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Tiberi S, Meili J, Cai P, Soneson C, He D, Sarkar H, Avalos-Pacheco A, Patro R, Robinson MD. DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes. Biostatistics 2024:kxae017. [PMID: 38887902 DOI: 10.1093/biostatistics/kxae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 03/21/2024] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
Although transcriptomics data is typically used to analyze mature spliced mRNA, recent attention has focused on jointly investigating spliced and unspliced (or precursor-) mRNA, which can be used to study gene regulation and changes in gene expression production. Nonetheless, most methods for spliced/unspliced inference (such as RNA velocity tools) focus on individual samples, and rarely allow comparisons between groups of samples (e.g. healthy vs. diseased). Furthermore, this kind of inference is challenging, because spliced and unspliced mRNA abundance is characterized by a high degree of quantification uncertainty, due to the prevalence of multi-mapping reads, ie reads compatible with multiple transcripts (or genes), and/or with both their spliced and unspliced versions. Here, we present DifferentialRegulation, a Bayesian hierarchical method to discover changes between experimental conditions with respect to the relative abundance of unspliced mRNA (over the total mRNA). We model the quantification uncertainty via a latent variable approach, where reads are allocated to their gene/transcript of origin, and to the respective splice version. We designed several benchmarks where our approach shows good performance, in terms of sensitivity and error control, vs. state-of-the-art competitors. Importantly, our tool is flexible, and works with both bulk and single-cell RNA-sequencing data. DifferentialRegulation is distributed as a Bioconductor R package.
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Affiliation(s)
- Simone Tiberi
- Department of Statistical Sciences, University of Bologna, Via delle Belle Arti 41, Bologna, 40126, Italy
- Department of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland
| | - Joël Meili
- Department of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland
| | - Peiying Cai
- Department of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland
| | - Charlotte Soneson
- Computational Biology Platform, Friedrich Miescher Institute for Biomedical Research and SIB Swiss Institute of Bioinformatics, Fabrikstrasse 24, Basel, 4056, Switzerland
| | - Dongze He
- Department of Cell Biology and Molecular Genetics, University of Maryland, 4062 Campus Drive, College Park, MD 20742, United States
- Center for Bioinformatics and Computational Biology, University of Maryland, 8125 Paint Branch Dr, College Park, MD 20742, United States
| | - Hirak Sarkar
- Department of Computer Science, Princeton University, 35 Olden St, Princeton, NJ 08540, United States
| | - Alejandra Avalos-Pacheco
- Research Unit of Applied Statistics, TU Wien, Wiedner Hauptstrabe 8-10/105, Wien 1040, Austria
- Harvard-MIT Center for Regulatory Science, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115200 Longwood Avenue, Boston, MA 02115, United States
| | - Rob Patro
- Center for Bioinformatics and Computational Biology, University of Maryland, 8125 Paint Branch Dr, College Park, MD 20742, United States
- Department of Computer Science, University of Maryland, 8125 Paint Branch Dr, College Park, MD 20742, United States
| | - Mark D Robinson
- Department of Molecular Life Sciences and SIB Swiss Institute of Bioinformatics, University of Zurich, Winterthurerstrasse 190, Zurich, 8057, Switzerland
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Tiberi S, Meili J, Cai P, Soneson C, He D, Sarkar H, Avalos-Pacheco A, Patro R, Robinson MD. DifferentialRegulation : a Bayesian hierarchical approach to identify differentially regulated genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.17.553679. [PMID: 37645841 PMCID: PMC10462127 DOI: 10.1101/2023.08.17.553679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Motivation Although transcriptomics data is typically used to analyse mature spliced mRNA, recent attention has focused on jointly investigating spliced and unspliced (or precursor-) mRNA, which can be used to study gene regulation and changes in gene expression production. Nonetheless, most methods for spliced/unspliced inference (such as RNA velocity tools) focus on individual samples, and rarely allow comparisons between groups of samples (e.g., healthy vs . diseased). Furthermore, this kind of inference is challenging, because spliced and unspliced mRNA abundance is characterized by a high degree of quantification uncertainty, due to the prevalence of multi-mapping reads, i.e., reads compatible with multiple transcripts (or genes), and/or with both their spliced and unspliced versions. Results Here, we present DifferentialRegulation , a Bayesian hierarchical method to discover changes between experimental conditions with respect to the relative abundance of unspliced mRNA (over the total mRNA). We model the quantification uncertainty via a latent variable approach, where reads are allocated to their gene/transcript of origin, and to the respective splice version. We designed several benchmarks where our approach shows good performance, in terms of sensitivity and error control, versus state-of-the-art competitors. Importantly, our tool is flexible, and works with both bulk and single-cell RNA-sequencing data. Availability and implementation DifferentialRegulation is distributed as a Bioconductor R package.
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3
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Diaz-Cuadros M. Mitochondrial metabolism and the continuing search for ultimate regulators of developmental rate. Curr Opin Genet Dev 2024; 86:102178. [PMID: 38461774 DOI: 10.1016/j.gde.2024.102178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/13/2024] [Accepted: 02/19/2024] [Indexed: 03/12/2024]
Abstract
The rate of embryonic development is a species-specific trait that depends on the properties of the intracellular environment, namely, the rate at which gene products flow through the central dogma of molecular biology. Although any given step in the production and degradation of gene products could theoretically be co-opted by evolution to modulate developmental speed, species are observed to accelerate or slow down all steps simultaneously. This suggests the rate of these molecular processes is jointly regulated by an upstream, ultimate factor. Mitochondrial metabolism was recently proposed to act as an ultimate regulator by controlling the pace of protein synthesis upstream of developmental tempo. Alternative candidates for ultimate regulators include species-specific gene expression levels of factors involved in the central dogma, as well as species-specific cell size. Overall, much work remains to be done before we can confidently identify the ultimate causes of species-specific developmental rates.
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Affiliation(s)
- Margarete Diaz-Cuadros
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA.
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Funk OH, Levy DL, Fay DS. Epidermal cell fusion promotes the transition from an embryonic to a larval transcriptome in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595354. [PMID: 38826300 PMCID: PMC11142173 DOI: 10.1101/2024.05.22.595354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Cell fusion is a fundamental process in the development of multicellular organisms, yet its impact on gene regulation, particularly during crucial developmental stages, remains poorly understood. The Caenorhabditis elegans epidermis comprises 8-10 syncytial cells, with the largest integrating 139 individual nuclei through cell-cell fusion governed by the fusogenic protein EFF-1. To explore the effects of cell fusion on developmental progression and associated gene expression changes, we conducted transcriptomic analyses of eff-1 fusion-deficient mutants. Our RNAseq findings showed widespread transcriptomic changes that were enriched for epidermal genes and key molecular pathways involved in epidermal function during larval development. Subsequent single-molecule fluorescence in situ hybridization validated the altered expression of mRNA transcripts, confirming quantifiable changes in gene expression in the absence of embryonic epidermal fusion. These results underscore the significance of cell-cell fusion in shaping transcriptional programs during development and raise questions regarding the precise identities and specialized functions of different subclasses of nuclei within developing syncytial cells and tissues.
