Distinct phases of Polycomb silencing to hold epigenetic memory of cold in
            <i>Arabidopsis</i>

Yang, Hongchun; Berry, Scott; Olsson, Tjelvar S. G.; Hartley, Matthew; Howard, Martin; Dean, Caroline

doi:10.1126/science.aan1121

Cited by 169 publications

(206 citation statements)

References 44 publications

(26 reference statements)

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“…Perhaps more interestingly, we also found genomic sites where loss of CLF led to a marked reduction of H3K27me3 in flanking regions, but not the peak summit, suggesting that CLF might help the spreading of H3K27me3 to flanking regions from a “core” area. Similar H3K27me3 pattern changes were also reported in previous studies (Li & Cui, ; Wang et al., ; Yang et al., ; Yuan et al., ). The remaining H3K27me3 signal at the summit in the clf‐29 mutants might be catalyzed by SWN.…”

Section: Discussionsupporting

confidence: 89%

Genome‐wide occupancy of histone H3K27 methyltransferases CURLY LEAF and SWINGER in Arabidopsis seedlings

et al. 2019

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The Polycomb Group (PcG) proteins form two protein complexes, PcG Repressive Complex 1 ( PRC 1) and PRC 2, which are key epigenetic regulators in eukaryotes. PRC 2 represses gene expression by catalyzing the trimethylation of histone H3 lysine 27 (H3K27me3). In Arabidopsis ( Arabidopsis thaliana ), CURLY LEAF ( CLF ) and SWINGER ( SWN ) are two major H3K27 methyltransferases and core components of PRC 2, playing essential roles in plant growth and development. Despite their importance, genome‐wide binding profiles of CLF and SWN have not been determined and compared yet. In this study, we generated transgenic lines expressing GFP ‐tagged CLF / SWN under their respective native promoters and used them for Ch IP ‐seq analyses to profile the genome‐wide distributions of CLF and SWN in Arabidopsis seedlings. We also profiled and compared the global H3K27me3 levels in wild‐type ( WT ) and PcG mutants ( clf , swn , and clf swn ). Our data show that CLF and SWN bind to almost the same set of genes, except that SWN has a few hundred more targets. Two short DNA sequences, the GAGA ‐like and Telo ‐box‐like motifs, were found enriched in the CLF and SWN binding regions. The H3K27me3 levels in clf , but not in swn , were markedly reduced compared with WT ; and the mark was undetectable in the clf swn double mutant. Further, we profiled the transcriptomes in clf , swn , and clf swn, and compared that with WT . Thus this work provides a useful resource for the plant epigenetics community for dissecting the functions of PRC 2 in plant growth and development.

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Section: Discussionsupporting

confidence: 89%

Genome‐wide occupancy of histone H3K27 methyltransferases CURLY LEAF and SWINGER in Arabidopsis seedlings

et al. 2019

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“…In wild-type plants, H3K27me3 and LHP1 subsequently "spread" to cover the entire locus in the weeks after cold. It is "spreading" rather than "nucleation" that is perturbed in lhp1 mutants (Yang et al 2017). We observed that wild-type LHP1 and LHP1-NLS both localized to the FLC nucleation region during cold and subsequently increased and spread across the entire locus after cold (Fig.…”

Section: The Lhp1 Rna-binding Region Is Required For Polycomb Target mentioning

confidence: 75%

“…ChIP experiments were performed as described previously (Yang et al 2017). Anti-GFP (Abcam, ab290) was used with Protein A agarose/salmon sperm DNA (Millipore,.…”

Section: Chipmentioning

confidence: 99%

Disruption of an RNA-binding hinge region abolishes LHP1-mediated epigenetic repression

et al. 2017

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Epigenetic maintenance of gene repression is essential for development. Polycomb complexes are central to this memory, but many aspects of the underlying mechanism remain unclear. LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) binds Polycomb-deposited H3K27me3 and is required for repression of many Polycomb target genes in Arabidopsis. Here we show that LHP1 binds RNA in vitro through the intrinsically disordered hinge region. By independently perturbing the RNA-binding hinge region and H3K27me3 (trimethylation of histone H3 at Lys27) recognition, we found that both facilitate LHP1 localization and H3K27me3 maintenance. Disruption of the RNAbinding hinge region also prevented formation of subnuclear foci, structures potentially important for epigenetic repression.

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“…It is possible that another sequence than the LTR is responsible for recruiting PRC2 and for the nucleation of a H3K27m3 domain over the TE; however, one would expect, in this scenario, to observe more H3K27m3 on ATR because it shares the same sequence as EVD —unless H3K27m3 is strongly antagonized by higher levels of DNA methylation than observed at EVD . Secondly, the specific genomic localization of EVD, next to PcG targets, as well as the almost complete loss of H3K27m3 at EVD‐LTR in plants mutated for CLF—which was recently shown to be involved in the spreading phase of H3K27m3 at the FLC locus C (Yang et al , )—rather support the hypothesis wherein H3K27 trimethylation at EVD is due to or at least favored by spreading from the neighboring genes marked by H3K27m3. Future studies should identify and delineate TEs that can potentially recruit PRC2 in cis from the ones that become H3K27m3‐marked due to an insertional effect, and the ones that exhibit both characteristics.…”

Section: Discussionmentioning

confidence: 87%

Transcriptional control and exploitation of an immune‐responsive family of plant retrotransposons

Zervudacki

Amesefe

et al. 2018

The EMBO Journal

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Mobilization of transposable elements (TEs) in plants has been recognized as a driving force of evolution and adaptation, in particular by providing genes with regulatory modules that impact their transcription. In this study, we employed an ATCOPIA93 long‐terminal repeat (LTR) promoter‐GUS fusion to show that this retrotransposon behaves like an immune‐responsive gene during pathogen defense in Arabidopsis. We also showed that the endogenous ATCOPIA93 copy “EVD”, which is activated in the presence of bacterial stress, is negatively regulated by both DNA methylation and polycomb‐mediated silencing, a mode of repression typically found at protein‐coding and microRNA genes. Interestingly, an ATCOPIA93‐derived soloLTR is located upstream of the disease resistance gene RPP4 and is devoid of DNA methylation and H3K27m3 marks. Through loss‐of‐function experiments, we demonstrate that this soloLTR is required for the proper expression of RPP4 during plant defense, thus linking the responsiveness of ATCOPIA93 to biotic stress and the co‐option of its LTR for plant immunity.

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Distinct phases of Polycomb silencing to hold epigenetic memory of cold in Arabidopsis

Cited by 169 publications

References 44 publications

Genome‐wide occupancy of histone H3K27 methyltransferases CURLY LEAF and SWINGER in Arabidopsis seedlings

Genome‐wide occupancy of histone H3K27 methyltransferases CURLY LEAF and SWINGER in Arabidopsis seedlings

Disruption of an RNA-binding hinge region abolishes LHP1-mediated epigenetic repression

Transcriptional control and exploitation of an immune‐responsive family of plant retrotransposons

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