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Mercier, R.

Publications and source records attributed to Mercier, R..

At least 19 recordsLinked to original sources

coelsch: Platform-agnostic single-cell analysis of meiotic recombination events

BackgroundMeiotic recombination creates genetic diversity through reciprocal exchange of haplotypes between homologous chromosomes. Scalable and robust methods for mapping recombination breakpoints are essential for understanding meiosis and for genetic mapping. Single cell sequencing of gametes offers a direct approach to recombination mapping, yet the effect of technical differences between single-cell sequencing methods for crossover detection remains unclear. ResultsWe benchmark single cell methods for droplet-based chromatin accessibility and RNA sequencing and plate-based whole-genome amplification for mapping meiotic recombination in Arabidopsis thaliana. For this purpose we introduce two novel open-source tools coelsch_mapping_pipeline and coelsch for haplotype-aware alignment and per-cell crossover detection, using them to recover known recombination frequencies and quantify the effects of coverage sparsity. We subsequently apply our approach to a panel of 40 recombinant F hybrids derived from crosses of 22 diverse natural accessions, successfully recovering genetic maps for 34 F1s in a single dataset. This analysis reveals substantial variation in recombination rate and identifies a [~]10 Mb pericentric inversion in the accession Zin-9, the largest natural inversion reported in A. thaliana to date. ConclusionsThese results demonstrate the applicability and scalability of single-cell gamete sequencing for high-throughput mapping of meiotic recombination, and highlight the strengths and limitations of different single-cell modalities. The accompanying open-source tools provide a framework for haplotyping and crossover detection analysis using sparse single-cell sequencing data. Our methodology enables parallel analysis of large numbers of hybrids in a single dataset, removing a major technical barrier to large-scale studies of natural variation in recombination rate.

bioinformatics↗

Host infection selects for sRNA variants that drive bacterial social cheating

Single-nucleotide mutations in regulatory small RNAs (sRNAs) represent a largely unexplored route to social cheating during bacterial infection. Here we show that arcZ, encoding a conserved Hfq-dependent sRNA in the plant pathogen Dickeya solani, undergoes recurrent single-nucleotide mutations during potato tuber infection. Five distinct arcZ alleles define a graded series of ArcZ functional impairment in which antifungal and protease activities are progressively reduced while virulence is compromised only in a subset of alleles. All five variants gain a fitness advantage exclusively during co-infection with wild-type arcZ1 cells. This advantage is strongest when variants are rare and declines as cheater frequency increases, ultimately correlating with reduced total bacterial productivity, the canonical signature of social cheating and a tragedy of the commons. No fitness benefit is detected in vitro. Transcriptomic profiling of five arcZ variants identifies a conserved core of 186 downregulated genes enriched in secreted and diffusible functions. Systematic genetic dissection, supported by quantitative proteomics, establishes BudAB-dependent acetoin production as the dominant cooperative public good exploited during infection. Wild-type arcZ1cells divert pyruvate flux toward acetoin via the BudAB pathway, maintaining a less acidic tissue environment that sustains disease progression; arcZ variants, which repress this pathway, exploit the resulting pH buffering without contributing to it. These results establish pleiotropic regulatory sRNAs as a previously unrecognized class of mutational targets for the emergence of social cheaters during host infection. StatementBacterial populations are not genetically uniform: variants that exploit the cooperative activities of their neighbors, social cheaters, can emerge rapidly within infected tissue and undermine collective bacterial productivity. We show that single-nucleotide mutations in the sRNA ArcZ of Dickeya solani are recurrently selected during potato infection, generating cheater variants that cease contributing to a shared metabolic benefit. Wild-type cells divert pyruvate toward acetoin, buffering tissue pH and sustaining disease; mutant variants exploit this pH maintenance without producing acetoin themselves. Because a single arcZ mutation simultaneously represses a conserved set of 186 genes, including genes involved in secreted and diffusible functions, regulatory sRNA genes represent a previously unrecognized and unusually efficient mutational target for the evolution of social cheating during infection.

