The Chaperone NASP Contributes to De Novo Deposition of the Centromeric Histone Variant CENH3 in Arabidopsis Early Embryogenesis

The centromere is an essential chromosome region where the kinetochore is formed to control equal chromosome distribution during cell division. The centromere-specific histone H3 variant CENH3 (also called CENP-A) is a prerequisite for the kinetochore formation. Since CENH3 evolves rapidly, associated factors, including histone chaperones mediating the deposition of CENH3 on the centromere, are thought to act through species-specific amino-acid sequences. The functions and interaction networks of CENH3 and histone chaperons have been well-characterized in animals and yeasts. However, molecular mechanisms involved in recognition and deposition of CENH3 are still unclear in plants. Here, we used a swapping strategy between domains of CENH3 of Arabidopsis thaliana and the liverwort Marchantia polymorpha to identify specific regions of CENH3 involved in targeting the centromeres and interacting with the general histone H3 chaperone, NASP (nuclear autoantigenic sperm protein). CENH3's LoopN-α1 region was necessary and sufficient for the centromere targeting in cooperation with the α2 region and was involved in interaction with NASP in cooperation with αN, suggesting a species-specific CENH3 recognition. In addition, by generating an Arabidopsis nasp knockout mutant in the background of a fully fertile GFP-CENH3/cenh3-1 line, we found that NASP was implicated for de novo CENH3 deposition after fertilization and thus for early embryo development. Our results imply that the NASP mediates the supply of CENH3 in the context of the rapidly evolving centromere identity in land plants.

Two imprinted genes primed by DEMETER in the central cell and activated by WRKY10 in the endosperm

The early development of the endosperm is crucial for balancing the allocation of maternal nutrients to offspring. This process is believed to be evolutionarily associated with genomic imprinting, resulting in parentally biased allelic gene expression. Beyond FertilizationIndependentSeed (FIS) genes, the number of imprinted genes involved in early endosperm development and seed size determination remains limited. This study introduces two early endosperm-expressed HAIKU (IKU) downstream Candidate F-box 1 (ICF1) and ICF2, as maternally expressed imprinted genes (MEGs). Although these genes are also demethylated by DEMETER (DME) in the central cell, their activation differs from the direct DME-mediated activation seen in classical MEGs such as the FIS genes. Instead, ICF maternal alleles carry pre-established hypomethylation in their promoters, priming them for activation by the WRKY10 transcription factor in the endosperm. On the contrary, paternal alleles are predominantly suppressed by CG methylation. Furthermore, we find that ICF genes partially contribute to the small seed size observed in iku mutants. Our discovery reveals a two-step regulatory mechanism that highlights the important role of conventional transcription factors in the activation of imprinted genes, which was previously not fully recognized. Therefore, the mechanism provides a new dimension to understand the transcriptional regulation of imprinting in plant reproduction and development.

Identification of plants' functional counterpart of the metazoan mediator of DNA Damage checkpoint 1

Induction of DNA damage triggers rapid phosphorylation of the histone H2A.X (γH2A.X). In animals, mediator of DNA damage checkpoint 1 (MDC1) binds γH2A.X through a tandem BRCA1 carboxyl-terminal (tBRCT) domain and mediates recruitment of downstream effectors of DNA damage response (DDR). However, readers of this modification in plants have remained elusive. We show that from the Arabidopsis BRCT domain proteome, BCP1-4 proteins with tBRCT domains are involved in DDR. Through its tBRCT domain BCP4 binds γH2A.X in vitro and localizes to DNA damage-induced foci in an H2A.X-dependent manner. BCP4 also contains a domain that interacts directly with NBS1 and thus acts as a functional counterpart of MDC1. We also show that BCP1, that contains two tBRCT domains, co-localizes with γH2A.X but it does not bind γH2A.X suggesting functional similarity with human PAXIP1. A phylogenetic analysis supports that PAXIP1 and MDC1 in metazoa and their plant counterparts evolved independently from common ancestors with tBRCT domains. Collectively, our study reveals missing components and provides mechanistic and evolutionary insights into plant DDR.

Micropillar arrays, wide window acquisition and AI-based data analysis improve comprehensiveness in multiple proteomic applications

Comprehensive proteomic analysis is essential to elucidate molecular pathways and protein functions. Despite tremendous progress in proteomics, current studies still suffer from limited proteomic coverage and dynamic range. Here, we utilize micropillar array columns (µPACs) together with wide-window acquisition and the AI-based CHIMERYS search engine to achieve excellent proteomic comprehensiveness for bulk proteomics, affinity purification mass spectrometry and single cell proteomics. Our data show that µPACs identify ≤50% more peptides and ≤24% more proteins, while offering improved throughput, which is critical for large (clinical) proteomics studies. Combining wide precursor isolation widths of m/z 4-12 with the CHIMERYS search engine identified +51-74% and +59-150% more proteins and peptides, respectively, for single cell, co-immunoprecipitation, and multi-species samples over a conventional workflow at well-controlled false discovery rates. The workflow further offers excellent precision, with CVs <7% for low input bulk samples, and accuracy, with deviations <10% from expected fold changes for regular abundance two-proteome mixes. Compared to a conventional workflow, our entire optimized platform discovered 92% more potential interactors in a protein-protein interaction study on the chromatin remodeler Smarca5/Snf2h. These include previously described Smarca5 binding partners and undescribed ones including Arid1a, another chromatin remodeler with key roles in neurodevelopmental and malignant disorders.

