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

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.

Genome-Wide Identification and Analysis of the Polycomb Group Family in Medicago truncatula

“…We found 64 PcG members in the M. truncatula genome, which was higher than the number found in previous research [ 57 , 58 , 59 , 60 ]. Several researchers identified 10 PcG proteins in M. truncatula [ 57 , 58 ] and 48 PcG proteins in T. aestivum [ 62 ]. Therefore, it is more likely that the number of PcG members in different species was associated with the genome size of the species, ploidy level, analytical method used, and other factors.…”

“…It is noted that the previously reported MtLHP1 gene was identified based on another genome database (Mt3.5v5 version) [ 60 ], whereas the LHP1 gene of M. truncatula was not identified in this study. Moreover, it was previously reported that the members of FIS2 and MEA have not been identified in O. sativa , T. aestivum , Z. mays , and M. truncatula [ 57 , 58 , 62 , 63 ]. Similarly, we did not identify the member of the FIS2 component in the present study.…”

“…A previous report suggested that the number of B3 domains in 27 VRN1 homologous proteins ranged from two to four. Among them, the VRN1 protein in hexaploid bread wheat contained four B3 conserved domains, and only two B3 domains were found in the VRN1 protein of A. thaliana [ 62 ]. The types of domains conserved among PRC1 members in M. truncatula were quite different, suggesting that these members had independent functions.…”

“…Additionally, the AtFIE gene was located on chromosome 3 [ 37 ], the AtVRN2 and AtSWN genes were located on chromosome 4 [ 75 ], and the AtEMF1 and AtEMF2 genes were located on chromosome 5 [ 27 , 76 ]. The E(z) genes of T. aestivum were distributed on chromosomes 4 and 7, the Su(z) genes were distributed on chromosomes 2 and 5, the FIE genes were distributed on chromosomes 4 and 7, the MSI and BMI genes were located on chromosome 5, the LHP1 genes were located on chromosome 7, the RING1 and EMF1 genes were located on chromosome 3, and the RING2 genes were located on chromosome 1 [ 62 ]. The E(z) genes of H. vulgare were located on chromosome 4, the FIE genes were located on chromosome 7, and the Su(z) genes were located on chromosomes 2 and 5 [ 77 ].…”

Post-Embryonic Phase Transitions Mediated by Polycomb Repressive Complexes in Plants

“…Evolutionary studies on the PRC1 subunits (LHP1, Ring1A/1B, BMI1A/1B/1C, EMF1, and VRN1) show that the PRC1 core subunits are conserved in angiosperms [ 34 ], indicating that PRC1 may play similar important regulatory roles in flowering plants. Homologous genes of LHP1 , BMI1A/1B/1C , RING1A/1B , and EMF1 have been discovered in the allohexaploid bread wheat ( Triticum aestivum ) [ 106 ], providing vital tools for studying and manipulating PRC1 in this plant. RING1 , BMI1 and LHP1 are also present in early plant homologs, and have been found in mosses, lycophytes and ferns [ 34 , 107 ].…”