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Martinez-Perez, E.

Publications and source records attributed to Martinez-Perez, E..

16 recordsLinked to original sources

Functional modelling of human infertility-associated genetic variants using C. elegans and mice

Infertility affects one in six couples worldwide and has a significant genetic component. Genome sequencing efforts have identified increasing numbers of potentially pathogenic variants, including in conserved meiotic genes. However, the lack of functional validation remains a major barrier to establishing variant pathogenicity and clinical diagnoses. Here, we establish an experimental pipeline integrating C. elegans and mouse in vivo models with in silico protein structure predictions to functionally validate potentially pathogenic infertility-associated variants. Using CRISPR-Cas9 we generated worm and mouse models of a homozygous missense variant (P638L) in MSH4, a mismatch repair protein essential for meiotic recombination, identified in a patient with non-obstructive azoospermia (NOA). Homozygous msh-4P546L worms exhibited severe meiotic defects including an absence of chiasmata, accumulation of DNA damage, and loss of crossover markers. Comparable defects were observed in spermatocytes of homozygous Msh4P660L/P660L mice, while Msh4P660L/P660L ovaries lacked oocyte-containing follicles, demonstrating that this variant causes infertility in both sexes. Together, these findings support a model in which the MSH4 P638L substitution disrupts the conversion of early recombination events into crossovers, leading to NOA in men and primary ovarian insufficiency in women. Further worm modelling of human MSH4 genetic variants identified exclusively in heterozygosity (G649R) or also in homozygosity (Y589C) demonstrates the potential of worm models to predict the pathogenicity of missense variants in meiotic proteins found in the human population. We propose that this integrated worm-mouse pipeline provides a powerful framework for accelerating the genetic diagnosis of infertility and informing the clinical management of affected individuals.

cell biology↗

A step towards animal models with self-sustained fungal bioluminescence

Engineering animal models with self-sustained luminescence could enable non-invasive longitudinal monitoring of molecular events in living animals. To create animal models that report physiology with autoluminescence, both luciferin biosynthesis enzymes and the luciferase need to be optimised. Previous work on engineering the autoluminescence pathway from fungi resulted in the development of nnLuz_v3, a version of Neonothopanus nambi luciferase with enhanced thermal stability. Here, we generated an nnLuz_v3 reporter of endogenous Cyp1a1 expression as a measure of aryl hydrocarbon receptor (AHR) activation, assessing the performance of nnLuz_v3 in vivo at physiologically relevant expression levels. As AHR dynamically responds to metabolic, environmental and dietary changes it provides a validated platform to assess novel luminescence approaches. In Cyp1a1-nnLuz mice bioluminescence signal was stable, allowing the generation of well-resolved luminescence images both on standard in vivo imaging equipment and consumer-grade cameras. Using mice and nematode models, we demonstrated limited oral availability of the fungal luciferin, potentially compatible with delivering the substrate via food or the microbiome. Our results are an encouraging first step in the generation of an autoluminescent mammalian model of a molecular event and encourage optimisation of other enzymes of the fungal luciferase pathway.

genetics↗

Loss of meiotic double strand breaks triggers recruitment of recombination-independent pro-crossover factors in C. elegans spermatogenesis

