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Arabidopsis TRB Proteins Form Two Closely Related Complexes to Mediate H3K4me3 Demethylation and Transcriptional Repression

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE287725 | GEO | 2025/09/17

REPOSITORIES: GEO

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Project description:The telomere repeat binding factors TRB1, TRB2, and TRB3 (TRB1/2/3) in Arabidopsis thaliana not only function as components of the PEAT complex involved in histone acetylation and H2A deubiquitination but also interact with Polycomb Repressive Complex 2 (PRC2) involved in H3 lysine 27 trimethylation (H3K27me3). In this study, we demonstrate that TRB1/2/3 form two additional chromatin-associated complexes, which we term TRB1/2/3-HTH1/2/3 (TRHT) and TRB1/2/3-HISTONE-DEMETHYLASE (TRHD). The TRHT complex comprises TRB1/2/3, ICU11, and HTH1/2/3, whereas the TRHD complex is composed of TRB1/2/3, ICU11, ZDP2, JMJ14, and NAC050/052. The TRHT and TRHD (TRHT/TRHD) complexes occupy a common set of target genes and cooperate to mediate JMJ14-mediated H3K4me3 demethylation and transcriptional repression. Compared with PEAT and PRC2 target genes, which are characterized by high and low levels of H3K4me3, respectively, the TRHT/TRHD target genes exhibit low to medium levels of H3K4me3. At the whole-genome level, TRB1/2/3 repress transcription at TRHT/TRHD and PRC2 target genes, while facilitating transcription at PEAT target genes. At the TRHT/TRHD target genes, the TRHT/TRHD complexes mediate transcriptional repression through both H3K4me3 demethylation-dependent and –independent mechanisms. These findings reveal the molecular mechanisms by which how the TRHT/TRHD complexes are coordinated with the PEAT and PRC2 complex to ensure the orchestration of multiple histone modifications at the whole-genome level.

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Project description:Two closely related TRB-containing complexes cooperate to mediate H3K4me3 demethylation and transcriptional repression

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Arabidopsis TRB proteins function in H3K4me3 demethylation by recruiting JMJ14.

Project description:Arabidopsis telomeric repeat binding factors (TRBs) can bind telomeric DNA sequences to protect telomeres from degradation. TRBs can also recruit Polycomb Repressive Complex 2 (PRC2) to deposit tri-methylation of H3 lysine 27 (H3K27me3) over certain target loci. Here, we demonstrate that TRBs also associate and colocalize with JUMONJI14 (JMJ14) and trigger H3K4me3 demethylation at some loci. The trb1/2/3 triple mutant and the jmj14-1 mutant show an increased level of H3K4me3 over TRB and JMJ14 binding sites, resulting in up-regulation of their target genes. Furthermore, tethering TRBs to the promoter region of genes with an artificial zinc finger (TRB-ZF) successfully triggers target gene silencing, as well as H3K27me3 deposition, and H3K4me3 removal. Interestingly, JMJ14 is predominantly recruited to ZF off-target sites with low levels of H3K4me3, which is accompanied with TRB-ZFs triggered H3K4me3 removal at these loci. These results suggest that TRB proteins coordinate PRC2 and JMJ14 activities to repress target genes via H3K27me3 deposition and H3K4me3 removal.

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Project description:Two closely related TRB-containing complexes cooperate to mediate H3K4me3 demethylation and transcriptional repression [RNA-seq]

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Project description:Two closely related TRB-containing complexes cooperate to mediate H3K4me3 demethylation and transcriptional repression [ChIP-seq]

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Arabidopsis TRB proteins function in H3K4me3 demethylation by recruiting the JMJ14 complex

Project description:Histone marks H3K27me3 and H3K4me3 are mutual exclusive over plant genome, however, the underlying mechanism is not fully understood. Arabidopsis telomeric repeat binding factors (TRBs) are required for the deposition of H3K27me3 by recruiting Polycomb repressive complexes (PRCs). Here, we demonstrate that TRBs associate and colocalize with JUMONJI 14 (JMJ14) over gene body regions and trigger H3K4me3 demethylation. The trb1/2/3 triple mutant and jmj14-1 mutant show an increased level of H3K4me3 over TRB and JMJ14 binding sites, resulting in up-regulation of their targeting genes. Furthermore, tethering TRBs to the promoter region of genes with an artificial zinc finger successfully triggers target gene silencing. These results suggest that TRB proteins cooperate with PRC2 and JMJ14 complex to repress target gene by H3K4me3 demethylation and H3K27me3 deposition.

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Arabidopsis TRB proteins function in H3K4me3 demethylation by recruiting JMJ14

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Project description:Arabidopsis TRB proteins function in H3K4me3 demethylation by recruiting the JMJ14 complex

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HP1 proteins form distinct complexes and mediate heterochromatic gene silencing by nonoverlapping mechanisms.

Project description:HP1 proteins are a highly conserved family of eukaryotic proteins that bind to methylated histone H3 lysine 9 (H3K9) and are required for heterochromatic gene silencing. In fission yeast, two HP1 homologs, Swi6 and Chp2, function in heterochromatic gene silencing, but their relative contribution to silencing remains unknown. Here we show that Swi6 and Chp2 exist in nonoverlapping complexes and make distinct contributions to silencing. Chp2 associates with the SHREC histone deacetylase complex (SHREC2), is required for histone H3 lysine 14 (H3K14) deacetylation, and mediates transcriptional repression by limiting RNA polymerase II access to heterochromatin. In contrast, Swi6 associates with a different set of nuclear proteins and with noncoding centromeric transcripts and is required for efficient RNAi-dependent processing of these transcripts. Our findings reveal an unexpected role for Swi6 in RNAi-mediated gene silencing and suggest that different HP1 proteins ensure full heterochromatic gene silencing through largely nonoverlapping inhibitory mechanisms.

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