Biology subjects

Pereira, C.

Publications and source records attributed to Pereira, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Shape2Fate: a morphology-aware deep learning framework for tracking endocytic and exocytic carriers at nanoscale.

Plasma membrane homeostasis requires balanced exocytosis and endocytosis, yet their coordination at the single-event level in non-neuronal cells is unresolved. We present Shape2Fate, a morphology-aware deep-learning pipeline that detects, tracks, and classifies individual exocytic and endocytic carriers in live-cell total internal reflection fluorescence structured illumination microscopy (TIRF-SIM) movies at [~]100 nm resolution. Trained on synthetic data and exploiting carrier shape evolution rather than fluorescence intensity, Shape2Fate achieves expert-level tracking and outcome classification across diverse cell types, imaging conditions, and microscope platforms. Applying Shape2Fate to constitutive secretion and insulin-stimulated GLUT4 exocytosis in adipocytes, we uncover two opposing exo-endocytic coupling architectures: exocytic fusion locally nucleates de novo clathrin-coated pits, whereas GLUT4 vesicles target pre-existing pits for rapid cargo capture. These findings establish that the spatial rules governing exo-endocytic coordination are not universal but are pathway-specific. Shape2Fate is openly available, enabling direct event-level mechanistic dissection of exo-endocytic coordination across pathways in living cells.

cell biology↗

bioRxiv2025

Data-driven Cognitive Clusters in Persistent Developmental Dyslexia

Developmental dyslexia is a neurodevelopmental condition characterized by persistent reading difficulties despite adequate intelligence and educational opportunities. The cognitive underpinnings of dyslexia remain incompletely understood. Although multiple causal pathways have been proposed, there is a gap in studies that can reliably identify dyslexia subtypes based on comprehensive evaluations that go beyond measures of reading and phonology. We employed one of the largest detailed samples of children with developmental dyslexia resistant to intervention, consisting of 147 extensively phenotyped school-age children aged 7-14 years who were recruited from specialized schools for students with learning differences. We implemented data-driven analyses leveraging a comprehensive neuropsychological assessment to delineate cognitive subdomains and characterize the heterogeneity in the sample. Hierarchical clustering of 24 cognitive measures aided in constructing a framework to subsequently interpret emerging clusters. Four clusters emerged, predominantly associated with: Processing Speed & Executive Function, Visuospatial & Mathematical Reasoning, Phonological Manipulation, and Verbal Short-term Memory & Word Retrieval. Subsequent latent profile analysis identified two distinct dyslexia profiles: one characterized by marked difficulties in executive functioning and processing speed, and another displaying impairments primarily in verbal short-term memory and word retrieval relative to the other profile. Importantly, both profiles exhibited comparable severity of persistent reading difficulties despite their divergent cognitive profiles. These findings show that phenotypically similar reading impairments can arise from distinct underlying cognitive factors, emphasizing the role of comprehensive neuropsychological evaluation in developing tailored interventions for affected children.

neuroscience↗

bioRxiv2025

The Golgi vesicle tether p115/USO1 can bind directly to the ER exit site organiser Sec16A

Newly-made secretory and membrane proteins exit the endoplasmic reticulum (ER) in COPII vesicles that form at specialised ER exit sites. These exit sites are typically near to the early Golgi compartments that receive these vesicles. A key player in the delivery of vesicles to the early Golgi is p115 (USO1), a homodimer with a folded head domain and a coiled-coil tail that is anchored to Golgi membranes. p115 has been shown to capture vesicles and to bind to SNARE proteins to promote membrane fusion. Here we report that the head domain of human p115 can bind directly to Sec16A, a large scaffolding protein that organises ER sites and promotes COPII vesicle formation. Structural prediction and deletion mapping define the region of interaction to a conserved motif in the unstructured N-terminal region of Sec16A, and mutations in p115 that block motif binding reduce the efficiency of secretion. This interaction could potentially allow a subset of p115 molecules to reach across from the early Golgi to the ER exit sites to contribute to the large-scale organisation of the early secretory pathway.

