Biology subjects

Mango, S. E.

Publications and source records attributed to Mango, S. E..

16 recordsLinked to original sources

bioRxiv2026

Safeguarding epithelial junctions by a novel quality control pathway

Cell junctions establish and maintain epithelial architecture despite fluctuating environmental and developmental conditions. A central question is how cells respond to challenging conditions to preserve junctional integrity. Here, we report the discovery of a previously unrecognized quality control pathway that monitors epithelial junctions (J-QC). We used the (I)Caenorhabditis elegans(/I) epidermis as a model to investigate the DLG-1-AJM-1 complex (DAC), a junctional domain that is critical for embryonic morphogenesis. We identify two mechanisms that sustain junctional integrity: first, localized (I)dlg-1(/I) mRNA ensures appropriate DLG-1 protein levels at the junction; repositioning (I)dlg-1(/I) RNA reduces DLG-1 levels, leading to gaps between epithelial cells. Second, transcription of DAC components responds to perturbations that disrupt the DAC. This response is sequence-independent, distinguishing it from other quality control mechanisms. It is activated by perturbations of the DAC or cytoskeleton and requires the LINC complex component ZYG-12/HOOK1-3 to transduce information about junctional integrity to the nucleus. These findings define a novel junctional QC for epithelial maintenance.

cell biology↗

bioRxiv2026

The One Click Wonder: a retrained automated segmentation pipeline that enables quantitative and modular analysis of C. elegans embryos

High-throughput approaches have transformed the study of gene regulation by enabling quantitative, genome-scale analyses in both genomics and imaging. However, applying these methods to intact organisms remains challenging, particularly for high-throughput, 3D imaging. In Caenorhabditis elegans, generalist segmentation models often perform poorly due to rapid changes in nuclear size, shape, and density. To overcome this obstacle, we developed One Click Wonder (OCW), an automated pipeline that pairs a retrained Cellpose model with stage-specific parameter selection to deliver accurate, high-throughput segmentation of embryos. We further introduce the Biological Annotation and Association Mapper (BAAM), which integrates segmentation with spot detection, to enable single-cell quantitation. Applied to the pioneer factor pha-4/FoxA, this pipeline revealed distinct cell populations with an eight-fold range in transcriptional burst frequency. These findings demonstrate that OCW and BAAM provide a modular, scalable pipeline for quantitative, single-cell analysis of gene expression in C. elegans embryos.

bioinformatics↗

bioRxiv2025

Rapid canalization of chromosome conformation-transcription fingerprints during embryogenesis revealed by fully-automated cell identity decoding with CeSCALE

Genome organization into higher-order active and inactive compartments exhibits cell-type specific patterns, which are widely implicated in the regulation of transcriptional activity. During embryogenesis, epigenetic regulation controls cell type specification along cellular lineages with similar transcriptional identities through the coordinated action of chromatin states. However, prevalent single-molecule variability in higher-order chromosome conformation and a lack of precise cell lineage information have previously limited our understanding of the relationship between conformation and transcriptional activity in vivo. Specifically, how the conformation-transcription relationship is inherited along cellular lineages through cell divisions is poorly understood. Here, we developed a novel algorithm for cell lineage identification (C. elegans Sinkhorn-based Cell ALignmEnt, CeSCALE) combined with single cell genomics to reveal that local conformation-transcription fingerprints are associated with, and inherited along the stereotyped cellular lineages of C. elegans embryos. Inspired by Optimal Transport theory, CeSCALE provides a fully automated framework for quantifying lineage-resolved individual cell phenotypes in situ, across a wide developmental window. Combining CeSCALE with single-molecule chromosome tracing uncovered higher-order interchromosomal block associations, which surprisingly coalesce transcriptionally diverse domains and are independent of lineage identity. Instead, by integrating lineage-resolved chromosome conformations with single-cell transcriptomics, we find that local conformation-transcription spatial relationships ( fingerprints), containing both hubs and islands of transcriptional activity, are robustly inherited along lineages. Finally, we find that the canalization of these fingerprints represent the rewiring of chromatin states at key developmental stages. Our results suggest that local chromatin environments, but not large-scale compartments, coordinate the dramatically changing transcriptome during embryogenesis.