Paternal imprinting in Marchantia polymorpha

We are becoming aware of a growing number of organisms that do not express genetic information equally from both parents as a result of an epigenetic phenomenon called genomic imprinting. Recently, it was shown that the entire paternal genome is repressed during the diploid phase of the life cycle of the liverwort Marchantia polymorpha. The deposition of the repressive epigenetic mark H3K27me3 on the male pronucleus is responsible for the imprinted state, which is reset by the end of meiosis. Here, we put these recent reports in perspective of other forms of imprinting and discuss the potential mechanisms of imprinting in bryophytes and the causes of its evolution.

Cell cycle status of male and female gametes during Arabidopsis reproduction

Fertilization in Arabidopsis (Arabidopsis thaliana) is a highly coordinated process that begins with a pollen tube delivering the 2 sperm cells into the embryo sac. Each sperm cell can then fertilize either the egg or the central cell to initiate embryo or endosperm development, respectively. The success of this double fertilization process requires a tight cell cycle synchrony between the male and female gametes to allow karyogamy (nuclei fusion). However, the cell cycle status of the male and female gametes during fertilization remains elusive as DNA quantification and DNA replication assays have given conflicting results. Here, to reconcile these results, we quantified the DNA replication state by DNA sequencing and performed microscopic analyses of fluorescent markers covering all phases of the cell cycle. We show that male and female Arabidopsis gametes are both arrested prior to DNA replication at maturity and initiate their DNA replication only during fertilization.

The ancestral chromatin landscape of land plants

Recent studies have shown that correlations between chromatin modifications and transcription vary among eukaryotes. This is the case for marked differences between the chromatin of the moss Physcomitrium patens and the liverwort Marchantia polymorpha. Mosses and liverworts diverged from hornworts, altogether forming the lineage of bryophytes that shared a common ancestor with land plants. We aimed to describe chromatin in hornworts to establish synapomorphies across bryophytes and approach a definition of the ancestral chromatin organization of land plants. We used genomic methods to define the 3D organization of chromatin and map the chromatin landscape of the model hornwort Anthoceros agrestis. We report that nearly half of the hornwort transposons were associated with facultative heterochromatin and euchromatin and formed the center of topologically associated domains delimited by protein coding genes. Transposons were scattered across autosomes, which contrasted with the dense compartments of constitutive heterochromatin surrounding the centromeres in flowering plants. Most of the features observed in hornworts are also present in liverworts or in mosses but are distinct from flowering plants. Hence, the ancestral genome of bryophytes was likely a patchwork of units of euchromatin interspersed within facultative and constitutive heterochromatin. We propose this genome organization was ancestral to land plants.

Plant reproduction: Ancient origins of male germline differentiation

Despite the wide diversity in male sexual development across land plants, new work reveals the conservation of a heterodimer of transcription factors as master regulators of the male germline.

The chromatin source-sink hypothesis: a shared mode of chromatin-mediated regulations

We propose that several chromatin-mediated regulatory processes are dominated by source-sink relationships in which factors operate as 'sources' to produce or provide a resource and compete with each other to occupy separate 'sinks'. In this model, large portions of genomic DNA operate as 'sinks', which are filled by 'sources', such as available histone variants, covalent modifications to histones, the readers of these modifications and non-coding RNAs. Competing occupation for the sinks by different sources leads to distinct states of genomic equilibrium in differentiated cells. During dynamic developmental events, such as sexual reproduction, we propose that dramatic and rapid reconfiguration of source-sink relationships modifies chromatin states. We envision that re-routing of sources could occur by altering the dimensions of the sink, by reconfiguration of existing sink occupation or by varying the size of the source, providing a central mechanism to explain a plethora of epigenetic phenomena, which contribute to phenotypic variegation, zygotic genome activation and nucleolar dominance.

The Polycomb repressive complex 2 deposits H3K27me3 and represses transposable elements in a broad range of eukaryotes

