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Polycomb-mediated gene silencing by the BAH–EMF1 complex in plants


Polycomb proteins implement genome-wide transcriptional repression in multicellular organisms. The evolutionarily conserved Polycomb repressive complex 2 (PRC2) catalyzes histone H3 Lys27 trimethylation (H3K27me3) that is read and effected by Polycomb repressive complex 1 (PRC1) in animals, but the interpretation of this mark remains unclear in plants. Here we report that in the eudicot Arabidopsis thaliana two homologous BAH (Bromo adjacent homology) domain–containing proteins form a plant-specific complex with EMBRYONIC FLOWER 1 (EMF1), and that the BAH–EMF1 complex (BAH–EMF1c) reads and effects the H3K27me3 mark and mediates genome-wide transcriptional repression. Furthermore, in the monocot rice a homolog of the Arabidopsis BAH-domain proteins also binds methylated H3K27 and forms a complex with the rice homolog of EMF1, suggesting that BAH–EMF1c is conserved in flowering plants. Therefore, our results show that the plant-specific BAH–EMF1c fulfills PRC1-like functions in higher plants, suggesting a convergent evolution of PRC1 activity in plants and animals.

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We thank J. Du and X. Zhong for exchange of unpublished information; G. Xu, X. Gu, H. Zhang and the in-house genomics facility for assistance; and R. J. Schmitz for critically reading this manuscript. This work was supported in part by funding from the National Natural Science Foundation of China (grant no. 31721001) and the Chinese Academy of Sciences.

Author information

Y.H. conceived and supervised the project. Z.L. and Y.W. performed the experimental work. X.F. and R.L. carried out all bioinformatic analyses. Z.L., X.F., Y.W., R.L. and Y.H. analyzed the data. Y.H. and Z.L. wrote the manuscript.

Competing interests

The authors declare no competing interests.

Correspondence to Yuehui He.

Supplementary information

Supplementary Figures

Supplementary Figures 1–14 and Supplementary Table 3

Reporting Summary

Supplementary Table 1

List of genes differentially expressed in lhp1, ebs shl, ebs shl lhp1 and emf1, compared to WT seedlings

Supplementary Table 2

List of genes occupied by SHL and EBS at a seedling stage

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Further reading

Fig. 1: SHL and EBS directly associate with EMF1 and At BMI1a.
Fig. 2: Functional analysis of the BAH domains from the SHL- and EBS-family proteins.
Fig. 3: SHL and EBS function in partial redundancy to regulate genome-wide gene expression.
Fig. 4: EBS, SHL, and EMF1 co-occupy a large number of genomic regions marked by H3K27me3.
Fig. 5: Analysis of a set of selected EBS and/or SHL loci and characterization of histone modifications upon loss of EBS, SHL and/or LHP1 function.