developmental biology↗

bioRxiv2025

Nuclear lamina-associated domain biogenesis is regulated by nuclear pore density during embryogenesis and mediates UV protection

Lamina-associated domains (LADs) are critical for genome organization and function, but their formation during development is not well understood. Here, we use DamID and image analysis to reveal the dynamics of LAD biogenesis during C. elegans embryogenesis. At early stages, DNA at the lamina is transcriptionally active and lacks lamina-associated heterochromatin. This state depends on abundant nuclear pores, which prevent heterochromatin accumulation at the nuclear periphery. As development proceeds, pore numbers decline, enabling heterochromatin to access the lamina. Reducing nuclear-pore components induces precocious accumulation of heterochromatin to the lamina. Functionally, we find that heterochromatic LADs confer protection against ultraviolet (UV) radiation. Older embryos are resistant to UV light and concentrate DNA damage at the nuclear periphery, whereas early embryos are UV sensitive and accumulate damage throughout nuclei when unshielded by their mothers in utero. These findings identify embryonic dissipation of nuclear pores as a key step in heterochromatic LAD assembly, allowing older embryos to withstand exposure to UV irradiation.

developmental biology↗

bioRxiv2025

Single-molecule chromosome tracing reveals a diversity of megabase heterochromatin domains

Chromosomes fold into distinct domains that regulate transcription, replication, and repair. Beyond well-characterized TADs and compartments, the diversity of heterochromatin domains remains poorly defined at the sequence level. Using single-molecule tracing of nascent heterochromatin in C. elegans, we identify three classes of megabase-scale domains: (i) sharp-boundary, Condensin I-dependent Topological Associating Domain-like domains (TADLs); (ii) similarly sized, but Condensin-independent, elegans Condensin-Independent Domains (elCIDs); and (iii) weaker, diffuse structures that are abundant in the population. TADLs arise early in development, preceding elCIDs, and both become progressively compacted through H3K9 methylation, which promotes intra- and inter-domain proximity. Condensin mutations disrupt TADLs, yet single molecules can still form domain-like structures, as recapitulated by free polymer simulations. However, these differ markedly in boundary positioning and biophysical properties. Our results uncover previously unrecognized heterochromatin architectures and demonstrate that single-molecule analysis and mutational dissection provide valuable approaches for distinguishing between domain types.

genomics↗

bioRxiv2025

A short conserved sequence in the HOT region of the C. elegans dlg-1 gene largely recapitulates its transcriptional behavior during embryogenesis

High occupancy target (HOT) regions, genomic sites bound by many transcription factors, are found across eukaryotes, but their physiological roles remain unclear. We characterized two HOT regions in the Caenorhabditis elegans dlg-1 locus containing transcription start sites: one upstream the coding sequence and one in the first intron. The upstream region is essential for proper transcription and proper animal development, while the intronic region modestly enhances transcription in epidermal cells. Our findings reveal the functions of HOT regions in animal development, expanding the repertoire of gene regulation strategies in C. elegans.

genetics↗

bioRxiv2025

The mechanosensory DEG/ENaC channel DEGT-1 is a proprioceptor of C. elegans foregut movement

