Danhua Jiang

Repression of FLOWERING LOCUS C and FLOWERING LOCUS T by the Arabidopsis Polycomb repressive complex 2 components.

Polycomb group (PcG) proteins are evolutionarily conserved in animals and plants, and play critical roles in the regulation of developmental gene expression. Here we show that the Arabidopsis Polycomb repressive complex 2 (PRC2) subunits CURLY LEAF (CLF), EMBRYONIC FLOWER 2 (EMF2) and FERTILIZATION INDEPENDENT ENDOSPERM (FIE) repress the expression of FLOWERING LOCUS C (FLC), a central repressor of the floral transition in Arabidopsis and FLC relatives. In addition, CLF directly interacts with and mediates the deposition of repressive histone H3 lysine 27 trimethylation (H3K27me3) into FLC and FLC relatives, which suppresses active histone H3 lysine 4 trimethylation (H3K4me3) in these loci. Furthermore, we show that during vegetative development CLF and FIE strongly repress the expression of FLOWERING LOCUS T (FT), a key flowering-time integrator, and that CLF also directly interacts with and mediates the deposition of H3K27me3 into FT chromatin. Our results suggest that PRC2-like complexes containing CLF, EMF2 and FIE, directly interact with and deposit into FT, FLC and FLC relatives repressive trimethyl H3K27 leading to the suppression of active H3K4me3 in these loci, and thus repress the expression of these flowering genes. Given the central roles of FLC and FT in flowering-time regulation in Arabidopsis, these findings suggest that the CLF-containing PRC2-like complexes play a significant role in control of flowering in Arabidopsis.

Arabidopsis Relatives of the Human Lysine-Specific Demethylase1 Repress the Expression of FWA and FLOWERING LOCUS C and Thus Promote the Floral Transition

The timing of the developmental transition to flowering is critical to reproductive success in plants. Here, we show that Arabidopsis thaliana homologs of human Lysine-Specific Demethylase1 (LSD1; a histone H3-Lys 4 demethylase) reduce the levels of histone H3-Lys 4 methylation in chromatin of the floral repressor FLOWERING LOCUS C (FLC) and the sporophytically silenced floral repressor FWA. Two of the homologs, LSD1-LIKE1 (LDL1) and LSD1-LIKE2 (LDL2), act in partial redundancy with FLOWERING LOCUS D (FLD; an additional homolog of LSD1) to repress FLC expression. However, LDL1 and LDL2 appear to act independently of FLD in the silencing of FWA, indicating that there is target gene specialization within this histone demethylase family. Loss of function of LDL1 and LDL2 affects DNA methylation on FWA, whereas FLC repression does not appear to involve DNA methylation; thus, members of the LDL family can participate in a range of silencing mechanisms.

Repression of the floral transition via histone H2B monoubiquitination

The Rad6-Bre1 complex monoubiquitinates histone H2B in target gene chromatin, and plays an important role in positively regulating gene expression in yeast. Here, we show that the Arabidopsis relatives of the yeast Rad6, ubiquitin-conjugating enzyme 1 (UBC1) and UBC2, redundantly mediate histone H2B monoubiquitination, and upregulate the expression of FLOWERING LOCUS C (FLC; a central flowering repressor in Arabidopsis) and FLC relatives, and also redundantly repress flowering, the developmental transition from a vegetative to a reproductive phase that is critical in the plant life cycle. Moreover, we have found that Arabidopsis relatives of the yeast Bre1, including HISTONE MONOUBIQUITINATION 1 (HUB1) and HUB2, also upregulate the expression of FLC and FLC relatives, and that HUB1 genetically interacts with UBC1 and UBC2 to repress the floral transition. These findings are consistent with a model in which HUB1 and HUB2 specifically interact with and direct UBC1 and UBC2 to monoubiquitinate H2B in developmental genes, and thus regulate developmental processes in plants.

Establishment of the Winter-Annual Growth Habit via FRIGIDA-Mediated Histone Methylation at FLOWERING LOCUS C in Arabidopsis

