Biology subjects

Thevenon, E.

Publications and source records attributed to Thevenon, E..

8 recordsLinked to original sources

bioRxiv2026

ULTRAPETALA1 remodels PRC2 recruitment to nucleosomes

Polycomb Repressive Complex 2 (PRC2) establishes transcriptional repression through trimethylation of histone H3 lysine 27 (H3K27me3), a modification essential for developmental patterning. Here, we describe a novel plant-specific PRC2 variant (PRC2.3) that employs a distinct nucleosome-targeting mechanism mediated by accessory factor ULTRAPETALA1 (ULT1), which promotes H3K27me3 deposition at over 1,300 developmental genes. The cryo-EM structure of the PRC2SWN-ULT1-nucleosome complex reveals that ULT1 antagonizes the canonical PRC2 binding mode and instead bridges PRC2 to the nucleosome using its own interaction surfaces. ULT1 binds consecutive purines in the nucleosomal DNA and the histone H2A/H2B acidic patch, while enabling PRC2 to accommodate H3K36 modifications. We further show that in planta ULT1 enhances H3K27me3 at purine-rich loci and at genes associated with H3K36 marks, and identify the ULT1-H2A/H2B interface as required for reproductive transition and flower organogenesis. Our findings demonstrate that PRC2 can deploy mechanistically distinct recruitment strategies to control key developmental switches.

Molecular Biology↗

bioRxiv2026

Structural Evolution of LEAFY Reveals DNA-Mediated Cooperativity and Dimerization Shifts at the Water-to-Land Transition

The evolution of transcription factor (TF) DNA-binding specificity is a major driver of gene regulatory innovation. Unlike most TFs, which diversify through gene duplication and neofunctionalization, the plant-specific LEAFY (LFY) TF evolved novel binding specificities without extensive duplication. Here, we combine experimental structural determination and biochemical assays to reveal how LFYs dimerization and DNA-binding preferences shifted during the water-to-land transition. We present crystal structures of the LFY DNA-binding domain (DBD) from the hornwort Nothoceros aenigmaticus and the alga Interfilum paradoxum bound to DNA, demonstrating two distinct dimerization mechanisms: one mediated by direct protein-protein interactions and another driven by DNA-mediated cooperativity. In the ancestral state, LFY likely bound DNA as a dimer through DNA-mediated cooperativity, with protein-protein dimerization emerging later, enforcing new DNA-binding preferences. Our findings support a revised evolutionary scenario for LFY, highlighting the dynamic interplay between protein-DNA and protein-protein interactions as key drivers of TF binding specificity. This work deepens our understanding of how structural adaptations in TFs underpin evolutionary transitions in gene regulation.

plant biology↗

bioRxiv2025

Rsc1 DNA-binding bromodomain drives RSC activity at A-rich promoters

In yeast, the SWI/SNF chromatin remodeler RSC orchestrates nucleosome positioning at promoters, yet the molecular determinants guiding RSC to chromatin remain unclear. Here, we investigate the RSC subunit Rsc1 in Candida albicans and Saccharomyces cerevisiae. We identify a non-canonical role for its second bromodomain, Rsc1-BD2, which lacks a functional acetyllysine-binding pocket. Instead, Rsc1-BD2, together with the adjacent AT-hook and BAH domains, forms a conserved DNA-binding surface that is critical for RSC-dependent nucleosome remodeling and essential for viability in both species. Genome-wide motif analysis reveals that promoter regions are enriched in polyA sequences, whose distribution correlates with nucleosome positioning and gene expression. We show that Rsc1 preferentially binds polyA motifs and that nucleosome positioning at polyA-rich promoters depends on Rsc1 DNA binding module. These findings establish Rsc1 as a sequence-specific DNA-binding factor that mediates RSC stimulation by polyA motifs at yeast promoters. Overall, this study expands our understanding of the functional diversity of bromodomains and provides insights into the mechanisms governing RSC targeting to chromatin.

molecular biology↗

bioRxiv2024

The dual trxG/PcG protein ULTRAPETALA1 modulates H3K27me3 and directly enhances POLYCOMB REPRESSIVE COMPLEX 2 activity for fine-tuned reproductive transitions

AbstractThe antagonistic POLYCOMB (PcG) REPRESSIVE COMPLEX 2 (PRC2) and trithorax (trxG) chromatin machineries play a major role in orchestrating gene expression during the development of multicellular eukaryotes. These complexes are well known for depositing and maintaining the repressive H3K27me3 and activating H3K4me3 marks, respectively. However, the mechanisms that govern the switch between these functions remains elusive, especially in plants, whose lifelong, flexible development relies heavily on this process. Here we demonstrate that the plant specific ULTRAPETALA1 (ULT1) protein, previously reported as a trxG factor that antagonizes the PRC2 enzymatic subunit CURLY LEAF (CLF), also exhibits a repressive function, increasing H3K27me3 levels at over a thousand genes. We discovered a physical interaction between ULT1 and PRC2 components, particularly the SWINGER (SWN) enzymatic subunit. We further show that in vitro ULT1 significantly enhances the enzymatic activity of PRC2SWN, and to a lesser extent also that of PRC2CLF, corroborating our epigenomic and developmental genetic data that reveal different ULT1 activity depending on the catalytic subunit of the PRC2 complex. This study provides new insights into the relative activities of CLF and SWN and introduces a novel mechanistic framework for a chromatin switch mediated by a bivalent trxG/PcG factor. Key messageULTRAPETALA1 counteracts or promotes PRC2 activity at hundreds of developmental genes in Arabidopsis thaliana, and activates the deposition of the repressive H3K27me3 chromatin mark via direct interaction with PRC2. This is the first instance of a bivalent factor which functions as a cofactor of PRC2 HMTs.

