Mutagenesis of a Quintuple Mutant Impaired in Environmental Responses Reveals Roles for CHROMATIN REMODELING4 in the Arabidopsis Floral Transition

Composition and function of plant chromatin remodeling complexes

ATP-dependent chromatin remodelers play a crucial role in modifying chromatin configuration by utilizing the energy of ATP hydrolysis. They are involved in various processes, including transcription, DNA replication, and maintaining genome stability. These remodeling remodelers usually form multi-subunit chromatin remodeling complexes in eukaryotes. In plants, chromatin remodeling complexes have diverse functions in regulating plant development and stress response. Recent studies have conducted extensive research on plant chromatin remodeling complexes. This review focuses on recent advances in the classification and composition of plant chromatin remodeling complexes, the protein-protein interactions within the complexes, their impact on chromatin configuration, and their interactions with chromatin modifications and transcription factors.

BLA1 Affects Leaf Angles by Altering Brassinosteroid Biosynthesis in Rice (Oryza sativa L.)

Brassinosteroids (BRs) are crucial plant hormones influencing diverse developmental processes in rice. While several enzymes in BR biosynthesis have been identified, their regulatory mechanisms remain largely unknown. This study highlights a novel regulatory pathway wherein the CHD3 chromatin remodeler, BLA1, epigenetically modulates the expression of key BR biosynthesis genes, BRD1 and D2. Phenotypic analysis of bla1 mutants revealed significant alterations, such as increased leaf angles and longer mesocotyls, which were alleviated by BR synthesis inhibitors. Moreover, the bla1 mutants showed elevated BR levels that correlated with the significant upregulation of the expression levels of BRD1 and D2, particularly at the lamina joint sites. Mechanistically, the yeast one-hybrid and chromatin immunoprecipitation assays revealed specific binding of BLA1 to the promoter regions of BRD1 and D2, accompanied by a marked enrichment of the transcriptionally active histone modification, H3K4me3, on these loci in the bla1 mutant. Functional assessments of the brd1 and d2 mutants confirmed their reduced sensitivity to BR, further underscoring their critical regulatory roles in BR-mediated developmental processes. Our findings uncovered an epigenetic mechanism that governs BR biosynthesis and orchestrates the expression of BRD1 and D2 to modulate BR levels and influence rice growth and development.

Loss of cold tolerance is conferred by absence of the WRKY34 promoter fragment during tomato evolution

Natural evolution has resulted in reduced cold tolerance in cultivated tomato (Solanum lycopersicum). Herein, we perform a combined analysis of ATAC-Seq and RNA-Seq in cold-sensitive cultivated tomato and cold-tolerant wild tomato (S. habrochaites). We identify that WRKY34 has the most significant association with differential chromatin accessibility and expression patterns under cold stress. We find that a 60 bp InDel in the WRKY34 promoter causes differences in its transcription and cold tolerance among 376 tomato accessions. This 60 bp fragment contains a GATA cis-regulatory element that binds to SWIBs and GATA29, which synergistically suppress WRKY34 expression under cold stress. Moreover, WRKY34 interferes with the CBF cold response pathway through regulating transcription and protein levels. Our findings emphasize the importance of polymorphisms in cis-regulatory regions and their effects on chromatin structure and gene expression during crop evolution.

Genetic and epigenetic basis of phytohormonal control of floral transition in plants

The timing of the developmental transition from the vegetative to the reproductive stage is critical for angiosperms, and is fine-tuned by the integration of endogenous factors and external environmental cues to ensure successful reproduction. Plants have evolved sophisticated mechanisms to response to diverse environmental or stress signals, and these can be mediated by hormones to coordinate flowering time. Phytohormones such as gibberellin, auxin, cytokinin, jasmonate, abscisic acid, ethylene, and brassinosteroids and the cross-talk among them are critical for the precise regulation of flowering time. Recent studies of the model flowering plant Arabidopsis have revealed that diverse transcription factors and epigenetic regulators play key roles in relation to the phytohormones that regulate floral transition. This review aims to summarize our current knowledge of the genetic and epigenetic mechanisms that underlie the phytohormonal control of floral transition in Arabidopsis, offering insights into how these processes are regulated and their implications for plant biology.

