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. 2020 Oct 14;20(Suppl 1):175.
doi: 10.1186/s12870-020-02384-6.

Identification of polycomb repressive complex 1 and 2 core components in hexaploid bread wheat

Beáta Strejčková  1 , Radim Čegan  1   2 , Ales Pecinka  1 , Zbyněk Milec  1 , Jan Šafář  3
Affiliations

Identification of polycomb repressive complex 1 and 2 core components in hexaploid bread wheat

Beáta Strejčková et al. BMC Plant Biol. .

Erratum in

Abstract

Background: Polycomb repressive complexes 1 and 2 play important roles in epigenetic gene regulation by posttranslationally modifying specific histone residues. Polycomb repressive complex 2 is responsible for the trimethylation of lysine 27 on histone H3; Polycomb repressive complex 1 catalyzes the monoubiquitination of histone H2A at lysine 119. Both complexes have been thoroughly studied in Arabidopsis, but the evolution of polycomb group gene families in monocots, particularly those with complex allopolyploid origins, is unknown.

Results: Here, we present the in silico identification of the Polycomb repressive complex 1 and 2 (PRC2, PRC1) subunits in allohexaploid bread wheat, the reconstruction of their evolutionary history and a transcriptional analysis over a series of 33 developmental stages. We identified four main subunits of PRC2 [E(z), Su(z), FIE and MSI] and three main subunits of PRC1 (Pc, Psc and Sce) and determined their chromosomal locations. We found that most of the genes coding for subunit proteins are present as paralogs in bread wheat. Using bread wheat RNA-seq data from different tissues and developmental stages throughout plant ontogenesis revealed variable transcriptional activity for individual paralogs. Phylogenetic analysis showed a high level of protein conservation among temperate cereals.

Conclusions: The identification and chromosomal location of the Polycomb repressive complex 1 and 2 core components in bread wheat may enable a deeper understanding of developmental processes, including vernalization, in commonly grown winter wheat.

Keywords: Epigenetics; Histone methylation; PRC2; Polycomb repressive complex; Wheat.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Schematic representation of the conserved protein domain architecture of Polycomb group (PcG) complexes. The in silico identification of the PRC2 and PRC1 core components in hexaploid wheat was supported by protein alignment with known homologs from Arabidopsis and barley PRC2 and PRC1 and by prediction of main functional protein domains. Homologs of the PRC2 (a) and PRC1 (b) core subunits share highly conserved protein domains among Arabidopsis thaliana (At), Hordeum vulgare (Hv), Triticum dicoccoides (Td) and Triticum aestivum (Ta). Proteins in the figure are representatives of each homologous group from Hv, Td and Ta, which share the same domains and differ only by protein length
Fig. 2
Fig. 2
Phylogenetic analysis of the plant PRC2 components E(z) (a), Su(z) (b), FIE (c) and MSI (d). The analysis was performed using the maximum likelihood method and JTT matrix-based model in MEGA X. The bootstrap consensus tree was inferred from 1000 replicates. E(z) tree is midpoint rooted. Su(z), FIE and MSI trees are rooted in the outgroup Drosophila melanogaster (Dm). Aegilops tauschii (Ata), Arabidopsis thaliana (Ath), Brachypodium distachyon (Bd), Helianthus annuus (Ha), Nicotiana attenuata (Na), Populus trichocarpa (Pt), Solanum lycopersicum (Sl), Sorghum bicolor (Sb), Hordeum vulgare (Hv), Oryza sativa indica (OsI), Oryza sativa japonica (OsJ), Triticum aestivum (Ta), Triticum dicoccoides (Td), Triticum urartu (Tu) and Zea mays (Zm). An asterisk (*) indicates the gene not assigned to any chromosome based on a BLAST search - the chromosome location was determined by a colinearity with T. urartu and T. turgidum
Fig. 3
Fig. 3
Phylogenetic analysis of the plant PRC1 components LHP1 (a), RING1 (b), BMI1 (c) and EMF1 (d). The analysis was performed using the maximum likelihood method and JTT matrix-based model in MEGA X. The bootstrap consensus tree was inferred from 1000 replicates. Trees are rooted in the outgroup Drosophila melanogaster (Dm), with the exception of the EMF1 tree, which is rooted in Arabidopsis thaliana (Ath). Aegilops tauschii (Ata), Brachypodium distachyon (Bd), Hordeum vulgare (Hv), Oryza sativa indica (OsI), Oryza sativa japonica (OsJ), Triticum aestivum (Ta), Triticum dicoccoides (Td), Triticum urartu (Tu) and Zea mays (Zm)
Fig. 4
Fig. 4
Heat map of PRC1 and PRC2 mRNA levels at different wheat developmental stages. The publicly available RNA-seq data of candidate genes from the cultivar Azhurnaya were clustered based on the transcription profile similarities between the genes (rows) and tissues (columns). Each tissue is characterized as “high-level age_age_tissue”. The high-level stages S – seedling (blue), V – vegetative (green) and R – reproductive (red) are also highlighted by a horizontal color stripe. For a detailed description of the developmental samples and input values, see Additional file 3: Table S2. The color key shows transcripts per million (TPM) after log2 transformation
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