Biology subjects

Simonini, S.

Publications and source records attributed to Simonini, S..

7 recordsLinked to original sources

bioRxiv2026

An oxygen-sensing Polycomb-group protein encodes flooding stress memory in plants

Most organisms, including plants, can encode stress memories that improve resilience to repeated environmental challenges. Flooding events expose plants to recurrent hypoxia, yet whether plants establish an adaptive memory of flooding is unclear. Here we show that somatic flooding stress memory is a conserved feature across multiple angiosperm species. In Arabidopsis, this memory depends on the oxygen-sensitive Polycomb Repressive Complex 2 (PRC2) subunit VERNALIZATION2 (VRN2). Loss of VRN2 impairs epigenetic memory formation and disrupts transcriptional memory at key genes that promote anthocyanin accumulation and repress leaf senescence, adaptive responses that enhance flooding tolerance. Collectively, we reveal a molecular mechanism where VRN2-PRC2 acts as both an oxygen sensor and chromatin effector to establish adaptive flooding stress memory in plants. ShortOur work defines a molecular mechanism for flooding stress memory in plants, actioned via the PRC2 subunit VRN2, that acts as the direct molecular (low) oxygen sensor and transducer. Coupled to its role in cold sensing, this identifies VRN2 as a master sensor subunit of the plant PRC2 that integrates multiple environmental cues to modulate the chromatin landscape and encode environmental memory.

plant biology↗

bioRxiv2025

ALFIN-LIKE Proteins Orchestrate H3K4me3-H3K27me3 Crosstalk to Regulate Plant Embryogenesis

In multicellular organisms such as animals and plants, development requires the precise regulation of gene expression, mediated not only by transcription factors but also by chromatin-based mechanisms. Among these, histone modifications like H3K4me3 and H3K27me3 play opposing roles in gene activation and repression, respectively. In Arabidopsis thaliana, H3K27me3 is deposited by the Polycomb Repressive Complex 2 (PRC2), while Trithorax group (TrxG) proteins mediate H3K4me3 deposition. While the functions of these writer complexes have been extensively studied, far less is known about the histone mark readers that interpret these modifications during development. Here, we investigate the antagonistic interplay between H3K27me3 and H3K4me3 during Arabidopsis embryogenesis. We identify a developmentally specific interaction between the FIS-PRC2 complex and ALFIN-LIKE (AL) proteins--a family of plant-specific PHD domain proteins that read H3K4me3. Our findings reveal a dynamic competition between these two marks during early embryogenesis that helps shape the epigenomic landscape of the developing seed. Disruption of AL function leads to severe developmental defects and loss of cell identity in early embryos. Moreover, loss of ALs impairs H3K4me3 deposition, resulting in aberrant spreading of H3K27me3, misregulation of developmental genes, and defects that persist into adult plant traits. Together, our results show that proper embryonic development relies on a finely tuned antagonism between activating and repressive chromatin states--an interplay orchestrated not only by their writers but also by specific readers that translate these epigenetic cues into developmental outcomes.

plant biology↗

bioRxiv2024

CUT&Tag for high-resolution epigenomic profiling from a low amount of Arabidopsis tissue