A key event in meiosis is the conversion of a small subset of double strand breaks into interhomolog crossovers. In this study, we demonstrate that Caenorhabditis elegans male spermatogenesis has less robust mechanisms than hermaphrodite oogenesis for ensuring and limiting the conversion of double strand breaks into crossovers. This is not a consequence of differences in meiotic prophase timing, sex chromosome genotype, or the presence or absence of germline apoptosis. Using the cyclin-like crossover marker COSA-1, we show that males have a linear response in converting increasing numbers of double strand breaks into crossovers, suggesting weakened crossover homeostasis. While the topoisomerase SPO-11, responsible for initiating meiotic double strand breaks, has an extended period of activity in males as in hermaphrodites, we discovered that COSA-1 foci form at the very end of meiotic prophase in the absence of SPO-11 during spermatogenesis. These COSA-1-marked sites are also independent of homologous recombination, and Topoisomerases I and II. We find that the synaptonemal complex, which holds homologs in proximity, differently modulates COSA-1 enrichment to chromosomes in the absence of SPO-11 in males and hermaphrodites. Together, these findings suggest that males have less robust crossover control and that there are previously unrecognized lesions or structures at the end of meiotic prophase in spermatocytes that can accumulate CO markers. Author SummaryFormation of healthy gametes depends on the accurate partitioning of genetic material in the daughter cells through meiosis. A hallmark of meiosis is the establishment of crossovers, which arise from physical exchange of DNA between the parental chromosomes during homologous recombination. Recombination is initiated via the induction of physiological DNA damage by the topoisomerase SPO-11 and its auxiliary factors. Abrogating SPO-11 activity prevents crossover formation, resulting in random chromosome segregation and generation of aneuploid gametes. While the underlying mechanisms of crossover formation are conserved between the sexes, several pieces of evidence indicate extensive sexual dimorphism. In our work we describe novel features of C. elegans spermatogenesis that reveal significant differences in the regulation of recombination compared to oogenesis. We find that in spermatogenesis crossover-promoting proteins can be recruited to chromosomes even in the absence of SPO-11 activity, a phenomenon not observed in the oogenic hermaphrodite germ line. Furthermore, removal of some auxiliary factors required for physiological break formation during oogenesis does not prevent crossover designation in spermatocytes. We show that the synaptonemal complex, tasked with keeping homologous chromosomes in proximity, exerts opposing roles in males and hermaphrodites by promoting and limiting the recruitment of SPO-11-independent crossover factors, respectively.

genetics↗

High-throughput behavioural phenotyping of 25 C. elegans disease models including patient-specific mutations

Genetic diagnosis is fast and cheap, challenging our capacity to evaluate the functional impact of novel disease-causing variants or identify potential therapeutics. Model organisms including C. elegans present the possibility of systematically modelling genetic diseases, yet robust, high-throughput methods have been lacking. Here we show that automated multi-dimensional behaviour tracking can detect phenotypes in 25 new C. elegans disease models spanning homozygous loss-of-function alleles and patient-specific single-amino-acid substitutions. We find that homozygous loss-of-function (LoF) mutants across diverse genetic pathways (including BORC, FLCN, and FNIP-2) exhibit strong, readily detectable abnormalities in posture, locomotion, and stimulus responses compared to wild-type animals. An smc-3 mutant strain--modelled by introducing a patient-identified missense change--causes developmental anomalies and distinct behavioural profiles even though complete loss of SMC-3 is lethal. In contrast, patient-derived missense mutations in another essential gene, tnpo-2, did not show a strong phenotype initially but it could be "sensitized" chemically (e.g., with aldicarb), potentially facilitating future drug screens. Our findings show that scalable behavioural phenotyping can capture a wide range of mutant effects--from strong to subtle--in patient-avatar worm lines. We anticipate that this standardized approach will enable systematic drug repurposing for rare genetic disorders as new disease variants are discovered.

animal behavior and cognition↗

Two structurally mobile regions control the conformation and function of metamorphic meiotic HORMAD proteins