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Nahar S, Morales Moya LJ, Brunner J, Hendriks GJ, Towbin B, Hauser Y, Brancati G, Gaidatzis D, Großhans H. Dynamics of miRNA accumulation during C. elegans larval development. Nucleic Acids Res 2024; 52:5336-5355. [PMID: 38381904 PMCID: PMC11109986 DOI: 10.1093/nar/gkae115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/23/2024] Open
Abstract
Temporally and spatially controlled accumulation underlies the functions of microRNAs (miRNAs) in various developmental processes. In Caenorhabditis elegans, this is exemplified by the temporal patterning miRNAs lin-4 and let-7, but for most miRNAs, developmental expression patterns remain poorly resolved. Indeed, experimentally observed long half-lives may constrain possible dynamics. Here, we profile miRNA expression throughout C. elegans postembryonic development at high temporal resolution, which identifies dynamically expressed miRNAs. We use mathematical models to explore the underlying mechanisms. For let-7, we can explain, and experimentally confirm, a striking stepwise accumulation pattern through a combination of rhythmic transcription and stage-specific regulation of precursor processing by the RNA-binding protein LIN-28. By contrast, the dynamics of several other miRNAs cannot be explained by regulation of production rates alone. Specifically, we show that a combination of oscillatory transcription and rhythmic decay drive rhythmic accumulation of miR-235, orthologous to miR-92 in other animals. We demonstrate that decay of miR-235 and additional miRNAs depends on EBAX-1, previously implicated in target-directed miRNA degradation (TDMD). Taken together, our results provide insight into dynamic miRNA decay and establish a resource to studying both the developmental functions of, and the regulatory mechanisms acting on, miRNAs.
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Affiliation(s)
- Smita Nahar
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
| | | | - Jana Brunner
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Gert-Jan Hendriks
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
| | - Benjamin Towbin
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
- University of Bern, Bern, Switzerland
| | - Yannick P Hauser
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Giovanna Brancati
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Dimos Gaidatzis
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
- University of Basel, Basel, Switzerland
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Ragle JM, Turzo A, Levenson MT, Jonnalagadda K, Jackson A, Vo AA, Pham VT, Ward JD. MLT-11 is a transient apical extracellular matrix component required for cuticle patterning and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.12.593762. [PMID: 38766248 PMCID: PMC11100798 DOI: 10.1101/2024.05.12.593762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Apical extracellular matrices (aECMs) are associated with all epithelia and form a protective layer against biotic and abiotic threats in the environment. Despite their importance, we lack a deep understanding of their structure and dynamics in development and disease. C. elegans molting offers a powerful entry point to understanding developmentally programmed aECM remodeling. A transient matrix is formed in embryos and at the end of each larval stage, presumably to pattern the new cuticle. Focusing on targets of NHR-23, a key transcription factor which drives molting, we identified the Kunitz family protease inhibitor gene mlt-11 as an NHR-23 target. We identified NHR-23-binding sites that are necessary and sufficient for epithelial expression. mlt-11 is necessary to pattern every layer of the adult cuticle, suggesting a broad patterning role prior to the formation of the mature cuticle. MLT-11::mNeonGreen::3xFLAG transiently localized to the aECM in the cuticle and embryo. It was also detected in lining openings to the exterior (vulva, rectum, mouth). Reduction of mlt-11 function disrupted the barrier function of the cuticle. Tissue-specific RNAi suggested mlt-11 activity is primarily necessary in seam cells and we observed alae and seam cell fusion defects upon mlt-11 inactivation. Predicted mlt-11 null mutations caused fully penetrant embryonic lethality and elongation defects suggesting mlt-11 also plays an important role in patterning the embryonic sheath. Finally, we found that mlt-11 inactivation suppressed the blistered cuticle phenotype of mutants of bli-4 mutants, a subtilisin protease gene but did not affect BLI-4::sfGFP expression. These data could suggest that MLT-11 may be necessary to assure proper levels of BLI-4 activity.
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Affiliation(s)
- James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Ariela Turzo
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Max T. Levenson
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Keya Jonnalagadda
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Anton Jackson
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - An A. Vo
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Vivian T. Pham
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jordan D. Ward
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
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Spangler RK, Ashley GE, Braun K, Wruck D, Ramos-Coronado A, Ragle JM, Iesmantavicius V, Hess D, Partch CL, Großhans H, Ward JD. A conserved chronobiological complex times C. elegans development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593322. [PMID: 38766223 PMCID: PMC11100808 DOI: 10.1101/2024.05.09.593322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The mammalian PAS-domain protein PERIOD (PER) and its C. elegans orthologue LIN-42 have been proposed to constitute an evolutionary link between two distinct, circadian and developmental, timing systems. However, while the function of PER in animal circadian rhythms is well understood molecularly and mechanistically, this is not true for the function of LIN-42 in timing rhythmic development. Here, using targeted deletions, we find that the LIN-42 PAS domains are dispensable for the protein's function in timing molts. Instead, we observe arrhythmic molts upon deletion of a distinct sequence element, conserved with PER. We show that this element mediates stable binding to KIN-20, the C. elegans CK1δ/ε orthologue. We demonstrate that CK1δ phosphorylates LIN-42 and define two conserved helical motifs, CK1δ-binding domain A (CK1BD-A) and CK1BD-B, that have distinct roles in controlling CK1δ-binding and kinase activity in vitro. KIN-20 and the LIN-42 CK1BD are required for proper molting timing in vivo. These interactions mirror the central role of a stable circadian PER-CK1 complex in setting a robust ~24-hour period. Hence, our results establish LIN-42/PER - KIN-20/CK1δ/ε as a functionally conserved signaling module of two distinct chronobiological systems.
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Affiliation(s)
- Rebecca K Spangler
- Department of Chemistry and Biochemistry, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Guinevere E Ashley
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Kathrin Braun
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Daniel Wruck
- Department of Chemistry and Biochemistry, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Andrea Ramos-Coronado
- Department of Chemistry and Biochemistry, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
- University of Basel, 4002 Basel, Switzerland
| | - Jordan D Ward
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
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Patil G, van Zon JS. Timers, variability, and body-wide coordination: C. elegans as a model system for whole-animal developmental timing. Curr Opin Genet Dev 2024; 85:102172. [PMID: 38432125 DOI: 10.1016/j.gde.2024.102172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Successful development requires both precise timing of cellular processes, such as division and differentiation, and tight coordination of timing between tissues and organs. Yet, how time information is encoded with high precision and synchronized between tissues, despite inherent molecular noise, is unsolved. Here, we propose the nematode C. elegans as a unique model system for studying body-wide control of developmental timing. Recent studies combining genetics, quantitative analysis, and simulations have 1) mapped core timers controlling larval development, indicating temporal gradients as an underlying mechanism, and 2) elucidated general principles that make timing insensitive to inherent fluctuations and variation in environmental conditions. As the molecular regulators of C. elegans developmental timing are broadly conserved, these mechanisms likely apply also to higher organisms.
