence to flower at a later season favourable for seed production1,2. In Arabidopsis thaliana, prolonged cold induces silencing of the potent floral repressor FLOWERING LOCUS C (FLC) by Polycomb group (PcG) chromatin modifiers. This Polycomb-repressed chromatin state is epigenetically maintained and thus ‘memorized’ in subsequent growth and development upon return to warmth1,3. ‘Memory of winter cold’ has been viewed as being mitotically stable but meiotically unstable3,4,5, and thus not to be transmitted intergenerationally. In general, whether and how chromatin-mediated environmental memories are transmitted across generations are unknown in plants. Here, we show that the cold-induced Polycomb-repressed chromatin state at FLC or memory of winter cold is maintained in the egg cell, that is meiotically stable in the process of female gamete formation, and provide evidence that this Polycomb-mediated memory is not maintained in the sperm cell. Moreover, we show that this cold memory is inherited maternally but not paternally to the zygote and early embryos. Our study demonstrates and further provides mechanistic insights into intergenerational transmission of chromatin state-mediated environmental memories in plants.

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Fig. 1: Analyses of Polycomb-mediated FLC repression and subsequent FLC reactivation in the course of embryogenesis following parental vernalization.
Fig. 2: FLC expression is maternally imprinted from proembryo through the transition embryo.
Fig. 3: Maternally transmitted Polycomb-repressed state at FLC is essential for its repression in early embryo cells.
Fig. 4: FLC chromatin remains to be a Polycomb-repressed state in the egg cell and is maternally transmitted to early embryos.

Data availability

The data supporting the findings in this study are included in this article and its extended data and Supplementary Information or available from the corresponding authors on request. Source data are provided with this paper.

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Acknowledgements

We are grateful to R. M. Amasino for kindly providing the FRI-Col seeds and I. E. Somssich for the pJawohl8-RNAi plasmid. We thank Y. Li for assistance with constructing the FRI clf and FRI lhp1 lines and Z. Gao for assistance with genetic crossing. This work was supported by the National Natural Science Foundation of China (grant nos. 31721001 and 31830049 to Y.H.) and the Chinese Academy of Sciences (grant no. XDB27030202 to Y.H.).

Author information

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Authors

Contributions

Y.H., X.L., Y.O. and R.L. conceived and designed the experiments. X.L., Y.O. and R.L. performed the experiments. All authors took part in data analysis. Y.H. wrote the manuscript.

Corresponding author

Correspondence to Yuehui He.

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The authors declare no competing interests.

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Peer review information Nature Plants thanks Daniel Woods 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 Analysis of embryonic FLC reactivation following parental vernalization.

a, Embryonic FLC::GUS reactivation in the plants vernalized for 35 d (V35). Shown are representative FLC::GUS expression patterns in the indicated F1 developing seeds. Number of each staining out of all scored seeds is indicated at bottom left of each image. Scale bars, 100 μm. b, Levels of FLC mRNA in the developing seeds of FRI-Col (WT) vernalized for 35 d or 45 d. Transcript levels were normalized directly to PP2A. Values were are means ± s.d. of three biological replicates. Lower-case letters denote statistically distinct differences (two-way ANOVA, p < 0.05).

Extended Data Fig. 2 Analyses of fertilization and de novo FLC transcription in early developing seeds.

a, Ovules from WT plants (vernalized for 45 d) are fertilized, 6 h after pollination. Pollen tubes were stained by aniline blue, and shown is a representative micrograph of two independent experiments with similar results. Scale bar, 100 μm. b, A DNA gel image to show that residue genomic DNA was completely removed by a DNase treatment in the indicated samples. cDNAs are reverse transcribed from DNase-treated total RNAs, extracted from the F1 developing seeds of NV x V35. The experiment was repeated independently twice with similar results. c, Levels of primary FLC transcripts (unspliced) in the indicated F1 developing seeds. Transcript levels were normalized directly to PP2A. Values are means ± s.d. of three biological replicates.

Source data

Extended Data Fig. 3 Temporal and spatial expression patterns of LEC1 from gametophytes through the heart-stage embryo.

A LEC1pro-LEC1:GUS line12 that reflects the endogenous LEC1 expression was examined. Each shown micrograph is a representative from over 26 examined samples; scale bars, 100 μm.

Extended Data Fig. 4 Molecular characterization of the FLC locus in the Se-0 accession.

a, Levels of FLC transcripts in the indicated seedlings. Total RNAs were extracted from non-vernalized (NV) WT (FRI-Col) and Se-0 seedlings, as well as vernalized seedlings (V45) that were grown for 3 d at normal temperature (22 °C) following a 45-d cold exposure. Transcript levels were normalized to PP2A. Values are means ± s.d. of three biological replicates; relative expression to WT (NV) is presented. b, Levels of H3K27me3 on FLC chromatin in the indicated seedlings. NV, non-vernalized; V45, 5 d at normal temperature following 45-d cold. Shown are relative levels of H3K27me3 in the examined two FLC regions (as illustrated in Fig. 1d), following a normalization to the reference gene SHOOTMERISTEMLESS (STM)10. Values are means ± s.d. of three biological replicates. c, d, Genomic polymorphisms of FLC (c) and UBC21 (d) between WT (FRI-Col) and Se-0. The genotype-specific forward primers used to amplify genomic and cDNAs of FLC or UBC21 are denoted. Black boxes for exons, and A of ATG as +1.

Extended Data Fig. 5 Expression of LHP1 and CLF proteins in the egg cell, sperm cell and/or early embryo cells.

a, LHP1:GFP in the nuclei of mature ovule cells. ECN, egg-cell nucleus; CCN, central-cell nucleus; SYN, synergid cell nucleus. Shown is a representative micrograph from over 50 examined ovules; scale bars, 10 μm. b, c, LHP1:GFP protein is absent in mature pollen grains (b) and germinating pollen grains (c). Nuclei were stained with Hoechst. SN, sperm cell nucleus; VN, vegetative cell nucleus. Scale bars, 10 μm. Note that there is green autofluorescence from the pollen grain wall. d, LHP1:GFP and CLF:GFP expression in 2-DAP F1 embryos of the indicated crosses. Scale bars, 10 μm. bd, Experiments were repeated independently once with similar results.

Extended Data Fig. 6 Analysis of egg-cell or central-cell knockdown of FIE, CLF, SWN and/or MEA expression.

a, b, Levels of FIE, CLF, SWN and MEA transcripts in mature ovules (a) and 2-DAP developing seeds (b) of the indicated lines. Transcript levels were normalized to PP2A, and values are means ± s.d. of three biological replicates. Statistically significant differences are indicated by lower-case letters (one-way ANOVA, p < 0.001) or p values (two tailed t-test); n.s., not significant. c, FLC::GUS expression patterns in the indicated F1 developing seeds (plants were vernalized for 35 d). Number of each staining out of all scored seeds is indicated at bottom left of each image. Scale bars, 100 μm. d, Normal seed development in the indicated lines. Shown are siliques at around 7 DAP.

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Luo, X., Ou, Y., Li, R. et al. Maternal transmission of the epigenetic ‘memory of winter cold’ in Arabidopsis. Nat. Plants 6, 1211–1218 (2020). https://doi.org/10.1038/s41477-020-00774-0

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