Chromatin regulation of flowering

The putative PRC1 RING-finger protein AtRING1A regulates flowering through repressing MADS AFFECTING FLOWERING genes in Arabidopsis

Polycomb group proteins play essential roles in the epigenetic control of gene expression in plants and animals. Although some components of Polycomb repressive complex 1 (PRC1)-like complexes have recently been reported in the model plant Arabidopsis, how they contribute to gene repression remains largely unknown. Here we show that a putative PRC1 RING-finger protein, AtRING1A, plays a hitherto unknown role in mediating the transition from vegetative to reproductive development in Arabidopsis. Loss of function of AtRING1A results in the late-flowering phenotype, which is attributed to derepression of two floral repressors, MADS AFFECTING FLOWERING 4/5 (MAF4/5), which in turn downregulate two floral pathway integrators, FLOWERING LOCUS T and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1. Levels of the H3K27me3 repressive mark at MAF4 and MAF5 loci, which is deposited by CURLY LEAF (CLF)-containing PRC2-like complexes and bound by LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), are affected by AtRING1A, which interacts with both CLF and LHP1. Levels of the H3K4me3 activation mark correlate inversely with H3K27me3 levels at MAF4 and MAF5 loci. Our results suggest that AtRING1A suppresses the expression of MAF4 and MAF5 through affecting H3K27me3 levels at these loci to regulate the floral transition in Arabidopsis.

Plant chromatin warms up in Madrid: meeting summary of the 3rd European Workshop on Plant Chromatin 2013, Madrid, Spain

The 3rd European Workshop on Plant Chromatin (EWPC) was held on August 2013 in Madrid, Spain. A number of different topics on plant chromatin were presented during the meeting, including new factors mediating Polycomb Group protein function in plants, chromatin-mediated reprogramming in plant developmental transitions, the role of histone variants, and newly identified chromatin remodeling factors. The function of interactions between chromatin and transcription factors in the modulation of gene expression, the role of chromatin dynamics in the control of nuclear processes and the influence of environmental factors on chromatin organization were also reported. In this report, we highlight some of the new insights emerging in this growing area of research, presented at the 3rd EWPC.

Functional and evolutionary characterization of the CONSTANS gene family in short-day photoperiodic flowering in soybean

CONSTANS (CO) plays a central role in photoperiodic flowering control of plants. However, much remains unknown about the function of the CO gene family in soybean and the molecular mechanisms underlying short-day photoperiodic flowering of soybean. We identified 26 CO homologs (GmCOLs) in the soybean genome, many of them previously unreported. Phylogenic analysis classified GmCOLs into three clades conserved among flowering plants. Two homeologous pairs in Clade I, GmCOL1a/GmCOL1b and GmCOL2a/GmCOL2b, showed the highest sequence similarity to Arabidopsis CO. The mRNA abundance of GmCOL1a and GmCOL1b exhibited a strong diurnal rhythm under flowering-inductive short days and peaked at dawn, which coincided with the rise of GmFT5a expression. In contrast, the mRNA abundance of GmCOL2a and GmCOL2b was extremely low. Our transgenic study demonstrated that GmCOL1a, GmCOL1b, GmCOL2a and GmCOL2b fully complemented the late flowering effect of the co-1 mutant in Arabidopsis. Together, these results indicate that GmCOL1a and GmCOL1b are potential inducers of flowering in soybean. Our data also indicate rapid regulatory divergence between GmCOL1a/GmCOL1b and GmCOL2a/GmCOL2b but conservation of their protein function. Dynamic evolution of GmCOL regulatory mechanisms may underlie the evolution of photoperiodic signaling in soybean.

Combinatorial functions of diverse histone methylations in Arabidopsis thaliana flowering time regulation

Previous studies in Arabidopsis thaliana have identified several histone methylation enzymes, including Arabidopsis trithorax1 (ATX1)/set domain group 27 (SDG27), ATX2/SDG30, LSD1-LIKE1 (LDL1), LDL2, SDG8, SDG25, and curly leaf (CLF)/SDG1, as regulators of the key flowering repressor flowering locus C (FLC) and the florigen flowering locus T (FT). However, the combinatorial functions of these enzymes remain largely uninvestigated. Here, we investigated functional interplays of different histone methylation enzymes by studying higher order combinations of their corresponding gene mutants. We showed that H3K4me2/me3 and H3K36me3 depositions occur largely independently and that SDG8-mediated H3K36me3 overrides ATX1/ATX2-mediated H3K4me2/me3 or LDL1/LDL2-mediated H3K4 demethylation in regulating FLC expression and flowering time. By contrast, a reciprocal inhibition was observed between deposition of the active mark H3K4me2/me3 and/or H3K36me3 and deposition of the repressive mark H3K27me3 at both FLC and FT chromatin; and the double mutants sdg8 clf and sdg25 clf displayed enhanced early-flowering phenotypes of the respective single mutants. Collectively, our results provide important insights into the interactions of different types of histone methylation and enzymes in the regulation of FLC and FT expression in flowering time control.