The mobility of transposable elements (TEs) contributes to evolution of genomes. Their uncontrolled activity causes genomic instability; therefore, expression of TEs is silenced by host genomes. TEs are marked with DNA and H3K9 methylation, which are associated with silencing in flowering plants, animals, and fungi. However, in distantly related groups of eukaryotes, TEs are marked by H3K27me3 deposited by the Polycomb repressive complex 2 (PRC2), an epigenetic mark associated with gene silencing in flowering plants and animals. The direct silencing of TEs by PRC2 has so far only been shown in one species of ciliates. To test if PRC2 silences TEs in a broader range of eukaryotes, we generated mutants with reduced PRC2 activity and analyzed the role of PRC2 in extant species along the lineage of Archaeplastida and in the diatom P. tricornutum. In this diatom and the red alga C. merolae, a greater proportion of TEs than genes were repressed by PRC2, whereas a greater proportion of genes than TEs were repressed by PRC2 in bryophytes. In flowering plants, TEs contained potential cis-elements recognized by transcription factors and associated with neighbor genes as transcriptional units repressed by PRC2. Thus, silencing of TEs by PRC2 is observed not only in Archaeplastida but also in diatoms and ciliates, suggesting that PRC2 deposited H3K27me3 to silence TEs in the last common ancestor of eukaryotes. We hypothesize that during the evolution of Archaeplastida, TE fragments marked with H3K27me3 were selected to shape transcriptional regulation, controlling networks of genes regulated by PRC2.

Variation is important: Warranting chromatin function and dynamics by histone variants

The chromatin of flowering plants exhibits a wide range of sequence variants of the core and linker histones. Recent studies have demonstrated that specific histone variant enrichment, combined with post-translational modifications (PTMs) of histones, defines distinct chromatin states that impact specific chromatin functions. Chromatin remodelers are emerging as key regulators of histone variant dynamics, contributing to shaping chromatin states and regulating gene transcription in response to environment. Recognizing the histone variants by their specific readers, controlled by histone PTMs, is crucial for maintaining genome and chromatin integrity. In addition, various histone variants have been shown to play essential roles in remodeling chromatin domains to facilitate important programmed transitions throughout the plant life cycle. In this review, we discuss recent findings in this exciting field of research, which holds immense promise for many surprising discoveries related to the evolution of complexity in plant organization through a seemingly simple protein family.

Histone variants shape chromatin states in Arabidopsis

How different intrinsic sequence variations and regulatory modifications of histones combine in nucleosomes remain unclear. To test the importance of histone variants in the organization of chromatin we investigated how histone variants and histone modifications assemble in the Arabidopsis thaliana genome. We showed that a limited number of chromatin states divide euchromatin and heterochromatin into several subdomains. We found that histone variants are as significant as histone modifications in determining the composition of chromatin states. Particularly strong associations were observed between H2A variants and specific combinations of histone modifications. To study the role of H2A variants in organizing chromatin states we determined the role of the chromatin remodeler DECREASED IN DNA METHYLATION (DDM1) in the organization of chromatin states. We showed that the loss of DDM1 prevented the exchange of the histone variant H2A.Z to H2A.W in constitutive heterochromatin, resulting in significant effects on the definition and distribution of chromatin states in and outside of constitutive heterochromatin. We thus propose that dynamic exchanges of histone variants control the organization of histone modifications into chromatin states, acting as molecular landmarks.

Elongation factor 1 is a component of the Arabidopsis RNA polymerase II elongation complex and associates with a subset of transcribed genes

Elongation factors modulate the efficiency of mRNA synthesis by RNA polymerase II (RNAPII) in the context of chromatin, thus contributing to implement proper gene expression programmes. The zinc-finger protein elongation factor 1 (ELF1) is a conserved transcript elongation factor (TEF), whose molecular function so far has not been studied in plants. Using biochemical approaches, we examined the interaction of Arabidopsis ELF1 with DNA and histones in vitro and with the RNAPII elongation complex in vivo. In addition, cytological assays demonstrated the nuclear localisation of the protein, and by means of double-mutant analyses, interplay with genes encoding other elongation factors was explored. The genome-wide distribution of ELF1 was addressed by chromatin immunoprecipitation. ELF1 isolated from Arabidopsis cells robustly copurified with RNAPII and various other elongation factors including SPT4-SPT5, SPT6, IWS1, FACT and PAF1C. Analysis of a CRISPR-Cas9-mediated gene editing mutant of ELF1 revealed distinct genetic interactions with mutants deficient in other elongation factors. Moreover, ELF1 associated with genomic regions actively transcribed by RNAPII. However, ELF1 occupied only c. 33% of the RNAPII transcribed loci with preference for inducible rather than constitutively expressed genes. Collectively, these results establish that Arabidopsis ELF1 shares several characteristic attributes with RNAPII TEFs.

Seminars in cell and development biology on histone variants remodelers of H2A variants associated with heterochromatin

Variants of the histone H2A occupy distinct locations in the genome. There is relatively little known about the mechanisms responsible for deposition of specific H2A variants. Notable exceptions are chromatin remodelers that control the dynamics of H2A.Z at promoters. Here we review the steps that identified the role of a specific class of chromatin remodelers, including LSH and DDM1 that deposit the variants macroH2A in mammals and H2A.W in plants, respectively. The function of these remodelers in heterochromatin is discussed together with their multiple roles in genome stability.