cell biology↗

bioRxiv2025

LLM-Assisted Functional Gene Annotation

Functional gene annotation is a highly manual and subjective process that requires analysis of large amounts of statistical and literature results. Here we present Artificial Intelligence Gene Enrichment (AIGE), a careful automation of the current state of the art process used by bioinformatic experts to deter-mine functions enriched in novel or experimentally derived gene lists. In 1206 test cases, AIGE is able to accurately recover 87% of biological functions, path-ways, and cell types, is robust to noise contamination, and accurately assesses its own self-confidence. AIGE reports provide accurate functional annotations and encourage further research in a broad set of contexts.

bioinformatics↗

bioRxiv2025

External and Internal Load Profiles of Male and Female Participants during a Walking Football Practice

BACKGROUNDHigh levels of sedentary behavior among older adults highlight the importance of walking football (WF) in promoting physical activity for healthy aging. This study examines the external and internal load profiles of male and female participants during a WF tournament, addressing a gap in research on game demands and induced load. METHODSThe study involved 176 players aged 50+ participating in a 40-min, 5v5 WF tournament with unlimited substitutions. External load (total and categorized distances) was measured using Global Positioning System (GPS), while heart rate (HR) monitors assessed internal load, including absolute HR and intensity zones based on %HRmax. RESULTSThe proportion of male participants (n=123; 70.3%) was higher than females (n=52; 29.7%), p<.001. They were similar in age (61.6{+/-}8.6 and 60.8{+/-}6.9, respectively). Males covered a higher distance per minute than females, with sex showing a moderate effect (63.3{+/-}10.7 m/min vs. 54.7{+/-}15.8 m/min; p < .001; Cohens dunbiased = 0.69 [0.36; 1.03]), especially in fast walking (41.7{+/-}12.2 m/min vs. 32.6{+/-}16.7 m/min; p < .001; Cohens dunbiased = 0.66 [0.33; 1.00]). Males played more time than females (22:26{+/-}09:47 min:ss vs. 15:41{+/-}07:46 min:ss; p<.001), with moderate effect (Cohens dunbiased = 0.73 [0.40; 1.06]). However, no differences between sexes were identified in the internal load variables, such that the female average %HRmax was 80{+/-}11% and the male was 82{+/-}8% during the practice. CONCLUSIONSOverall, while males generally exhibit higher external loads in WF, both sexes experience similar internal load demands, highlighting WFs potential as a scalable, health-promoting intervention for aging populations.

physiology↗

bioRxiv2024

Myocardial disarray drives metabolic inefficiency in human cardiomyocytes

Adult cardiomyocytes are embedded within a highly organized myocardial microenvironment that imposes critical geometric cues essential for the alignment and distribution of organelles and the shaping of their unique, rectangular cellular morphology. Despite the association of cardiomyocyte disarray with human heart disease, the functional consequences of this cellular disorganization remain poorly understood. Here, we leveraged micropatterned substrates to promote structural alignment in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), contrasting the effects of mechanical alignment on mitochondrial form and function with hiPSC-CMs cultured under standard unconstrained conditions. Cardiomyocytes cultured under unconstrained conditions exhibited misaligned sarcomeres and a perinuclear mitochondrial distribution while micropatterned hiPSC-CMs developed linear myofibrils and reconfigured sarcomere and mitochondrial organization, which increased mitochondrial respiration without augmenting mitochondrial mass. Notably, micropatterned hiPSC-CMs exhibited an increased number of mitochondrial-associated membranes, as determined by proximity ligation assays and transmission electron microscopy, suggesting enhanced interactions between the sarcoplasmic reticulum and mitochondria. Together, these findings demonstrate that mitochondrial-sarcoplasmic architecture and geometry are critical spatial features that ensure bioenergetic efficiency of cardiomyocytes. This work underscores the importance of cellular organization in cardiomyocyte metabolism and function, providing insights into the pathophysiology of cardiac diseases marked by cellular disarray.

cell biology↗

bioRxiv2024

Shifting Routes: Plant Specific Insert trafficking and function in Arabidopsis seedlings under abiotic stress