FLC-mediated flowering repression is positively regulated by sumoylation

Flowering locus C (FLC), a floral repressor, is a critical factor for the transition from the vegetative to the reproductive phase. Here, the mechanisms regulating the activity and stability of the FLC protein were investigated. Bimolecular fluorescence complementation and in vitro pull-down analyses showed that FLC interacts with the E3 small ubiquitin-like modifier (SUMO) ligase AtSIZ1, suggesting that AtSIZ1 is an E3 SUMO ligase for FLC. In vitro sumoylation assays showed that FLC is modified by SUMO in the presence of SUMO-activating enzyme E1 and conjugating enzyme E2, but its sumoylation is inhibited by AtSIZ1. In transgenic plants, inducible AtSIZ1 overexpression led to an increase in the concentration of FLC and delayed the post-translational decay of FLC, indicating that AtSIZ1 stabilizes FLC through direct binding. Also, the flowering time in mutant FLC (K154R, a mutation of the sumoylation site)-overexpressing plants was comparable with that in the wild type, whereas flowering was considerably delayed in FLC-overexpressing plants, supporting the notion that sumoylation is an important mechanism for FLC function. The data indicate that the sumoylation of FLC is critical for its role in the control of flowering time and that AtSIZ1 positively regulates FLC-mediated floral suppression.

Epigenetic regulation of bud dormancy events in perennial plants

Release of bud dormancy in perennial plants resembles vernalization in Arabidopsis thaliana and cereals. In both cases, a certain period of chilling is required for accomplishing the reproductive phase, and several transcription factors with the MADS-box domain perform a central regulatory role in these processes. The expression of DORMANCY-ASSOCIATED MADS-box (DAM)-related genes has been found to be up-regulated in dormant buds of numerous plant species, such as poplar, raspberry, leafy spurge, blackcurrant, Japanese apricot, and peach. Moreover, functional evidence suggests the involvement of DAM genes in the regulation of seasonal dormancy in peach. Recent findings highlight the presence of genome-wide epigenetic modifications related to dormancy events, and more specifically the epigenetic regulation of DAM-related genes in a similar way to FLOWERING LOCUS C, a key integrator of vernalization effectors on flowering initiation in Arabidopsis. We revise the most relevant molecular and genomic contributions in the field of bud dormancy, and discuss the increasing evidence for chromatin modification involvement in the epigenetic regulation of seasonal dormancy cycles in perennial plants.

Epigenetic regulation of rice flowering and reproduction

Current understanding of the epigenetic regulator roles in plant growth and development has largely derived from studies in the dicotyledonous model plant Arabidopsis thaliana. Rice (Oryza sativa) is one of the most important food crops in the world and has more recently becoming a monocotyledonous model plant in functional genomics research. During the past few years, an increasing number of studies have reported the impact of DNA methylation, non-coding RNAs and histone modifications on transcription regulation, flowering time control, and reproduction in rice. Here, we review these studies to provide an updated complete view about chromatin modifiers characterized in rice and in particular on their roles in epigenetic regulation of flowering time, reproduction, and seed development.

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.

Flowering time is a critical developmental transition for a plant’s reproductive success and it depends on endogenous and environmental signals. Here Gu et al. show that MADS-domain floral repressors form protein complexes that coordinate Arabidopsis responses to these cues and regulate its flowering time.

Flowering time regulation: photoperiod- and temperature-sensing in leaves

Plants monitor changes in photoperiod and temperature to synchronize their flowering with seasonal changes to maximize fitness. In the Arabidopsis photoperiodic flowering pathway, the circadian clock-regulated components, such as FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 and CONSTANS, both of which have light-controlled functions, are crucial to induce the day-length specific expression of the FLOWERING LOCUS T (FT) gene in leaves. Recent advances indicate that FT transcriptional regulation is central for integrating the information derived from other important internal and external factors, such as developmental age, amount of gibberellic acid, and the ambient temperature. In this review, we describe how these factors interactively regulate the expression of FT, the main component of florigen, in leaves.

MIDGET cooperates with COP1 and SPA1 to repress flowering in Arabidopsis thaliana

The life cycle of plants is strictly regulated by light, which directly influences the initiation of developmental programs such as photomorphogenesis of seedlings and induction of flowering. When environmental conditions are unsuitable, both processes are actively repressed by the action of COP1/SPA protein complexes which participate in ubiquitylation and subsequent degradation of transcription factors. We have shown recently that MIDGET (MID), a regulator of the TOPOISOMERASE VI complex, physically interacts with COP1 and is required for its function as suppressor of photomorphogenesis. Here we show that in Arabidopsis thaliana, the MID protein similarly plays a role in COP1/SPA1-controlled repression of flowering under short-day conditions.