Cellular dynamics of coenocytic endosperm development in Arabidopsis thaliana

After double fertilization, the endosperm in the seeds of many flowering plants undergoes repeated mitotic nuclear divisions without cytokinesis, resulting in a large coenocytic endosperm that then cellularizes. Growth during the coenocytic phase is strongly associated with the final seed size; however, a detailed description of the cellular dynamics controlling the unique coenocytic development in flowering plants has remained elusive. By integrating confocal microscopy live-cell imaging and genetics, we have characterized the entire development of the coenocytic endosperm of Arabidopsis thaliana including nuclear divisions, their timing intervals, nuclear movement and cytoskeleton dynamics. Around each nucleus, microtubules organize into aster-shaped structures that drive actin filament (F-actin) organization. Microtubules promote nuclear movement after division, while F-actin restricts it. F-actin is also involved in controlling the size of both the coenocytic endosperm and the mature seed. The characterization of cytoskeleton dynamics in real time throughout the entire coenocyte endosperm period provides foundational knowledge of plant coenocytic development, insights into the coordination of F-actin and microtubules in nuclear dynamics, and new opportunities to increase seed size and our food security.

Histone H3.3 deposition in seed is essential for the post-embryonic developmental competence in Arabidopsis

The acquisition of germination and post-embryonic developmental ability during seed maturation is vital for seed vigor, an important trait for plant propagation and crop production. How seed vigor is established in seeds is still poorly understood. Here, we report the crucial function of Arabidopsis histone variant H3.3 in endowing seeds with post-embryonic developmental potentials. H3.3 is not essential for seed formation, but loss of H3.3 results in severely impaired germination and post-embryonic development. H3.3 exhibits a seed-specific 5' gene end distribution and facilitates chromatin opening at regulatory regions in seeds. During germination, H3.3 is essential for proper gene transcriptional regulation. Moreover, H3.3 is constantly loaded at the 3' gene end, correlating with gene body DNA methylation and the restriction of chromatin accessibility and cryptic transcription at this region. Our results suggest a fundamental role of H3.3 in initiating chromatin accessibility at regulatory regions in seed and licensing the embryonic to post-embryonic transition.

The efficacy and safety of macitentan in Fontan-palliated patients: results of the 52-week randomised, placebo-controlled RUBATO trial

Background

The clinical utility and long-term effects of endothelin receptor antagonists (ERAs) in Fontan-palliated patients remain unclear and there are currently no approved therapies. A decline in peak VO2 between consecutive cardiopulmonary exercise tests (CPETs) is highly prognostic for death or transplant in adult Fontan patients, hence its use as a primary endpoint in clinical trials of ERAs in patients with Fontan circulation.

Purpose

The RUBATO trial aimed to assess the efficacy and safety of macitentan, an endothelin receptor antagonist, in Fontan-palliated patients over 52 weeks.

Methods

In the multicentre, double-blind, randomised, placebo-controlled, phase 3 RUBATO trial, Fontan-palliated patients were randomised 1:1 to macitentan 10 mg once-daily or placebo for 52 weeks. Eligible patients were aged ≥12 years, in New York Heart Association functional class II or III, had no limitations for CPET (including no pacemakers), had undergone lateral tunnel or extracardiac conduit Fontan (total cavopulmonary connection) &gt;1 year before screening and showed no signs of Fontan failure or clinical deterioration within 3 months before screening. Primary efficacy endpoint was change in peak VO2 from baseline to week 16. Secondary endpoints were change in peak VO2 from baseline over 52 weeks and change in mean count per minute of daily physical activity from baseline to week 16 as measured by an accelerometer. Adverse events were also assessed.

Results

137 patients were randomised to macitentan (n=68) or placebo (n=69). 92.7% of patients completed 52 weeks of double-blind treatment: 7 and 3 patients prematurely discontinued study treatment in macitentan and placebo arms, respectively. Patient baseline characteristics are shown in Table 1. At week 16, the mean (SD) change from baseline in peak VO2 was –0.16 (2.86) with macitentan vs –0.67 (2.66) mL/kg/min with placebo (median unbiased estimate of the difference between macitentan and placebo: 0.62 mL/kg/min [99% repeated confidence interval –0.62; 1.85], p=0.1930). No treatment effect was observed in the two secondary endpoints (Table 2): mean (SD) count per minute of daily physical activity decreased from baseline to week 16 by 3.02 (92.44) with macitentan and by 14.34 (117.56) with placebo (p=0.4512). The most common AEs were headache (10.3% vs 8.7% on placebo), nasopharyngitis (5.9% vs 4.3%), and pyrexia (5.9% vs 4.3%). AEs leading to treatment discontinuation were reported in 3 (4.4%) and 1 (1.4%) of macitentan and placebo patients.

Conclusion

The 52-week RUBATO trial provides an important addition to data on the clinical utility of ERAs in Fontan-palliated patients. The primary efficacy endpoint was not met and no treatment effect was observed for the two secondary endpoints. Macitentan was well tolerated; safety findings were consistent with the known safety profile of macitentan 10 mg.

Funding Acknowledgement

Type of funding sources: Private company. Main funding source(s): Actelion Pharmaceuticals Ltd., a Janssen pharmaceutical company of Johnson & Johnson.