In Arabidopsis thaliana, flowering-time variation exists among accessions, and the winter-annual (late-flowering without vernalization) versus rapid-cycling (early flowering) growth habit is typically determined by allelic variation at FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). FRI upregulates the expression of FLC, a central floral repressor, to levels that inhibit flowering, resulting in the winter-annual habit. Here, we show that FRI promotes histone H3 lysine-4 trimethylation (H3K4me3) in FLC to upregulate its expression. We identified an Arabidopsis homolog of the human WDR5, namely, WDR5a, which is a conserved core component of the human H3K4 methyltransferase complexes called COMPASS-like. We found that recombinant WDR5a binds H3K4-methylated peptides and that WDR5a also directly interacts with an H3K4 methyltransferase, ARABIDOPSIS TRITHORAX1. FRI mediates WDR5a enrichment at the FLC locus, leading to increased H3K4me3 and FLC upregulation. WDR5a enrichment is not required for elevated H3K4me3 in FLC upon loss of function of an FLC repressor, suggesting that two distinct mechanisms underlie elevated H3K4me3 in FLC. Our findings suggest that FRI is involved in the enrichment of a WDR5a-containing COMPASS-like complex at FLC chromatin that methylates H3K4, leading to FLC upregulation and thus the establishment of the winter-annual growth habit.

Arabidopsis FLC clade members form flowering-repressor complexes coordinating responses to endogenous and environmental cues

The developmental transition to flowering is timed by endogenous and environmental signals through multiple genetic pathways. In Arabidopsis, the MADS-domain protein FLOWERING LOCUS C is a potent flowering repressor. Here, we report that the FLOWERING LOCUS C clade member MADS AFFECTING FLOWERING3 acts redundantly with another clade member to directly repress expression of the florigen FLOWERING LOCUS T and inhibit flowering. FLOWERING LOCUS C clade members act in partial redundancy in floral repression and mediate flowering responses to temperature, in addition to their participation in the flowering-time regulation by vernalization and photoperiod. We show that FLOWERING LOCUS C, MADS AFFECTING FLOWERING3 and three other clade members can directly interact with each other and form nuclear complexes, and that FLOWERING LOCUS C-dependent floral repression requires other clade members. Our results collectively suggest that the FLOWERING LOCUS C clade members act as part of several MADS-domain complexes with partial redundancy, which integrate responses to endogenous and environmental cues to control flowering.

Arabidopsis COMPASS-Like Complexes Mediate Histone H3 Lysine-4 Trimethylation to Control Floral Transition and Plant Development

Histone H3 lysine-4 (H3K4) methylation is associated with transcribed genes in eukaryotes. In Drosophila and mammals, both di- and tri-methylation of H3K4 are associated with gene activation. In contrast to animals, in Arabidopsis H3K4 trimethylation, but not mono- or di-methylation of H3K4, has been implicated in transcriptional activation. H3K4 methylation is catalyzed by the H3K4 methyltransferase complexes known as COMPASS or COMPASS-like in yeast and mammals. Here, we report that Arabidopsis homologs of the COMPASS and COMPASS-like complex core components known as Ash2, RbBP5, and WDR5 in humans form a nuclear subcomplex during vegetative and reproductive development, which can associate with multiple putative H3K4 methyltransferases. Loss of function of ARABIDOPSIS Ash2 RELATIVE (ASH2R) causes a great decrease in genome-wide H3K4 trimethylation, but not in di- or mono-methylation. Knockdown of ASH2R or the RbBP5 homolog suppresses the expression of a crucial Arabidopsis floral repressor, FLOWERING LOCUS C (FLC), and FLC homologs resulting in accelerated floral transition. ASH2R binds to the chromatin of FLC and FLC homologs in vivo and is required for H3K4 trimethylation, but not for H3K4 dimethylation in these loci; overexpression of ASH2R causes elevated H3K4 trimethylation, but not H3K4 dimethylation, in its target genes FLC and FLC homologs, resulting in activation of these gene expression and consequent late flowering. These results strongly suggest that H3K4 trimethylation in FLC and its homologs can activate their expression, providing concrete evidence that H3K4 trimethylation accumulation can activate eukaryotic gene expression. Furthermore, our findings suggest that there are multiple COMPASS-like complexes in Arabidopsis and that these complexes deposit trimethyl but not di- or mono-methyl H3K4 in target genes to promote their expression, providing a molecular explanation for the observed coupling of H3K4 trimethylation (but not H3K4 dimethylation) with active gene expression in Arabidopsis.

A plant‐specific histone H3 lysine 4 demethylase represses the floral transition in Arabidopsis

Histone demethylation regulates chromatin structure and gene expression, and is catalyzed by various histone demethylases. Trimethylation of histone H3 at lysine 4 (H3K4) is coupled to active gene expression; trimethyl H3K4 is demethylated by Jumonj C (JmjC) domain-containing demethylases in mammals. Here we report that a plant-specific JmjC domain-containing protein known as PKDM7B (At4g20400) demethylates trimethyl H3K4. PKDM7B mediates H3K4 demethylation in a key floral promoter, FLOWERING LOCUS T (FT), and an FT homolog, TWIN SISTER OF FT (TSF), and represses their expression to inhibit the floral transition in Arabidopsis. Our findings suggest that there are at least two distinct sub-families of JmjC domain-containing demethylases that demethylate the active trimethyl H3K4 mark in eukaryotic genes, and reveal a plant-specific JmjC domain enzyme capable of H3K4 demethylation.

