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.

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Identification of Polycomb Repressive Complex 1 and 2 Core Components in Hexaploid Bread Wheat

10.1101/703546 ◽

2019 ◽

Author(s):

Beáta Strejčková ◽

Radim Čegan ◽

Ales Pecinka ◽

Zbyněk Milec ◽

Jan Šafář

Keyword(s):

Bread Wheat ◽

Developmental Stages ◽

Gene Families ◽

Polycomb Group ◽

Transcriptional Analysis ◽

Histone H2a ◽

Polycomb Repressive Complex ◽

Polycomb Repressive Complex 2 ◽

Core Components ◽

Polycomb Repressive Complex 1

ABSTRACTPolycomb repressive complex 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, while Polycomb repressive complex 1 catalyzes the monoubiquitination of histone H2A at lysine 119. Although these biochemical functions are evolutionarily conserved, studies in animals and plants, mainly Arabidopsis thaliana, showed that specific subunits have evolved into small gene families, with individual members acting at different developmental stages or responding to specific environmental stimuli. However, the evolution of polycomb group gene families in monocots, particularly those with complex allopolyploid origins, is unknown. Here, we present the in silico identification of the Polycomb repressive complex 1 and 2 subunits in allohexaploid bread wheat, the reconstruction of their evolutionary history and a transcriptional analysis over a series of 33 developmental stages. 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.

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The genetic basis for PRC1 complex diversity emerged early in animal evolution

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2005136117 ◽

2020 ◽

Vol 117 (37) ◽

pp. 22880-22889 ◽

Cited By ~ 1

Author(s):

James M. Gahan ◽

Fabian Rentzsch ◽

Christine E. Schnitzler

Keyword(s):

Classical Model ◽

Ring Finger ◽

Polycomb Group ◽

Model Systems ◽

Vertebrate Lineage ◽

Animal Evolution ◽

Chromatin Regulators ◽

Core Components ◽

Mammalian Counterpart ◽

Polycomb Repressive Complex 1

Polycomb group proteins are essential regulators of developmental processes across animals. Despite their importance, studies on Polycomb are often restricted to classical model systems and, as such, little is known about the evolution of these important chromatin regulators. Here we focus on Polycomb Repressive Complex 1 (PRC1) and trace the evolution of core components of canonical and non-canonical PRC1 complexes in animals. Previous work suggested that a major expansion in the number of PRC1 complexes occurred in the vertebrate lineage. We show that the expansion of the Polycomb Group RING Finger (PCGF) protein family, an essential step for the establishment of the large diversity of PRC1 complexes found in vertebrates, predates the bilaterian–cnidarian ancestor. This means that the genetic repertoire necessary to form all major vertebrate PRC1 complexes emerged early in animal evolution, over 550 million years ago. We further show that PCGF5, a gene conserved in cnidarians and vertebrates but lost in all other studied groups, is expressed in the nervous system in the sea anemone Nematostella vectensis, similar to its mammalian counterpart. Together this work provides a framework for understanding the evolution of PRC1 complex diversity and it establishes Nematostella as a promising model system in which the functional ramifications of this diversification can be further explored.

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USP7 Cooperates with SCML2 To Regulate the Activity of PRC1

Molecular and Cellular Biology ◽

10.1128/mcb.01197-14 ◽

2015 ◽

Vol 35 (7) ◽

pp. 1157-1168 ◽

Cited By ~ 37

Author(s):

Emilio Lecona ◽

Varun Narendra ◽

Danny Reinberg

Keyword(s):

Chromatin Immunoprecipitation ◽

Essential Role ◽

Target Genes ◽

Polycomb Group ◽

Histone H2a ◽

Polycomb Group Protein ◽

Specific Component ◽

Group Protein ◽

The Common ◽

Polycomb Repressive Complex 1

USP7 is a protein deubiquitinase with an essential role in development. Here, we provide evidence that USP7 regulates the activity of Polycomb repressive complex 1 (PRC1) in coordination with SCML2. There are six versions of PRC1 defined by the association of one of the PCGF homologues (PCGF1 to PCGF6) with the common catalytic subunit RING1B. First, we show that SCML2, a Polycomb group protein that associates with PRC1.2 (containing PCGF2/MEL18) and PRC1.4 (containing PCGF4/BMI1), modulates the localization of USP7 and bridges USP7 with PRC1.4, allowing for the stabilization of BMI1. Chromatin immunoprecipitation (ChIP) experiments demonstrate that USP7 is found at SCML2 and BMI1 target genes. Second, inhibition of USP7 leads to a reduction in the level of ubiquitinated histone H2A (H2Aub), the catalytic product of PRC1 and key for its repressive activity. USP7 regulates the posttranslational status of RING1B and BMI1, a specific component of PRC1.4. Thus, not only does USP7 stabilize PRC1 components, its catalytic activity is also necessary to maintain a functional PRC1, thereby ensuring appropriate levels of repressive H2Aub.