Polycomb-mediated repression of paternal chromosomes maintains haploid dosage in diploid embryos of Marchantia

Complex mechanisms regulate gene dosage throughout eukaryotic life cycles. Mechanisms controlling gene dosage have been extensively studied in animals, however it is unknown how generalizable these mechanisms are to diverse eukaryotes. Here, we use the haploid plant Marchantia polymorpha to assess gene dosage control in its short-lived diploid embryo. We show that throughout embryogenesis, paternal chromosomes are repressed resulting in functional haploidy. The paternal genome is targeted for genomic imprinting by the Polycomb mark H3K27me3 starting at fertilization, rendering the maternal genome in control of embryogenesis. Maintaining haploid gene dosage by this new form of imprinting is essential for embryonic development. Our findings illustrate how haploid-dominant species can regulate gene dosage through paternal chromosome inactivation and initiates the exploration of the link between life cycle history and gene dosage in a broader range of organisms.

Modeling Active Non-Markovian Oscillations

Modeling noisy oscillations of active systems is one of the current challenges in physics and biology. Because the physical mechanisms of such processes are often difficult to identify, we propose a linear stochastic model driven by a non-Markovian bistable noise that is capable of generating self-sustained periodic oscillation. We derive analytical predictions for most relevant dynamical and thermodynamic properties of the model. This minimal model turns out to describe accurately bistablelike oscillatory motion of hair bundles in bullfrog sacculus, extracted from experimental data. Based on and in agreement with these data, we estimate the power required to sustain such active oscillations to be of the order of 100  k_{B}T per oscillation cycle.

Which field of research would Gregor Mendel choose in the 21st century?

Gregor Mendel's work on segregation of traits in plants established the basic methodology and rules of genetics. The interruption of Mendel's research activities in 1870 impeded the immediate recognition of the value of his work until the dawn of the 20th century. Only then were his founding laws of genetics validated, propelling the development of biological research toward the birth of molecular biology in the second half of the 20th century. While molecular plant genetics can be viewed as the spiritual heir of Mendel's research, one might wonder whether in the 21st century Gregor Mendel would prefer to practice scientific approaches other than molecular genetics such as population genetics, comparative genomics, or the emerging field of evo-chromo. In this perspective, I review aspects of these fields that might have attracted or perplexed a 21st century Mendel.

Phosphorylation of the FACT histone chaperone subunit SPT16 affects chromatin at RNA polymerase II transcriptional start sites in Arabidopsis

The heterodimeric histone chaperone FACT, consisting of SSRP1 and SPT16, contributes to dynamic nucleosome rearrangements during various DNA-dependent processes including transcription. In search of post-translational modifications that may regulate the activity of FACT, SSRP1 and SPT16 were isolated from Arabidopsis cells and analysed by mass spectrometry. Four acetylated lysine residues could be mapped within the basic C-terminal region of SSRP1, while three phosphorylated serine/threonine residues were identified in the acidic C-terminal region of SPT16. Mutational analysis of the SSRP1 acetylation sites revealed only mild effects. However, phosphorylation of SPT16 that is catalysed by protein kinase CK2, modulates histone interactions. A non-phosphorylatable version of SPT16 displayed reduced histone binding and proved inactive in complementing the growth and developmental phenotypes of spt16 mutant plants. In plants expressing the non-phosphorylatable SPT16 version we detected at a subset of genes enrichment of histone H3 directly upstream of RNA polymerase II transcriptional start sites (TSSs) in a region that usually is nucleosome-depleted. This suggests that some genes require phosphorylation of the SPT16 acidic region for establishing the correct nucleosome occupancy at the TSS of active genes.

One residue-one function

The histone H3.1 variant deposited at replication forks docks DNA repair machinery.

Diversification of chromatin organization in eukaryotes

Our knowledge of the chromatin landscape and its regulation was originally discovered using yeast and a limited number of animals models. A wealth of studies in model plants now strongly demonstrates the conservation of certain features while illuminating the diversification of others. Here we summarize recent advances that describe specific features of chromatin organization of transcriptional units and specific regulation of heterochromatin in flowering plants. We highlight the importance of transcriptional regulation in plant chromatin organization and the need to investigate a more diverse range of species to understand the chromatin landscape in eukaryotes.

Identification of the sex-determining factor in the liverwort Marchantia polymorpha reveals unique evolution of sex chromosomes in a haploid system

Sex determination is a central process for sexual reproduction and is often regulated by a sex determinant encoded on a sex chromosome. Rules that govern the evolution of sex chromosomes via specialization and degeneration following the evolution of a sex determinant have been well studied in diploid organisms. However, distinct predictions apply to sex chromosomes in organisms where sex is determined in the haploid phase of the life cycle: both sex chromosomes, female U and male V, are expected to maintain their gene functions, even though both are non-recombining. This is in contrast to the X-Y (or Z-W) asymmetry and Y (W) chromosome degeneration in XY (ZW) systems of diploids. Here, we provide evidence that sex chromosomes diverged early during the evolution of haploid liverworts and identify the sex determinant on the Marchantia polymorpha U chromosome. This gene, Feminizer, encodes a member of the plant-specific BASIC PENTACYSTEINE transcription factor family. It triggers female differentiation via regulation of the autosomal sex-determining locus of FEMALE GAMETOPHYTE MYB and SUPPRESSOR OF FEMINIZATION. Phylogenetic analyses of Feminizer and other sex chromosome genes indicate dimorphic sex chromosomes had already been established 430 mya in the ancestral liverwort. Feminizer also plays a role in reproductive induction that is shared with its gametolog on the V chromosome, suggesting an ancestral function, distinct from sex determination, was retained by the gametologs. This implies ancestral functions can be preserved after the acquisition of a sex determination mechanism during the evolution of a dominant haploid sex chromosome system.