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Gandasi NR, Gao R, Kothegala L, Pearce A, Santos C, Acreman S, Basco D, Benrick A, Chibalina MV, Clark A, Guida C, Harris M, Johnson PRV, Knudsen JG, Ma J, Miranda C, Shigeto M, Tarasov AI, Yeung HY, Thorens B, Asterholm IW, Zhang Q, Ramracheya R, Ladds G, Rorsman P. GLP-1 metabolite GLP-1(9-36) is a systemic inhibitor of mouse and human pancreatic islet glucagon secretion. Diabetologia 2024; 67:528-546. [PMID: 38127123 PMCID: PMC10844371 DOI: 10.1007/s00125-023-06060-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/18/2023] [Indexed: 12/23/2023]
Abstract
AIMS/HYPOTHESIS Diabetes mellitus is associated with impaired insulin secretion, often aggravated by oversecretion of glucagon. Therapeutic interventions should ideally correct both defects. Glucagon-like peptide 1 (GLP-1) has this capability but exactly how it exerts its glucagonostatic effect remains obscure. Following its release GLP-1 is rapidly degraded from GLP-1(7-36) to GLP-1(9-36). We hypothesised that the metabolite GLP-1(9-36) (previously believed to be biologically inactive) exerts a direct inhibitory effect on glucagon secretion and that this mechanism becomes impaired in diabetes. METHODS We used a combination of glucagon secretion measurements in mouse and human islets (including islets from donors with type 2 diabetes), total internal reflection fluorescence microscopy imaging of secretory granule dynamics, recordings of cytoplasmic Ca2+ and measurements of protein kinase A activity, immunocytochemistry, in vivo physiology and GTP-binding protein dissociation studies to explore how GLP-1 exerts its inhibitory effect on glucagon secretion and the role of the metabolite GLP-1(9-36). RESULTS GLP-1(7-36) inhibited glucagon secretion in isolated islets with an IC50 of 2.5 pmol/l. The effect was particularly strong at low glucose concentrations. The degradation product GLP-1(9-36) shared this capacity. GLP-1(9-36) retained its glucagonostatic effects after genetic/pharmacological inactivation of the GLP-1 receptor. GLP-1(9-36) also potently inhibited glucagon secretion evoked by β-adrenergic stimulation, amino acids and membrane depolarisation. In islet alpha cells, GLP-1(9-36) led to inhibition of Ca2+ entry via voltage-gated Ca2+ channels sensitive to ω-agatoxin, with consequential pertussis-toxin-sensitive depletion of the docked pool of secretory granules, effects that were prevented by the glucagon receptor antagonists REMD2.59 and L-168049. The capacity of GLP-1(9-36) to inhibit glucagon secretion and reduce the number of docked granules was lost in alpha cells from human donors with type 2 diabetes. In vivo, high exogenous concentrations of GLP-1(9-36) (>100 pmol/l) resulted in a small (30%) lowering of circulating glucagon during insulin-induced hypoglycaemia. This effect was abolished by REMD2.59, which promptly increased circulating glucagon by >225% (adjusted for the change in plasma glucose) without affecting pancreatic glucagon content. CONCLUSIONS/INTERPRETATION We conclude that the GLP-1 metabolite GLP-1(9-36) is a systemic inhibitor of glucagon secretion. We propose that the increase in circulating glucagon observed following genetic/pharmacological inactivation of glucagon signalling in mice and in people with type 2 diabetes reflects the removal of GLP-1(9-36)'s glucagonostatic action.
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Affiliation(s)
- Nikhil R Gandasi
- Metabolic Physiology Unit, Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, Gothenburg, Sweden
- Cell Metabolism Lab (GA-08), Department of Developmental Biology and Genetics, Indian Institute of Science, Bangalore, India
| | - Rui Gao
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - Lakshmi Kothegala
- Metabolic Physiology Unit, Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, Gothenburg, Sweden
| | - Abigail Pearce
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Cristiano Santos
- Metabolic Physiology Unit, Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, Gothenburg, Sweden
| | - Samuel Acreman
- Metabolic Physiology Unit, Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, Gothenburg, Sweden
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - Davide Basco
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Anna Benrick
- Metabolic Physiology Unit, Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, Gothenburg, Sweden
| | - Margarita V Chibalina
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - Anne Clark
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - Claudia Guida
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - Matthew Harris
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Paul R V Johnson
- Nuffield Department of Surgical Sciences, John Radcliffe Hospital, Oxford, UK
- Biomedical Research Centre, Oxford National Institute for Health Research, Churchill Hospital, Oxford, UK
| | - Jakob G Knudsen
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jinfang Ma
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - Caroline Miranda
- Metabolic Physiology Unit, Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, Gothenburg, Sweden
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - Makoto Shigeto
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - Andrei I Tarasov
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
- School of Biomedical Sciences, University of Ulster, Coleraine, Northern Ireland, UK
| | - Ho Yan Yeung
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Bernard Thorens
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Ingrid W Asterholm
- Metabolic Physiology Unit, Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, Gothenburg, Sweden
| | - Quan Zhang
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - Reshma Ramracheya
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK
| | - Graham Ladds
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Patrik Rorsman
- Metabolic Physiology Unit, Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, Gothenburg, Sweden.
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Oxford, UK.
- Biomedical Research Centre, Oxford National Institute for Health Research, Churchill Hospital, Oxford, UK.
- School of Biomedical Sciences, University of Ulster, Coleraine, Northern Ireland, UK.
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Hiroki S, Yoshitane H. Ror homolog nhr-23 is essential for both developmental clock and circadian clock in C. elegans. Commun Biol 2024; 7:243. [PMID: 38418700 PMCID: PMC10902330 DOI: 10.1038/s42003-024-05894-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
Animals have internal clocks that generate biological rhythms. In mammals, clock genes such as Period form the circadian clock to generate approximately 24-h biological rhythms. In C. elegans, the clock gene homologs constitute the "developmental clock", which has an 8-h period during larval development to determine the timing of molting. Thus, the ancestral circadian clock has been believed to evolve into the oscillator with a shorter period in C. elegans. However, circadian rhythms have also been observed in adult C. elegans, albeit relatively weak. This prompts the question: if the clock gene homologs drive the developmental rhythm with 8-h period, which genes generate the circadian rhythms in C. elegans? In this study, we discovered that nhr-23, a homolog of the mammalian circadian clock gene Ror, is essential for circadian transcriptional rhythms in adult C. elegans. Interestingly, nhr-23 was also known to be essential for the molting clock. The bilaterian ancestral circadian clock genes might have evolved to function over multiple periods depending on developmental contexts rather than a single 8-h period in C. elegans.
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Affiliation(s)
- Shingo Hiroki
- Tokyo Metropolitan Institute of Medical Sciences, Tokyo, Japan.
| | - Hikari Yoshitane
- Tokyo Metropolitan Institute of Medical Sciences, Tokyo, Japan.
- Department of Biological Sciences, School of Science, University of Tokyo, Tokyo, Japan.
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11
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van Eijnatten AL, Sterken MG, Kammenga JE, Nijveen H, Snoek BL. The effect of developmental variation on expression QTLs in a multi parental Caenorhabditis elegans population. G3 (BETHESDA, MD.) 2024; 14:jkad273. [PMID: 38015660 PMCID: PMC10849341 DOI: 10.1093/g3journal/jkad273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 09/21/2023] [Accepted: 10/27/2023] [Indexed: 11/30/2023]
Abstract
Regulation of gene expression plays a crucial role in developmental processes and adaptation to changing environments. expression quantitative trait locus (eQTL) mapping is a technique used to study the genetic regulation of gene expression using the transcriptomes of recombinant inbred lines (RILs). Typically, the age of the inbred lines at the time of RNA sampling is carefully controlled. This is necessary because the developmental process causes changes in gene expression, complicating the interpretation of eQTL mapping experiments. However, due to genetics and variation in ambient micro-environments, organisms can differ in their "developmental age," even if they are of the same chronological age. As a result, eQTL patterns are affected by developmental variation in gene expression. The model organism Caenorhabditis elegans is particularly suited for studying the effect of developmental variation on eQTL mapping patterns. In a span of days, C. elegans transitions from embryo through 4 larval stages to adult while undergoing massive changes to its transcriptome. Here, we use C. elegans to investigate the effect of developmental age variation on eQTL patterns and present a normalization procedure. We used dynamical eQTL mapping, which includes the developmental age as a cofactor, to separate the variation in development from genotypic variation and explain variation in gene expression levels. We compare classical single marker eQTL mapping and dynamical eQTL mapping using RNA-seq data of ∼200 multi-parental RILs of C. elegans. The results show that (1) many eQTLs are caused by developmental variation, (2) most trans-bands are developmental QTLs, and (3) dynamical eQTL mapping detects additional eQTLs not found with classical eQTL mapping. We recommend that correction for variation in developmental age should be strongly considered in eQTL mapping studies given the large impact of processes like development on the transcriptome.
