Dynamic and stable histone H3 methylation patterns at the Arabidopsis FLC and AP1 loci
Introduction
Plant development, differentiation, and environmental adaptation involve global reprogramming of the genome. Dynamic changes of chromatin structure are forces driving controlled shifts in genome activity. Specific chemical modifications of histone tails may trigger events leading to the establishment of transcriptionally active/silent chromatin domains. The Polycomb- and the Trithorax-Group (PcG/TrxG) complexes, known to regulate animal developmental genes, establish tri-methyl groups on lysine 27 of histone H3 (H3K27me3) and on lysine 4 (H3K4me3), respectively (Grimaud et al., 2006, Kouzarides, 2007). Similar to the metazoan counterparts, Arabidopsis PCR2 complexes deposit H3K27me3 through the biochemical activity of E(z) homologs (Goodrich et al., 1997, Chanvivattana et al., 2004, Schubert et al., 2005, Schubert et al., 2006), while Trithorax family members specifically tri-methylate histone H3K4 (Alvarez-Venegas et al., 2003, Pien and Grossniklaus, 2007). H3K27me3 and H3K4me3 marks are considered hallmarks of silent and actively transcribed genes, respectively. Emerging evidence, however, is suggesting more complex roles for histone modifications beyond simply ‘activating-silencing’ marks. Thus, histone deacetylase Rpd3 and histone deacetylation of the coding regions in actively transcribed genes are directly linked with methylated H3K36 labeling active genes (Kaplan et al., 2003, Keogh, 2005, Brown et al., 2006); simultaneously present K4me3 and K27me3 marks at promotor nucleosomes of embryonic stem cells establish a bivalent chromatin state for genes poised for expression later in development (Bernstein et al., 2006). In addition to pluripotent cells, K4me3–K27me3 co-localization is functional in more differentiated cells as well (rev. in Sharov and Ko, 2007). Here, we report that dual H3K27me3 and H3K4me3 marks co-exist on the nucleosomes of two related genes from the MADS-box family, FLC and AP1. We found that dual H3K27me3 and H3K4me3 marks at the 5′-transcription start site (TSS) have a different meaning from dual-marks labeling downstream gene (G)-nucleosomes. Distribution of H3K4me3 and H3K27me3 at TSS nucleosomes is dynamic and gene-specific. Erasure of both H3K27me3–H3K4me3 marks at the AP1-TSS region upon AP1 activation reflects removal of a nucleosome from the site. Changes in the methylation patterns of 5′-TSS nucleosomes of both FLC and AP1 reflect the genes' transcriptional activity, while dual marks on downstream nucleosomes remain unchanged. Thereby, preserved H3K27me3–H3K4me3 were passed on as stable marks independent of the FLC- and AP1 activity and/or developmental transitions. ATX1 modifies FLC, but not AP1, nucleosomes. However, CLF does not appear involved in modifying either the FLC or AP1 nucleosomes.
Section snippets
Plant material, growth conditions and chromatin isolation
Arabidopsis thaliana Ws seeds were sterilized and grown in either 40 ml of germination media or in pots, at 24 °C under long-day (16 h light/8 h darkness). The atx1 mutant line was described in Alvarez-Venegas et al. (2003). Seeds for the clf mutant line were kind gift by J. Goodrich. Tissues for analysis were harvested from 10-day old seedlings, from the rosette leaves of plants upon bolting and from buds and flowers of five-week old plants. Chromatins were isolated from wild type and from the
H3K4me3 and H3K27me3 patterns of FLC- and AP1-nucleosomes in transcribed and non-transcribed chromatins
The FLOWERING LOCUS C (FLC) indirectly represses the activity of APETALA1 (AP1) blocking the transition from vegetative to reproductive stages in Arabidopsis (Levy et al., 2002, Schonrock et al., 2006). After bolting, FLC transcripts were no longer detected in inflorescences or in rosette leaves while AP1-expression changed in reverse (Fig. 1a). To determine the nucleosomal methylation patterns of the two reciprocally expressed transcription factors, we analyzed chromatin H3K4me3 and H3K27me3
Discussion
Generally, H3K4me3 and H3K27me3 are interpreted as ‘activating’ and ‘silencing’ marks, respectively. Here, we provide strong evidence that neither modification, alone, could serve as an indicator of expression status even for related genes. The two antagonistic marks on downstream nucleosomes remained unchanged throughout developmental transitions, independently of the transcriptional activity of AP1 or FLC. In a stark contrast, the H3K4me3/H3K27me3 profile at 5′-TSS nucleosomes changed
Acknowledgements
I am grateful to Drs. S. Pien (U. of Zurich) and P. Crevillen (John Innes Center) for critically reading the manuscript and helpful suggestions. This work was partially supported by NSF-MCB-0343934 grant award ZA and by NSF grant EPS-0701892.