Arabidopsis Homologs of Retinoblastoma-Associated Protein 46/48 Associate with a Histone Deacetylase to Act Redundantly in Chromatin Silencing

RNA molecules such as small-interfering RNAs (siRNAs) and antisense RNAs (asRNAs) trigger chromatin silencing of target loci. In the model plant Arabidopsis, RNA–triggered chromatin silencing involves repressive histone modifications such as histone deacetylation, histone H3 lysine-9 methylation, and H3 lysine-27 monomethylation. Here, we report that two Arabidopsis homologs of the human histone-binding proteins Retinoblastoma-Associated Protein 46/48 (RbAp46/48), known as MSI4 (or FVE) and MSI5, function in partial redundancy in chromatin silencing of various loci targeted by siRNAs or asRNAs. We show that MSI5 acts in partial redundancy with FVE to silence FLOWERING LOCUS C (FLC), which is a crucial floral repressor subject to asRNA–mediated silencing, FLC homologs, and other loci including transposable and repetitive elements which are targets of siRNA–directed DNA Methylation (RdDM). Both FVE and MSI5 associate with HISTONE DEACETYLASE 6 (HDA6) to form complexes and directly interact with the target loci, leading to histone deacetylation and transcriptional silencing. In addition, these two genes function in de novo CHH (H = A, T, or C) methylation and maintenance of symmetric cytosine methylation (mainly CHG methylation) at endogenous RdDM target loci, and they are also required for establishment of cytosine methylation in the previously unmethylated sequences directed by the RdDM pathway. This reveals an important functional divergence of the plant RbAp46/48 relatives from animal counterparts.

Coupling of histone methylation and RNA processing by the nuclear mRNA cap-binding complex.

In eukaryotes, genes are transcribed into pre-mRNAs that are subsequently processed into mature mRNAs by adding a 5′-cap and a 3′-polyA tail and splicing introns. Pre-mRNA processing involves their binding proteins and processing factors, whereas gene transcription often involves chromatin modifiers. It has been unclear how the factors involved in chromatin modifications and RNA processing function in concert to control mRNA production. Here, we show that in Arabidopsis thaliana, the evolutionarily conserved nuclear mRNA cap-binding complex (CBC) forms multi-protein complexes with a conserved histone 3 lysine 4 (H3K4) methyltransferase complex called COMPASS-like and a histone 3 lysine 36 (H3K36) methyltransferase to integrate active histone methylations with co-transcriptional mRNA processing and cap preservation, leading to a high level of mature mRNA production. We further show that CBC is required for H3K4 and H3K36 trimethylation, and the histone methyltransferases are required for CBC-mediated mRNA cap preservation and efficient pre-mRNA splicing at their target loci, suggesting that these factors are functionally interdependent. Our study reveals novel roles for histone methyltransferases in RNA-processing-related events and provides mechanistic insights into how the ‘downstream’ RNA CBC controls eukaryotic gene transcription.

FRIGIDA establishes a local chromosomal environment for FLOWERING LOCUS C mRNA production

FRIGIDA (FRI) upregulates the expression of the potent floral repressor FLOWERING LOCUS C (FLC) to confer the winter-annual growth habit in Arabidopsis thaliana: accelerated transition to flowering after prolonged cold exposure (vernalization). Here, we show that FRI, histone acetyltransferases, the histone methyltransferase COMPASS-like and other chromatin modifiers are part of a FRI-containing supercomplex enriched in a region around the FLC transcription start site (TSS) to promote its expression. Several FRI partners are also enriched in a 3’ region flanking FLC and, together with FRI, they function to increase the frequency of physical association of the region around TSS with the 3’ region and promote the expression of both sense FLC and antisense non-coding RNAs. Our results show that the FRI supercomplex establishes a local chromosomal environment at FLC with active chromatin modifications and topology to promote transcriptional activation, fast elongation and efficient pre-messenger RNA splicing, leading to a high-level production of FLC mRNAs.FLOWERING LOCUS C (FLC) is a central floral repressor in Arabidopsis, whose expression is vernalization-responsive and controlled by a plant-specific scaffold protein FRIGIDA (FRI). Now, the detailed mechanism of FRI-controlled FLC transcription is elucidated.