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Affiliation(s)
- Abraham L van Eijnatten
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8,3584 CH Utrecht, The Netherlands
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Jan E Kammenga
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Harm Nijveen
- Laboratory of Bioinformatics, Wageningen University, Droevendaalsesteeg 1, Radix West, Building 107, 6708 PB Wageningen, The Netherlands
| | - Basten L Snoek
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8,3584 CH Utrecht, The Netherlands
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12
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Egan BM, Pohl F, Anderson X, Williams SC, Gregory Adodo I, Hunt P, Wang Z, Chiu CH, Scharf A, Mosley M, Kumar S, Schneider DL, Fujiwara H, Hsu FF, Kornfeld K. The ACE inhibitor captopril inhibits ACN-1 to control dauer formation and aging. Development 2024; 151:dev202146. [PMID: 38284547 PMCID: PMC10911126 DOI: 10.1242/dev.202146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 01/02/2024] [Indexed: 01/30/2024]
Abstract
The renin-angiotensin-aldosterone system (RAAS) plays a well-characterized role regulating blood pressure in mammals. Pharmacological and genetic manipulation of the RAAS has been shown to extend lifespan in Caenorhabditis elegans, Drosophila and rodents, but its mechanism is not well defined. Here, we investigate the angiotensin-converting enzyme (ACE) inhibitor drug captopril, which extends lifespan in worms and mice. To investigate the mechanism, we performed a forward genetic screen for captopril-hypersensitive mutants. We identified a missense mutation that causes a partial loss of function of the daf-2 receptor tyrosine kinase gene, a powerful regulator of aging. The homologous mutation in the human insulin receptor causes Donohue syndrome, establishing these mutant worms as an invertebrate model of this disease. Captopril functions in C. elegans by inhibiting ACN-1, the worm homolog of ACE. Reducing the activity of acn-1 via captopril or RNA interference promoted dauer larvae formation, suggesting that acn-1 is a daf gene. Captopril-mediated lifespan extension was abrogated by daf-16(lf) and daf-12(lf) mutations. Our results indicate that captopril and acn-1 influence lifespan by modulating dauer formation pathways. We speculate that this represents a conserved mechanism of lifespan control.
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Affiliation(s)
- Brian M. Egan
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Franziska Pohl
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xavier Anderson
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shoshana C. Williams
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Patrick Hunt
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Zuoxu Wang
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chen-Hao Chiu
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrea Scharf
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Biological Sciences, Missouri University of Science and Technology, Rolla, MO 65409, USA
| | - Matthew Mosley
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sandeep Kumar
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Daniel L. Schneider
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hideji Fujiwara
- Division of Endocrinology, Metabolism & Lipid Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Fong-Fu Hsu
- Division of Endocrinology, Metabolism & Lipid Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kerry Kornfeld
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
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13
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Kiontke K, Herrera RA, Mason DA, Woronik A, Vernooy S, Patel Y, Fitch DHA. Tissue-specific RNA-seq defines genes governing male tail tip morphogenesis in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.12.575210. [PMID: 38260477 PMCID: PMC10802606 DOI: 10.1101/2024.01.12.575210] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Caenorhabditis elegans males undergo sex-specific tail tip morphogenesis (TTM) under the control of the transcription factor DMD-3. To find genes regulated by DMD-3, We performed RNA-seq of laser-dissected tail tips. We identified 564 genes differentially expressed (DE) in wild-type males vs. dmd-3(-) males and hermaphrodites. The transcription profile of dmd-3(-) tail tips is similar to that in hermaphrodites. For validation, we analyzed transcriptional reporters for 49 genes and found male-specific or male-biased expression for 26 genes. Only 11 DE genes overlapped with genes found in a previous RNAi screen for defective TTM. GO enrichment analysis of DE genes finds upregulation of genes within the UPR (unfolded protein response) pathway and downregulation of genes involved in cuticle maintenance. Of the DE genes, 40 are transcription factors, indicating that the gene network downstream of DMD-3 is complex and potentially modular. We propose modules of genes that act together in TTM and are coregulated by DMD-3, among them the chondroitin synthesis pathway and the hypertonic stress response.
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Affiliation(s)
- Karin Kiontke
- Department of Biology, New York University, 100 Washington Square E., New York, NY 10003
| | | | - D Adam Mason
- Biology Department, Siena College, 515 Loudon Road, Loudonville, NY 12211
| | - Alyssa Woronik
- Sacred Heart University, 5151 Park Avenue, Fairfield, CT 06825
| | - Stephanie Vernooy
- Biology Department, Siena College, 515 Loudon Road, Loudonville, NY 12211
| | - Yash Patel
- Department of Biology, New York University, 100 Washington Square E., New York, NY 10003
| | - David H A Fitch
- Department of Biology, New York University, 100 Washington Square E., New York, NY 10003
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14
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Serra ND, Darwin CB, Sundaram MV. C. elegans Hedgehog-related proteins are tissue- and substructure-specific components of the cuticle and pre-cuticle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.26.573316. [PMID: 38234847 PMCID: PMC10793445 DOI: 10.1101/2023.12.26.573316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
In C. elegans, divergent Hedgehog-related (Hh-r) and Patched-related (PTR) proteins promote numerous processes ranging from epithelial and sense organ development to pathogen responses to cuticle shedding during the molt cycle. Here we show that Hh-r proteins are actual components of the cuticle and pre-cuticle apical extracellular matrices (aECMs) that coat, shape, and protect external epithelia. Different Hh-r proteins stably associate with the aECMs of specific tissues and with specific substructures such as furrows and alae. Hh-r mutations can disrupt matrix structure. These results provide a unifying model for the function of nematode Hh-r proteins and highlight ancient connections between Hh proteins and the extracellular matrix.
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Affiliation(s)
- Nicholas D. Serra
- Dept. of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA
| | - Chelsea B. Darwin
- Dept. of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA
| | - Meera V. Sundaram
- Dept. of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA
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15
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Emans SW, Yerevanian A, Ahsan FM, Rotti JF, Zhou Y, Cedillo L, Soukas AA. GRD-1/PTR-11, the C. elegans hedgehog/patched-like morphogen-receptor pair, modulates developmental rate. Development 2023; 150:dev201974. [PMID: 37982457 PMCID: PMC10753586 DOI: 10.1242/dev.201974] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/08/2023] [Indexed: 11/21/2023]
Abstract
Both hedgehog (Hh) and target of rapamycin complex 2 (TORC2) are central, evolutionarily conserved signaling pathways that regulate development and metabolism. In C. elegans, loss of the essential TORC2 component RICTOR (rict-1) causes delayed development, shortened lifespan, reduced brood, small size and increased fat. Here, we report that knockdown of both the hedgehog-related morphogen grd-1 and its patched-related receptor ptr-11 rescues delayed development in TORC2 loss-of-function mutants, and grd-1 and ptr-11 overexpression delays wild-type development to a similar level to that in TORC2 loss-of-function animals. These findings potentially indicate an unexpected role for grd-1 and ptr-11 in slowing developmental rate downstream of a nutrient-sensing pathway. Furthermore, we implicate the chronic stress transcription factor pqm-1 as a key transcriptional effector in this slowing of whole-organism growth by grd-1 and ptr-11. We propose that TORC2, grd-1 and ptr-11 may act linearly or converge on pqm-1 to delay organismal development.
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Affiliation(s)
- Sinclair W. Emans
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Biological and Biomedical Sciences, Division of Medical Science, Harvard Medical School, Boston, MA 02115, USA
| | - Armen Yerevanian
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Fasih M. Ahsan
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Biological and Biomedical Sciences, Division of Medical Science, Harvard Medical School, Boston, MA 02115, USA
| | - Jen F. Rotti
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Yifei Zhou
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lucydalila Cedillo
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Biological and Biomedical Sciences, Division of Medical Science, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander A. Soukas
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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16
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Diaz-Cuadros M, Pourquié O. The Clockwork Embryo: Mechanisms Regulating Developmental Rate. Annu Rev Genet 2023; 57:117-134. [PMID: 38012023 DOI: 10.1146/annurev-genet-022123-104503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Organismal development requires the reproducible unfolding of an ordered sequence of discrete steps (cell fate determination, migration, tissue folding, etc.) in both time and space. Here, we review the mechanisms that grant temporal specificity to developmental steps, including molecular clocks and timers. Individual timing mechanisms must be coordinated with each other to maintain the overall developmental sequence. However, phenotypic novelties can also arise through the modification of temporal patterns over the course of evolution. Two main types of variation in temporal patterning characterize interspecies differences in developmental time: allochrony, where the overall developmental sequence is either accelerated or slowed down while maintaining the relative duration of individual steps, and heterochrony, where the duration of specific developmental steps is altered relative to the rest. New advances in in vitro modeling of mammalian development using stem cells have recently enabled the revival of mechanistic studies of allochrony and heterochrony. In both cases, differences in the rate of basic cellular functions such as splicing, translation, protein degradation, and metabolism seem to underlie differences in developmental time. In the coming years, these studies should identify the genetic differences that drive divergence in developmental time between species.