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Dependency on the polycomb gene Ezh2 distinguishes fetal from adult hematopoietic stem cells

Blood ◽

10.1182/blood-2011-03-340554 ◽

2011 ◽

Vol 118 (25) ◽

pp. 6553-6561 ◽

Cited By ~ 129

Author(s):

Makiko Mochizuki-Kashio ◽

Yuta Mishima ◽

Satoru Miyagi ◽

Masamitsu Negishi ◽

Atsunori Saraya ◽

...

Keyword(s):

Stem Cells ◽

Hematopoietic Stem Cells ◽

Progenitor Cells ◽

Fetal Liver ◽

Polycomb Group ◽

Gene Encoding ◽

Hematopoietic Stem ◽

High Level ◽

Polycomb Repressive Complex 1

Abstract Polycomb-group (PcG) proteins are essential regulators of hematopoietic stem cells (HSCs). In contrast to Bmi1, a component of Polycomb repressive complex 1 (PRC1), the role of PRC2 and its components in hematopoiesis remains elusive. Here we show that Ezh2, a core component of PRC2, is essential for fetal, but not adult, HSCs. Ezh2-deficient embryos died of anemia because of insufficient expansion of HSCs/progenitor cells and defective erythropoiesis in fetal liver. Deletion of Ezh2 in adult BM, however, did not significantly compromise hematopoiesis, except for lymphopoiesis. Of note, Ezh2-deficient fetal liver cells showed a drastic reduction in trimethylation of histone H3 at lysine 27 (H3K27me3) accompanied by derepression of a large cohort of genes, whereas on homing to BM, they acquired a high level of H3K27me3 and long-term repopulating capacity. Quantitative RT-PCR revealed that Ezh1, the gene encoding a backup enzyme, is highly expressed in HSCs/progenitor cells in BM compared with those in fetal liver, whereas Ezh2 is ubiquitously expressed. These findings suggest that Ezh1 complements Ezh2 in the BM, but not in the fetal liver, and reveal that the reinforcement of PcG-mediated gene silencing occurs during the transition from proliferative fetal HSCs to quiescent adult HSCs.

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KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands

eLife ◽

10.7554/elife.00205 ◽

2012 ◽

Vol 1 ◽

Cited By ~ 280

Author(s):

Anca M Farcas ◽

Neil P Blackledge ◽

Ian Sudbery ◽

Hannah K Long ◽

Joanna F McGouran ◽

...

Keyword(s):

Cpg Islands ◽

Gene Promoters ◽

Histone H2a ◽

Polycomb Repressive Complex ◽

Expression Of Genes ◽

Nucleation Sites ◽

Polycomb Response Elements ◽

Low Levels ◽

Polycomb Repressive Complexes ◽

Polycomb Repressive Complex 1

CpG islands (CGIs) are associated with most mammalian gene promoters. A subset of CGIs act as polycomb response elements (PREs) and are recognized by the polycomb silencing systems to regulate expression of genes involved in early development. How CGIs function mechanistically as nucleation sites for polycomb repressive complexes remains unknown. Here we discover that KDM2B (FBXL10) specifically recognizes non-methylated DNA in CGIs and recruits the polycomb repressive complex 1 (PRC1). This contributes to histone H2A lysine 119 ubiquitylation (H2AK119ub1) and gene repression. Unexpectedly, we also find that CGIs are occupied by low levels of PRC1 throughout the genome, suggesting that the KDM2B-PRC1 complex may sample CGI-associated genes for susceptibility to polycomb-mediated silencing. These observations demonstrate an unexpected and direct link between recognition of CGIs by KDM2B and targeting of the polycomb repressive system. This provides the basis for a new model describing the functionality of CGIs as mammalian PREs.

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The genetic basis for PRC1 complex diversity emerged early in animal evolution

10.1101/2020.03.18.997064 ◽

2020 ◽

Author(s):

James M Gahan ◽

Fabian Rentzsch ◽

Christine E Schnitzler

Keyword(s):

Genetic Basis ◽

Classical Model ◽

Polycomb Group ◽

Model Systems ◽

Vertebrate Lineage ◽

Animal Evolution ◽

Chromatin Regulators ◽

Core Components ◽

Mammalian Counterpart ◽

Polycomb Repressive Complex 1

AbstractPolycomb group proteins are essential regulators of developmental processes across animals. Despite their importance, studies on Polycomb are often restricted to classical model systems and, as such, little is known about the evolution of these important chromatin regulators. Here we focus on Polycomb Repressive Complex 1 (PRC1) and trace the evolution of core components of canonical and non-canonical PRC1 complexes in animals. Previous work suggested that a major expansion in the number of PRC1 complexes occurred in the vertebrate lineage. Here we show that the expansion of the PCGF protein family, an essential step for the establishment of the large diversity of PRC1 complexes found in vertebrates, predates the bilaterian-cnidarian ancestor. This means that the genetic repertoire necessary to form all major vertebrate PRC1 complexes emerged early in animal evolution, over 550 million years ago. We further show that PCGF5, a gene conserved in cnidarians and vertebrates but lost in all other studied groups, is expressed in the nervous system in the sea anemone Nematostella vectensis, similar to its mammalian counterpart. Together this work provides an evolutionary framework to understand PRC1 complex diversity and evolution and establishes Nematostella as a promising model system in which this can be further explored.

