scholarly journals The VIL gene CRAWLING ELEPHANT controls maturation and differentiation in tomato via polycomb silencing

2021 ◽  
Author(s):  
Ido Shwartz ◽  
Chen Yahav ◽  
Neta Kovetz ◽  
Alon Israeli ◽  
Maya Bar ◽  
...  

VERNALIZATION INSENSITIVE 3-LIKE (VIL) proteins are PHD-finger proteins that recruit the repressor complex Polycomb Repressive Complex 2 (PRC2) to the promoters of target genes. Most known VIL targets are flowering repressor genes. Here, we show that the tomato VIL gene CRAWLING ELEPHANT ( CREL ) promotes differentiation throughout plant development by facilitating the trimethylation of Histone H3 on lysine 27 (H3K27me3). We identified the crel mutant in a screen for suppressors of the simple-leaf phenotype of entire ( e ), a mutant in the AUX/IAA gene ENTIRE/SlIAA9, involved in compound-leaf development in tomato. crel mutants have increased leaf complexity, and suppress the ectopic blade growth of e mutants. In addition, crel mutants are late flowering, and have delayed and aberrant stem, root and flower development. Consistent with a role for CREL in recruiting PRC2, crel mutants present altered H3K27me3 modifications at a subset of PRC2 targets throughout the genome. Our results uncover a wide role for CREL in plant and organ differentiation in tomato and suggest that CREL is required for targeting PRC2 activity to, and thus silencing, a specific subset of polycomb targets.

2021 ◽  
Author(s):  
Manuel Tavares ◽  
Garima Khandelwal ◽  
Joanne Mutter ◽  
Keijo Viiri ◽  
Manuel Beltran ◽  
...  

Polycomb repressive complex 2 (PRC2) methylates histone H3 lysine 27 (H3K27me3) to maintain repression of genes specific for other cell types and is essential for cell differentiation. In endometrial stromal sarcoma, the PRC2 subunit SUZ12 is often fused with the NuA4/TIP60 subunit JAZF1. Here, we show that JAZF1-SUZ12 dysregulates PRC2 composition, recruitment, histone modification, gene expression and cell differentiation. The loss of the SUZ12 N-terminus in the fusion protein disrupted interaction with the PRC2 accessory factors JARID2, EPOP and PALI1 and prevented recruitment of PRC2 from RNA to chromatin. In undifferentiated cells, JAZF1-SUZ12 occupied PRC2 target genes but gained a JAZF1-like binding profile during cell differentiation. JAZF1-SUZ12 reduced H3K27me3 and increased H4Kac at PRC2 target genes, and this was associated with disruption in gene expression and cell differentiation programs. These results reveal the defects in chromatin regulation caused by JAZF1-SUZ12, which may underlie its role in oncogenesis.


2021 ◽  
Author(s):  
Jianji Chen ◽  
John Horton ◽  
Cari Sagum ◽  
Jujun Zhou ◽  
Xiaodong Cheng ◽  
...  

The reader ability of PHD fingers is largely limited to the recognition of the histone H3 N-terminal tail. Distinct subsets of PHDs bind either H3K4me3 (a transcriptional activator mark) or H3K4me0 (a transcriptional repressor state). Structural studies have identified common features among the different H3K4me3 effector PHDs, including 1) removal of the initiator methionine residue of H3 to prevent steric interference, 2) a groove where arginine-2 binds, and 3) an aromatic cage that engages methylated lysine-4. We hypothesize that  PHDs  have the ability to engage with non-histone ligands, as long as they adhere to these three rules. A search of the human proteome revealed an enrichment of chromatin-binding proteins that met these criteria, which we termed H3 N-terminal mimicry proteins (H3TMs). Seven H3TMs were selected, and used to screen a protein domain microarray for potential effector domains, and they all had the ability to bind H3K4me3-interacting effector domains. Furthermore, the binding affinity between the VRK1 peptide and the PHD domain of PHF2 is ~3-fold stronger than that of PHF2 and H3K4me3 interaction. The crystal structure of PHF2 PHD finger bound with VRK1 K4me3 peptide provides a molecular basis for stronger binding of VRK1 peptide. In addition, a number of the H3TMs peptides, in their unmethylated form, interact with NuRD transcriptional repressor complex. Our findings provide in vitro evidence that methylation of H3TMs can promote interactions with PHD and Tudor domain-containing proteins and potentially block interactions with the NuRD complex. We propose that these interactions can occur in vivo as well.