microbiology↗

HEIP1 orchestrates pro-crossover protein activity during mammalian meiosis

Meiotic crossovers are needed to produce genetically balanced gametes. In mammals, crossover formation is mediated by a conserved set of pro-crossover proteins via mechanisms that remain unclear. Here, we characterize a mammalian pro-crossover factor HEIP1. In mouse HEIP1 is essential for crossing over and fertility of both sexes. HEIP1 promotes crossing over by orchestrating the recruitment of other pro-crossover proteins, including the MutS{gamma} complex (MSH4- MSH5) and E3 ligases (HEI10, RNF212, and RNF212B), that are required to mature crossover sites and recruit the crossover-specific resolution complex MutL{gamma}. Moreover, HEIP1 directly interacts with HEI10, suggesting a direct role in controlling the recruitment of pro-crossover E3 ligases. During early stages of meiotic prophase I, HEIP1 interacts with the chromosome axes, independently of recombination, before relocalizing to the central region of the synaptonemal complex. We propose that HEIP1 is a new conserved master regulator of crossover proteins that controls different crossover maturation steps. Significance StatementCrossovers are essential to produce gametes by promoting the proper segregation of the homologous chromosomes. But, if misregulated, they can lead to genetic disorders, miscarriage and infertility. Their formation depends on the conserved pro-crossover factors, which repertoire is expanding and mode of action tightly regulated. This study highlights how the HEIP1 protein organizes pro-crossover protein activities in the mouse. Our findings show that HEIP1, by interacting early with chromosomes independently of recombination initiation, and orchestrating the recruitment of pro-crossover factors, including the MutSg complex and the RING proteins HEI10, RNF212 and RNF212B, is pivotal in this regulation. Our work is of significance to unravel crossover control during meiotic recombination, a conserved mechanism essential for gametes formation.

genetics↗

Collaboration between two conserved sequence motifs drives ATPase stimulation of Hsp90 by Aha1

AbstractHsp90 is a dimeric molecular chaperone essential for the folding, stabilization, activation, and maturation of hundreds of client proteins, which are critical for cellular function. Co-chaperones, such as Aha1, play a key role in regulating the ATP-dependent Hsp90 client activation cycle by modulating Hsp90s ATPase activity and controlling progression through the cycle. Two highly conserved motifs in Aha1--the NxNNWHW and RKxK motifs--are known to regulate specific aspects of the Hsp90 ATPase cycle. In this study, we demonstrate that the K60 residue within the RKxK motif facilitates the structural organization of the NxNNWHW motif prior to ATP hydrolysis. Mutation of the K60 residue partially impairs the in vivo functionality of yeast Aha1. Additionally, we reveal that each individual residue within the NxNNWHW motif modulates the ATPase rate and apparent affinity for ATP of Hsp90. These findings provide new insights into how conserved regions of Aha-type co-chaperones influence Hsp90 kinetics and its regulation of client protein folding.

biochemistry↗

The 1001G+ project: A curated collection of Arabidopsis thaliana long-read genome assemblies to advance plant research

Arabidopsis thaliana was the first plant for which a high-quality genome sequence became available. The publication of the first reference genome sequence almost 25 years ago was already accompanied by genome-wide data on sequence polymorphisms in another accession, or naturally occurring strain. Since then, inventories of genome-wide diversity have been generated at increasingly precise levels. High-density genotype data for A. thaliana, including those from the 1001 Genomes Project, were key to demonstrating the enormous power of GWAS in inbred populations of wild plants, and the comparison of intraspecific polymorphism with interspecific divergence has illuminated many aspects of plant genome evolution. Over the past decade, an increasing number of nearly complete genome sequences have been published for many more accessions. Here, we highlight the diversity of a curated collection of previously published and so far unpublished genome sequences assembled using different types of long reads, including PacBio Continuous Long Reads (CLR), PacBio High Fidelity (HiFi) reads, and Oxford Nanopore Technologies (ONT) reads. This 1001 Genomes Plus (1001G+) resource is being made available at http://1001genomes.org. We invite colleagues with yet unpublished genome assemblies from A. thaliana accessions to contribute to this effort.

genomics↗

FIGL1 limits the formation of meiotic non crossover events in Arabidopsis thaliana

Meiotic recombination produces both crossover and non crossover events that are essential in the history of population genetics and evolution of species. In Arabidopsis thaliana, several pathways control the rate and distribution of crossovers. Here, by sequencing the four products of a series of tetrads, we confirm the antiCO role of RECQ4A, RECQ4B, FIGL1 and FANCM. Moreover, when one of this gene is mutated, complex chimeric gene conversion events associated to crossover are observed suggesting a role of these proteins in limiting the multiple strand invasions. Nothing was known about the factors that could limit or increase NCOs. Here, we show that FIGL1 plays a major role in controlling the NCO number.