Metamorphic HORMA domain proteins (HORMADs) nucleate protein complex formation by refolding their mobile safety belt region to bind short motifs on interactors. Meiotic HORMADs (mHORMADs) bind proteinaceous axial elements to orchestrate complex chromosomal events that underpin fertility, including pairing and recombination between homologous chromosomes. However, the mechanisms supporting the diverse roles of mHORMADs remain unclear. Here, we show that mHORMADs have a second structurally mobile region, the {beta}5-C loop, which controls mHORMAD conformation and function. Molecular dynamics and in vivo approaches show that functional specialisation of C. elegans paralogs HTP-1 and HTP-2 depends on the interplay between their {beta}5-C loop and safety belt. The {beta}5-C loop can interact with the same HORMA core surface as the safety belt, forming a "loop engaged" conformation. The {beta}5-C loop HORMA core interaction is essential for axis loading of HTP-1 and its paralog HTP-3, and is also present in yeast, plant, and mammalian mHORMADs, suggesting that it represents a conserved functional feature of mHORMADs. Our study reveals that mHORMADs have expanded the bimodal folding landscape first identified in Mad2, paving the way to elucidate how non-canonical HORMAD conformations control meiotic chromosome function to ensure fertility.

molecular biology↗

Pipeline for transferring annotations between proteins beyond globular domains

BackgroundDisProt is the primary repository of Intrinsically Disordered Proteins. This database is manually curated and the annotations there have strong experimental support. Currently DisProt contains a relatively small number of proteins highlighting the importance of transferring verified disorder and other annotations, in such a way as to increase the number of proteins that could benefit from this valuable information. While the principles and practicalities of homology transfer are well-established for globular proteins, these are largely lacking for disordered proteins. MethodsWe used DisProt to evaluate the transferability of the annotation terms to orthologous proteins. For each protein, we looked for their orthologs, with the assumption that they will have a similar function. Then, for each protein and their orthologs we made multiple sequence alignments (MSAs). Global and regional quality of the MSAs was evaluated with the NorMD score. ResultsWe have designed a pipeline to obtain good quality MSAs and to transfer annotations from any protein to their orthologs. Applying the pipeline to DisProt proteins, from the 1931 entries with 5,623 annotations we can reach 97,555 orthologs and transfer a total of 301,190 terms by homology. We also provide a web server for consulting the results of DisProt proteins and execute the pipeline for any other protein. The server Homology Transfer IDP (HoTIDP) is accessible at http://hotidp.leloir.org.ar.

bioinformatics↗

The kleisin subunit controls the function of meiotic cohesins by determining the mode of DNA binding and differential regulation by SCC-2 and WAPL-1

The cohesin complex plays essential roles in chromosome segregation, 3D genome organisation, and DNA damage repair through its ability to modify DNA topology. In higher eukaryotes, meiotic chromosome function, and therefore fertility, requires cohesin complexes containing meiosis-specific kleisin subunits: REC8 and RAD21L in mammals and REC-8 and COH-3/4 in C. elegans. How these complexes perform the multiple functions of cohesin during meiosis and whether this involves different modes of DNA binding or dynamic association with chromosomes is poorly understood. Combining time-resolved methods of protein removal with live imaging and exploiting the temporospatial organisation of the C. elegans germline, we show that REC-8 complexes provide sister chromatid cohesion (SCC) and DNA repair, while COH-3/4 complexes control higher-order chromosome structure. High-abundance COH-3/4 complexes associate dynamically with individual chromatids in a manner dependent on cohesin loading (SCC-2) and removal (WAPL-1) factors. In contrast, low-abundance REC-8 complexes associate stably with chromosomes, tethering sister chromatids from S-phase until the meiotic divisions. Our results reveal that kleisin identity determines the function of meiotic cohesin by controlling the mode and regulation of cohesin-DNA association, and are consistent with a model in which SCC and DNA looping are performed by variant cohesin complexes that coexist on chromosomes.

cell biology↗

GRAS-1 is a conserved novel regulator of early meiotic chromosome dynamics in C. elegans