The bZIP transcription factor AREB3 mediates FT signalling and floral transition at the Arabidopsis shoot apical meristem

The floral transition occurs at the shoot apical meristem (SAM) in response to favourable external and internal signals. Among these signals, variations in daylength (photoperiod) act as robust seasonal cues to activate flowering. In Arabidopsis, long-day photoperiods stimulate production in the leaf vasculature of a systemic florigenic signal that is translocated to the SAM. According to the current model, FLOWERING LOCUS T (FT), the main Arabidopsis florigen, causes transcriptional reprogramming at the SAM, so that lateral primordia eventually acquire floral identity. FT functions as a transcriptional coregulator with the bZIP transcription factor FD, which binds DNA at specific promoters. FD can also interact with TERMINAL FLOWER 1 (TFL1), a protein related to FT that acts as a floral repressor. Thus, the balance between FT-TFL1 at the SAM influences the expression levels of floral genes targeted by FD. Here, we show that the FD-related bZIP transcription factor AREB3, which was previously studied in the context of phytohormone abscisic acid signalling, is expressed at the SAM in a spatio-temporal pattern that strongly overlaps with FD and contributes to FT signalling. Mutant analyses demonstrate that AREB3 relays FT signals redundantly with FD, and the presence of a conserved carboxy-terminal SAP motif is required for downstream signalling. AREB3 shows unique and common patterns of expression with FD, and AREB3 expression levels are negatively regulated by FD thus forming a compensatory feedback loop. Mutations in another bZIP, FDP, further aggravate the late flowering phenotypes of fd areb3 mutants. Therefore, multiple florigen-interacting bZIP transcription factors have redundant functions in flowering at the SAM.

Floral Homeotic Factors: A Question of Specificity

MADS-domain transcription factors are involved in the control of a multitude of processes in eukaryotes, and in plants, they play particularly important roles during reproductive development. Among the members of this large family of regulatory proteins are the floral organ identity factors, which specify the identities of the different types of floral organs in a combinatorial manner. Much has been learned over the past three decades about the function of these master regulators. For example, it has been shown that they have similar DNA-binding activities and that their genome-wide binding patterns exhibit large overlaps. At the same time, it appears that only a minority of binding events lead to changes in gene expression and that the different floral organ identity factors have distinct sets of target genes. Thus, binding of these transcription factors to the promoters of target genes alone may not be sufficient for their regulation. How these master regulators achieve specificity in a developmental context is currently not well understood. Here, we review what is known about their activities and highlight open questions that need to be addressed to gain more detailed insights into the molecular mechanisms underlying their functions. We discuss evidence for the involvement of cofactors as well as the results from studies on transcription factors in animals that may be instructive for a better understanding of how the floral organ identity factors achieve regulatory specificity.

MicroRNA172 controls inflorescence meristem size through regulation of APETALA2 in Arabidopsis

The APETALA2 (AP2) transcription factor regulates flower development, floral transition and shoot apical meristem (SAM) maintenance in Arabidopsis. AP2 is also regulated at the post-transcriptional level by microRNA172 (miR172), but the contribution of this to SAM maintenance is poorly understood. We generated transgenic plants carrying a form of AP2 that is resistant to miR172 (rAP2) or carrying a wild-type AP2 susceptible to miR172. Phenotypic and genetic analyses were performed on these lines and mir172 mutants to study the role of AP2 regulation by miR172 on meristem size and the rate of flower production. We found that rAP2 enlarges the inflorescence meristem by increasing cell size and cell number. Misexpression of rAP2 from heterologous promoters showed that AP2 acts in the central zone (CZ) and organizing center (OC) to increase SAM size. Furthermore, we found that AP2 is negatively regulated by AUXIN RESPONSE FACTOR 3 (ARF3). However, genetic analyses indicated that ARF3 also influences SAM size and flower production rate independently of AP2. The study identifies miR172/AP2 as a regulatory module controlling inflorescence meristem size and suggests that transcriptional regulation of AP2 by ARF3 fine-tunes SAM size determination.