genetics↗

MutLgamma enforces meiotic crossovers in Arabidopsis thaliana

During meiosis, each chromosome pair experiences at least one crossover (CO), which directs their balanced segregation in addition to shuffling genetic information. COs tend to be away from each other, a phenomenon known as CO interference. The main biochemical pathway for CO formation, which is conserved in distant eukaryotes, involves the ZMM proteins together with the MLH1-MLH3 complex (MutL{gamma}). Here, we aim to clarify the role of MutL{gamma} in CO formation in Arabidopsis thaliana. We show that AtMutL{gamma} is partially dispensable for ZMM-dependant CO formation. HEI10 large foci - that mark CO sites in wild-type-form at a normal level in mlh1 and mlh3 mutants, but are inefficiently maturated into COs. Mutating the MUS81 nuclease in either mlh1 or mlh3 leads to chromosome fragmentation, which is suppressed by further mutating the zmm msh5. This suggests that in the absence of MutL{gamma}, recombination intermediates produced by ZMMs are resolved by MUS81, which does not ensure CO formation. Finally, CO interference is not affected in mlh1, which is compatible with a random sub-sampling of normally patterned CO sites. We conclude that AtMutL{gamma} imposes designated recombination intermediates to be resolved exclusively as COs, supporting the view that MutL{gamma} asymmetrically resolves double-Holliday junctions, yielding COs.

genetics↗

Interference Length reveals regularity of crossover placement across species

Crossover interference is a phenomenon that affects the number and positioning of crossovers in meiosis and thus affects genetic diversity and chromosome segregation. Yet, the underlying mechanism is not fully understood, partly because quantification is difficult. To overcome this challenge, we introduce the interference length Lint that quantifies changes in crossover patterning due to interference. We show that it faithfully captures known aspects of crossover interference and provides superior statistical power over previous methods. We apply our analysis to empirical data and unveil a similar behavior of Lint across species, which hints at a common mechanism. A recently proposed coarsening model generally captures these aspects, providing a unified view of crossover interference. Consequently, Lint facilitates model refinements and general comparisons between alternative models of crossover interference.

genetics↗

Structural variation and DNA methylation shape the centromere-proximal meiotic crossover landscape in Arabidopsis

BackgroundCentromeres load kinetochore complexes onto chromosomes, which mediate spindle attachment and allow segregation during cell division. Although centromeres perform a conserved cellular function, their underlying DNA sequences are highly divergent within and between species. Despite variability in DNA sequence, centromeres are also universally suppressed for meiotic crossover recombination, across eukaryotes. However, the genetic and epigenetic factors responsible for suppression of centromeric crossovers remain to be completely defined. ResultsTo explore the centromere-proximal recombination landscape, we mapped 14,397 crossovers against fully assembled Arabidopsis thaliana genomes. A. thaliana centromeres comprise megabase-scale satellite repeat arrays that load nucleosomes containing the CENH3 histone variant. Each chromosome possesses a structurally polymorphic 3-4 megabase region where crossovers were absent, that includes the satellite arrays, flanked by 1-2 megabase low-recombination zones. The recombination-suppressed regions are enriched for Gypsy/Ty3 retrotransposons, and additionally contain expressed genes with high genetic diversity that initiate meiotic recombination, yet do not crossover. We mapped crossovers at high-resolution in proximity to CEN3, which resolved punctate centromere-proximal hotspots that overlapped gene islands embedded in heterochromatin. Centromeres are densely DNA methylated and the recombination landscape was remodelled in DNA methylation mutants. We observed that the centromeric low-recombining zones decreased and increased crossovers in CG (met1) and non-CG (cmt3) mutants, respectively, whereas the core non recombining zones remained suppressed. ConclusionOur work relates the genetic and epigenetic organisation of the A. thaliana centromeres and flanking pericentromeric heterochromatin to the zones of crossover suppression that surround the CENH3-occupied satellite repeat arrays.

genomics↗

Remarkably high rate of meiotic recombination in the fission yeast Schizosaccharomyces pombe