BackgroundThe genome-wide profiling of chromatin states that are defined by different histone post-translational modifications, known as epigenomic profiling, is crucial for understanding the epigenetic regulations of gene expression, both in animal and plant systems. CUT&Tag (Cleavage Under Targets and Tagmentation, [1]) is a novel enzyme-tethering method for epigenomic profiling, initially developed for mammalian cells. CUT&Tag has several advantages compared to the most commonly used epigenomic profiling methods such as Chromatin Immunoprecipitation followed by high-throughput sequencing (ChIP-seq). CUT&Tag allows epigenenomic profiling from a much less amount of starting material compared to ChIP-seq. CUT&Tag is based on the in situ cleavage of DNA by enzymes tethered to antibodies, while in ChIP-seq, the cleavage is done by a nearly random fragmentation step. In theory, this difference in the way of cleaving DNA allows CUT&Tag to reach a higher resolution compared to ChIP-seq. Therefore, CUT&Tag holds the potential to profile the genome-wide distribution at a high resolution even from a small amount of plant tissues. ResultsWe profiled the genome-wide distribution of three histone modifications, H3K27me3, H3K4me3 and H3K27Ac, from a few seedlings of Arabidopsis that weighed around 0.01 grams. By comparing the H3K27me3 profiles generated from ChIP-seq and CUT&Tag, we showed that CUT&Tag and ChIP-seq capture the same broad lines of the epigenomes, but they also revealed different sets of peaks. Analysis using the CUT&Tag datasets for the three histone modifications revealed their genomic locations and their relationship with the gene expression level, which are consistent with the expected effect of these histone marks on gene transcription. By comparing to the nucleosome occupancy data, we show that CUT&Tag reached nucleosomal resolution, a much higher resolution than ChIP-seq. In the end, we presented that the increased resolution of CUT&Tag could better reveal the exon enrichment of histone modifications and the epigenetic states of the +1 nucleosome, showing benefits and advantages that this technique could bring to the field of plant epigenetics and chromatin study in general. ConclusionCUT&Tag is a valid, easy-to-perform, cost-effective, and reliable approach for efficient epigenomic profiling in Arabidopsis, even with limited amount of starting material and provides a higher resolution compared to ChIP-seq. Because the CUT&Tag protocol starting input is isolated nuclei, it is also applicable to other model and non-model plants.

plant biology↗

bioRxiv2023

Unequal genetic redundancy among the rice transcription factors OsMADS2 and OsMADS4 reveals distinct roles in floret organ development

Diversification of transcription factors and of their downstream targets can contribute to new organ morphologies. An example is rice lodicule, a small fleshy petal homolog that aids floret opening, thus facilitates pollination and fertility. To understand mechanisms underlying its specification, we investigated the developmental functions of the rice PISTILLATA (PI) paralogs, OsMADS2 and OsMADS4. Null osmads2 mutants reiterated OsMADS2 nonredundant lodicule specification roles and revealed new roles in flowering time and floral organ number and fate. Doubly perturbed osmads2d8/d8 osmads4kd florets had severe abnormalities, were female infertile, yet initiated parthenocarpy. Ubiquitous OsMADS4 overexpression rescued osmads2 abnormalities. Target genes whose regulation can contribute to OsMADS2 functions were discovered by its genome-wide binding analyses and transcriptome profiling. Several targets are implicated in lodicule and stamen development, floral organ number, cell wall, cell shape and osmotic homeostasis processes. Some targets relevant to lodicule development are cell division regulators (Cyclin D6, Cyclin P4-1-like), aquaporin (PIP1A), peptide transporter (PTR2), vascular development regulator (HOX1) and cell wall modulator (GH9B16). Their deregulation underscores the perturbed cell division, tissue differentiation patterns and physiology of the malformed osmads2 and osmads2d8/d8 osmads4kd lodicules. Altogether, we reveal novel roles for the rice PI paralogs in flowering time, panicle exsertion and embryo sac differentiation, divulge gene targets for lodicule development and provide mechanistic insights on the functional diversification of rice PI paralogs.

plant biology↗

bioRxiv2023

HISTONE DEACETYLASE 19 REGULATES SHOOT MERISTEMLESS EXPRESSION IN THE CARPEL MARGIN MERISTEM CONTRIBUTING TO OVULE NUMBER DETERMINATION AND TRANSMITTING TRACT DIFFERENTIATION