2018 ◽  
Vol 293 (47) ◽  
pp. 18031-18039 ◽  
Author(s):  
Mónica Ferreira ◽  
Iris Verbinnen ◽  
Margarida Fardilha ◽  
Aleyde Van Eynde ◽  
Mathieu Bollen

Germ cell proliferation is epigenetically controlled, mainly through DNA methylation and histone modifications. However, the pivotal epigenetic regulators of germ cell self-renewal and differentiation in postnatal testis are still poorly defined. The histone methyltransferase enhancer of zeste homolog 2 (EZH2) is the catalytic subunit of Polycomb repressive complex 2, represses target genes through trimethylation of histone H3 at Lys-27 (H3K27me3), and interacts (in)directly with both protein phosphatase 1 (PP1) and nuclear inhibitor of PP1 (NIPP1). Here, we report that postnatal, testis-specific ablation of NIPP1 in mice results in loss of EZH2 and reduces H3K27me3 levels. Mechanistically, the NIPP1 deletion abrogated PP1-mediated EZH2 dephosphorylation at two cyclin-dependent kinase sites (Thr-345/487), thereby generating hyperphosphorylated EZH2, which is a substrate for proteolytic degradation. Accordingly, alanine mutation of these residues prolonged the half-life of EZH2 in male germ cells. Our study discloses a key role for the PP1:NIPP1 holoenzyme in stabilizing EZH2 and maintaining the H3K27me3 mark on genes that are important for germ cell development and spermatogenesis.


Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 4386-4386
Author(s):  
Shujun Liu ◽  
M. I. Klisovic ◽  
T. Shen ◽  
J. Yu ◽  
G. Dai ◽  
...  

Abstract In t(8;21) AML, the AML1/ETO fusion protein promotes leukemogenesis by recruiting histone deacetylase (HDAC) and silencing target genes important for hematopoiesis. In addition to its anticonvulsant properties, valproic acid (VPA), an eight-carbon branched-chain fatty acid, has shown a significant antitumor activity mediated, at least in part, by inhibition of the HDAC enzymatic activity. The molecular mechanisms through which VPA inhibits HDACs and restore gene expression in cancer cells remain, however, to be fully elucidated. Herein, we showed that in AML1/ETO-positive cells, VPA modulates HDAC activity by releasing HDAC1 and AML1/ETO from the DNA binding sites at concentrations attainable in pts. Nuclear and whole cells extracts were obtained from AML1/ETO-positive Kasumi-1 cells untreated or treated with VPA (0.3 to 3 mM) for 24 hours and subjected to immunoblotting with AML1, ETO or HDAC1 antibody. Decreased levels of HDAC1 was noticed in the nuclear extract, but not in the unfractionated cell lysates following VPA treatment. These changes correlated with a dose-dependent inhibition of HDAC enzymatic activity and global hyperacetylation of histone H3 and H4. Decrease of HDAC1 and AML1/ETO in the nucleus was likely due to dissociation of the repressor complex proteins from DNA and relocation in the cytoplasm as indicated by a “band-depletion” assay. Untreated or VPA treated Kasumi-1 cells were cross-linked with 1% formaldehyde to stabilize the binding of proteins to their target DNA sequences, and subjected to immublotting with HADC1, AML1 or ETO antibody. While free protein can be resolved on a polyacrylamide gel by immunoblotting, high-molecular weight DNA-protein complexes cannot. Following formaldehyde cross-linking, in untreated cells, the AML1/ETO-HDAC1 complex was stabilized onto the DNA binding sites thereby forming a low-mobility DNA-protein complex which resulted in the absence of the corresponding gel band. In contrast, following VPA treatment, high-intensity AML1/ETO and HDAC1 bands were visualized, suggesting a decrease in DNA binding and an increase in the free-pools of the AML1/ETO and HDAC1 proteins. No changes were observed in HDAC1 and AML1/ETO RNA or protein levels in cells not cross-linked with formaldehyde, thereby excluding upregulation of the corresponding genes following VPA treatment. Similar results were confirmed at the promoter of specific AML1/ETO-target genes (i.e., IL-3). Following VPA exposure, decreased levels of HDAC1 and AML1/ETO, and histone H3 and H4 hyperacetylation were detected on the IL-3 promoter by chromatin immunoprecipitation. The functional relevance of these changes was supported by detection of mRNA expression of IL-3, which was otherwise silenced in untreated cells. Notably, the activity of VPA to HDAC1 and AML1/ETO appeared quite specific, as levels of other factors that initiate histone acetylation and/or gene transcription such as HAT1 and Pol II did not decrease, rather increased on the IL-3 promoter. Further, following VPA exposure, we observed posttranslational changes of specific H3 and H4 lysine residues associated with gene transcription (H3K9 and H4K16 acetylation and H3K4 methylation), partial cell differentiation, cell cycle arrest via upregulation of p21 and caspase-induced apoptosis. Taken together, these data suggest VPA as a promising compound for targeting molecular subgroups of AML, especially those in which leukemogenesis is promoted by aberrant HDAC activity.