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

BMC Genomics ◽

10.1186/s12864-019-5905-9 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 5

Author(s):

Yong Huang ◽

Ling Jiang ◽

Bo-Yu Liu ◽

Cheng-Fang Tan ◽

Dong-Hong Chen ◽

...

Keyword(s):

Associated Factors ◽

Polycomb Repressive Complex ◽

Core Components ◽

Polycomb Repressive Complex 1 ◽

Green Lineage

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Polycomb repressive complex 1 defines the nucleosome landscape but not accessibility at target genes

10.1101/280305 ◽

2018 ◽

Author(s):

Hamish W King ◽

Robert J Klose

Keyword(s):

Target Genes ◽

Nucleosome Occupancy ◽

Embryonic Stem ◽

Chromatin Accessibility ◽

Polycomb Group ◽

Gene Promoters ◽

Polycomb Repressive Complex ◽

Chromatin Domains ◽

Genetic Ablation ◽

Polycomb Repressive Complex 1

ABSTRACTPolycomb group (PcG) proteins are transcriptional repressors that play important roles regulating gene expression during animal development. In vitro experiments have shown that PcG protein complexes can compact chromatin limiting the activity of chromatin remodelling enzymes and access of the transcriptional machinery to DNA. In fitting with these ideas, gene promoters associated with PcG proteins have been reported to be less accessible than other gene promotors. However, it remains largely untested in vivo whether PcG proteins define chromatin accessibility or other chromatin features. To address this important question, we measured chromatin accessibility and examined the nucleosome landscape at PcG protein-bound promoters in mouse embryonic stem cells using the assay for transposase accessible chromatin (ATAC)-seq. Combined with genetic ablation strategies, we unexpectedly discover that although PcG protein-occupied gene promoters exhibit reduced accessibility, this does not rely on PcG proteins. Instead, the Polycomb repressive complex 1 (PRC1) appears to play a unique role in driving elevated nucleosome occupancy and decreased nucleosomal spacing in Polycomb chromatin domains. Our new genome-scale observations argue, in contrast to the prevailing view, that PcG proteins and Polycomb chromatin domains do not significantly affect chromatin accessibility and highlight an underappreciated complexity in the relationship between chromatin accessibility, the nucleosome landscape and PcG-mediated transcriptional repression.

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Arabidopsis Genes Essential for Seedling Viability: Isolation of Insertional Mutants and Molecular Cloning

Genetics ◽

10.1093/genetics/159.4.1765 ◽

2001 ◽

Vol 159 (4) ◽

pp. 1765-1778

Author(s):

Gregory J Budziszewski ◽

Sharon Potter Lewis ◽

Lyn Wegrich Glover ◽

Jennifer Reineke ◽

Gary Jones ◽

...

Keyword(s):

Large Scale ◽

Protein Translocation ◽

Gene Families ◽

Mutant Phenotype ◽

Lethal Mutant ◽

A Genome ◽

Genes Encoding ◽

High Level ◽

Mutant Lines ◽

Genome Scale

Abstract We have undertaken a large-scale genetic screen to identify genes with a seedling-lethal mutant phenotype. From screening ~38,000 insertional mutant lines, we identified >500 seedling-lethal mutants, completed cosegregation analysis of the insertion and the lethal phenotype for >200 mutants, molecularly characterized 54 mutants, and provided a detailed description for 22 of them. Most of the seedling-lethal mutants seem to affect chloroplast function because they display altered pigmentation and affect genes encoding proteins predicted to have chloroplast localization. Although a high level of functional redundancy in Arabidopsis might be expected because 65% of genes are members of gene families, we found that 41% of the essential genes found in this study are members of Arabidopsis gene families. In addition, we isolated several interesting classes of mutants and genes. We found three mutants in the recently discovered nonmevalonate isoprenoid biosynthetic pathway and mutants disrupting genes similar to Tic40 and tatC, which are likely to be involved in chloroplast protein translocation. Finally, we directly compared T-DNA and Ac/Ds transposon mutagenesis methods in Arabidopsis on a genome scale. In each population, we found only about one-third of the insertion mutations cosegregated with a mutant phenotype.

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