Transcriptome-wide analysis of vernalization reveals conserved and species-specific mechanisms in Brachypodium

Several temperate cereals need vernalization to promote flowering. Little, however, is known about the vernalization-memory-related genes, and almost no comparative analysis has been performed. Here, RNA-Seq was used for transcriptome analysis in non-vernalized, vernalized and post-vernalized Brachypodium distachyon (L.) Beauv. seedlings. In total, the expression of 1,665 genes showed significant changes (fold change ≥4) in response to vernalization. Among them, 674 putative vernalization-memory-related genes with a constant response to vernalization were significantly enriched in transcriptional regulation and monooxygenase-mediated biological processes. Comparative analysis of vernalization-memory-related genes with barley demonstrated that the oxidative-stress response was the most conserved pathway between these two plant species. Moreover, Brachypodium preferred to regulate transcription and protein phosphorylation processes, while vernalization-memory-related genes, whose products are cytoplasmic membrane-bound-vesicle-located proteins, were preferred to be regulated in barley. Correlation analysis of the vernalization-related genes with barley revealed that the vernalization mechanism was conserved between these two plant species. In summary, vernalization, including its memory mechanism, is conserved between Brachypodium and barley, although several species-specific features also exist. The data reported here will provide primary resources for subsequent functional research in vernalization.

Genetic identification of a novel locus, ACCELERATED FLOWERING 1 that controls chromatin modification associated with histone H3 lysine 27 trimethylation in Arabidopsis thaliana

Flowering on time is a critically important for successful reproduction of plants. Here we report an early-flowering mutant in Arabidopsis thaliana, accelerated flowering 1-1D (afl1-1D) that exhibited pleiotropic developmental defects including semi-dwarfism, curly leaf, and increased branching. Genetic analysis showed that afl1-1D mutant is a single, dominant mutant. Chromosomal mapping indicates that AFL1 resides at the middle of chromosome 4, around which no known flowering-related genes have been characterized. Expression analysis and double mutant studies with late flowering mutants in various floral pathways indicated that elevated FT is responsible for the early-flowering of afl1-1D mutant. Interestingly, not only flowering-related genes, but also several floral homeotic genes were ectopically overexpressed in the afl1-1D mutants in both FT-dependent and -independent manner. The degree of histone H3 Lys27-trimethylation (H3K27me3) was reduced in several chromatin including FT, FLC, AG and SEP3 in the afl1-1D, suggesting that afl1-1D might be involved in chromatin modification. In support, double mutant analysis of afl1-1D and lhp1-4 revealed epistatic interaction between afl1-1D and lhp1-4 in regard to flowering control. Taken together, we propose that AFL1 regulate various aspect of development through chromatin modification, particularly associated with H3K27me3 in A. thaliana.

Structure and function of florigen and the receptor complex

In the 1930s, the flowering hormone, florigen, was proposed to be synthesized in leaves under inductive day length and transported to the shoot apex, where it induces flowering. More recently, generated genetic and biochemical data suggest that florigen is a protein encoded by the gene, FLOWERING LOCUS T (FT). A rice (Oryza sativa) FT homolog, Hd3a, interacts with the rice FD homolog, OsFD1, via a 14-3-3 protein. Formation of this tri-protein complex is essential for flowering promotion by Hd3a in rice. In addition, the multifunctionality of FT homologs, other than for flowering promotion, is an emerging concept. Here we review the structural and biochemical features of the florigen protein complex and discuss the molecular basis for the multifunctionality of FT proteins.

The polycomb complex PRC1: composition and function in plants

Polycomb group (PcG) proteins are crucial epigenetic regulators conferring transcriptional memory to cell lineages. They assemble into multi-protein complexes, e.g., Polycomb Repressive Complex 1 and 2 (PRC1, PRC2), which are thought to act in a sequential manner to stably maintain gene repression. PRC2 induces histone H3 lysine 27 (H3K27) trimethylation (H3K27me3), which is subsequently read by PRC1 that further catalyzes H2A monoubiquitination (H2Aub1), creating a transcriptional silent chromatin conformation. PRC2 components are conserved in plants and have been extensively characterized in Arabidopsis. In contrast, PRC1 composition and function are more diverged between animals and plants. Only more recently, PRC1 existence in plants has been documented. Here we review the aspects of plant specific and conserved PRC1 and highlight critical roles of PRC1 components in seed embryonic trait determinacy, shoot stem cell fate determinacy, and flower development in Arabidopsis.