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Affiliation(s)
- Margarete Diaz-Cuadros
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA;
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA;
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA;
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA
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17
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Kinney B, Sahu S, Stec N, Hills-Muckey K, Adams DW, Wang J, Jaremko M, Joshua-Tor L, Keil W, Hammell CM. A circadian-like gene network programs the timing and dosage of heterochronic miRNA transcription during C. elegans development. Dev Cell 2023; 58:2563-2579.e8. [PMID: 37643611 PMCID: PMC10840721 DOI: 10.1016/j.devcel.2023.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/10/2023] [Accepted: 08/02/2023] [Indexed: 08/31/2023]
Abstract
Development relies on the exquisite control of both the timing and the levels of gene expression to achieve robust developmental transitions. How cis- and trans-acting factors control both aspects simultaneously is unclear. We show that transcriptional pulses of the temporal patterning microRNA (miRNA) lin-4 are generated by two nuclear hormone receptors (NHRs) in C. elegans, NHR-85 and NHR-23, whose mammalian orthologs, Rev-Erb and ROR, function in the circadian clock. Although Rev-Erb and ROR antagonize each other to control once-daily transcription in mammals, NHR-85/NHR-23 heterodimers bind cooperatively to lin-4 regulatory elements to induce a single pulse of expression during each larval stage. Each pulse's timing, amplitude, and duration are dictated by the phased expression of these NHRs and the C. elegans Period ortholog, LIN-42, that binds to and represses NHR-85. Therefore, during nematode temporal patterning, an evolutionary rewiring of circadian clock components couples the timing of gene expression to the control of transcriptional dosage.
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Affiliation(s)
- Brian Kinney
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Shubham Sahu
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168 Laboratoire Physico Chimie Curie, Paris 75005, France
| | - Natalia Stec
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | | | - Dexter W Adams
- Howard Hughes Medical Institute, W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jing Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Matt Jaremko
- Howard Hughes Medical Institute, W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Leemor Joshua-Tor
- Howard Hughes Medical Institute, W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Wolfgang Keil
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR168 Laboratoire Physico Chimie Curie, Paris 75005, France.
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18
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Adams JRG, Pooranachithra M, Jyo EM, Zheng SL, Goncharov A, Crew JR, Kramer JM, Jin Y, Ernst AM, Chisholm AD. Nanoscale patterning of collagens in C. elegans apical extracellular matrix. Nat Commun 2023; 14:7506. [PMID: 37980413 PMCID: PMC10657453 DOI: 10.1038/s41467-023-43058-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 10/30/2023] [Indexed: 11/20/2023] Open
Abstract
Apical extracellular matrices (aECMs) are complex extracellular compartments that form important interfaces between animals and their environment. In the adult C. elegans cuticle, layers are connected by regularly spaced columnar structures known as struts. Defects in struts result in swelling of the fluid-filled medial cuticle layer ('blistering', Bli). Here we show that three cuticle collagens BLI-1, BLI-2, and BLI-6, play key roles in struts. BLI-1 and BLI-2 are essential for strut formation whereas activating mutations in BLI-6 disrupt strut formation. BLI-1, BLI-2, and BLI-6 precisely colocalize to arrays of puncta in the adult cuticle, corresponding to struts, initially deposited in diffuse stripes adjacent to cuticle furrows. They eventually exhibit tube-like morphology, with the basal ends of BLI-containing struts contact regularly spaced holes in the cuticle. Genetic interaction studies indicate that BLI strut patterning involves interactions with other cuticle components. Our results reveal strut formation as a tractable example of precise aECM patterning at the nanoscale.
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Affiliation(s)
- Jennifer R G Adams
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Murugesan Pooranachithra
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Erin M Jyo
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Sherry Li Zheng
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Alexandr Goncharov
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jennifer R Crew
- Northwestern University School of Medicine, Department of Cell and Molecular Biology, Chicago, IL, 60611, USA
| | - James M Kramer
- Northwestern University School of Medicine, Department of Cell and Molecular Biology, Chicago, IL, 60611, USA
| | - Yishi Jin
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Andreas M Ernst
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA
| | - Andrew D Chisholm
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA.
- Department of Neurobiology, School of Biological Sciences, University of California San Diego, La Jolla, CA, 92093, USA.
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19
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Jordan DJ, Miska EA. Canalisation and plasticity on the developmental manifold of Caenorhabditis elegans. Mol Syst Biol 2023; 19:e11835. [PMID: 37850520 PMCID: PMC10632735 DOI: 10.15252/msb.202311835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/26/2023] [Accepted: 10/05/2023] [Indexed: 10/19/2023] Open
Abstract
How do the same mechanisms that faithfully regenerate complex developmental programmes in spite of environmental and genetic perturbations also allow responsiveness to environmental signals, adaptation and genetic evolution? Using the nematode Caenorhabditis elegans as a model, we explore the phenotypic space of growth and development in various genetic and environmental contexts. Our data are growth curves and developmental parameters obtained by automated microscopy. Using these, we show that among the traits that make up the developmental space, correlations within a particular context are predictive of correlations among different contexts. Furthermore, we find that the developmental variability of this animal can be captured on a relatively low-dimensional phenotypic manifold and that on this manifold, genetic and environmental contributions to plasticity can be deconvolved independently. Our perspective offers a new way of understanding the relationship between robustness and flexibility in complex systems, suggesting that projection and concentration of dimension can naturally align these forces as complementary rather than competing.
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Affiliation(s)
- David J Jordan
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Eric A Miska
- Department of BiochemistryUniversity of CambridgeCambridgeUK
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20
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Reich H, Savage-Dunn C. Signaling circuits and the apical extracellular matrix in aging: connections identified in the nematode Caenorhabditis elegans. Am J Physiol Cell Physiol 2023; 325:C1201-C1211. [PMID: 37721005 PMCID: PMC10861026 DOI: 10.1152/ajpcell.00195.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/24/2023] [Accepted: 09/11/2023] [Indexed: 09/19/2023]
Abstract
Numerous conserved signaling pathways play critical roles in aging, including insulin/IGF-1, TGF-β, and Wnt pathways. Some of these pathways also play prominent roles in the formation and maintenance of the extracellular matrix. The nematode Caenorhabditis elegans has been an enduringly productive system for the identification of conserved mechanisms of biological aging. Recent studies in C. elegans highlight the regulatory circuits between conserved signaling pathways and the extracellular matrix, revealing a bidirectional relationship between these factors and providing a platform to address how regulation of and by the extracellular matrix can impact lifespan and organismal health during aging. These discoveries provide new opportunities for clinical advances and novel therapeutic strategies.