The evolution of imprinting in plants: beyond the seed

Genomic imprinting results in the biased expression of alleles depending on if the allele was inherited from the mother or the father. Despite the prevalence of sexual reproduction across eukaryotes, imprinting is only found in placental mammals, flowering plants, and some insects, suggesting independent evolutionary origins. Numerous hypotheses have been proposed to explain the selective pressures that favour the innovation of imprinted gene expression and each differs in their experimental support and predictions. Due to the lack of investigation of imprinting in land plants, other than angiosperms with triploid endosperm, we do not know whether imprinting occurs in species lacking endosperm and with embryos developing on maternal plants. Here, we discuss the potential for uncovering additional examples of imprinting in land plants and how these observations may provide additional support for one or more existing imprinting hypotheses.

The genetic and epigenetic landscape of the Arabidopsis centromeres

Centromeres attach chromosomes to spindle microtubules during cell division and, despite this conserved role, show paradoxically rapid evolution and are typified by complex repeats. We used long-read sequencing to generate the Col-CEN Arabidopsis thaliana genome assembly that resolves all five centromeres. The centromeres consist of megabase-scale tandemly repeated satellite arrays, which support CENTROMERE SPECIFIC HISTONE H3 (CENH3) occupancy and are densely DNA methylated, with satellite variants private to each chromosome. CENH3 preferentially occupies satellites that show the least amount of divergence and occur in higher-order repeats. The centromeres are invaded by ATHILA retrotransposons, which disrupt genetic and epigenetic organization. Centromeric crossover recombination is suppressed, yet low levels of meiotic DNA double-strand breaks occur that are regulated by DNA methylation. We propose that Arabidopsis centromeres are evolving through cycles of satellite homogenization and retrotransposon-driven diversification.

Corona-specific health literacy: a longitudinal study in the German-speaking part of Switzerland

Background

The COVID-19 pandemic is accompanied by an infodemic, i.e. a flood of conflicting infor-mation through numerous channels and mis-/disinformation. To cope with these challenges and to make sound health-decisions, people need skills that enable them to access, under-stand, appraise, and use health-related information, i.e. adequate health literacy (HL). Thus, the present study investigates how people in the German-speaking part of Switzerland handle with Corona-specific information, what their difficulties are and what potential improvement measures could be.

Methods

Three representative samples of 1'000 individuals each were interviewed online in early sum-mer, autumn and winter 2020 using a modified version of the HLS-EU-Q16 questionnaire. Da-ta were analyzed using descriptive methods and an index for Corona-specific HL was built.

Results

In early summer, 55% of the German-speaking Swiss population reported adequate Corona-specific HL, with a tendency to increase with the duration of the pandemic (autumn: 62%; winter: 63%). Nonetheless, a great proportion reported difficulties, especially with assessing the trustworthiness of information from the media. With the progress of the pandemic, partici-pants felt less informed and the proportion of (very) poorly informed increased from 8% in early summer to 16% in winter 2020.

Conclusions

Participants often found it difficult to assess the trustworthiness of information on COVID-19 and to derive consequences for their own behavior. Hence, it is important that all relevant stakeholders such as health organizations, authorities and media support the population with tools to facilitate the use of health information and to empower them to take responsibility for their own health as well as for their community.

Key messages

People need adequate HL to handle the amount and complexity of COVID-19-related information. Relevant stakeholders need to take over responsibility to empower the population and to enhance their HL.

Aortic Z-scores in paediatric patients with marfan syndrome and other hereditary thoracic aortic diseases

Introduction

Marfan syndrome (MFS) and other hereditary thoracic aortic diseases (HTAD) are characterized by dilatation of the aorta caused by mutations in the FBN1-gene and other aortic genes. To prevent aortic dissection or rupture, patients are prophylactically treated by aortic surgery. Different z-scores of the aortic root are used for diagnosis and monitoring in paediatric patients.

Purpose

What are the differences between the various aortic Z-scores in their use for monitoring, assessing the severity of the aortic disease, and establishing the indication for surgery in this age group?

