Trans-acting small RNA determines dominance relationships in Brassica self-incompatibility

Abstract

A diploid organism has two copies of each gene, one inherited from each parent. The expression of two inherited alleles is sometimes biased by the effects known as dominant/recessive relationships, which determine the final phenotype of the organism. To explore the mechanisms underlying these relationships, we have examined the monoallelic expression of S-locus protein 11 genes (SP11), which encode the male determinants of self-incompatibility in Brassica. We previously reported that SP11 expression was monoallelic in some S heterozygotes, and that the promoter regions of recessive SP11 alleles were specifically methylated in the anther tapetum1,2,3. Here we show that this methylation is controlled by trans-acting small non-coding RNA (sRNA). We identified inverted genomic sequences that were similar to the recessive SP11 promoters in the flanking regions of dominant SP11 alleles. These sequences were specifically expressed in the anther tapetum and processed into 24-nucleotide sRNA, named SP11 methylation inducer (Smi). Introduction of the Smi genomic region into the recessive S homozygotes triggered the methylation of the promoter of recessive SP11 alleles and repressed their transcription. This is an example showing sRNA encoded in the flanking region of a dominant allele acts in trans to induce transcriptional silencing of the recessive allele. Our finding may provide new insights into the widespread monoallelic gene expression systems.

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Figure 1: Smi sequences homologous to the methylated region of the recessive SP11 alleles.
Figure 2: Expression analyses of Smi.
Figure 3: Effect of S9-Smi transgene on self-incompatibility phenotype and DNA methylation.

Accession codes

Primary accessions

GenBank/EMBL/DDBJ

Data deposits

Sequence data have been deposited in GenBank under accession numbers GQ473178–GQ473187 and GQ847769.

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Acknowledgements

We thank Q. A. Ngo and P. Kaothien-Nakayama for critical comments and discussion; K. Nakashima for helpful comments; and H. Ichikawa, T. Ohnishi, F. Yamamoto, M. Kawashima and R. Nagai for technical assistance. This work was supported by the Program for Promotion of Basic Research Activities for Innovative Biosciences (to S.T.) from the Bio-oriented Technology Research Advancement Institution (BRAIN), by Grants-in-Aid for Creative Scientific Research (to A.I., M.W. and S.T.) from the Japan Society for the Promotion of Science (JSPS), and by Grants-in-Aid for Scientific Research on Priority Area (to H.S., M.W. and S.T.) and Grants-in-Aid for the Global Center of Excellence Program to NAIST from the Ministry of Education, Culture, Sports, Science and Technology (MEXT).

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Y.T. designed and performed the experiments, and wrote the paper. H.S., A.I. and S.T. initiated the study, provided advice regarding the experiments, and wrote the paper. M.I. performed the in situ hybridization. T.K., G.S. and M.W. provided plant materials and performed the sequence analyses of the S locus.

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Correspondence to Seiji Takayama.

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The authors declare no competing financial interests.

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Tarutani, Y., Shiba, H., Iwano, M. et al. Trans-acting small RNA determines dominance relationships in Brassica self-incompatibility. Nature 466, 983–986 (2010). https://doi.org/10.1038/nature09308

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