Polycomb repressive complex 2 (PRC2) is involved in maintaining transcriptionally silent chromatin states through methylating lysine 27 of histone H3 by the catalytic subunit enhancer of zeste [E(z)]. Here, we report the diversity of PRC2 core subunit proteins in different eukaryotic supergroups with emphasis on the early-diverged lineages and explore the molecular evolution of PRC2 subunits by phylogenetics. For the first time, we identify the putative ortholog of E(z) in Discoba, a lineage hypothetically proximal to the eukaryotic root, strongly supporting emergence of PRC2 before the diversification of eukaryotes. Analyzing 283 species, we robustly detect a common presence of E(z) and ESC, indicating a conserved functional core. Full-length Su(z)12 orthologs were identified in some lineages and species only, indicating, nonexclusively, high divergence of VEFS-Box-containing Su(z)12-like proteins, functional convergence of sequence-unrelated proteins, or Su(z)12 dispensability. Our results trace E(z) evolution within the SET-domain protein family, proposing a substrate specificity shift during E(z) evolution based on SET-domain and H3 histone interaction prediction.
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.
- Klíčová slova
- Epigenetics, Histone methylation, PRC2, Polycomb repressive complex, Wheat,
- MeSH
- chromozomy rostlin MeSH
- fylogeneze MeSH
- mapování chromozomů MeSH
- molekulární evoluce MeSH
- počítačová simulace MeSH
- PRC1 genetika MeSH
- PRC2 genetika MeSH
- pšenice genetika MeSH
- RNA rostlin MeSH
- sekvenování transkriptomu MeSH
- stanovení celkové genové exprese MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- PRC1 MeSH
- PRC2 MeSH
- RNA rostlin MeSH
In mammals, the noncoding Xist RNA triggers transcriptional silencing of one of the two X chromosomes in female cells. Here, we report a genetic screen for silencing factors in X chromosome inactivation using haploid mouse embryonic stem cells (ESCs) that carry an engineered selectable reporter system. This system was able to identify several candidate factors that are genetically required for chromosomal repression by Xist. Among the list of candidates, we identify the RNA-binding protein Spen, the homolog of split ends. Independent validation through gene deletion in ESCs confirms that Spen is required for gene repression by Xist. However, Spen is not required for Xist RNA localization and the recruitment of chromatin modifications, including Polycomb protein Ezh2. The identification of Spen opens avenues for further investigation into the gene-silencing pathway of Xist and shows the usefulness of haploid ESCs for genetic screening of epigenetic pathways.
- MeSH
- DNA vazebné proteiny MeSH
- embryonální kmenové buňky metabolismus MeSH
- EZH2 protein MeSH
- haploidie MeSH
- jaderné proteiny genetika metabolismus MeSH
- kultivované buňky MeSH
- myši MeSH
- PRC2 genetika metabolismus MeSH
- proteiny vázající RNA MeSH
- RNA dlouhá nekódující genetika MeSH
- umlčování genů * MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- DNA vazebné proteiny MeSH
- Ezh2 protein, mouse MeSH Prohlížeč
- EZH2 protein MeSH
- jaderné proteiny MeSH
- PRC2 MeSH
- proteiny vázající RNA MeSH
- RNA dlouhá nekódující MeSH
- Spen protein, mouse MeSH Prohlížeč
- XIST non-coding RNA MeSH Prohlížeč