Chromosome movements and licensing of synapsis must be tightly regulated during early meiosis to ensure accurate chromosome segregation and avoid aneuploidy, although how these steps are coordinated is not fully understood. Here we show that GRAS-1, the worm homolog of mammalian GRASP/Tamalin and CYTIP, coordinates early meiotic events with cytoskeletal forces outside the nucleus. GRAS-1 localizes close to the nuclear envelope (NE) in early prophase I and interacts with NE and cytoskeleton proteins. Delayed homologous chromosome pairing, synaptonemal complex (SC) assembly, and DNA double-strand break repair progression are partially rescued by the expression of human CYTIP in gras-1 mutants, supporting functional conservation. However, Tamalin, Cytip double knockout mice do not exhibit obvious fertility or meiotic defects, suggesting evolutionary differences between mammals. gras-1 mutants show accelerated chromosome movement during early prophase I, implicating GRAS-1 in regulating chromosome dynamics. GRAS-1-mediated regulation of chromosome movement is DHC-1-dependent, placing it acting within the LINC-controlled pathway, and depends on GRAS-1 phosphorylation at a C-terminal S/T cluster. We propose that GRAS-1 serves as a scaffold for a multi-protein complex coordinating the early steps of homology search and licensing of SC assembly by regulating the pace of chromosome movement in early prophase I.

cell biology↗

Cohesin is required for meiotic spindle assembly independent of its role in cohesion in C. elegans

Accurate chromosome segregation requires a cohesin-mediated physical attachment between chromosomes that are to be segregated apart, and a bipolar spindle with microtubule plus ends emanating from exactly two poles toward the paired chromosomes. We asked whether the striking bipolar structure of C. elegans meiotic chromosomes is required for bipolarity of acentriolar female meiotic spindles by analyzing mutants that lack cohesion between chromosomes. Both a spo-11, rec-8, coh-3, coh-4 quadruple mutant and a spo-11, rec-8 double mutant entered M phase with single chromatids lacking any cohesion. However, the quadruple mutant formed an apolar spindle whereas the double mutant formed a bipolar spindle that segregated chromatids into two roughly equal masses. Residual non-cohesive COH-3/4-dependent cohesin on single chromatids of the double mutant was sufficient to recruit haspin- dependent Aurora B kinase, which regulated the localization of the spindle-assembly factors CLASP-2 and kinesin-13 to mediate bipolar spindle assembly in the apparent absence of chromosomal bipolarity. These results demonstrate that cohesin is essential for spindle assembly and chromosome segregation independent of its role in sister chromatid cohesion.

cell biology↗

DisPhaseDB, an integrative database of diseases related variations in liquid-liquid phase separation proteins

MotivationProteins involved in liquid-liquid phase separation (LLPS) and membraneless organelles (MLOs) are recognized to be decisive for many biological processes and also responsible for several diseases. The recent explosion of research in the area still lacks tools for the analysis and data integration among different repositories. Currently, there is not a comprehensive and dedicated database that collects all disease-related variations in combination with the protein location, biological role in the MLO and all the metadata available for each protein and disease. Disease related protein variants and additional features are dispersed and the user has to navigate many databases, with different focus, formats and often not user friendly. ResultsWe present DisPhaseDB, a database dedicated to disease related variants of LLPS proteins and/or are involved in MLOs. It integrates 10 databases, contains 5.741 proteins, 1.660.059 variants and 4.051 disease terms. It also offers intuitive navigation and an informative display. It constitutes a pivotal starting point for further analysis, encouraging the development of new computational tools. Availability and ImplementationThe database is freely available at http://disphasedb.leloir.org.ar. Contactjiserte@leloir.org.ar and cmb@leloir.org.ar Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=169 SRC="FIGDIR/small/479026v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@b4e706org.highwire.dtl.DTLVardef@ab75bforg.highwire.dtl.DTLVardef@bf70cborg.highwire.dtl.DTLVardef@8622e3_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

Single-molecule analysis reveals cooperative stimulation of Rad51 filament nucleation and growth by mediator proteins