In most eukaryotes, the number of meiotic crossovers (COs) is limited to 1-3 per chromosome, which are prevented from occurring close to one another by CO interference. The fission yeast Schizosaccharomyces pombe, an exception to this general rule, lacks CO interference and seems to have the highest CO number per chromosome. However, global CO frequency was indirectly estimated in this species, raising doubts about this exceptional recombination level. Here, we used an innovative strategy to directly determine COs genome-wide in S. pombe. We confirm the absence of crossover interference and reveal the presence of co-variation in CO number across chromosomes within tetrads, suggesting that a limiting pro-CO factor varies stochastically between meiocytes. CO number per chromosome varies linearly with chromosome size, with the three chromosomes having, on average, 15.9, 12.5, and 7.0 COs, respectively. This is significantly lower than previous estimates but reinforces S. pombes exceptional status as the eukaryote with the highest CO number per chromosome described to date and among the species with the highest rate of COs per unit of DNA.

genetics↗

High-frequency synthetic apomixis in hybrid rice

Introducing asexual reproduction through seeds - apomixis - into crop species could revolutionize agriculture by allowing F1 hybrids with enhanced yield and stability to be clonally propagated. Engineering synthetic apomixis has proven feasible in inbred rice through the inactivation of three genes (MiMe), which results in the conversion of meiosis into mitosis in a line ectopically expressing the BABYBOOM1 (BBM1) parthenogenetic trigger in egg cells. However, only 10-30% of the seeds were clonal. We show here that synthetic apomixis can be induced in a F1 hybrid of rice by inducing MiMe mutations and egg cell expression of BBM1 in a single step. We generated hybrid plants that produced more than 95% of clonal seeds across multiple generations. Clonal apomictic plants maintained the phenotype of the F1 hybrid along successive generations. Our results demonstrate that there is no barrier to almost fully penetrant synthetic apomixis in an important crop species, rendering it compatible with use in agriculture.

plant biology↗

The FANCC-FANCE-FANCF complex is evolutionarily conserved and regulates meiotic recombination

At meiosis, programmed meiotic DNA double-strand breaks are repaired via homologous recombination, resulting in crossovers (COs). From a large excess of DNA double-strand breaks that are formed, only a small proportion gets converted into COs because of active mechanisms that restrict CO formation. The Fanconi anemia (FA) complex proteins AtFANCM, MHF1, and MHF2 were previously identified in a genetic screen as anti-CO factors that function during meiosis in Arabidopsis thaliana. Here, pursuing the same screen, we identify FANCC as a new anti-CO gene. FANCC was previously only identified in mammals because of low primary sequence conservation. We show that FANCC, and its physical interaction with FANCE-FANCF, is conserved from vertebrates to plants. Further, we show that FANCC, together with its subcomplex partners FANCE and FANCF, regulates meiotic recombination. Mutations of any of these three genes partially rescues CO-defective mutants, which is particularly marked in female meiosis. Functional loss of FANCC, FANCE, or FANCF results in synthetic meiotic catastrophe with the pro-CO factor MUS81. This work reveals that FANCC is conserved outside mammals and has an anti-CO role during meiosis together with FANCE and FANCF.

genetics↗

Extensive NEUROG3 occupancy in the human pancreatic endocrine gene regulatory network

