Conservation and diversification of polycomb repressive complex 2 (PRC2) proteins in the green lineage

Huang, Yong; Chen, Donghong; Liu, Boyu; Shen, Wen‐Hui; Ruan, Ying

doi:10.1093/bfgp/elw007

Cited by 25 publications

(60 citation statements)

References 120 publications

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“…Phylogenetic analyses on the conserved domains or full sequences of core PRC2 homologs in lower and higher plants with the creation of Neighbor-Joining (NJ) trees revealed grouping into several distinct classes ( Shaver et al, 2010 ; Kim et al, 2013 ; Huang et al, 2016 ). In a different approach, we extracted amino acid sequences from the most abundant PRC2 members, aligned them and automatically selected only the conserved blocks in the multiple alignment (see Material and Methods).…”

Section: Resultsmentioning

confidence: 99%

Characterization of the Polycomb-Group Mark H3K27me3 in Unicellular Algae

et al. 2017

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Polycomb Group (PcG) proteins mediate chromatin repression in plants and animals by catalyzing H3K27 methylation and H2AK118/119 mono-ubiquitination through the activity of the Polycomb repressive complex 2 (PRC2) and PRC1, respectively. PcG proteins were extensively studied in higher plants, but their function and target genes in unicellular branches of the green lineage remain largely unknown. To shed light on PcG function and modus operandi in a broad evolutionary context, we demonstrate phylogenetic relationship of core PRC1 and PRC2 proteins and H3K27me3 biochemical presence in several unicellular algae of different phylogenetic subclades. We focus then on one of the species, the model red alga Cyanidioschizon merolae, and show that H3K27me3 occupies both, genes and repetitive elements, and mediates the strength of repression depending on the differential occupancy over gene bodies. Furthermore, we report that H3K27me3 in C. merolae is enriched in telomeric and subtelomeric regions of the chromosomes and has unique preferential binding toward intein-containing genes involved in protein splicing. Thus, our study gives important insight for Polycombmediated repression in lower eukaryotes, uncovering a previously unknown link between H3K27me3 targets and protein splicing.

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Section: Resultsmentioning

confidence: 99%

Characterization of the Polycomb-Group Mark H3K27me3 in Unicellular Algae

et al. 2017

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“…The presence of PRC2 complex in lower plants including algae has been reported [41, 98]. PRC1 is also evolutionarily ancient, and its subunits are found in mammals, plants, insects, and other species, but are lost in several primitive organisms [41].…”

Section: Discussionmentioning

confidence: 99%

Evolution and conservation of polycomb repressive complex 1 core components and putative associated factors in the green lineage

et al. 2019

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Background: Polycomb group (PcG) proteins play important roles in animal and plant development and stress response. Polycomb repressive complex 1 (PRC1) and PRC2 are the key epigenetic regulators of gene expression, and are involved in almost all developmental stages. PRC1 catalyzes H2A monoubiquitination resulting in transcriptional silencing or activation. The PRC1 components in the green lineage were identified and evolution and conservation was analyzed by bioinformatics techniques. RING Finger Protein 1 (RING1), B lymphoma Mo-MLV insertion region 1 homolog (BMI1), Like Heterochromatin Protein 1 (LHP1) and Embryonic Flower 1 (EMF1) are the PRC1 core components and Vernalization 1 (VRN1), VP1/ABI3-Like 1/2/3 (VAL1/2/3), Alfin-like 1-7 (AL1-7), Inhibitor of growth 1/2 (ING1/2), and Early Bolting in Short Days (EBS) / Short Life (SHL) are the associated factors. Results: Each PRC1 subunit possesses special domain organizations, such as RING and the ring finger and WD40associated ubiquitin-like (RAWUL) domains for RING1 and BMI1, chromatin organization modifier (CHROMO) and chromo shadow (ChSh) domains for LHP1, one or two B3 DNA binding domain(s) for VRN1, B3 and zf-CW domains for VAL1/2/3, Alfin and Plant HomeoDomain (PHD) domains for AL1-7, ING and PHD domains for ING1/2, Bromoadjacent homology (BAT) and PHD domains for EBS/SHL. Six new motifs are uncovered in EMF1. The PRC1 core components RING1 and BMI1, and the associated factors VAL1/2/3, AL1-7, ING1/2, and EBS/SHL exist from alga to higher plants, whereas LHP1 only occurs in higher plants. EMF1 and VRN1 are present only in eudicots. PRC1 components undergo duplication in the plant evolution. Most of plants carry the homologous core component LHP1, the associated factor EMF1, and several homologs in RING1, BMI1, VRN1, AL1-7, ING1/2/3, and EBS/SHL. Cabbage, cotton, poplar, orange and maize often exhibit more gene copies than other species. Domain organization analysis shows that duplicated gene functions may be of diverse. Conclusions: The PRC1 core components RING1 and BMI1, and the associated factors VAL1/2/3, AL1-7, ING1/2, and EBS/SHL originate from algae. The core component LHP1 is from moss and the associated factors EMF1 and VRN1 are from dicotyledon. PRC1 components are of functional redundancy and diversity in evolution.

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“…AtKMT1A;1 ( SDG33 / SUVH4 ), homologous gene to GrKMT1A;1a is involved in host defense system by regulating target genes H3K9me48. KMT6B;1 ( SDG1 / CLF ) is one of core components of PRC2 and mainly contributes to the H3K27 activity49, whose increase at stress gene loci will repress heat shock response (HSR)50. However, the function of AtKMT3;3 ( SDG4 / ASHR / SET4 ) in resistance response is unknown.…”

Section: Discussionmentioning

confidence: 99%

Identification of SET Domain-Containing Proteins in Gossypium raimondii and Their Response to High Temperature Stress

Huang

Chen

et al. 2016

Sci Rep

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SET (Su(var), E(z), and Trithorax) domain-containing proteins play an important role in plant development and stress responses through modifying lysine methylation status of histone. Gossypium raimondii may be the putative contributor of the D-subgenome of economical crops allotetraploid G. hirsutum and G. barbadense and therefore can potentially provide resistance genes. In this study, we identified 52 SET domain-containing genes from G. raimondii genome. Based on conserved sequences, these genes are grouped into seven classes and are predicted to catalyze the methylation of different substrates: GrKMT1 for H3K9me, GrKMT2 and GrKMT7 for H3K4me, GrKMT3 for H3K36me, GrKMT6 for H3K27me, but GrRBCMT and GrS-ET for nonhistones substrate-specific methylation. Seven pairs of GrKMT and GrRBCMT homologous genes are found to be duplicated, possibly one originating from tandem duplication and five from a large scale or whole genome duplication event. The gene structure, domain organization and expression patterns analyses suggest that these genes’ functions are diversified. A few of GrKMTs and GrRBCMTs, especially for GrKMT1A;1a, GrKMT3;3 and GrKMT6B;1 were affected by high temperature (HT) stress, demonstrating dramatically changed expression patterns. The characterization of SET domain-containing genes in G. raimondii provides useful clues for further revealing epigenetic regulation under HT and function diversification during evolution.

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Conservation and diversification of polycomb repressive complex 2 (PRC2) proteins in the green lineage

Cited by 25 publications

References 120 publications

Characterization of the Polycomb-Group Mark H3K27me3 in Unicellular Algae

Characterization of the Polycomb-Group Mark H3K27me3 in Unicellular Algae

Evolution and conservation of polycomb repressive complex 1 core components and putative associated factors in the green lineage

Identification of SET Domain-Containing Proteins in Gossypium raimondii and Their Response to High Temperature Stress

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