Methods

We retrospectively analyzed the diameters of aortic roots measured by echocardiography in 180 children and young adults (1 month to 25 years) with MFS and other HTADs presenting at our specialized outpatient clinic between January 2010 and August 2019. Thirteen patients underwent surgery during this period and 121 were monitored for a duration of one up to nine years. Five aortic z-scores were compared: Pettersen, Gautier, Cantinotti, Lopez, Boston. For evaluation of the severity of dilatation and indication for surgery, we used the last value before operation or the last follow-up value. For monitoring, we used the difference between the first and the last value. For comparison of the z-scores, values of the sinuses of Valsalva were analyzed. We investigated theoretic backgrounds and reference groups of each z-score.

Results

The z-score values differ significantly (p&lt;0,001) for each score. The medians reach from 2.06 to 3.45, in operated patients 4.90 to 8.52, non-operated patients 1.86 to 3.31 (p&lt;0,001). 93 aortic diameters to 136 were classified as dilatated (z-score ≥2). There were significant differences of almost all z-scores in the comparison with one another. During follow-up, the increase of the median z-score ranged from 0.11 to 0.24, in operated patients from 0.73 to 1.93, in non-operated patients from 0.02 to 0.21, respectively. The median monitoring time was 4.14 years and 2.93 years, for patients monitored for more than one year and all patients, respectively. In the operated subgroup, a weak correlation showed that the longer the monitoring time and the closer the surgery arrived, the faster the z-scores rose. Lopez, Boston and Cantinotti have higher values and label a value quicker than dilatated, but also reveal the severity of dilatation and the potential necessity of surgery.

Conclusions

Our data show that the various z-scores differ significantly. No z-score was superior regarding above-mentioned aspects, their differences in monitoring were small. However, it seems important to consistently use one same z-score. Expectedly, z-score values of each score were higher in the operated subgroup than in patients without surgery. However, there is no z-score value that determines a clear-cut indication for surgery.

Funding Acknowledgement

Type of funding sources: None.

First results of a regenerative transcatheter heart valve implant from autologous tissue in a long-term animal model

Background

The perfect heart valve replacement remains to be found regarding longevity, freedom of anticoagulation and availability in each size.

Purpose

Examination of a new technique for a regenerative, immunocompatible, transcatheter pulmonary valve implant from autologous pericardium was performed in an adult sheep model.

Methods

For each valve implant a pericardial patch was harvested by left antero-lateral mini-thoracotomy, placed on one of two slightly different shaped moulds either made of acrylic glass (AG) or printed in a 3D Printer (3D) and transferred into a container filled with a biological crosslinking agent at a non-toxic concentration to stabilize the given shape. After a median of 3 days (d) they were unpacked, sewn into a self-expandable nitinol stent with a diameter of 26 or 30mm and implanted via the jugular vein into pulmonary valve position of the same animal using a custom-made delivery system (1). Three groups (Gr) were planned: Gr 1) 4 animals with at least 6 d of crosslinking and AG mould; Gr 2) 5 animals with at least 3 d of crosslinking and AG mould; Gr 3) 6 animals with at least 3 d crosslinking and 3D mould. Follow ups (FU) were performed every 3 months (mo) evaluating valve function by intracardiac echocardiography (ICE) and cardiac MRI for up to 20.5 mo. All experiments were approved and conducted according to German federal law.

Results

In 11 of 13 animals minimally-invasive implantation was successful. One animal died because of ventricular fibrillation, in the other the implant dislocated into the right ventricle, so it had to be sacrificed. Direct post-implantation valve insufficiency was evaluated in 9 animals using ICE or angiography. In Gr 1 insufficiency was non-existent (n=2), in Gr 2 moderate or severe (n=2) and in Gr 3 non-existent or mild (n=5). Long term function as shown in figure 1 decreased rapidly in Gr 1 and 2 with median MRI regurgitation fractions (RF) in Gr 1 of 31% at 3 mo (n=3), 41% at 6 mo (n=3), 48% at 9 mo (n=2), 47% at 12 mo (n=3) and in Gr 2 of 43% at 3 and 54% at 6 mo (n=1) after implantation. Median RF in Gr 3 was small with 9% at 3 mo (n=4), 8% at 6 mo (n=3), 8% at 9 mo (n=3), 12% at 13 mo (n=3), 8% at 17 mo (n=2) and 20.5 mo (n=2). We never witnessed valve stenosis in any group at any point in time.

Conclusion

Gr 3 showed promising results regarding long time function of the implant which encourages further research with higher validity. The reason for failing of Gr 1 and 2 remains a topic of discussion. Regardless, valuable experience was gained in crafting and conducting the implantation of this new regenerative heart valve implant.

Funding Acknowledgement

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): EXIST research transfer program of the federal ministry of education and research

Deep evolutionary origin of gamete-directed zygote activation by KNOX/BELL transcription factors in green plants

KNOX and BELL transcription factors regulate distinct steps of diploid development in plants. In the green alga Chlamydomonas reinhardtii, KNOX and BELL proteins are inherited by gametes of the opposite mating types and heterodimerize in zygotes to activate diploid development. By contrast, in land plants such as Physcomitrium patens and Arabidopsis thaliana, KNOX and BELL proteins function in sporophyte and spore formation, meristem maintenance and organogenesis during the later stages of diploid development. However, whether the contrasting functions of KNOX and BELL were acquired independently in algae and land plants is currently unknown. Here, we show that in the basal land plant species Marchantia polymorpha, gamete-expressed KNOX and BELL are required to initiate zygotic development by promoting nuclear fusion in a manner strikingly similar to that in C. reinhardtii. Our results indicate that zygote activation is the ancestral role of KNOX/BELL transcription factors, which shifted toward meristem maintenance as land plants evolved.

Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants

The appearance of plant organs mediated the explosive radiation of land plants, which shaped the biosphere and allowed the establishment of terrestrial animal life. The evolution of organs and immobile gametes required the coordinated acquisition of novel gene functions, the co-option of existing genes and the development of novel regulatory programmes. However, no large-scale analyses of genomic and transcriptomic data have been performed for land plants. To remedy this, we generated gene expression atlases for various organs and gametes of ten plant species comprising bryophytes, vascular plants, gymnosperms and flowering plants. A comparative analysis of the atlases identified hundreds of organ- and gamete-specific orthogroups and revealed that most of the specific transcriptomes are significantly conserved. Interestingly, our results suggest that co-option of existing genes is the main mechanism for evolving new organs. In contrast to female gametes, male gametes showed a high number and conservation of specific genes, which indicates that male reproduction is highly specialized. The expression atlas capturing pollen development revealed numerous transcription factors and kinases essential for pollen biogenesis and function.

Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants

The appearance of plant organs mediated the explosive radiation of land plants, which shaped the biosphere and allowed the establishment of terrestrial animal life. The evolution of organs and immobile gametes required the coordinated acquisition of novel gene functions, the co-option of existing genes and the development of novel regulatory programmes. However, no large-scale analyses of genomic and transcriptomic data have been performed for land plants. To remedy this, we generated gene expression atlases for various organs and gametes of ten plant species comprising bryophytes, vascular plants, gymnosperms and flowering plants. A comparative analysis of the atlases identified hundreds of organ- and gamete-specific orthogroups and revealed that most of the specific transcriptomes are significantly conserved. Interestingly, our results suggest that co-option of existing genes is the main mechanism for evolving new organs. In contrast to female gametes, male gametes showed a high number and conservation of specific genes, which indicates that male reproduction is highly specialized. The expression atlas capturing pollen development revealed numerous transcription factors and kinases essential for pollen biogenesis and function.

Role of Polycomb in the control of transposable elements

It is generally considered that Polycomb Repressive Complex (PRC)2 deposits the histone mark H3K27me3 on silent protein-coding genes, while transposable elements are repressed by DNA and/or H3K9 methylation. Yet, there is increasing evidence that PRC2 also targets and even silences transposable elements in representatives of several distantly related eukaryotic lineages. In plants and animals, H3K27me3 is present on transposable elements in mutants and specific cell types devoid of DNA methylation. In this Opinion, we summarize the experimental evidence for this phenomenon across the eukaryotic kingdom, and discuss its functional and evolutionary significance. We hypothesize that an ancestral role of Polycomb group (PcG) proteins was to silence transposable elements.

Crosstalk between H2A variant-specific modifications impacts vital cell functions

Selection of C-terminal motifs participated in evolution of distinct histone H2A variants. Hybrid types of variants combining motifs from distinct H2A classes are extremely rare. This suggests that the proximity between the motif cases interferes with their function. We studied this question in flowering plants that evolved sporadically a hybrid H2A variant combining the SQ motif of H2A.X that participates in the DNA damage response with the KSPK motif of H2A.W that stabilizes heterochromatin. Our inventory of PTMs of H2A.W variants showed that in vivo the cell cycle-dependent kinase CDKA phosphorylates the KSPK motif of H2A.W but only in absence of an SQ motif. Phosphomimicry of KSPK prevented DNA damage response by the SQ motif of the hybrid H2A.W/X variant. In a synthetic yeast expressing the hybrid H2A.W/X variant, phosphorylation of KSPK prevented binding of the BRCT-domain protein Mdb1 to phosphorylated SQ and impaired response to DNA damage. Our findings illustrate that PTMs mediate interference between the function of H2A variant specific C-terminal motifs. Such interference could explain the mutual exclusion of motifs that led to evolution of H2A variants.

Histone variants take center stage in shaping the epigenome

The dynamic properties of the nucleosome are central to genomic activity. Variants of the core histones that form the nucleosome play a pivotal role in modulating nucleosome structure and function. Despite often small differences in sequence, histone variants display remarkable diversity in genomic deposition and post-translational modification. Here, we summarize the roles played by histone variants in the establishment, maintenance and reprogramming of plant chromatin landscapes, with a focus on histone H3 variants. Deposition of replicative H3.1 during DNA replication controls epigenetic inheritance, while local replacement of H3.1 with H3.3 marks cells undergoing terminal differentiation. Deposition of specialized H3 variants in specific cell types is emerging as a novel mechanism of selective epigenetic reprogramming during the plant life cycle.