genetics↗

bioRxiv2024

Phototropin connects blue light perception to starch metabolism in green algae

In photosynthetic organisms light acts as an environmental signal to control their development and physiology, and as energy source to drive the conversion of CO2 into carbohydrates used for growth or storage. The main storage carbohydrate in green algae is starch, which accumulates during the day and is broken down at night to meet cellular energy demands. The signalling role of light quality in the regulation of starch accumulation remains unexplored. Here, we identify PHOTOTROPIN-MEDIATED SIGNALLING KINASE 1 (PMSK1) as a key regulator of starch metabolism in Chlamydomonas reinhardtii. In its phosphorylated form (PMSK1-P), it activates GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (GAP1), promoting starch biosynthesis. We show that blue light, perceived by PHOTOTROPIN, induces PMSK1 dephosphorylation that in turn represses GAP1 mRNA levels and reduces starch accumulation. These findings reveal a novel blue light-mediated signaling pathway that advances our understanding of photoreceptor-controlled carbon metabolism in microalgae. One-Sentence SummaryBlue light perception by PHOTOTROPIN triggers kinase-mediated signaling to inhibit starch accumulation in the green alga Chlamydomonas.

plant biology↗

bioRxiv2023

The ALOG domain defines a new family of plant-specific transcription factors acting during Arabidopsis flower development

The ALOGs (Arabidopsis LIGHT-DEPENDENT SHORT HYPOCOTYLS 1 and Oryza G1) are Transcription Factors (TFs) from an evolutionarily conserved plant-specific family shown to play critical roles in meristem identity, inflorescence architecture and organ boundaries in diverse species from mosses to higher flowering plants. However, the DNA binding-specificity and molecular determinants of protein-DNA interactions of this family were uncharacterized. Using in vitro genome-wide studies, we identified the conserved DNA motif bound by ALOG proteins from the liverwort Marchantia polymorpha and the flowering plants Arabidopsis, tomato and rice. In order to determine the amino acids responsible for DNA-binding specificity, we solved the 2.1[A] structure of the ALOG DNA binding domain in complex with its cognate DNA. The ALOG DBD is an all-alpha helical domain with a structural zinc ribbon insertion and an N-terminal disordered NLS. The NLS sequence forms an integral part of the DNA binding domain and contributes to direct base read-out. To define the function of a group of redundant ALOG proteins in the model plant Arabidopsis thaliana, we generated a series of alog mutants and uncovered their participation in a gene regulatory network involving the other floral regulators LEAFY, BLADE-ON-PETIOLE and PUCHI, all active in defining boundary regions between reproductive meristems and repressing bracts development. Taken together, this work provides the biochemical and structural basis for DNA-binding specificity of an evolutionarily conserved TF family and reveals its role as a key player in defining organ boundaries in Arabidopsis. Significance StatementTranscription Factors (TFs) are key proteins that bind specific regions in the genome and regulate the expression of associated genes. Not all organisms possess the same set of TFs and some, like the ALOGs, are specific to the plant kingdom. These TFs have been shown to play important roles from mosses to flowering plants. However, it was not known what DNA motif they recognize and how they bind DNA. Here we identify this motif, we show it is widely conserved in evolution and we understand how this new type of DNA binding domain works at the structural level. In addition, we also show that several ALOG genes from Arabidopsis share a redundant function within the genetic network underlying correct floral meristem development.

plant biology↗

bioRxiv2022

The F-box cofactor UFO redirects the LEAFY floral regulator to novel cis-elements

In angiosperms, flower patterning requires the localized expression of the APETALA3 (AP3) floral homeotic gene involved in petal and stamen development. AP3 is synergistically induced by the master transcription factor (TF) LEAFY (LFY) and the F-box protein UNUSUAL FLORAL ORGANS (UFO), but the molecular mechanism underlying this synergy has remained unknown. Here we show that the connection to ubiquitination pathways suggested by the F-box domain of UFO is mostly dispensable for its function and that UFO instead acts by forming a transcriptional complex with LFY and binds to newly discovered regulatory elements. Cryo-electron microscopy explains how a LFY-UFO complex forms on these novel DNA sites due to direct interaction of UFO with LFY and DNA. Finally, we show that this complex has a deep evolutionary origin, largely predating flowering plants. This work reveals a novel mechanism of an F-box protein in directly modulating the DNA-binding specificity of a master TF.

plant biology↗

bioRxiv2021

The LEAFY floral regulator displays pioneer transcription factor properties

Pioneer transcription factors (TFs) are a special category of TFs with the capacity to bind to closed chromatin regions in which DNA is wrapped around histones and often highly methylated. Subsequently, they are able to modify the chromatin state to initiate gene expression. In plants, LEAFY (LFY) is a master floral regulator and has been suggested to act as a pioneer TF in Arabidopsis. Here, we demonstrate that LFY is able to bind both methylated and non-methylated DNA using a combination of in vitro genome-wide binding experiments and structural modeling. Comparisons between regions bound by LFY in vivo and chromatin accessibility data suggest that LFY binds a subset of regions occupied by nucleosomes. We confirm that LFY is able to bind nucleosomal DNA in vitro using reconstituted nucleosomes. Finally, we show that constitutive LFY expression in seedling tissues is sufficient to induce chromatin accessibility in the LFY direct target genes, APETALA1 and AGAMOUS. Taken together, our study suggests that LFY possesses key pioneer TF features that contribute to launch the floral gene expression program.

plant biology↗