Homologous recombination (HR) is an essential DNA double-strand break (DSBs) repair mechanism frequently inactivated in cancer. During HR, RAD51 forms nucleoprotein filaments on RPA-coated resected DNA and catalyses strand invasion into homologous duplex DNA. How RAD51 displaces RPA and assembles into long HR-proficient filaments remains uncertain. Here, we employ single-molecule imaging to investigate the mechanism of nematode RAD-51 filament growth in the presence of BRC-2 (BRCA2) and RAD-51 paralogs, RFS-1/RIP-1. BRC-2 nucleates RAD-51 on RPA-coated DNA, while RFS-1/RIP-1 acts as a chaperone to promote 3 to 5 filament growth via highly dynamic engagement with 5 filament ends. Inhibiting ATPase or mutation in RFS-1 Walker box leads to RFS-1/RIP-1 retention on RAD-51 filaments and hinders growth. rfs-1 Walker box mutants display sensitivity to DNA damage and accumulate RAD-51 complexes non-functional for HR in vivo. Our work reveals the mechanism of RAD-51 nucleation and filament growth in the presence of recombination mediators.

biophysics↗

Phosphoregulation of HORMA domain protein HIM-3 promotes asymmetric synaptonemal complex disassembly in meiotic prophase in C. elegans

In the two cell divisions of meiosis, diploid genomes are reduced into complementary haploid sets through the discrete, two-step removal of chromosome cohesion, a task carried out in most eukaryotes by protecting cohesion at the centromere until the second division. In eukaryotes without defined centromeres, however, alternative strategies have been innovated. The best-understood of these is that used by the nematode Caenorhabditis elegans, where upon division of the chromosome into two segments or arms by the single off-center crossover, several chromosome-associated proteins or post-translational modifications become specifically partitioned to either the short or long arm, where they affect the timing of cohesion loss through as-yet unknown mechanisms. Here, we investigate the meiotic axis HORMA-domain protein HIM-3 and show that it becomes phosphorylated at its C-terminus, within the conserved “closure motif” region bound by the related HORMA-domain proteins HTP-1 and HTP-2. Binding of HTP-2 is abrogated by phosphorylation of the closure motif in in vitro assays, strongly suggesting that in vivo phosphorylation of HIM-3 likely modulates the hierarchical structure of the chromosome axis. Phosphorylation of HIM-3 only occurs on synapsed chromosomes, and similarly to previously-described phosphorylated proteins of the synaptonemal complex, becomes restricted to the short arm after designation of crossover recombination sites. Regulation of HIM-3 phosphorylation status is required for timely disassembly of synaptonemal complex central elements from the long arm, and is also required for proper timing of HTP-1 and HTP-2 dissociation from the short arm. Phosphorylation of HIM-3 thus plays a role in establishing the identity of short and long arms, thereby contributing to the robustness of the two-step chromosome segregation.Competing Interest StatementThe authors have declared no competing interest.View Full Text

cell biology↗

Reactivation of chromosome signalling induces reversal of the meiotic program

Chromosome movements and programmed DNA double-strand breaks (DSBs) promote homologue pairing and initiate recombination at meiosis onset. Meiotic progression involves checkpoint-controlled termination of these events when all homologue pairs achieve synapsis and form crossover precursors. We show that termination of chromosome movement and DSB formation is reversible and is continuously implemented by the synaptonemal complex (SC), which silences chromosome signals that promote CHK-2 activity. Forced removal of the SC or different meiosis-specific cohesin complexes, which are individually required for SC stability, causes rapid CHK-2-dependent reinstallation of the DSB-formation and chromosome-movement machinery. This nuclear reorganization occurs without transcriptional changes, but requires signalling from HORMA protein HTP-1. Conversely, CHK-2 inactivation causes rapid disassembly of the DSB-formation and chromosome-movement machinery. Thus, nuclear organization is constantly controlled by the level of CHK-2 activity. Our results uncover an unexpected plasticity of the meiotic program and show how chromosome signalling integrates nuclear organization with meiotic progression.

cell biology↗

Spatial Regulation of Polo-like Kinase Activity during C. elegans Meiosis by the Nucleoplasmic HAL-2/HAL-3 Complex