ObjectiveMice lacking the bHLH transcription factor (TF) Neurog3 do not form pancreatic islet cells, including insulin secreting beta cells, causing diabetes. In human, homozygous mutations of NEUROG3 manifest with neonatal or childhood diabetes. Despite this critical role in islet cell development, the precise function and downstream genetic programs regulated directly by NEUROG3 remain elusive. We therefore mapped genome-wide NEUROG3 occupancy in human induced pluripotent stem cell (iPSC)-derived endocrine progenitors and determined NEUROG3 dependency of associated genes to uncover direct targets. MethodsWe generated a novel hiPSC line (NEUROG3-HA-P2A-Venus), where NEUROG3 is HA-tagged and fused to a self-cleaving fluorescent VENUS reporter. We used the CUT&RUN technique to map NEUROG3 occupancy and epigenetic marks in pancreatic endocrine progenitors (PEP) differentiated from this hiPSC line. We integrated NEUROG3 occupancy data with chromatin status and gene expression in PEPs and their NEUROG3-dependence. In addition, we searched whether NEUROG3 binds type 2 diabetes mellitus (T2DM)-associated variants at the PEP stage. ResultsCUT&RUN revealed a total of 863 NEUROG3 binding sites assigned to 1268 unique genes. NEUROG3 occupancy was found at promoters as well as at distant cis-regulatory elements frequently overlapping within PEP active enhancers. De novo motif analyses defined a NEUROG3 consensus binding motif and suggested potential co-regulation of NEUROG3 target genes by FOXA, RFX or PBX transcription factors. Moreover, we found that 22% of the genes downregulated in NEUROG3-/- hESC-derived PEPs are bound by NEUROG3 and thus likely to be directly regulated. NEUROG3 targets include transcription factors known to have important roles in islet cell development or function, such as NEUROD1, PAX4, NKX2-2, SOX4, MLXIPL, LMX1B, RFX3, and NEUROG3 itself. Remarkably, we uncovered that NEUROG3 binds transcriptional regulator genes with enriched expression in human fetal pancreatic alpha (e.g., IRX1, IRX2), beta (e.g., NKX6-1, SMAD9, ISX, TFCP2L1) and delta cells (ERBB4) suggesting that NEUROG3 could control islets subtype programs. Moreover, NEUROG3 targets genes critical for insulin secretion in beta cells (e.g., GCK, ABCC8/KCNJ11, CACNA1A, CHGA, SCG2, SLC30A8 and PCSK1). In addition, we unveiled a panel of ncRNA potentially regulated by NEUROG3. Lastly, we identified several T2DM risk SNPs within NEUROG3 peaks suggesting a possible developmental role of NEUROG3 in T2DM susceptibility. ConclusionMapping of NEUROG3 genome occupancy in PEPs uncovers an unexpectedly broad, direct control of the endocrine gene regulatory network (GRN) and raises novel hypotheses on how this master regulator controls islet and beta cell differentiation. HighlightsO_LINEUROG3 CUT&RUN analysis revealed 1268 target genes in human pancreatic endocrine progenitors (PEPs) C_LIO_LINEUROG3 binding sites overlap with active chromatin regions in PEPs. C_LIO_LI1/5 of the genes downregulated in NEUROG3-/- hESC-derived PEPs are bound by NEUROG3. C_LIO_LINEUROG3 targets islet specific TFs and regulators of insulin secretion. C_LIO_LISeveral T2DM risk allelles lie within NEUROG3 bound regions. C_LI

genomics↗

A Tad-like apparatus is required for contact-dependent prey killing in predatory social bacteria

Myxococcus xanthus, a soil bacterium, predates collectively using motility to invade prey colonies. Prey lysis is mostly thought to rely on secreted factors, cocktails of antibiotics and enzymes, and direct contac with Myxococcus cells. In this study, we show that on surfaces the coupling of A-motility and contact-dependent killing is the central predatory mechanism driving effective prey colony invasion and consumption. At the molecular level, contact-dependent killing involves a newly discovered type IV filament-like machinery (Kil) that both promotes motility arrest and prey cell plasmolysis. In this process, Kil proteins assemble at the predator-prey contact site, suggesting that they allow tight contact with prey cells for their intoxication. Kil-like systems form a new class of Tad-like machineries in predatory bacteria, suggesting a conserved function in predator-prey interactions. This study further reveals a novel cell-cell interaction function for bacterial pili-like assemblages.

microbiology↗

Patronus is the elusive plant securin, preventing chromosome separation by antagonizing separase

Chromosome distribution at anaphase of mitosis and meiosis is triggered by separase, an evolutionarily conserved protease. Separase must be tightly regulated to prevent the untimely release of chromatid cohesion and disastrous chromosome distribution defects. Securin is the key inhibitor of separase in animals and fungi, but has not been identified in other eukaryotic lineages. Here, we identified PATRONUS1 and PATRONUS2 (PANS1 and PANS2) as the Arabidopsis homologues of securin. Disruption of PANS1 is known to lead to the premature separation of chromosomes at meiosis, and the simultaneous disruption of PANS1 and PANS2 is lethal. Here, we show that PANS1 targeting by the anaphase-promoting-complex is required to trigger chromosome separation, mirroring the regulation of securin. We showed that PANS1 acts independently from Shugosins. In a genetic screen for pans1 suppressors, we identified SEPARASE mutants, showing that PANS1 and SEPARASE have antagonistic functions in vivo. Finally, we showed that the PANS1 and PANS2 proteins interact directly with SEPARASE. Altogether, our results show that PANS1 and PANS2 act as a plant securin. Remote sequence similarity was identified between the plant patronus family and animal securins, suggesting that they indeed derive from a common ancestor. Identification of patronus as the elusive plant securin illustrates the extreme sequence divergence of this central regulator of mitosis and meiosis.