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Affiliation(s)
- Hannah Reich
- Department of Biology, Queens College, City University of New York, Flushing, New York, United States
| | - Cathy Savage-Dunn
- Department of Biology, Queens College, City University of New York, Flushing, New York, United States
- PhD Program in Biology, The Graduate Center, City University of New York, New York, New York, United States
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21
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Kamal M, Tokmakjian L, Knox J, Han D, Moshiri H, Magomedova L, Nguyen KCQ, Zheng H, Burns AR, Cooke B, Lacoste J, Yeo M, Hall DH, Cummins CL, Roy PJ. PGP-14 establishes a polar lipid permeability barrier within the C. elegans pharyngeal cuticle. PLoS Genet 2023; 19:e1011008. [PMID: 37930961 PMCID: PMC10653525 DOI: 10.1371/journal.pgen.1011008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 11/16/2023] [Accepted: 10/05/2023] [Indexed: 11/08/2023] Open
Abstract
The cuticles of ecdysozoan animals are barriers to material loss and xenobiotic insult. Key to this barrier is lipid content, the establishment of which is poorly understood. Here, we show that the p-glycoprotein PGP-14 functions coincidently with the sphingomyelin synthase SMS-5 to establish a polar lipid barrier within the pharyngeal cuticle of the nematode C. elegans. We show that PGP-14 and SMS-5 are coincidentally expressed in the epithelium that surrounds the anterior pharyngeal cuticle where PGP-14 localizes to the apical membrane. pgp-14 and sms-5 also peak in expression at the time of new cuticle synthesis. Loss of PGP-14 and SMS-5 dramatically reduces pharyngeal cuticle staining by Nile Red, a key marker of polar lipids, and coincidently alters the nematode's response to a wide-range of xenobiotics. We infer that PGP-14 exports polar lipids into the developing pharyngeal cuticle in an SMS-5-dependent manner to safeguard the nematode from environmental insult.
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Affiliation(s)
- Muntasir Kamal
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Levon Tokmakjian
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Jessica Knox
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Duhyun Han
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Houtan Moshiri
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Lilia Magomedova
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Ken CQ Nguyen
- Department of Neuroscience, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Hong Zheng
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Andrew R. Burns
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Brittany Cooke
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Jessica Lacoste
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - May Yeo
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - David H. Hall
- Department of Neuroscience, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Carolyn L. Cummins
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Peter J. Roy
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
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22
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Myles KM, Clancy JC, Johnson LC, Ashley G, Manzano J, Ragle JM, Ward JD. An nhr-85::GFP::AID*::3xFLAG knock-in allele for investigation of molting and oscillatory gene regulation. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000993. [PMID: 37927911 PMCID: PMC10620605 DOI: 10.17912/micropub.biology.000993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/14/2023] [Accepted: 10/17/2023] [Indexed: 11/07/2023]
Abstract
C. elegans NHR-85 is a poorly characterized nuclear hormone receptor transcription factor with an emerging role in regulating microRNA expression to control developmental timing. We generated the first NHR-85 translational fusion by knocking a GFP::AID*::3xFLAG cassette into the endogenous locus to tag all known isoforms. nhr-85 ::GFP::AID*::3xFLAG animals have wild-type broodsizes and NHR-85 ::GFP peaks in expression at the start of the L4 stage in epithelial cells. NHR-85 is not expressed in the germline, suggesting that while it might cooperate with the NHR-23 transcription factor to control microRNA expression, NHR-23 promotes spermatogenesis independent of NHR-85 . This nhr-85 ::GFP::AID*::3xFLAG strain will be a valuable resource for studying when and where NHR-85 acts to promote developmental timing.
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Affiliation(s)
- Krista M. Myles
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, United States
| | - John C. Clancy
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, United States
| | - Londen C. Johnson
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, United States
| | - Guinevere Ashley
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, United States
| | - Jesus Manzano
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, United States
| | - James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, United States
| | - Jordan D. Ward
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, United States
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23
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Birnbaum SK, Cohen JD, Belfi A, Murray JI, Adams JRG, Chisholm AD, Sundaram MV. The proprotein convertase BLI-4 promotes collagen secretion prior to assembly of the Caenorhabditis elegans cuticle. PLoS Genet 2023; 19:e1010944. [PMID: 37721936 PMCID: PMC10538796 DOI: 10.1371/journal.pgen.1010944] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/28/2023] [Accepted: 08/30/2023] [Indexed: 09/20/2023] Open
Abstract
Some types of collagens, including transmembrane MACIT collagens and C. elegans cuticle collagens, are N-terminally cleaved at a dibasic site that resembles the consensus for furin or other proprotein convertases of the subtilisin/kexin (PCSK) family. Such cleavage may release transmembrane collagens from the plasma membrane and affect extracellular matrix assembly or structure. However, the functional consequences of such cleavage are unclear and evidence for the role of specific PCSKs is lacking. Here, we used endogenous collagen fusions to fluorescent proteins to visualize the secretion and assembly of the first collagen-based cuticle in C. elegans and then tested the role of the PCSK BLI-4 in these processes. Unexpectedly, we found that cuticle collagens SQT-3 and DPY-17 are secreted into the extraembryonic space several hours before cuticle matrix assembly. Furthermore, this early secretion depends on BLI-4/PCSK; in bli-4 and cleavage-site mutants, SQT-3 and DPY-17 are not efficiently secreted and instead form large intracellular puncta. Their later assembly into cuticle matrix is reduced but not entirely blocked. These data reveal a role for collagen N-terminal processing in intracellular trafficking and the control of matrix assembly in vivo. Our observations also prompt a revision of the classic model for C. elegans cuticle matrix assembly and the pre-cuticle-to-cuticle transition, suggesting that cuticle layer assembly proceeds via a series of regulated steps and not simply by sequential secretion and deposition.
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Affiliation(s)
- Susanna K. Birnbaum
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jennifer D. Cohen
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Alexandra Belfi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - John I. Murray
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jennifer R. G. Adams
- Departments of Neurobiology and Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Andrew D. Chisholm
- Departments of Neurobiology and Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego, California, United States of America
| | - Meera V. Sundaram
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
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24
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Faerberg DF, Aprison EZ, Ruvinsky I. Periods of environmental sensitivity couple larval behavior and development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552015. [PMID: 37609125 PMCID: PMC10441318 DOI: 10.1101/2023.08.04.552015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The typical life cycle in most animal phyla includes a larval period that bridges embryogenesis and adulthood1. Despite the great diversity of larval forms, all larvae grow, acquire adult morphology and function, while navigating their habitats to obtain resources necessary for development. How larval development is coordinated with behavior remains substantially unclear. Here, we describe features of the iterative organization of larval stages that serve to assess the environment and procure resources prior to costly developmental commitments. We found that male-excreted pheromones accelerate2-4 the onset of adulthood in C. elegans hermaphrodites by coordinately advancing multiple developmental events and growth during the last larval stage. The larvae are sensitive to the accelerating male pheromones only at the end of the penultimate larval stage, just before the acceleration begins. Other larval stages also contain windows of sensitivity to environmental inputs. Importantly, behaviors associated with search and consumption of food are distinct between early and late portions of larval stages. We infer that each larval stage in C. elegans is subdivided into two epochs: A) global assessment of the environment to identify the most suitable patch and B) consumption of sufficient food and acquisition of salient information for developmental events in the next stage. We predict that in larvae of other species behavior is also divided into distinct epochs optimized either for assessing the habitat or obtaining the resources. Thus, a major role of larval behavior is to coordinate the orderly progression of development in variable environments.
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Affiliation(s)
- Denis F. Faerberg
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Erin Z. Aprison
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Ilya Ruvinsky
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
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25
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Egan BM, Pohl F, Anderson X, Williams SC, Adodo IG, Hunt P, Wang Z, Chiu CH, Scharf A, Mosley M, Kumar S, Schneider DL, Fujiwara H, Hsu FF, Kornfeld K. The ACE-inhibitor drug captopril inhibits ACN-1 to control dauer formation and aging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.17.549402. [PMID: 37502959 PMCID: PMC10370070 DOI: 10.1101/2023.07.17.549402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The renin-angiotensin-aldosterone system (RAAS) plays a well-characterized role regulating blood pressure in mammals. Pharmacological and genetic manipulation of the RAAS has been shown to extend lifespan in C. elegans , Drosophila , and rodents, but its mechanism is not well defined. Here we investigate the angiotensin-converting enzyme (ACE) inhibitor drug captopril, which extends lifespan in worms and mice. To investigate the mechanism, we performed a forward genetic screen for captopril hypersensitive mutants. We identified a missense mutation that causes a partial loss-of-function of the daf-2 receptor tyrosine kinase gene, a powerful regulator of aging. The homologous mutation in the human insulin receptor causes Donohue syndrome, establishing these mutant worms as an invertebrate model of this disease. Captopril functions in C. elegans by inhibiting ACN-1, the worm homolog of ACE. Reducing the activity of acn-1 via captopril or RNAi promoted dauer larvae formation, suggesting acn-1 is a daf gene. Captopril-mediated lifespan extension xwas abrogated by daf-16(lf) and daf-12(lf) mutations. Our results indicate that captopril and acn-1 control aging by modulating dauer formation pathways. We speculate that this represents a conserved mechanism of lifespan control. Summary Statement Captopril and acn-1 control aging. By demonstrating they regulate dauer formation and interact with daf genes, including a new DAF-2(A261V) mutant corresponding to a human disease variant, we clarified the mechanism.