The gastrointestinal tract is subjected to extensive mechanosensory stimulation during food ingestion. However, the identities of mechanosensory receptors in the enteric nervous system are largely unknown. The pharynx of C. elegans is a structurally and functionally homologous model of the vertebrate foregut, but is comprised of only 20 neurons that are embedded within the muscles and epithelial cells of the organ. Here we report that the DEG/ENaC family ion channel DEGT-1 is a proprioceptor of pharynx movement. DEGT-1 protein is expressed in 4 pharyngeal neurons (MI, M3, I4, and M5) and localized to their neuronal soma in direct contact with the collagenous pharyngeal basement membrane. degt-1 mutants display abnormally rapid feeding in the presence of food, causing global changes in lipid accumulation. degt-1 mutants also pump rapidly when pumping is induced by the presence of serotonin alone, suggesting that DEGT-1 is required for proprioception of pharyngeal pumping itself, rather than sensing ingested food. DEGT-1 is required in only two pharyngeal neurons (I4 and M5) to control pumping rate. Taken together, these results suggest that DEGT-1 modulates pharyngeal pumping rate by relaying proprioceptive feedback generated by the shear force of the pharynx against its own basement membrane. Thus, mechanosensors in enteric nervous systems modulate organ function not only by detecting forces from ingested contents, but also the movements of the organ itself.

neuroscience↗

bioRxiv2024

H3K9 methylation-independent activity for HPL-2/HP1 in heterochromatin foci, gene repression, and organogenesis

In differentiated cells, genome segregation into heterochromatin and euchromatin is mediated by modified histones, which recruit so-called reader proteins. Surprisingly, many histone modifiers remain functional in the absence of catalytic activity, but the underlying mechanism remains unclear. To explore this puzzle, we examined the relationship between C. elegans MET-2/SETDB1, a histone H3 lysine (H3K9me) methyltransferase that also has non-catalytic roles, and the canonical H3K9me reader HPL-2 (HP1). We show that HPL-2 represses transcription and supports organogenesis independently of H3K9me binding, whereas complete loss of met-2 and hpl-2 causes severe transcriptional and developmental defects. MET-2 and HPL-2 rely on different binding partners - the disordered protein LIN-65/ATF7IP and the multi-zinc finger protein LIN-13, respectively - for localization and function. The results suggest that HPL-2 can operate through alternative protein interactions, and that HPL-2 and MET-2 function in parallel, H3K9me-independent pathways, with H3K9me acting as a reinforcing but non-essential contributor to these processes.

molecular biology↗

bioRxiv2024

Whole-embryo Spatial Transcriptomics at Subcellular Resolution from Gastrulation to Organogenesis

Spatiotemporal patterns of gene expression underlie embryogenesis. Despite progress in single-cell genomics, mapping these patterns across whole embryos with comprehensive gene coverage and at high resolution has remained elusive. Here, we introduce a whole-embryo imaging platform using multiplexed error-robust fluorescent in-situ hybridization (weMERFISH). We quantified the expression of 495 genes in whole-mount zebrafish embryos at subcellular resolution. Integration with single-cell multiomics data generated an atlas detailing the expression of 25,872 genes and the accessibility of 294,954 chromatin regions, explorable with an online interface MERFISHEYES (beta version). We found that temporal gene expression aligns with cellular maturation and morphogenetic movements, diverse expression patterns correspond to composites of tissue-specific accessible elements, and changes in gene expression generate sharp boundaries during gastrulation. These results establish a novel approach for whole-organism spatial transcriptomics, provide a comprehensive spatially resolved atlas of gene expression and chromatin accessibility, and reveal the diversity, precision and emergence of embryonic patterns.

developmental biology↗

bioRxiv2023

An adapted MS2-MCP system to visualize endogenous cytoplasmic mRNA with live imaging in Caenorhabditis elegans

Live imaging of RNA molecules constitutes an invaluable means to track the dynamics of mRNAs, but live imaging in Caenorhabditis elegans has been difficult to achieve. Endogenous transcripts have been observed in nuclei, but endogenous mRNAs have not been detected in the cytoplasm, and functional mRNAs have not been generated. Here, we have adapted live imaging methods to visualize mRNA in embryonic epithelial cells. We have tagged endogenous transcripts with MS2 hairpins in the 3 Untranslated Region (UTR) and visualized them after adjusting MS2 Coat Protein (MCP) expression. A reduced number of these transcripts accumulate in the cytoplasm, leading to loss-of-function phenotypes. In addition, mRNAs for dlg-1 fail to associate with the adherens junction, as observed for the endogenous mRNA. These defects are reversed by inactivating the nonsense-mediated decay pathway. RNA accumulates in the cytoplasm, dlg-1 associates with the adherens junction, and mutant phenotypes are rescued. These data suggest that MS2 repeats can induce the degradation of endogenous targets and alter the cytoplasmic distribution. Although our focus is RNAs expressed in epithelial cells during morphogenesis, this method can likely be applied to other cell types and stages. Summary statementAn adapted MS2-MCP method to tag endogenous transcripts in C. elegans embryos for live imaging without affecting mRNA stability.