The gynoecium is critical for the reproduction of flowering species as it contains the ovules and the tissues required for pollen germination and guidance. These tissues are collectively known as the reproductive tract (ReT) and comprise stigma, style and transmitting tract (TT). The ovules and the ReT originate from a meristem within the pistil named carpel margin meristem (CMM). SHOOT MERISTEMLESS (STM) is a key transcription factor required for meristem formation and maintenance. In all above-ground meristems, including the CMM, STM has to be locally downregulated to allow proper organ differentiation. However, how this downregulation is achieved in the CMM is unknown. In this work, we have studied HISTONE DEACETYLASE 19 (HDA19) role in ovule and ReT differentiation, based on the observation that hda19-3 mutant displays reduced ovule number and fails to properly differentiate the TT. Fluorescence activated cell sorting (FACS) coupled with RNA-seq revealed that in the CMM of hda19-3 mutant, genes promoting organ development are downregulated while meristematic markers, including STM, are upregulated. We found that HDA19 is fundamental to downregulate STM in the CMM, allowing ovule formation and TT differentiation. STM is ectopically expressed in hda19-3 at intermediate stages of pistil development, and its downregulation by RNA interference alleviated hda19-3 phenotypic defects. Furthermore, chromatin immunoprecipitation assays indicated that STM is a direct target of HDA19 during pistil development and that SEEDSTICK (STK) is required for the histone acetylation-mediated regulation of STM. Our results have led to the identification of the factors required for STM silencing in the gynoecium allowing organogenesis and tissue differentiation from the CMM.

plant biology↗

bioRxiv2023

A paternal signal induces endosperm proliferation upon fertilization in Arabidopsis

In multicellular organisms, sexual reproduction relies on the formation of highly specialized, differentiated cells, the gametes. At maturity, male and female gametes are quiescent, awaiting fertilization, with their cell cycle being arrested at a precise stage. Failure to establish quiescence leads to unwanted proliferation, abortion of the offspring, and a waste of resources. Upon fertilization, the cell cycle resumes, allowing the newly formed zygote to divide rapidly. Successful development requires that male and female gametes are in the same phase of the cell cycle. The molecular mechanisms that enforce quiescence and reinstate cell division only after fertilization occurs are poorly understood. Here, we describe a sperm-derived signal that induces proliferation of the Arabidopsis central cell precisely upon fertilization. We show that the mature central cell is arrested in S phase, caused by the activity of the conserved RETINOBLASTOMA RELATED1 (RBR1) protein. Paternal delivery of the core cell cycle component CYCD7;1 triggers RBR1 degradation, thereby stimulating S phase progression. Absence of CYCD7;1 delays RBR1 depletion, S phase reactivation, and central cell division, whereas its constitutive expression triggers proliferation of unfertilized central cells. In summary, we show that CYCD7;1 is a paternal signal that informs the central cell that fertilization occurred, thus unlocking quiescence and ensuring that cell division initiates just at the right time to ensure functional endosperm formation.

plant biology↗

bioRxiv2020

The Polycomb group protein MEDEA controls cell proliferation and embryonic patterning in Arabidopsis

Establishing the body plan of a multicellular organism relies on precisely orchestrated cell divisions coupled with pattern formation. In animals, cell proliferation and embryonic patterning are regulated by Polycomb group (PcG) proteins that form various multisubunit complexes (Grossniklaus and Paro, 2014). The evolutionary conserved Polycomb Repressive Complex 2 (PRC2) trimethylates histone H3 at lysine 27 (H3K27me3) and comes in different flavors in the model plant Arabidopsis thaliana (Forderer et al., 2016; Grossniklaus and Paro, 2014). The histone methyltransferase MEDEA (MEA) is part of the FERTILIZATION INDEPENDENT SEED (FIS)-PRC2 required for seed development4. Although embryos derived from mea mutant egg cells show morphological abnormalities (Grossniklaus et al., 1998), defects in the development of the placenta-like endosperm are considered the main cause of seed abortion (Kinoshita et al., 1999; Scott et al., 1998), and a role of FIS-PRC2 in embryonic patterning was dismissed (Bouyer et al., 2011; Leroy et al., 2007). Here, we demonstrate that endosperm lacking MEA activity sustains normal embryo development and that embryos derived from mea mutant eggs abort even in presence of a wild-type endosperm because MEA is required for embryonic patterning and cell lineage determination. We show that, similar to PcG proteins in mammals, MEA regulates embryonic growth by repressing the transcription of core cell cycle components. Our work demonstrates that Arabidopsis embryogenesis is under epigenetic control of maternally expressed PcG proteins, revealing that PRC2 was independently recruited to control embryonic cell proliferation and patterning in animals and plants.

developmental biology↗