Due to plants inability to escape adverse conditions, they must adapt and adjust their endomembrane system through protein sorting and distribution. Cardosins A and B are key models for studying intracellular trafficking. They are aspartic proteinases in thistle flowers that mediate different vacuolar pathways despite sharing high sequence similarity, and both are responsive to stress conditions. The Plant Specific Insert (PSI) is a 100 amino acid domain found in these proteins. It is known that stress can impact protein sorting, shifting it from the conventional pathway (ER-Golgi) to a Golgi-independent route. In this work we assessed changes in the expression and localization of PSI from Cardosin B (PSI B) in Arabidopsis plants overexpressing PSI B-mCherry submitted to different abiotic stress conditions (saline, hydric, oxidative, metals). Aside from potential PSI B localization changes, we focused on characterizing the homozygous line, alongside assessing several biometric parameters and biochemical endpoints. The results revealed that the PSI B line responded differently depending on the stress conditions. Biometric and biochemical analyses emphasized the roles of PSI B in enhancing plant fitness and supporting adaptation to abiotic stress. Besides, confocal microscopy allowed us to find PSI B accumulation in Endoplasmic Reticulum-derived vesicles (ER bodies), indicating a shift from the common PSI B-mediated route. These findings underscore the role of PSI B in enhancing plant fitness and adaptation to abiotic stress through altered protein trafficking. HighlightPSI B has an active role in enhancing plant fitness, revealing its value in adaptation and tolerance to abiotic stress by adjusting its localization and trafficking under challenging environments.

plant biology↗

bioRxiv2024

The p.H222P lamin A/C mutation induces heart failure via impaired mitochondrial calcium uptake in human cardiac laminopathy

BackgroundMutations in the LMNA gene, which encodes lamin A/C, cause a variety of diseases known as laminopathies. Some mutations are particularly associated with the occurrence of dilated cardiomyopathy and heart failure, but the genotype-phenotype relationship and underlying mechanisms are unclear. Here, we used induced pluripotent stem cells (hiPSCs) from a patient carrying a LMNA point mutation (c.665A>C, p.His222Pro) to investigate the mechanisms leading to contractile dysfunction. MethodsLMNA p.H222P mutant and a CRISPR/Cas9 corrected isogenic control hiPSCs clones were differentiated into cardiomyocytes (hiPSC-CMs). Immunofluorescence staining was performed on hiPSC-CMs to quantify their sarcomere organization (SarcOrgScore) using a Matlab code. Ring-shaped cardiac 3D organoids were generated to compare the contractile properties of the two clones. Calcium transients in mutant and corrected hiPSC-CMs were measured by live confocal imaging. Mitochondrial respiration parameters were measured by Seahorse. ResultshiPSC-CMs were generated from the LMNA mutant and the corrected hiPSCs with no difference in the differentiation yield (proportion of troponin-positive cells: 95.0% for LMNA p.H222P vs. 95.1% for Ctrl-iso1, p=0.726). hiPSC-CMs displayed well-formed sarcomeres and their organization was similar between the two cell lines. However, cardiac 3D organoids generated with LMNA p.H222P hiPSC-CMs showed an impaired contractility compared to control organoids. Calcium transient recordings in LMNA p.H222P mutant cardiomyocytes showed a significantly higher calcium transient amplitude with a significantly slower calcium re-uptake. Transcriptomic analyses suggested a global mitochondrial dysfunction and in particular an impaired mitochondrial calcium uptake with a significantly decreased expression of the mitochondrial calcium uniporter (MCU). This decrease in MCU expression was confirmed by western blot and was accompanied by an increased MICU1:MCU, as well as an increased PDH Ser232 and PDH Ser300 phosphorylation, indicating a decreased mitochondrial calcium uptake in the LMNA mutant hiPSC-CMs. Measurement of mitochondrial respiration showed lower basal and maximal respiration in LMNA p.H222P hiPSC-CMs. Consistently, the ATP levels were significantly lower in LMNA p.H222P hiPSC-CMs as compared to isogenic controls. ConclusionsLMNA p.H222P mutant hiPSC-CMs exhibit contractile dysfunction associated with mitochondrial dysfunction with impaired MCU complex activity, decreased mitochondrial calcium homeostasis and reduced mitochondrial energy production. NOVELTY AND SIGNIFICANCEO_ST_ABSWhat is known?C_ST_ABS- Mutations in LMNA, which encodes the nuclear lamins A/C, cause a variety of diseases (called laminopathies), which can involve the cardiac muscle leading to dilated cardiomyopathy and systolic heart failure. - The pathological mechanisms linking the nuclear envelope abnormalities induced by LMNA mutations to the development of a reduced cardiac muscle contractility are not well understood. What new information does this article contribute?- LMNA mutant cardiomyocytes have a profound mitochondrial dysfunction with impaired MCU complex activity, decreased mitochondrial calcium homeostasis, and reduced mitochondrial energy production. - Our study uncovers an unappreciated pathophysiological mechanism and opens new possibilities by suggesting MCU activators as a novel therapeutic for patients with LMNA cardiomyopathy.