Comparative Expression Profiling of Snf2 Family Genes During Reproductive Development and Stress Responses in Rice

Sucrose non-fermenting 2 (Snf2) protein family, as chromatin remodeling factors, is an enormous and the most diverse protein family, which contributes to biological processes of replication, transcription, and DNA repair using the energy of adenosine triphosphate (ATP) hydrolysis. The members of Snf2 family proteins have been well characterized in Arabidopsis, rice, and tomato. Although this family received significant attention, few genes were identified uniquely for their roles in mediating reproductive development and stress tolerance in rice. In the present study, we comprehensively analyzed the expression profiling of Snf2 genes during reproductive development and biotic/abiotic stresses. Our results showed that five proteins (OsCHR712/715/720/726/739) were mainly localized in the nucleus, while OsCHR715/739 were also slightly expressed in the cell membrane. There were abundant cis-acting elements in the putative promoter of Snf2 genes, including dehydration, MeJA, MYB binding site for drought, ABA-responsive, and stress-responsive element. Most of the genes were induced immediately after Magnaporthe oryzae infection at 12 h post-infection (hpi). About 55% of the total genes were upregulated under salt and drought stresses during the entire time, and 22-35% of the total genes were upregulated at 3 h. It was noteworthy that the seven genes (OsCHR705, OsCHR706, OsCHR710, OsCHR714, OsCHR721, OsCHR726, and OsCHR737) were upregulated, and one gene (OsCHR712) was downregulated under salt and drought stresses, respectively. The deficiency of OsCHR726 mutations displayed a hypersensitive phenotype under salt stress. These results will be significantly useful features for the validation of the rice Snf2 genes and facilitate understanding of the genetic engineering of crops with improved biotic and abiotic stresses.

OsDDM1b Controls Grain Size by Influencing Cell Cycling and Regulating Homeostasis and Signaling of Brassinosteroid in Rice

Snf2 family proteins are the crucial subunits of chromatin-remodeling complexes (CRCs), which contributes to the biological processes of transcription, replication, and DNA repair using ATP as energy. Some CRC subunits have been confirmed to be the critical regulators in various aspects of plant growth and development and in epigenetic mechanisms such as histone modification, DNA methylation, and histone variants. However, the functions of Snf2 family genes in rice were poorly investigated. In this study, the relative expression profile of 40 members of Snf2 family in rice was studied at certain developmental stages of seed. Our results revealed that OsCHR741/OsDDM1b (Decrease in DNA methylation 1) was accumulated highly in the early developmental stage of seeds. We further analyzed the OsDDM1b T-DNA insertion loss-of-function of mutant, which exhibited dwarfism, smaller organ size, and shorter and wider grain size than the wild type (Hwayoung, HY), yet no difference in 1,000-grain weight. Consistent with the grain size, the outer parenchyma cell layers of lemma in osddm1b developed more cells with decreased size. OsDDM1b encoded a nucleus, membrane-localized protein and was distributed predominately in young spikelets and seeds, asserting its role in grain size. Meanwhile, the osddm1b was less sensitive to brassinosteroids (BRs) while the endogenous BR levels increased. We detected changes in the expression levels of the BR signaling pathway and feedback-inhibited genes with and without exogenous BR application, and the alterations of expression were also observed in grain size-related genes in the osddm1b. Altogether, our results suggest that OsDDM1b plays a crucial role in grain size via influencing cell proliferation and regulating BR signaling and homeostasis.

Resequencing and genome-wide association studies of autotetraploid potato

Potato is the fourth most important food crop in the world. Although with a long history for breeding approaches, genomic information and association between genes and agronomic traits remain largely unknown particularly in autotetraploid potato cultivars, which limit the molecular breeding progression. By resequencing the genome of 108 main cultivar potato accessions with rich genetic diversity and population structure from International Potato Center, with approximate 20-fold coverage, we revealed more than 27 million Single Nucleotide Polymorphisms and ~ 3 million Insertion and Deletions with high quality and accuracy. Domestication analysis and genome-wide association studies (GWAS) identified candidate loci related to photoperiodic flowering time and temperature sensitivity as well as disease resistance, providing informative insights into the selection and domestication of cultivar potato. In addition, GWAS with GWASploy for 25 agronomic traits identified candidate loci by association signals, especially those related to tuber size, small-sized tuber weight and tuber thickness that was also validated by transcriptome analysis. Our study provides a valuable resource that facilitates the elucidation of domestication process as well as the genetic studies and agronomic improvement of autotetraploid potato.

