SUMMARYArbuscular mycorrhizal (AM) symbiosis is a widespread mutualism formed between vascular plants and fungi of the Glomeromycota. In this endosymbiosis, fungal hyphae enter the roots, growing through epidermal cells to the cortex where they establish differentiated hyphae called arbuscules in the cortical cells. Reprogramming of the plant epidermal and cortical cells occurs to enable intracellular growth of the fungal symbiont; however, the plant genes underlying this process are largely unknown. Here, through the use of RNAi, we demonstrate that the expression of a Medicago truncatula gene named Vapyrin is essential for arbuscule formation, and also for efficient epidermal penetration by AM fungi. Vapyrin is induced transiently in the epidermis coincident with hyphal penetration, and then in the cortex during arbuscule formation. The Vapyrin protein is cytoplasmic, and in cells containing AM fungal hyphae, the protein accumulates in small puncta that move through the cytoplasm. Vapyrin is a novel protein composed of two domains that mediate protein-protein interactions: an N-terminal VAMP-associated protein (VAP)/major sperm protein (MSP) domain and a C-terminal ankyrin-repeat domain. Putative Vapyrin orthologs exist widely in the plant kingdom, but not in Arabidopsis, or in non-plant species. The data suggest a role for Vapyrin in cellular remodeling to support the intracellular development of fungal hyphae during AM symbiosis.

During meiosis, homologous chromosomes undergo reciprocal crossovers, which generate genetic diversity and underpin classical crop improvement. Meiotic recombination initiates from DNA double-strand breaks (DSBs), which are processed into single-stranded DNA that can invade a homologous chromosome. The resulting joint molecules can ultimately be resolved as crossovers. In , competing pathways balance the repair of ∼100-200 meiotic DSBs into ∼10 crossovers per meiosis, with the excess DSBs repaired as noncrossovers. To bias DSB repair toward crossovers, we simultaneously increased dosage of the procrossover E3 ligase gene and introduced mutations in the anticrossovers helicase genes and As and increase interfering and noninterfering crossover pathways, respectively, they combine additively to yield a massive meiotic recombination increase. Interestingly, we also show that increased dosage increases crossover coincidence, which indicates an effect on interference. We also show that patterns of interhomolog polymorphism and heterochromatin drive recombination increases distally towards the subtelomeres in both and backgrounds, while the centromeres remain crossover suppressed. These results provide a genetic framework for engineering meiotic recombination landscapes in plant genomes.

One-sentence summary: REC8 association with the genome correlates with multiple chromatin states and is required to organize meiotic chromosome architecture and interhomolog recombination.

Nodals are signaling factors of the transforming growth factor-β (TGFβ) superfamily with a key role in vertebrate development. They control a variety of cell fate decisions required for the establishment of the embryonic body plan. We have identified two highly conserved transmembrane proteins, Nicalin and Nomo (Nodal modulator, previously known as pM5), as novel antagonists of Nodal signaling. Nicalin is distantly related to Nicastrin, a component of the Alzheimer's disease-associated γ-secretase, and forms a complex with Nomo. Ectopic expression of both proteins in zebrafish embryos causes cyclopia, a phenotype that can arise from a defect in mesendoderm patterning mediated by the Nodal signaling pathway. Accordingly, downregulation of Nomo resulted in an increase in anterior axial mesendoderm and the development of an enlarged hatching gland. Inhibition of Nodal signaling by ectopic expression of Lefty was rescued by reducing Nomo levels. Furthermore, Nodal- as well as Activin-induced signaling was inhibited by Nicalin and Nomo in a cell-based reporter assay. Our data demonstrate that the Nicalin/Nomo complex antagonizes Nodal signaling during mesendodermal patterning in zebrafish

During meiosis, interhomolog recombination produces crossovers and noncrossovers to create genetic diversity. Meiotic recombination frequency varies at multiple scales, with high subtelomeric recombination and suppressed centromeric recombination typical in many eukaryotes. During recombination, sister chromatids are tethered as loops to a polymerized chromosome axis, which, in plants, includes the ASY1 HORMA domain protein and REC8–cohesin complexes. Using chromatin immunoprecipitation, we show an ascending telomere-to-centromere gradient of ASY1 enrichment, which correlates strongly with REC8–cohesin ChIP-seq data. We mapped crossovers genome-wide in the absence of ASY1 and observe that telomere-led recombination becomes dominant. Surprisingly,asy1/+heterozygotes also remodel crossovers toward subtelomeric regions at the expense of the pericentromeres. Telomeric recombination increases inasy1/+occur in distal regions where ASY1 and REC8 ChIP enrichment are lowest in wild type. In wild type, the majority of crossovers show interference, meaning that they are more widely spaced along the chromosomes than expected by chance. To measure interference, we analyzed double crossover distances, MLH1 foci, and fluorescent pollen tetrads. Interestingly, while crossover interference is normal inasy1/+, it is undetectable inasy1mutants, indicating that ASY1 is required to mediate crossover interference. Together, this is consistent with ASY1 antagonizing telomere-led recombination and promoting spaced crossover formation along the chromosomes via interference. These findings provide insight into the role of the meiotic axis in patterning recombination frequency within plant genomes.

