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

Huang, Yong; Jiang, Ling; Liu, Boyu; Tan, Chengfang; Chen, Dong Hong; Shen, Wen‐Hui; Ruan, Ying

doi:10.1186/s12864-019-5905-9

Cited by 29 publications

(26 citation statements)

References 109 publications

(177 reference statements)

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“…We demonstrate that EPR-1 forms nuclear foci, reminiscent of Polycomb bodies (24), and its genomic distribution is limited to, and dependent upon, H3K27-methylated chromatin, which it recognizes directly through its BAH domain. Finally, we discover that EPR-1 orthologs are widely distributed across eukaryotes, contrary to previous reports (21,25,26), suggesting an ancient role of EPR-1 homologs in Polycomb repression that was then lost on multiple occasions in certain lineages.…”

Section: Introductioncontrasting

confidence: 94%

Evolutionarily ancient BAH-PHD protein mediates Polycomb silencing

Wiles

McNaught

Silva

et al. 2019

Preprint

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AbstractMethylation of histone H3 lysine 27 (H3K27) is widely recognized as a transcriptionally repressive chromatin modification but the mechanism of repression remains unclear. We devised and implemented a forward genetic scheme to identify factors required for H3K27 methylation-mediated silencing in the filamentous fungus Neurospora crassa and identified a bromo-adjacent homology (BAH)-plant homeodomain (PHD)-containing protein, EPR-1 (Effector of Polycomb Repression 1; NCU07505). EPR-1 associates with H3K27 methylation in vivo and in vitro, and loss of EPR-1 de-represses H3K27-methylated genes without loss of H3K27 methylation. EPR-1 is not fungal-specific; orthologs of EPR-1 are present in a diverse array of eukaryotic lineages, suggesting an ancestral EPR-1 was a component of a primitive Polycomb repression pathway.SignificancePolycomb group (PcG) proteins are employed by a wide variety of eukaryotes for the maintenance of gene repression. Polycomb repressive complex 2 (PRC2), a multimeric complex of PcG proteins, catalyzes the methylation of histone H3 lysine 27 (H3K27). In the filamentous fungus, Neurospora crassa, H3K27 methylation represses scores of genes, despite the absence of canonical H3K27 methylation effectors that are present in plants and animals. We report the identification and characterization of an H3K27 methylation effector, EPR-1, in N. crassa and demonstrate its widespread presence and early eukaryotic origins with phylogenetic analyses. These findings indicate that an ancient EPR-1 may have been part of a nascent Polycomb repression system in eukaryotes.

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Section: Introductioncontrasting

confidence: 94%

Evolutionarily ancient BAH-PHD protein mediates Polycomb silencing

Wiles

McNaught

Silva

et al. 2019

Preprint

View full text Add to dashboard Cite

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“…We demonstrate that EPR-1 forms nuclear foci, reminiscent of Polycomb bodies (24), and its genomic distribution is limited to, and dependent upon, H3K27-methylated chromatin, which may be recognized through its BAH domain. Finally, we discovered that EPR-1 orthologs are widely distributed across eukaryotes, contrary to previous reports (21,25,26), suggesting an ancient role of EPR-1 homologs in Polycomb repression that was then lost on multiple occasions in certain lineages.…”

contrasting

confidence: 96%

“…6A). Notably, we determined the Arabidopsis thaliana paralogs EBS and SHL as orthologs of EPR-1 in our analyses, which have been erroneously reported as plant-unique proteins (21,25,26). Similar to EPR-1, the plant paralogs, EBS and SHL, bind H3K27 methylation and have been implicated in gene repression (17,18,21).…”

Section: Epr-1 Is a Homolog Of Plant Ebs/shl And Widely Distributed Amentioning

confidence: 99%

Evolutionarily ancient BAH–PHD protein mediates Polycomb silencing

Wiles

McNaught

Kaur

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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Methylation of histone H3 lysine 27 (H3K27) is widely recognized as a transcriptionally repressive chromatin modification but the mechanism of repression remains unclear. We devised and implemented a forward genetic scheme to identify factors required for H3K27 methylation-mediated silencing in the filamentous fungusNeurospora crassaand identified a bromo-adjacent homology (BAH)-plant homeodomain (PHD)-containing protein, EPR-1 (effector of polycomb repression 1; NCU07505). EPR-1 associates with H3K27-methylated chromatin, and loss of EPR-1 de-represses H3K27-methylated genes without loss of H3K27 methylation. EPR-1 is not fungal-specific; orthologs of EPR-1 are present in a diverse array of eukaryotic lineages, suggesting an ancestral EPR-1 was a component of a primitive Polycomb repression pathway.

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“…from Tetrahymena thermophila and a phosphorylated histone H3 peptide (aa. [5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23] showed that the HAT domain interacts with the sidechain of glutamine 5 (Q5), located 9 amino acids upstream of the target lysine (K14) on the H3 peptide (56). As H3K27 is similarly located 9 amino acids upstream H3K36, this suggests that the HAT domain of GCN5 in Arabidopsis may interact with the sidechain of H3K27 to regulate the catalytic activity of GCN5 at H3K36.…”

Section: Discussionmentioning

confidence: 99%

H3.1K27me1 maintains transcriptional silencing and genome stability by preventing GCN5-mediated histone acetylation

Dong

LeBlanc

Poulet

et al. 2020

Preprint

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In plants, genome stability is maintained during DNA replication by the H3.1K27 methyltransferases ATXR5 and ATXR6, which catalyze the deposition of K27me1 on replication-dependent H3.1 variants. Loss of H3.1K27me1 in atxr5 atxr6 double mutants leads to heterochromatin defects, including transcriptional de-repression and genomic instability, but the molecular mechanisms involved remain largely unknown. In this study, we identified the conserved histone acetyltransferase GCN5 as a mediator of transcriptional de-repression and genomic instability in the absence of H3.1K27me1. GCN5 is part of a SAGA-like complex in plants that requires ADA2b and CHR6 to mediate the heterochromatic defects of atxr5 atxr6 mutants. Our results show that Arabidopsis GCN5 acetylates multiple lysine residues on H3.1 variants in vitro, but that H3.1K27 and H3.1K36 play key roles in inducing genomic instability in the absence of H3.1K27me1. Overall, this work reveals a key molecular role for H3.1K27me1 in maintaining genome stability by restricting histone acetylation in plants.

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

Cited by 29 publications

References 109 publications

Evolutionarily ancient BAH-PHD protein mediates Polycomb silencing

Evolutionarily ancient BAH-PHD protein mediates Polycomb silencing

Evolutionarily ancient BAH–PHD protein mediates Polycomb silencing

H3.1K27me1 maintains transcriptional silencing and genome stability by preventing GCN5-mediated histone acetylation

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