genetics↗

bioRxiv2022

Multiplex DNA fluorescence in situ hybridization to analyze maternal vs. paternal C. elegans chromosomes

Recent advances in high-throughput microscopy have paved the way to study chromosome organization at the single-molecule level and have led to a better understanding of genome organization in space and time. During development, distinct maternal and paternal contributions ensure the formation of an embryo proper, yet little is known about the organization of chromosomes inherited from mothers versus fathers. To tackle this question, we have modified single-molecule chromosome tracing to distinguish between the chromosomes of two well-studied strains of C. elegans called Bristol and Hawaiian. We find that chromosomes from these two strains have similar folding patterns in homozygous hermaphrodites. However, crosses between Bristol and Hawaiian animals reveal that the paternal chromosome adopts the folding parameters of the maternal chromosome in embryos. This is accomplished by an increase in the polymer step size and decompaction of the chromosome. The data indicate that factors from the mother impact chromosome folding in trans. We also characterize the degree of intermixing between homologues within the chromosome territories. Sister chromosomes overlap frequently in C. elegans embryos, but pairing between homologues is rare, suggesting that transvection is unlikely to occur. This method constitutes a powerful tool to investigate chromosome architecture from mothers and fathers.

molecular biology↗

bioRxiv2021

Translation-dependent mRNA localization to Caenorhabditis elegans adherens junctions

mRNA localization is an evolutionarily widespread phenomenon that facilitates sub-cellular protein targeting. Extensive work has focused on mRNA targeting through "zip codes" within untranslated regions (UTRs), while much less is known about translation-dependent cues. Here, we examine mRNA localization in Caenorhabditis elegans embryonic epithelia. From an smFISH-based survey, we identified mRNAs associated with the cell membrane or cortex, and with apical junctions in a stage- and cell type-specific manner. Mutational analyses for one of these transcripts, dlg-1/discs large, revealed that it relied on a translation-dependent process and did not require its 5 or 3 UTR. We suggest a model in which dlg-1 transcripts are co-translationally colocalized with the encoded protein: first the translating complex goes to the cell membrane through sequences of the SH3 domain, and then to the apical junction by the L27 and PDZ sequences. In addition, the Hook and GuK sequences contribute to the second step: they are required for mRNA, but not protein, to accumulate at the apical junctions from locations at or near the membrane. These studies identify a translation-based process for mRNA localization within developing epithelia and determine the necessary cis-acting sequences for dlg-1 mRNA targeting. Summary statementAn smFISH-based survey identified a subset of mRNAs coding for junctional components that localize at or in the proximity of the adherent junction through a translation-dependent mechanism.

developmental biology↗

bioRxiv2021

Neuronal control of maternal provisioning in response to social cues

Mothers contribute cytoplasmic components to their progeny in a process called maternal provisioning. Provisioning is influenced by the parental environment, but the molecular pathways that transmit environmental cues from mother to progeny are not well understood. Here we show that in C. elegans, social cues modulate maternal provisioning to regulate gene silencing in offspring. Intergenerational signal transmission depends on a pheromone-sensing neuron and neuronal FMRF (Phe-Met-Arg-Phe)-like peptides. Parental FMRF signaling promotes the deposition of mRNAs for translational components in progeny, which in turn reduces gene silencing. Previous studies had implicated FMRF signaling in short-term responses such as modulated feeding behavior in response to the metabolic state1,2, but our data reveal a broader role, to coordinate energetically expensive processes such as translation and maternal provisioning. This study identifies a new pathway for intergenerational communication, distinct from previously discovered pathways involving small RNAs and chromatin, that links sensory perception to maternal provisioning.