pathology↗

bioRxiv2024

Evaluating phasic transcutaneous vagus nerve stimulation (taVNS) with pupil dilation: the importance of stimulation intensity and sensory perception

The efficacy of transcutaneous auricular vagus nerve stimulation (taVNS) as a non-invasive method to modulate physiological markers of noradrenergic activity of the Locus Coeruleus (LC), such as pupil dilation, is increasingly more discussed. However, taVNS studies show high heterogeneity of stimulation effects. Therefore, a taVNS setup was established here to test different frequencies (10 Hz and 25 Hz) and intensities (3 mA and 5 mA) during phasic stimulation (3 s) with time-synchronous recording of pupil dilation in younger adults. Specifically, phasic real taVNS and higher intensity led to increased pupil dilation, which is consistent with phasic invasive VNS studies in animals. The results also suggest that the influence of intensity on pupil dilation may be stronger than that of frequency. However, there was an attenuation of taVNS-induced pupil dilation when differences in perception of sensations were considered. Specifically, pupil dilation during phasic stimulation increased with perceived stimulation intensity. The extent to which the effect of taVNS induces pupil dilation and the involvement of sensory perception in the stimulation process are discussed here and require more extensive research. Additionally, it is crucial to strive for comparable stimulation sensations during systematic parameter testing in order to investigate possible effects of phasic taVNS on pupil dilation in more detail.

neuroscience↗

bioRxiv2024

The widely used cymoxanil fungicide impairs respiration in Saccharomyces cerevisiae via cytochrome c oxidase inhibition

Cymoxanil (CYM) is a synthetic acetamide fungicide that has been widely used to combat downy mildew diseases in grapevine cultures and late blight diseases in tomato and potato caused by the oomycetes Plasmopara viticola and Phytophthora infestans, respectively. Despite its extensive application, the biochemical mode of action of CYM remains elusive. Previous reports indicate that CYM affects growth, DNA and RNA synthesis in Phytophthora and inhibits cell growth, biomass production and respiration rate in the well-characterized fungal model Saccharomyces cerevisiae. We therefore used this model to further characterize the effect of CYM on mitochondria. We found that CYM inhibits oxygen consumption in whole cells after 3 h of exposure, which persists over time. Using isolated mitochondria, we demonstrated that CYM specifically inhibits cytochrome c oxidase (CcO) activity during oxidative phosphorylation. Based on molecular docking algorithms, we propose that CYM acts by blocking the interaction of cytochrome c (cyt c) with CcO, hampering electron transfer and inhibiting CcO catalytic activity. Although other targets cannot be excluded, our data offer valuable insights into the mode of action of CYM that can be instrumental to drive informed management of the use of this fungicide.

biochemistry↗

bioRxiv2023

Structural and functional characterization of the NF-κB-targeting toxin AIP56 from Photobacterium damselae subsp. piscicida reveals a novel mechanism for membrane interaction and translocation

Bacterial AB toxins are secreted virulence factors that are internalized by target cells through receptor-mediated endocytosis, translocating their enzymatic domain to the cytosol from endosomes (short-trip) or the endoplasmic reticulum (long-trip). To accomplish this, they evolved a multidomain structure organized into either a single polypeptide chain or non-covalently associated polypeptide chains. The prototypical short-trip single-chain toxin is characterized by a receptor-binding domain that confers cellular specificity and a translocation domain responsible for pore formation whereby the catalytic domain translocates to the cytosol in an endosomal acidification-dependent way. In this work, the resolution of the three-dimensional structure of AIP56 showed that instead of a two-domain organization, as previously predicted, AIP56 has a three-domain organization, with a NleC-like catalytic domain associated with a small middle domain that contains the linker-peptide, followed by the receptor-binding domain. In contrast to prototypical single-chain AB toxins, AIP56 does not comprise a typical structurally complex translocation domain; instead, the elements involved in translocation are scattered across its domains. Thus, the catalytic domain contains a helical hairpin that serves as a molecular switch for triggering the conformational changes necessary for membrane insertion only with endosomal acidification, whereas the middle and receptor-binding domains are required for pore formation. Considering the increasing number of putative AIP56 homologous toxins in databases, the data presented here have implications far beyond the AIP56 intoxication process and the virulence of Phdp.

