Biology subjects

Concia, L.

Publications and source records attributed to Concia, L..

9 recordsLinked to original sources

bioRxiv2025

Entry and exit of Fragilariopsis cylindrus diatoms from the polar night: evidence for chromatin-mediated genome control

Regulation of the epigenome landscape plays a crucial role in adaptation to environmental changes. However, the molecular mechanisms by which epigenome landscapes are established and tuned to adjust the cellular status to environmental cues remain poorly understood, especially in unicellular photosynthetic eukaryotes. Polar microalgae must adapt to extreme variations in light and temperature for survival and therefore represent excellent models to understand the diversity of gene regulatory mechanisms, yet chromatin-based mechanisms have never been explored in these organisms. In this study, we combined genome-wide profiling of histone and DNA modifications with transcriptomic analyses of the marine polar diatom Fragilariopsis cylindrus upon entry and exit of a 3-month-long polar night. We show that, in agreement with its established role in transcription facilitation, histone H2B monobiquitination (H2Bub) is modulated at active genes upon prolonged darkness to light re-exposure. In contrast, histone H3 lysine 27 trimethylation (H3K27me3) and DNA cytosine methylation (CG methylation), two modifications typically associated with the silencing of genes or transposable elements (TEs), remained stable throughout the transitions, reinforcing their role in transcriptional repression, particularly at TEs but also at a few genes. We further demonstrate that H3K27me3 and DNA methylation are physically associated at TEs, probably reflecting a dual locking system enabling F.cylindrus cells to cope with the invasive nature of these genetic elements under extreme environmental conditions. These findings enhance our understanding of genome and epigenome regulation in diatoms in response to environmental variability and open new avenues for exploring the role played by chromatin-level regulation in the unique evolutionary history of polar unicellular eukaryotes.

genomics↗

bioRxiv2023

A layer cake model for plant and metazoan chromatin

Early structural studies of chromosome organisation in eukaryotic nuclei led to the identification of euchromatin and heterochromatin, two main archetypes of chromatin visible through microscopy. Subsequently, the diversity of chromatin composition along the linear genome sequence was resolved using high throughput sequencing techniques to map a multitude of chromatin marks and unravel their functional organisation. Recent analyses of human chromosome conformation capture experiments tend to point to the existence of several chromosome sub-compartments that may correspond to epigenomic variations in chromatin composition. Here, we compare genome 3D organisations in representative eukaryotic species to explore the links between chromosomal sub-compartments and chromatin marks, genome replication timing, and genomic repeats in six model organisms, including vertebrates, plants and insects. We report that the 3D organisation of chromatin in organisms with different genome content and size can be described as layers characterised by distinct chromatin marks and activities. We propose a "layer cake" model for the genome 3D organisation as a more refined view than the prevalent "two compartments" model of chromatin organisation in multi-cellular organisms.

genomics↗

bioRxiv2023

Hypometabolism to survive the long polar night in the diatom Fragilariopsis cylindrus

Diatoms, the major eukaryotic phytoplankton in polar regions, are essential to sustain Arctic and Antarctic ecosystems. As such, it is fundamental to understand the physiological mechanisms and associated molecular basis of their resilience to the long polar night. Here, we report an integrative approach revealing that in prolonged darkness, diatom cells enter a state of quiescence associated with reduced metabolic and transcriptional activity during which no cell division occurs. We propose that minimal energy is provided by respiration and degradation of protein, carbohydrate, and lipid stores and that homeostasis is maintained by autophagy in prolonged darkness. We also report internal structural changes that manifest the morphological acclimation of cells to darkness. Our results further indicate that immediately following a return to light, diatom cells are able to use photoprotective mechanisms and rapidly resume photosynthesis. Cell division resumed rates similar to those before darkness. Our study demonstrates the remarkable robustness of polar diatoms to prolonged darkness at low temperatures. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=160 SRC="FIGDIR/small/524047v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@1da578corg.highwire.dtl.DTLVardef@1a9ac5borg.highwire.dtl.DTLVardef@729265org.highwire.dtl.DTLVardef@1e94c18_HPS_FORMAT_FIGEXP M_FIG C_FIG TeaserTo survive the long winter, polar diatoms slow down metabolism and express genes to assure survival following return to light.

ecology↗

bioRxiv2021

Arabidopsis Topless-related 1 mitigates physiological damage and growth penalties of induced immunity