During meiosis homologous chromosomes undergo reciprocal crossovers, which generate genetic diversity and underpin classical crop improvement. Meiotic recombination initiates from DNA double strand breaks, which are processed into single-stranded DNA that can invade a homologous chromosome. The resulting joint molecules can ultimately be resolved as crossovers. In Arabidopsis, competing pathways balance the repair of ∼100–200 meiotic DSBs into ∼10 crossovers per meiosis, with the excess DSBs repaired as non-crossovers. In order to bias DSB repair towards crossovers, we simultaneously increased dosage of the pro-crossover E3 ligase gene HEI10 and introduced mutations in the anti-crossover helicase genes RECQ4A and RECQ4B. As HEI10 and recq4a recq4b increase interfering and non-interfering crossover pathways respectively, they combine additively to yield a massive meiotic recombination increase. Interestingly, we also show that increased HEI10 dosage increases crossover coincidence, which indicates an effect of HEI10 on interference. We also show that patterns of interhomolog polymorphism and heterochromatin drive recombination increases towards the sub-telomeres in both HEI10 and recq4a recq4b backgrounds, while the centromeres remain crossover-suppressed. These results provide a genetic framework for engineering meiotic recombination landscapes in plant genomes.

18During meiosis chromosomes undergo DNA double-strand breaks (DSBs) that can be 19 repaired using a homolog to produce crossovers, which creates genetic diversity. 20Meiotic recombination occurs coincident with homolog pairing and polymerization of 21 the meiotic axis and synaptonemal complex (SC). REC8-cohesin is required to connect 22 chromosomes to the axis and to organize axis polymerization. However, control of 23 REC8 loading along chromosomes, in relation to chromatin, transcription and 24 recombination, is not yet fully understood. Therefore, we performed REC8 ChIP-seq in 25 Arabidopsis, which revealed strong enrichment in centromeric heterochromatin. REC8 26 abundance correlates with suppression of meiotic DSBs and crossovers, despite axis 27 loading of SPO11-1 in these regions. Loss of the heterochromatic marks H3K9me2 28 and non-CG DNA methylation in kyp/suvh4 suvh5 suvh6 mutants causes remodeling of 29 REC8 and gain of meiotic recombination locally in repeated sequences, although 30 centromere cohesion is maintained. In the chromosome arms, REC8 is enriched within 31 gene bodies, exons and GC-rich sequences, and anti-correlates with transcription. 32Highest REC8 occupancy occurred in facultatively silent, H3K27me3-modified genes. 33Using immunocytology we show that axis polycomplexes form in rec8 mutants that 34 recruit recombination foci with altered stoichiometry, leading to catastrophic non-35 homologous recombination. Therefore, REC8 plays a key role organizing meiotic 36 chromosome architecture and promoting high-fidelity interhomolog recombination. 37Despite this pro-recombination role, local REC8 enrichment associates with DSB 38 repression at the fine scale, which is consistent with the tethered-loop/axis model. 39Coincident with its organizational role during meiosis, REC8-cohesin occupancy along 40 the chromosomes is shaped by multiple chromatin states and transcription. 42Keywords: 44Cohesin, REC8, meiosis, recombination, crossover, H3K9me2, DNA methylation. 45 46 47 48 49 50 51 52 2 Introduction: 53 54 Cohesin complexes form ~35-50 nm rings that can topologically embrace one or more 55 DNA helices (Uhlmann 2016; Nasmyth and Haering 2009; Peters et al. 2008). Cohesin 56 rings consist of paired structural maintenance of chromosomes (SMC) proteins that 57 interact at hinge and ATPase head domains, with the head regions clamped by an α-58 kleisin (Gligoris and Löwe 2016). DNA can enter and exit cohesin rings at the subunit 59 interfaces, and the rings undergo dynamic cycles of association and disassociation 60 with chromosomes (