References (37)
- et al.
ATX1, an Arabidopsis homolog of trithorax, activates flower homeotic genes
Curr. Biol.
(2003) A bivalent chromatin structure marks key developmental genes in embryonic stem cells
Cell
(2006)- et al.
Chromosomal histone modification patterns—from conservation to diversity
Trends Plant Sci.
(2006) - et al.
Role of chromatin modification in flowering-time control
Trends Plant Sci.
(2005) Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex
Cell
(2005)Chromatin modifications and their function
Cell
(2007)- et al.
C2H2 zinc finger-SET histone methyltransferase is a plant-specific chromatin modifier
Dev. Biol.
(2007) - et al.
The Arabidopsis RNA-binding protein FCA requires a lysine-specific demethylase 1 homolog to downregulate FLC
Mol. Cell.
(2007) - et al.
Polycomb group and trithorax group proteins in Arabidopsis
Biophys. Biochem. Acta
(2007) Chromatin modifiers that control plant development
Curr. Opin. Plant Dev.
(2006)
Epigenetic control of plant development by Polycomb-group proteins
Curr. Opin. Plant Biol.
Human ES cell profiling broadens the reach of bivalent domains
Cell Stem Cell
Methylation patterns of histone H3 Lys 4, Lys 9 and Lys 27 in transcriptionally active and inactive Arabidopsis genes and in atx1 mutants
Nucleic Acids Res.
The Arabidopsis homolog of trithorax, ATX1, binds phosphoinositide 5-phosphate and the two regulate a common set of target genes
Proc. Natl. Acad. Sci.
Vernalization requires epigenetic silencing of FLC by histone methylation
Nature
Identification and characterization of Smyd2: a split SET/MYND domain-containing histone H3 lysine 36-specific methyltransferase that interacts with the Sin3 histone deacetylase complex
Mol. Cancer
Interaction of Polycomb-group proteins controlling flowering in Arabidopsis
Development
Repression of flowering in Arabidopsis requires activation of FLOWERING LOCUS C expression by the histone variant H2A
Z. Plant Cell
Cited by (40)
Identification of grape H3K4 genes and their expression profiles during grape fruit ripening and postharvest ROS treatment
2021, GenomicsCitation Excerpt :The loss of function of atx2 does not have any phenotype [44,45]. Different from the early-flowering phenotype of Arabidopsis atx1 [44,45], the orthormic rice mutant ostrx1/sdg723 showed late flowering by reducing the H3K4me3 level of the central flowering time integron Ehd1 [46]. OsTRX1 can rescue the Arabidopsis ATX1 phenotype [37,46,47,48], which shows that ATX1 proteins have conserved biochemical and molecular functions during evolution.
Arctigenin, a dietary phytoestrogen, induces apoptosis of estrogen receptor-negative breast cancer cells through the ROS/p38 MAPK pathway and epigenetic regulation
2014, Free Radical Biology and MedicineCitation Excerpt :p38 MAPK has been reported to phosphorylate ATF-2, a component of the activator protein 1 (AP-1) transcription factor, thereby inducing apoptosis in several cancers [30–35]. AP-1 has also been reported to regulate target genes by cooperating with histone modification [36,37]. We used the TFsearch computational tool to search for AP-1 binding sites in the Bcl-2 promoter.
SET domain proteins in plant development
2011, Biochimica et Biophysica Acta - Gene Regulatory MechanismsCitation Excerpt :Mutation in ATX1 has been reported to affect floral organ development and reduce expression levels of AP1, AP2, AGAMOUS (AG) in buds and flowers [103]. The effect on AP1 is indirect, but in rosette leaves ATX1 has been shown to target and deposit H3K4me3 at AG (Fig. 2B) [104,105]. However, ATX1 mutations are less severe than the ASH2R mutation, and it is therefore likely that the ASH2R core subcomplex associate with different H3K4 methyltransferases in different tissues and developmental stages, for instance with ATX3/SDG14 and ATX4/SDG16, which interact with WDR5a in yeast-two-hybrid assays [101].
Epigenetic regulatory mechanisms in plants
2011, Handbook of EpigeneticsEpigenetic Regulatory Mechanisms in Plants
2010, Handbook of Epigenetics: The New Molecular and Medical Genetics