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26
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Balasubramaniam B, Topalidou I, Kelley M, Meadows SM, Funk O, Ailion M, Fay DS. Effectors of anterior morphogenesis in C. elegans embryos. Biol Open 2023; 12:bio059982. [PMID: 37345480 PMCID: PMC10339035 DOI: 10.1242/bio.059982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 06/19/2023] [Indexed: 06/23/2023] Open
Abstract
During embryogenesis the nascent Caenorhabditis elegans epidermis secretes an apical extracellular matrix (aECM) that serves as an external stabilizer, preventing deformation of the epidermis by mechanical forces exerted during morphogenesis. At present, the factors that contribute to aECM function are mostly unknown, including the aECM components themselves, their posttranslational regulators, and the pathways required for their secretion. Here we showed that two proteins previously linked to aECM function, SYM-3/FAM102A and SYM-4/WDR44, colocalize to intracellular and membrane-associated puncta and likely function in a complex. Proteomics experiments also suggested potential roles for SYM-3/FAM102A and SYM-4/WDR44 family proteins in intracellular trafficking. Nonetheless, we found no evidence to support a critical function for SYM-3 or SYM-4 in the apical deposition of two aECM components, NOAH-1 and FBN-1. Moreover, loss of a key splicing regulator of fbn-1, MEC-8/RBPMS2, had surprisingly little effect on the abundance or deposition of FBN-1. Using a focused screening approach, we identified 32 additional proteins that likely contribute to the structure and function of the embryonic aECM. We also characterized morphogenesis defects in embryos lacking mir-51 microRNA family members, which display a similar phenotype to mec-8; sym double mutants. Collectively, these findings add to our knowledge of factors controlling embryonic morphogenesis.
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Affiliation(s)
- Boopathi Balasubramaniam
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie 82071-3944, WY, USA
| | - Irini Topalidou
- Department of Biochemistry, University of Washington, Seattle 98195-7350, WA, USA
| | - Melissa Kelley
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie 82071-3944, WY, USA
| | - Sarina M. Meadows
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie 82071-3944, WY, USA
| | - Owen Funk
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie 82071-3944, WY, USA
| | - Michael Ailion
- Department of Biochemistry, University of Washington, Seattle 98195-7350, WA, USA
| | - David S. Fay
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie 82071-3944, WY, USA
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27
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Birnbaum SK, Cohen JD, Belfi A, Murray JI, Adams JRG, Chisholm AD, Sundaram MV. The proprotein convertase BLI-4 promotes collagen secretion during assembly of the Caenorhabditis elegans cuticle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.542650. [PMID: 37333289 PMCID: PMC10274747 DOI: 10.1101/2023.06.06.542650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Some types of collagens, including transmembrane MACIT collagens and C. elegans cuticle collagens, are N-terminally cleaved at a dibasic site that resembles the consensus for furin or other proprotein convertases of the subtilisin/kexin (PCSK) family. Such cleavage may release transmembrane collagens from the plasma membrane and affect extracellular matrix assembly or structure. However, the functional consequences of such cleavage are unclear and evidence for the role of specific PCSKs is lacking. Here, we used endogenous collagen fusions to fluorescent proteins to visualize the secretion and assembly of the first collagen-based cuticle in C. elegans and then tested the role of the PCSK BLI-4 in these processes. Unexpectedly, we found that cuticle collagens SQT-3 and DPY-17 are secreted into the extraembryonic space several hours before cuticle matrix assembly. Furthermore, this early secretion depends on BLI-4/PCSK; in bli-4 and cleavage-site mutants, SQT-3 and DPY-17 are not efficiently secreted and instead form large intracellular aggregates. Their later assembly into cuticle matrix is reduced but not entirely blocked. These data reveal a role for collagen N-terminal processing in intracellular trafficking and in the spatial and temporal restriction of matrix assembly in vivo . Our observations also prompt a revision of the classic model for C. elegans cuticle matrix assembly and the pre-cuticle-to-cuticle transition, suggesting that cuticle layer assembly proceeds via a series of regulated steps and not simply by sequential secretion and deposition.
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Affiliation(s)
- Susanna K Birnbaum
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia PA
| | - Jennifer D Cohen
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia PA
| | - Alexandra Belfi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia PA
| | - John I Murray
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia PA
| | - Jennifer R G Adams
- Departments of Neurobiology and Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego CA
| | - Andrew D Chisholm
- Departments of Neurobiology and Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, San Diego CA
| | - Meera V Sundaram
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia PA
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28
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Johnson LC, Vo AA, Clancy JC, Myles KM, Pooranachithra M, Aguilera J, Levenson MT, Wohlenberg C, Rechtsteiner A, Ragle JM, Chisholm AD, Ward JD. NHR-23 activity is necessary for C. elegans developmental progression and apical extracellular matrix structure and function. Development 2023; 150:dev201085. [PMID: 37129010 PMCID: PMC10233720 DOI: 10.1242/dev.201085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 04/11/2023] [Indexed: 05/03/2023]
Abstract
Nematode molting is a remarkable process where animals must repeatedly build a new apical extracellular matrix (aECM) beneath a previously built aECM that is subsequently shed. The nuclear hormone receptor NHR-23 (also known as NR1F1) is an important regulator of C. elegans molting. NHR-23 expression oscillates in the epidermal epithelium, and soma-specific NHR-23 depletion causes severe developmental delay and death. Tissue-specific RNAi suggests that nhr-23 acts primarily in seam and hypodermal cells. NHR-23 coordinates the expression of factors involved in molting, lipid transport/metabolism and remodeling of the aECM. NHR-23 depletion causes dampened expression of a nas-37 promoter reporter and a loss of reporter oscillation. The cuticle collagen ROL-6 and zona pellucida protein NOAH-1 display aberrant annular localization and severe disorganization over the seam cells after NHR-23 depletion, while the expression of the adult-specific cuticle collagen BLI-1 is diminished and frequently found in patches. Consistent with these localization defects, the cuticle barrier is severely compromised when NHR-23 is depleted. Together, this work provides insight into how NHR-23 acts in the seam and hypodermal cells to coordinate aECM regeneration during development.