microbiology↗

bioRxiv2023

A versatile high-throughput assay based on 3D ring-shaped cardiac tissues generated from human induced pluripotent stem cell derived cardiomyocytes

We developed a 96-well plate assay which allows fast, reproducible and high-throughput generation of 3D cardiac rings around a deformable optically transparent hydrogel (PEG) pillar of known stiffness. Human induced pluripotent stem cell-derived cardiomyocytes, mixed with normal human adult dermal fibroblasts in an optimized 3:1 ratio, self-organized to form ring-shaped cardiac constructs. Immunostaining showed that the fibroblasts form a basal layer in contact with the glass, stabilizing the muscular fiber above. Tissues started contracting around the pillar at D1 and their fractional shortening increased until D7, reaching a plateau at 25{+/-}1%, that was maintained up to 14 days. The average stress, calculated from the compaction of the central pillar during contractions, was 1.4{+/-}0.4 mN/mm2. The cardiac constructs recapitulated expected inotropic responses to calcium and various drugs (isoproterenol, verapamil) as well as the arrhythmogenic effects of dofetilide. This versatile high-throughput assay allows multiple in situ mechanical and structural read-outs.

bioengineering↗

bioRxiv2022

Oxygen is a critical regulator of cellular metabolism and function in cell culture

Cell culture is generally considered to be hyperoxic. However, the importance of cellular oxygen consumption is often underappreciated, with rates of oxygen consumption often sufficient to cause hypoxia at cell monolayers. We initially focused on cultured adipocytes as a terminally differentiated cell-type with substantial oxygen consumption rates to support diverse cellular functions. Under standard conditions, cultured adipocytes are hypoxic and highly glycolytic. Increasing oxygen diverted glucose flux toward mitochondria and resulted in thousands of gene expression changes that pointed toward alleviated physiological transcriptional responses to hypoxia. Phenotypically, providing more oxygen increased adipokine secretion and rendered adipocytes more sensitive to insulin and lipolytic stimuli. The functional benefits of increasing pericellular oxygen were transferable to other cellular systems including hPSC-derived hepatocytes and cardiac organoids. Our findings suggest that oxygen is limiting in many terminally-differentiated cell culture systems, and that controlling oxygen availability can improve the quality and translatability of cell models.

cell biology↗

bioRxiv2022

The exocyst complex is an essential component of the mammalian constitutive secretory pathway

Secreted proteins fulfil a vast array of different functions, including adaptive immunity, cell signalling and extracellular matrix remodelling. In the trans-Golgi network, proteins destined for constitutive secretion are sorted into post-Golgi carriers which fuse with the plasma membrane to deliver their contents to the extracellular space. The molecular machinery involved is poorly understood. Here, we have used kinetic trafficking assays and transient CRISPR knock-outs to study the biosynthetic sorting route from the Golgi apparatus to the plasma membrane. Depletion of core-exocyst subunits reduces carrier fusion and causes cargo accumulation in the post-Golgi carriers. Exocyst subunits co-localise with carriers fusing at the plasma membrane and we show that the exocyst complex is recruited directly to these carriers. Abrogation of exocyst followed by kinetic trafficking assays with multiple different soluble cargoes results in cargo accumulation of all tested cargoes. Unbiased secretomics reveals a drastic reduction in the secretion of soluble proteins to the extracellular milieu after knock-out of exocyst subunits. Importantly, the knock-out of exocyst subunits in specialised secretory cell types prevents the constitutive secretion of antibodies in lymphocytes and of the hormones leptin and adiponectin in adipocytes. Together these data identify the exocyst complex as the functional tether of secretory post-Golgi carriers at the plasma membrane and an essential component of the mammalian constitutive secretory pathway.

cell biology↗

bioRxiv2022

Thermopriming-associated proteome and sugar content responses in Pinus radiata embryogenic tissue