Transcriptional corepressors of the Topless family are important regulators of plant hormone and immunity signaling. The lack of a genome-wide profile of their chromatin associations limits understanding of transcriptional regulation in plant immune responses. Chromatin immunoprecipitation with sequencing (ChIP-seq) was performed on GFP-tagged Topless-related 1 (TPR1) expressed in Arabidopsis thaliana lines with and without constitutive immunity dependent on Enhanced Disease Susceptibility 1 (EDS1). RNA-seq profiling of pathogen-infected tpl/tpr mutants and assessments of growth and physiological parameters were employed to determine TPL/TPR roles in transcriptional immunity and defense homeostasis. TPR1 bound to promoter regions of ~1,400 genes and ~10% of the detected binding required EDS1 immunity signaling. A tpr1 tpl tpr4 (t3) mutant displayed mildly enhanced defense-related transcriptional reprogramming upon bacterial infection but not increased bacterial resistance. Bacteria or pep1 phytocytokine-challenged t3 plants exhibited, respectively, photosystem II dysfunction and exacerbated root growth inhibition. Transgenic expression of TPR1 restored the t3 physiological defects. We propose that TPR1 and TPL-family proteins function in Arabidopsis to reduce detrimental effects associated with activated transcriptional immunity.

plant biology↗

bioRxiv2020

Histone H1 protects telomeric repeats from H3K27me3 invasion in Arabidopsis

While the pivotal role of linker histone H1 in shaping nucleosome organization is well established, its functional interplays with chromatin factors along the epigenome are just starting to emerge. Here we first report that in Arabidopsis, as in mammals, H1 occupies Polycomb Repressive Complex 2 (PRC2) target genes where it favors chromatin condensation and H3K27me3 deposition. We further show that, contrasting with its conserved function in PRC2 activation at genes, H1 selectively prevents H3K27me3 accumulation at telomeres and large pericentromeric interstitial telomeric repeat (ITR) domains by restricting DNA accessibility to Telomere Repeat Binding (TRB) proteins, a group of H1-related Myb factors mediating PRC2 cis recruitment. This study unveils a mechanistic framework by which H1 avoids the formation of gigantic H3K27me3-rich domains at telomeric sequences and contributes to safeguard nucleus architecture. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/402172v5_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@13cf29dorg.highwire.dtl.DTLVardef@5c5c86org.highwire.dtl.DTLVardef@1be7516org.highwire.dtl.DTLVardef@f935cb_HPS_FORMAT_FIGEXP M_FIG Teano et al. report that that linker histone H1 and a group of H1-related telomeric proteins interplay to selectively influence the Polycomb repressive landscape at genes and telomeric repeats in Arabidopsis. These findings provide a mechanistic framework by which H1 influences the epigenome and nuclear organization in a sequence-specific manner. C_FIG HighlightsO_LIH1 promotes PRC2 activity and limits accessibility at a majority of genes C_LIO_LIH1 prevents PRC2 activity at telomeric DNA sequences C_LIO_LIPRC2 repression is achieved by restricting accessibility to TRB proteins C_LIO_LIH1 orchestrates the spatial organization of telomeres and interstitial telomeres (ITRs) C_LI

molecular biology↗

bioRxiv2020

New insights into homoeologous copy number variations in the hexaploid wheat genome

Bread wheat is an allohexaploid species originating from two successive and recent rounds of hybridization between three diploid species that were very similar in terms of chromosome number, genome size, TE content, gene content and synteny. As a result, it has long been considered that most of the genes were in three pairs of homoeologous copies. However, these so-called triads represent only one half of wheat genes, while the remaining half belong to homoeologous groups with various number of copies across subgenomes. In this study, we examined and compared the distribution, conservation, function, expression and epigenetic profiles of triads with homoeologous groups having undergone a deletion (dyads) or a duplication (tetrads) in one subgenome. We show that dyads and tetrads are mostly located in distal regions and have lower expression level and breadth than triads. Moreover, they are enriched in functions related to adaptation and more associated with the repressive H3K27me3 modification. Altogether, these results suggest that triads mainly correspond to housekeeping genes and are part of the core genome, while dyads and tetrads belong to the Triticeae dispensable genome. In addition, by comparing the different categories of dyads and tetrads, we hypothesize that, unlike most of the allopolyploid species, subgenome dominance and biased fractionation are absent in hexaploid wheat. Differences observed between the three subgenomes are more likely related to two successive and ongoing waves of post-polyploid diploidization, that had impacted A and B more significantly than D, as a result of the evolutionary history of hexaploid wheat. Core ideasOnly one half of hexaploid wheat genes are in triads, i.e. in a 1:1:1 ratio across subgenomes Triads are likely part of the core genome; dyads and tetrads belong to the dispensable genome Subgenome dominance and biased fractionation are absent in hexaploid wheat Subgenome differences are related to two successive waves of post-polyploid diploidization