Unraveling the role of MADS transcription factor complexes in apple tree dormancy

A group of MADS transcription factors (TFs) are believed to control temperature-mediated bud dormancy. These TFs, called DORMANCY-ASSOCIATED MADS-BOX (DAM), are encoded by genes similar to SHORT VEGETATIVE PHASE (SVP) from Arabidopsis. MADS proteins form transcriptional complexes whose combinatory composition defines their molecular function. However, how MADS multimeric complexes control the dormancy cycle in trees is unclear. Apple MdDAM and other dormancy-related MADS proteins form complexes with MdSVPa, which is essential for the ability of transcriptional complexes to bind to DNA. Sequential DNA-affinity purification sequencing (seq-DAP-seq) was performed to identify the genome-wide binding sites of apple MADS TF complexes. Target genes associated with the binding sites were identified by combining seq-DAP-seq data with transcriptomics datasets obtained using a glucocorticoid receptor fusion system, and RNA-seq data related to apple dormancy. We describe a gene regulatory network (GRN) formed by MdSVPa-containing complexes, which regulate the dormancy cycle in response to environmental cues and hormonal signaling pathways. Additionally, novel molecular evidence regarding the evolutionary functional segregation between DAM and SVP proteins in the Rosaceae is presented. MdSVPa sequentially forms complexes with the MADS TFs that predominate at each dormancy phase, altering its DNA-binding specificity and, therefore, the transcriptional regulation of its target genes.

"Core" RxLR effectors in phytopathogenic oomycetes: A promising way to breeding for durable resistance in plants?

Phytopathogenic oomycetes are known to successfully infect their hosts due to their ability to secrete effector proteins. Of interest to many researchers are effectors with the N-terminal RxLR motif (Arginine-any amino acid-Leucine-Arginine). Owing to advances in genome sequencing, we can now comprehend the high level of diversity among oomycete effectors, and similarly, their conservation within and among species referred to here as "core" RxLR effectors (CREs). Currently, there is a considerable number of CREs that have been identified in oomycetes. Functional characterization of these CREs propose their virulence role with the potential of targeting central cellular processes that are conserved across diverse plant species. We reason that effectors that are highly conserved and recognized by the host, could be harnessed in engineering plants for durable as well as broad-spectrum resistance.

Genomic impact of stress-induced transposable element mobility in Arabidopsis

Transposable elements (TEs) have long been known to be major contributors to plant evolution, adaptation and crop domestication. Stress-induced TE mobilization is of particular interest because it may result in novel gene regulatory pathways responding to stresses and thereby contribute to stress adaptation. Here, we investigated the genomic impacts of stress induced TE mobilization in wild type Arabidopsis plants. We find that the heat-stress responsive ONSEN TE displays an insertion site preference that is associated with specific chromatin states, especially those rich in H2A.Z histone variant and H3K27me3 histone mark. In order to better understand how novel ONSEN insertions affect the plant's response to heat stress, we carried out an in-depth transcriptomic analysis. We find that in addition to simple gene knockouts, ONSEN can produce a plethora of gene expression changes such as: constitutive activation of gene expression, alternative splicing, acquisition of heat-responsiveness, exonisation and genesis of novel non-coding and antisense RNAs. This report shows how the mobilization of a single TE-family can lead to a rapid rise of its copy number increasing the host's genome size and contribute to a broad range of transcriptomic novelty on which natural selection can then act.

Dissection of floral transition by single-meristem transcriptomes at high temporal resolution

The vegetative-to-floral transition is a dramatic developmental change of the shoot apical meristem, promoted by the systemic florigen signal. However, poor molecular temporal resolution of this dynamic process has precluded characterization of how meristems respond to florigen induction. Here, we develop a technology that allows sensitive transcriptional profiling of individual shoot apical meristems. Computational ordering of hundreds of tomato samples reconstructed the floral transition process at fine temporal resolution and uncovered novel short-lived gene expression programs that are activated before flowering. These programs are annulled only when both florigen and a parallel signalling pathway are eliminated. Functional screening identified genes acting at the onset of pre-flowering programs that are involved in the regulation of meristem morphogenetic changes but dispensable for the timing of floral transition. Induced expression of these short-lived transition-state genes allowed us to determine their genetic hierarchies and to bypass the need for the main flowering pathways. Our findings illuminate how systemic and autonomous pathways are integrated to control a critical developmental switch.

Beyond the Genetic Pathways, Flowering Regulation Complexity in Arabidopsis thaliana

Flowering is one of the most critical developmental transitions in plants’ life. The irreversible change from the vegetative to the reproductive stage is strictly controlled to ensure the progeny’s success. In Arabidopsis thaliana, seven flowering genetic pathways have been described under specific growth conditions. However, the evidence condensed here suggest that these pathways are tightly interconnected in a complex multilevel regulatory network. In this review, we pursue an integrative approach emphasizing the molecular interactions among the flowering regulatory network components. We also consider that the same regulatory network prevents or induces flowering phase change in response to internal cues modulated by environmental signals. In this sense, we describe how during the vegetative phase of development it is essential to prevent the expression of flowering promoting genes until they are required. Then, we mention flowering regulation under suboptimal growing temperatures, such as those in autumn and winter. We next expose the requirement of endogenous signals in flowering, and finally, the acceleration of this transition by long-day photoperiod and temperature rise signals allowing A. thaliana to bloom in spring and summer seasons. With this approach, we aim to provide an initial systemic view to help the reader integrate this complex developmental process.