Improving the capacity of plants to face adverse environmental conditions requires a deep understanding of the molecular mechanisms governing stress response and adaptation. Proteomics, combined with metabolic analyses, offers a wide resource of information to be used in plant breeding programs. Previous studies have shown that somatic embryogenesis in Pinus spp. is a suitable tool not only to investigate stress response processes but also to modulate the behaviour of somatic plants. Based on this, the objective of this study was to analyse the protein and soluble sugar profiles of Pinus radiata embryonal masses after the application of high temperatures to unravel the mechanisms involved in thermopriming and memory acquisition at early stages of the somatic embryogenesis process. Results confirmed that heat provokes deep readjustments in the life-cycle of proteins, together with a significant reduction in the carbon-flux of central-metabolism pathways. Heat-priming also promotes the accumulation of proteins involved in oxidative stress defence, in the synthesis of specific amino acids such as isoleucine, influences cell division, the organization of the cytoskeleton and cell-walls, and modifies the levels of free soluble sugars like glucose or fructose. All this seems to be regulated by proteins linked with epigenetic, transcriptional and post-transcriptional mechanisms.

plant biology↗

bioRxiv2021

Sequencing Micronuclei Reveals the Landscape of Chromosomal Instability

Genome instability (GIN) is a main contributing factor to congenital and somatic diseases, but its sporadic occurrence in individual cell cycles makes it difficult to study mechanistically. One profound manifestation of GIN is the formation of micronuclei (MN), the engulfment of chromosomes or chromosome fragments in their own nuclear structures separate from the main nucleus. Here, we developed MN-seq, an approach for sequencing the DNA contained within micronuclei. We applied MN-seq to mice with mutations in Mcm4 and Rad9a, which disrupt DNA replication, repair, and damage responses. Data analysis and simulations show that centromere presence, fragment length, and a heterogenous landscape of chromosomal fragility all contribute to the patterns of DNA present within MN. In particular, we show that long genes, but also gene-poor regions, are associated with chromosome breaks that lead to the enrichment of particular genomic sequences in MN, in a genetic background-specific manner. Finally, we introduce single-cell micronucleus sequencing (scMN-seq), an approach to sequence the DNA present in MN of individual cells. Together, sequencing micronuclei provides a systematic approach for studying GIN and reveals novel molecular associations with chromosome breakage and segregation.

genomics↗

bioRxiv2021

Phosphoproteomics of ATR Signaling in Prophase I of Mouse Meiosis

During mammalian meiosis, the ATR kinase plays crucial roles in the coordination of DNA repair, meiotic sex chromosome inactivation and checkpoint signaling. Despite the importance of ATR in meiosis, the meiotic ATR signaling network remains largely unknown. Here we defined ATR signaling during prophase I in mice. Quantitative analysis of phosphoproteomes obtained after genetic ablation of the ATR-activating 9-1-1 complex or chemical inhibition of ATR revealed over 12,000 phosphorylation sites, of which 863 phosphorylation sites were dependent on both 9-1-1 and ATR. ATR and 9-1-1-dependent signaling was enriched for S/T-Q and S/T-X-X-K motifs and included proteins involved in DNA damage signaling, DNA repair, and piRNA and mRNA metabolism. We find that ATR targets the RNA processing factors SETX and RANBP3 and regulate their localization to the sex body. Overall, our analysis establishes a comprehensive map of ATR signaling in spermatocytes and highlights potential meiotic-specific actions of ATR during prophase I.

developmental biology↗

bioRxiv2021

Multiple 9-1-1 complexes promote homolog synapsis, DSB repair, and ATR signaling during mammalian meiosis

DNA damage response mechanisms have meiotic roles that ensure successful gamete formation. While completion of meiotic double-strand break (DSB) repair requires the canonical RAD9A-RAD1-HUS1 (9A-1-1) complex, mammalian meiocytes also express RAD9A and HUS1 paralogs, RAD9B and HUS1B, predicted to form alternative 9-1-1 complexes. The RAD1 subunit is shared by all predicted 9-1-1 complexes and localizes to meiotic chromosomes even in the absence of HUS1 and RAD9A. Here we report that testis-specific RAD1 disruption resulted in impaired DSB repair, germ cell depletion and infertility. Unlike Hus1 or Rad9a disruption, Rad1 loss also caused defects in homolog synapsis, ATR signaling and meiotic sex chromosome inactivation. Comprehensive testis phosphoproteomics revealed that RAD1 and ATR coordinately regulate numerous proteins involved in DSB repair, meiotic silencing, synaptonemal complex formation, and cohesion. Together, these results establish critical roles for both canonical and alternative 9-1-1 complexes in meiotic ATR activation and successful prophase I completion.

genetics↗