genetics↗

bioRxiv2018

MET-2, a SETDB1 family methyltransferase, coordinates embryo events through distinct histone H3 methylation states

During the first hours of embryogenesis, formation of higher-order heterochromatin coincides with the loss of developmental potential. Here we examine the relationship between these two processes, and we probe the determinants that contribute to their onset. Mutations that disrupt histone H3 lysine 9 (H3K9) methyltransferases reveal that the methyltransferase MET-2 helps terminate developmental plasticity, likely through mono- and di- methylation of H3K9 (me1/me2), and promotes heterochromatin formation, likely through H3K9me3. We examine how MET-2 is regulated and find that methylated H3K9 appears gradually and depends on the accumulated time of embryogenesis. H3K9me is independent of zygotic genome activation or cell counting. These data reveal how central events are synchronized during embryogenesis and distinguish distinct roles for different H3K9 methylation states.\n\nSummary StatementDuring early embryogenesis, heterochromatin formation and loss of developmental plasticity are coordinately regulated by distinct Histone H3 Lysine 9 (H3K9) methylation states, by the methyltransferase MET-2.

developmental biology↗

bioRxiv2018

A heterochromatic histone methyltransferase lowers nucleosome occupancy at euchromatic promoters

H3K9me3 (histone H3 modified with tri-methylation at lysine 9) is a hallmark of transcriptional silencing and heterochromatin. However, its global effects on the genome, including euchromatin, are less well understood. Here we develop Formaldehyde-Assisted Identification of Regulatory Elements (FAIRE) for C. elegans to examine the chromatin configuration of mutants that lack virtually all H3K9me3, while leaving H3K9me1 and H3K9me2 intact. We find that nucleosomes are mildly disrupted, and levels of H3K9me2 and H3K27me3 rise in mutant embryos. In addition to these expected changes, the most dramatic change occurs in euchromatin: many regions encompassing transcription start sites (TSSs) gain an average of two nucleosomes in mutants. The affected regions normally lack H3K9me3, revealing a locus non-autonomous role for H3K9me3. Affected TSSs are associated with genes that are active in epithelia and muscles, and implicated in development, locomotion, morphogenesis and transcription. Mutant embryos develop normally under ideal laboratory conditions but die when challenged, with defects in morphogenesis and development. Our findings reveal that H3K9me3 protects transcription start sites within euchromatin from nucleosome deposition. These results may be relevant to mammals, where diseases that disrupt the nuclear lamina and heterochromatin can alter epithelial and muscle gene expression.

developmental biology↗

bioRxiv2018

Regulated nuclear accumulation of a histone methyltransferase times the onset of heterochromatin formation in C. elegans embryos

Heterochromatin formation during early embryogenesis is timed precisely, but it has been elusive how this process is regulated. Here we report the discovery of a histone methyltransferase complex whose nuclear accumulation and activation establishes the onset of heterochromatin formation in C. elegans embryos. We find that the inception of heterochromatin generation coincides with the accumulation of the Histone H3 Lysine 9 (H3K9) methyltransferase MET-2 (SETDB) into nuclear hubs. The absence of MET-2 results in delayed and disturbed heterochromatin formation, whereas accelerated nuclear localization of the methyltransferase leads to precocious H3K9 methylation. We identify two factors that bind to and function with MET-2: LIN-65, which resembles ATF7IP, localizes MET-2 into nuclear hubs, and ARLE-14, orthologous to ARL14EP, promotes stable association of MET-2 with chromatin. These data reveal that nuclear accumulation of MET-2 in conjunction with LIN-65 and ARLE-14 regulates timing of heterochromatin domains during embryogenesis.\n\nONE SENTENCE SUMMARYMET-2/SETDB1 and interactors LIN-65/ATF7IP and ARLE-14/ARL14EP initiate heterochromatin formation during embryogenesis.

developmental biology↗