The Rice CHD3/Mi-2 Chromatin Remodeling Factor Rolled Fine Striped Promotes Flowering Independent of Photoperiod

Genetic studies have revealed that chromatin modifications affect flowering time, but the underlying mechanisms by which chromatin remodeling factors alter flowering remain largely unknown in rice (Oryza sativa). Here, we show that Rolled Fine Striped (RFS), a chromodomain helicase DNA-binding 3 (CHD3)/Mi-2 subfamily ATP-dependent chromatin remodeling factor, promotes flowering in rice. Diurnal expression of RFS peaked at night under short-day (SD) conditions and at dawn under long-day (LD) conditions. The rfs-1 and rfs-2 mutants (derived from different genetic backgrounds) displayed a late-flowering phenotype under SD and LD conditions. Reverse transcription-quantitative PCR analysis revealed that among the flowering time-related genes, the expression of the major floral repressor Grain number and heading date 7 (Ghd7) was mainly upregulated in rfs mutants, resulting in downregulation of its downstream floral inducers, including Early heading date 1 (Ehd1), Heading date 3a (Hd3a), and Rice FLOWERING LOCUS T 1 (RFT1). The rfs mutation had pleiotropic negative effects on rice grain yield and yield components, such as plant height and fertility. Taking these observations together, we propose that RFS participates in multiple aspects of rice development, including the promotion of flowering independent of photoperiod.

Photoperiodic Signaling and Senescence, an Ancient Solution to a Modern Problem?

The length of the day (photoperiod) is a robust seasonal signal originated by earth orbital and translational movements, a resilient external cue to the global climate change, and a predictable hint to initiate or complete different developmental programs. In eukaryotic algae, the gene expression network that controls the cellular response to photoperiod also regulates other basic physiological functions such as starch synthesis or redox homeostasis. Land plants, evolving in a novel and demanding environment, imbued these external signals within the regulatory networks controlling organogenesis and developmental programs. Unlike algae that largely have to deal with cellular physical cues, within the course of evolution land plants had to transfer this external information from the receiving organs to the target tissues, and mobile signals such as hormones were recruited and incorporated in the regulomes. Control of senescence by photoperiod, as suggested in this perspective, would be an accurate way to feed seasonal information into a newly developed function (senescence) using an ancient route (photoperiodic signaling). This way, the plant would assure that two coordinated aspects of development such as flowering and organ senescence were sequentially controlled. As in the case of senescence, there is growing evidence to support the idea that harnessing the reliability of photoperiod regulation over other, more labile signaling pathways could be used as a robust breeding tool to enhance plants against the harmful effects of climate change.

A Chromodomain-Helicase-DNA-Binding Factor Functions in Chromatin Modification and Gene Regulation

Proteins in the Chromodomain-Helicase/ATPase-DNA-binding domain (CHD) family are divided into three groups. The function of group I CHD proteins in nucleosome positioning is well established, while that of group II members (represented by CHD3/Mi2) remains unclear. Using high-throughput approaches, we investigated the function of the group II rice (Oryza sativa) CHD protein CHR729 in nucleosome positioning, gene expression, histone methylation, and binding. Our data revealed that the chr729 mutation led to increased nucleosome occupancy in the rice genome and altered the expression and histone H3K4me3 modification of many, mainly underexpressed, genes. Further analysis showed that the mutation affected both the deposition and depletion of H3K4me3 in distinct chromatin regions, with concomitant changes in H3K27me3 modification. Genetic and genomic analyses revealed that CHR729 and JMJ703, an H3K4 demethylase, had agonistic, antagonistic, and independent functions in modulating H3K4me3 and the expression of subsets of genes. In addition, CHR729 binding was enriched in H3K4me3-marked genic and H3K27me3-marked intergenic regions. The results indicate that CHR729 has distinct functions in regulating H3K4me3 and H3K27me3 modifications and gene expression at different chromatin domains and provide insight into chromatin regulation of bivalent genes marked by both H3K4me3 and H3K27me3.