cell biology↗

Clonal seeds in hybrid rice using CRISPR/Cas9

Heterosis, the observation that first generation hybrids outcompete the parental lines, is widely used in increasing the productivity and yield of agricultural crops1,2. However, heterosis is lost in the following generations because of genetic segregation. In addition, the high cost of hybrid seed production hinders the application of heterosis in many crops. Clonal reproduction through seeds could be revolutionary for agriculture by allowing self-propagation of F1 hybrids3,4. Here we show that heterozygosity of F1 hybrid rice can be fixed and thus propagated without additional crossing. First, we showed that multiplex editing of three key meiotic genes5,6 in hybrid rice leads to the production of clonal diploid gametes and tetraploid seeds. Next, editing of the MATRILINEAL (MTL) gene that involved in fertilization7,8 results in the induction of haploid seeds in hybrid rice. By simultaneous editing of these four endogenous genes in hybrid rice using the CRISPR/Cas9 system, we obtained in one generation plants able to propagate clonally through seeds. This opens the possibility to fix heterozygosity of hybrid varieties in food crops.

plant biology↗

Unleashing meiotic crossovers in hybrid plants

Meiotic crossovers shuffle parental genetic information, providing novel combinations of alleles on which natural or artificial selection can act. However, crossover events are relatively rare, typically one to three exchange points per chromosome pair. Recent work has identified three pathways limiting meiotic crossovers in Arabidopsis thaliana, that rely on the activity of FANCM1, RECQ42 and FIGL13, respectively. Here, we analyzed recombination in plants where one, two or three of these pathways were disrupted, in both pure line and hybrid contexts. The highest effect was observed when combining recq4 and figl1 mutations, which increased the hybrid genetic map length from 389 to 3037 centiMorgans. This corresponds to an unprecedented 7.8-fold increase in crossover frequency. Disrupting the three pathways do not further increases recombination, suggesting that some upper limit has been reached. The increase in crossovers is not uniform along chromosomes and rises from centromere to telomere. Finally, while in wild type recombination is much higher in male than in female meiosis (490 cM vs 290 cM), female recombination is higher than male in recq4 figl1 (3200 cM vs 2720 cM), suggesting that the factors that make wild-type female meiosis less recombinogenic than male wild-type meiosis do not apply in the mutant context. The massive increase of recombination observed in recq4 figl1 hybrids opens the possibility to manipulate recombination to enhance plant breeding efficiency.

genetics↗

FIGL1 and its novel partner FLIP form a conserved complex that regulates homologous recombination.

Homologous recombination is central to repair DNA double-strand breaks (DSB), either accidently arising in mitotic cells or in a programed manner at meiosis. Crossovers resulting from the repair of meiotic breaks are essential for proper chromosome segregation and increase genetic diversity of the progeny. However, mechanisms regulating CO formation remain elusive. Here, we identified through protein-protein interaction and genetic screens FIDGETIN-LIKE-1 INTERACTING PROTEIN (FLIP) as a new partner of the previously characterized anti-crossover factor FIDGETIN-LIKE-1 (FIGL1) in Arabidopsis thaliana. We showed that FLIP limits meiotic crossover together with FIGL1. Further, FLIP and FIGL1 form a protein complex conserved from Arabidopsis to Human. FIGL1 interacts with the recombinases RAD51 and DMC1, the enzymes that catalyze the DNA stand exchange step of homologous recombination. Arabidopsis flip mutants recapitulates the figl1 phenotype, with enhanced meiotic recombination associated with change in DMC1 dynamics. Our data thus suggest that FLIP and FIGL1 form a conserved complex that regulates the crucial step of strand invasion in homologous recombination.

genetics↗