Proper partitioning of homologous chromosomes during meiosis relies on the coordinated execution of multiple interconnected events: Homologs must locate, recognize and align with their correct pairing partners. Further, homolog pairing must be coupled to assembly of the synaptonemal complex (SC), a meiosis-specific tripartite structure that maintains stable associations between the axes of aligned homologs and regulates formation of crossovers between their DNA molecules to create linkages that enable their segregation. Here we identify HAL-3 (Homolog Alignment 3) as an important player in coordinating these key events during C. elegans meiosis. HAL-3 and the previously-identified HAL-2 are interacting and interdependent components of a protein complex that localizes to the nucleoplasm of germ cells. hal-3 (or hal-2) mutants exhibit multiple meiotic prophase defects including failure to establish homolog pairing, inappropriate loading of SC subunits onto unpaired chromosome axes, and premature loss of synapsis checkpoint protein PCH-2. Further, loss of hal function results in misregulation of the subcellular localization and activity of polo-like kinases (PLK-1 and PLK-2), which dynamically localize to different defined subnuclear sites during wild-type prophase progression to regulate distinct cellular events. Moreover, loss of PLK-2 activity partially restores tripartite SC structure in a hal mutant background, suggesting that the defect in pairwise SC assembly in hal mutants reflects inappropriate PLK activity. Together our data support a model in which the nucleoplasmic HAL-2/HAL-3 protein complex constrains both localization and activity of meiotic Polo-like kinases, thereby preventing premature interaction with stage-inappropriate targets.

genetics↗

Evolutionary analysis implicates RNA polymerase II pausing and chromatin structure in nematode piRNA biogenesis

Piwi-interacting RNAs (piRNAs) control transposable elements widely across metazoans but have rapidly evolving biogenesis pathways. In Caenorhabditis elegans, almost all piRNA loci are found within two 3Mb clusters on Chromosome IV. Each piRNA locus possesses an upstream motif that recruits RNA polymerase II to produce a [~]28 nt precursor transcript. Here, we use comparative epigenomics across nematodes to gain insight into piRNA biogenesis. We show that the piRNA upstream motif is derived from core promoter elements controlling snRNA biogenesis. We describe two alternative modes of piRNA organisation in nematodes: in C. elegans and closely related nematodes, piRNAs are clustered within repressive H3K27me3 chromatin, whilst in other species, typified by Pristionchus pacificus, piRNAs are distributed genome-wide within introns of actively transcribed genes. In both groups, piRNA production depends on downstream sequence signals associated with RNA polymerase II pausing, which synergise with the chromatin environment to control piRNA precursor transcription.

genomics↗

Co-mutation and exclusion analysis in human tumors, a means for cancer biology studies and treatment design

BackgroundMalignant tumors originate from genomic and epigenomic alterations, which lead to loss of control of the cellular circuitry. These alterations relate with each other in patterns of mutual exclusion and co-occurrence that affect prognosis and treatment response and highlight the need for multitargeted therapy. However, to the best of our knowledge, there are no systematic reports in the literature of co-dependent and mutually exclusive mutations across all types of cancer. In addition, the studies reported so far generally deal with whole genes instead of specific mutations, ignoring the fact that different alterations in the same gene can have widely different effects.\n\nResultsHere we present a systematic analysis of co-dependencies of somatic mutations across all cancer types. Combining multi testing with conditional and expected mutational probabilities, we have found pairs and networks of co-mutations and exclusions, some of them in particular types of cancer and others widespread. We have also determined that driver loci are present in more types of cancer than non driver loci, that they tend to pair within a single gene and that those pairs are more often exclusions than co-mutations.\n\nConclusionsBased on this properties, we propose new drivers that warrant experimental validation. Our analysis is potentially relevant for cancer biology and classification, as well as for the rational selection of multitargeted therapeutic approaches.

cancer biology↗