genomics↗

bioRxiv2020

Genome-wide chromatin binding of transcriptional corepressor Topless-related 1 in Arabidopsis

Timely and specific regulation of gene expression is critical for plant responses to environmental and developmental cues. Transcriptional coregulators have emerged as important factors in gene expression control, although they lack DNA-binding domains and the mechanisms by which they are recruited to and function at the chromatin are poorly understood. Plant Topless-related 1 (TPR1), belonging to a family of transcriptional corepressors found across eukaryotes, contributes to immunity signaling in Arabidopsis thaliana and wild tobacco. We performed chromatin immunoprecipitation and sequencing (ChIP-seq) on an Arabidopsis TPR1-GFP expressing transgenic line to characterize genome-wide TPR1-chromatin associations. The analysis revealed [~]1400 genes bound by TPR1, with the majority of binding sites located at gene upstream regions. Among the TPR1 bound genes, we find not only regulators of immunity but also genes controlling growth and development. To support further analysis of TPR1-chromatin complexes and other transcriptional corepressors in plants, we provide two ways to access the processed ChIP-seq data and enable their broader use by the research community.

plant biology↗

bioRxiv2019

Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in histone H3 Lys-4 trimethylation independently from histone H2B monoubiquitination

The functional determinants of histone H3 Lys-4 trimethylation (H3K4me3), their potential dependency on histone H2B monoubiquitination (H2Bub) and their contribution to defining transcriptional regimes are poorly defined in plant systems. Unlike in S. cerevisiae, where a single SET1 protein catalyzes H3 Lys-4 trimethylation as part of COMPASS (COMPlex of proteins ASsociated with Set1), in Arabidopsis thaliana this activity involves multiple histone methyltransferases (HMTs). Among these, the plant-specific SDG2 (SET DOMAIN GROUP2) has a prominent role. We report that SDG2 co-regulates hundreds of genes with SWD2-like b (S2Lb), a plant ortholog of the Swd2 axillary subunit of yeast COMPASS. S2Lb co-purifies with the AtCOMPASS core subunit WDR5 from a high-molecular weight complex, and both S2Lb and SDG2 directly influence H3K4me3 enrichment over highly transcribed genes. S2Lb knockout triggers pleiotropic developmental phenotypes at the vegetative and reproductive stages, including reduced fertility and seed dormancy. Notwithstanding, s2lb seedlings display little transcriptomic defects as compared to the large repertoire of genes targeted by S2Lb, SDG2 or H3 Lys-4 trimethylation, suggesting that H3K4me3 enrichment is important for optimal gene induction during cellular transitions rather than for determining on/off transcriptional status. Moreover, unlike in budding yeast, most of the S2Lb and H3K4me3 genomic distribution does not rely on a trans-histone crosstalk with histone H2B monoubiquitination. Collectively, this study unveils that the evolutionarily conserved COMPASS-like complex has been coopted by the plant-specific SDG2 HMT and mediates H3K4me3 deposition through an H2Bub-independent pathway in Arabidopsis.

plant biology↗

bioRxiv2016

Repliscan: a tool for classifying replication timing regions

BackgroundReplication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density, and possible results make traditional ChIP-Seq analysis methods inappropriate for use with replicating timing.\n\nResultsTo accurately detect and classify regions of replication across the genome, we present Repliscan. Repliscan robustly normalizes, automatically removes outlying and uninformative data points, and classifies Repli-seq signals into discrete combinations of replication signatures. The quality control steps and self-fitting methods makes Repliscan generally applicable and superior to previous methods with thresholds inapplicable to different genomes.\n\nConclusionsRepliscan is simple and effective to use on organisms with different magnitude genome sizes and sequencing coverage as low as 2.4x.

bioinformatics↗