Author(s):  
Akhil Gargey Iragavarapu ◽  
Liqi Yao ◽  
Vignesh Kasinath

Polycomb repressive complexes are a family of chromatin modifier enzymes which are critical for regulating gene expression and maintaining cell-type identity. The reversible chemical modifications of histone H3 and H2A by the Polycomb proteins are central to its ability to function as a gene silencer. PRC2 is both a reader and writer of the tri-methylation of histone H3 lysine 27 (H3K27me3) which serves as a marker for transcription repression, and heterochromatin boundaries. Over the last few years, several studies have provided key insights into the mechanisms regulating the recruitment and activation of PRC2 at Polycomb target genes. In this review, we highlight the recent structural studies which have elucidated the roles played by Polycomb cofactor proteins in mediating crosstalk between histone post-translational modifications and the recruitment of PRC2 and the stimulation of PRC2 methyltransferase activity.


Author(s):  
Shanshan Wang ◽  
Xuewen Xu ◽  
Yan Liu ◽  
Jianjun Jin ◽  
Feng Zhu ◽  
...  

Enhancer of zeste homolog 2 (EZH2) is the catalytic subunit of polycomb repressive complex 2 and contains a SET domain that catalyzes histone H3 trimethylation on lysine 27 (H3K27me3) to generate an epigenetic silencing mark. EZH2 interacts with transcription factors or RNA transcripts to perform its function. In this study, we applied RNA immunoprecipitation sequencing and long intergenic non-coding RNA (lincRNA) sequencing methods to identify EZH2-binding lincRNAs. A total of 356 novel EZH2-binding lincRNAs were identified by bioinformatics analysis and an EZH2-binding lincRNA TCONS-00036665 was characterized. TCONS-00036665 promoted pig skeletal satellite cell proliferation but inhibited cell differentiation, and this function was conserved between pigs and mice. Further mechanistic studies indicated that TCONS-00036665 can bind to EZH2 and recruits EZH2 to the promoters of the target genes p21, MyoG, and Myh4, which leads to the enrichment of H3K27me3 and the repression of target gene expression and pig myogenesis. In conclusion, the lincRNA TCONS-00036665 regulates pig myogenesis through its interaction with EZH2.


2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Peirong Li ◽  
Tongbing Su ◽  
Deshuang Zhang ◽  
Weihong Wang ◽  
Xiaoyun Xin ◽  
...  

AbstractHeterosis is a complex phenomenon in which hybrids show better phenotypic characteristics than their parents do. Chinese cabbage (Brassica rapa L. spp. pekinensis) is a popular leafy crop species, hybrids of which are widely used in commercial production; however, the molecular basis of heterosis for biomass of Chinese cabbage is poorly understood. We characterized heterosis in a Chinese cabbage F1 hybrid cultivar and its parental lines from the seedling stage to the heading stage; marked heterosis of leaf weight and biomass yield were observed. Small RNA sequencing revealed 63 and 50 differentially expressed microRNAs (DEMs) at the seedling and early-heading stages, respectively. The expression levels of the majority of miRNA clusters in the F1 hybrid were lower than the mid-parent values (MPVs). Using degradome sequencing, we identified 1,819 miRNA target genes. Gene ontology (GO) analyses demonstrated that the target genes of the MPV-DEMs and low parental expression level dominance (ELD) miRNAs were significantly enriched in leaf morphogenesis, leaf development, and leaf shaping. Transcriptome analysis revealed that the expression levels of photosynthesis and chlorophyll synthesis-related MPV-DEGs (differentially expressed genes) were significantly different in the F1 hybrid compared to the parental lines, resulting in increased photosynthesis capacity and chlorophyll content in the former. Furthermore, expression of genes known to regulate leaf development was also observed at the seedling stage. Arabidopsis plants overexpressing BrGRF4.2 and bra-miR396 presented increased and decreased leaf sizes, respectively. These results provide new insight into the regulation of target genes and miRNA expression patterns in leaf size and heterosis for biomass of B. rapa.


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