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Affiliation(s)
- Londen C. Johnson
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - An A. Vo
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - John C. Clancy
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Krista M. Myles
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Murugesan Pooranachithra
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Joseph Aguilera
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Max T. Levenson
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Chloe Wohlenberg
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Andreas Rechtsteiner
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Andrew D. Chisholm
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jordan D. Ward
- Department of Molecular, Cell, and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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29
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Boopathi B, Topalidou I, Kelley M, Meadows SM, Funk O, Ailion M, Fay DS. Pathways that affect anterior morphogenesis in C. elegans embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.23.537986. [PMID: 37163004 PMCID: PMC10168279 DOI: 10.1101/2023.04.23.537986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
During embryogenesis the nascent Caenorhabditis elegans epidermis secretes an apical extracellular matrix (aECM) that serves as an external stabilizer, preventing deformation of the epidermis by mechanical forces exerted during morphogenesis. We showed that two conserved proteins linked to this process, SYM-3/FAM102A and SYM-4/WDR44, colocalize to intracellular and membrane-associated puncta and likely function together in a complex. Proteomics data also suggested potential roles for FAM102A and WDR44 family proteins in intracellular trafficking, consistent with their localization patterns. Nonetheless, we found no evidence to support a clear function for SYM-3 or SYM-4 in the apical deposition of two aECM components, FBN-1 and NOAH. Surprisingly, loss of MEC-8/RBPMS2, a conserved splicing factor and regulator of fbn-1 , had little effect on the abundance or deposition of FBN-1 to the aECM. Using a focused screening approach, we identified 32 additional proteins that likely contribute to the structure and function of the embryonic aECM. Lastly, we examined morphogenesis defects in embryos lacking mir-51 microRNA family members, which display a related embryonic phenotype to mec-8; sym double mutants. Collectively, our findings add to our knowledge of pathways controlling embryonic morphogenesis. SUMMARY STATEMENT We identify new proteins in apical ECM biology in C. elegans and provide evidence that SYM-3/FAM102A and SYM-4/WDR44 function together in trafficking but do not regulate apical ECM protein deposition.
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Affiliation(s)
- Balasubramaniam Boopathi
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Irini Topalidou
- Department of Biochemistry, University of Washington, Seattle, United States of America
| | - Melissa Kelley
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Sarina M Meadows
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Owen Funk
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Michael Ailion
- Department of Biochemistry, University of Washington, Seattle, United States of America
| | - David S Fay
- Department of Molecular Biology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
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30
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Clancy JC, Vo AA, Myles KM, Levenson MT, Ragle JM, Ward JD. Experimental considerations for study of C. elegans lysosomal proteins. G3 (BETHESDA, MD.) 2023; 13:jkad032. [PMID: 36748711 PMCID: PMC10085801 DOI: 10.1093/g3journal/jkad032] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 06/20/2022] [Accepted: 01/27/2023] [Indexed: 02/08/2023]
Abstract
Lysosomes are an important organelle required for the degradation of a range of cellular components. Lysosome function is critical for development and homeostasis as dysfunction can lead to inherited genetic disorders, cancer, and neurodegenerative and metabolic diseases. The acidic and protease-rich environment of lysosomes poses experimental challenges. Many fluorescent proteins are quenched or degraded, while specific red fluorescent proteins can be cleaved from translational fusion partners and accumulate. While studying MLT-11, a Caenorhabditis elegans molting factor that localizes to lysosomes and the cuticle, we sought to optimize several experimental parameters. We found that, in contrast to mNeonGreen fusions, mScarlet fusions to MLT-11 missed cuticular and rectal epithelial localization. Rapid sample lysis and denaturation were critical for preventing MLT-11 fragmentation while preparing lysates for western blots. Using a model lysosomal substrate (NUC-1), we found that rigid polyproline linkers and truncated mCherry constructs do not prevent cleavage of mCherry from NUC-1. We provide evidence that extended localization in lysosomal environments prevents the detection of FLAG epitopes in western blots. Finally, we optimize an acid-tolerant green fluorescent protein (Gamillus) for use in C. elegans. These experiments provide important experimental considerations and new reagents for the study of C. elegans lysosomal proteins.
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Affiliation(s)
- John C Clancy
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - An A Vo
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Krista M Myles
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Max T Levenson
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - James Matthew Ragle
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jordan D Ward
- Department of Molecular, Cell, and Developmental Biology, University of California-Santa Cruz, Santa Cruz, CA 95064, USA
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31
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Blazie SM, Jin Y. Executing cell-specific cross-linking immunoprecipitation and sequencing (seCLIP) in C. elegans. STAR Protoc 2023; 4:101959. [PMID: 36566382 PMCID: PMC9803825 DOI: 10.1016/j.xpro.2022.101959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/03/2022] [Accepted: 12/02/2022] [Indexed: 12/25/2022] Open
Abstract
The single-end enhanced cross-linking immunoprecipitation (seCLIP) method is well suited for efficient and unbiased transcriptome-wide interrogation of RNA-binding protein (RBP) interaction sites. Here, we provide a protocol for executing cell-specific seCLIP for any desired RBP in Caenorhabditis elegans. We begin with steps and recommendations for transgene construction and Cas9-mediated chromosomal integration. We provide detailed procedures for isolation of RBP-associated RNA fragments, subsequent library preparation, and sequencing. We further discuss best practices for data analysis, interpretation of results, and troubleshooting. For complete details on the use and execution of this protocol, please refer to Blazie et al. (2021).1.
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Affiliation(s)
- Stephen M Blazie
- Department of Neurobiology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Yishi Jin
- Department of Neurobiology, School of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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32
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Meeuse MWM, Hauser YP, Nahar S, Smith AAT, Braun K, Azzi C, Rempfler M, Großhans H. C. elegans molting requires rhythmic accumulation of the Grainyhead/LSF transcription factor GRH-1. EMBO J 2023; 42:e111895. [PMID: 36688410 PMCID: PMC9929640 DOI: 10.15252/embj.2022111895] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/08/2022] [Accepted: 12/16/2022] [Indexed: 01/24/2023] Open
Abstract
C. elegans develops through four larval stages that are rhythmically terminated by molts, that is, the synthesis and shedding of a cuticular exoskeleton. Each larval cycle involves rhythmic accumulation of thousands of transcripts, which we show here relies on rhythmic transcription. To uncover the responsible gene regulatory networks (GRNs), we screened for transcription factors that promote progression through the larval stages and identified GRH-1, BLMP-1, NHR-23, NHR-25, MYRF-1, and BED-3. We further characterize GRH-1, a Grainyhead/LSF transcription factor, whose orthologues in other animals are key epithelial cell-fate regulators. We find that GRH-1 depletion extends molt durations, impairs cuticle integrity and shedding, and causes larval death. GRH-1 is required for, and accumulates prior to, each molt, and preferentially binds to the promoters of genes expressed during this time window. Binding to the promoters of additional genes identified in our screen furthermore suggests that we have identified components of a core molting-clock GRN. Since the mammalian orthologues of GRH-1, BLMP-1 and NHR-23, have been implicated in rhythmic homeostatic skin regeneration in mouse, the mechanisms underlying rhythmic C. elegans molting may apply beyond nematodes.
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Affiliation(s)
- Milou W M Meeuse
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
- University of BaselBaselSwitzerland
| | - Yannick P Hauser
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
- University of BaselBaselSwitzerland
| | - Smita Nahar
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
| | | | - Kathrin Braun
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
| | - Chiara Azzi
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
- University of BaselBaselSwitzerland
| | - Markus Rempfler
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research (FMI)BaselSwitzerland
- University of BaselBaselSwitzerland
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33
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Rodriguez Mendoza V, Chandler L, Liu Z, Buddendorff L, Al-Rajhi A, Choi T, Gibb G, Harvey J, Mihalik A, Moravec S, Pilcher W, Raju V, Choe KP. Extracellular proteins OSM-7 and OSM-8 are required for stress response gene regulation at all post-embryonic stages. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000688. [PMID: 36606078 PMCID: PMC9807463 DOI: 10.17912/micropub.biology.000688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 01/07/2023]
Abstract
Nematode cuticles are extracellular matrices (ECMs) that function as structural support and permeability barriers. Genetic disruption of specific cuticle collagen structures or secreted epidermal proteins in C. elegans activates stress response genes in epithelial cells suggesting the presence of an extracellular damage signaling mechanism. Cuticles are replaced during development via molting but investigations of extracellular signaling to stress responses have focused on adults. In our current study, we measured cuticle phenotypes and stress response gene expression in all post-embryonic stages of mutant strains for a collagen and two secreted epidermal proteins to gain insights into developmental patterns.
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Affiliation(s)
| | - Luke Chandler
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL USA
| | - Zhexin Liu
- University of Florida, Gainesville, FL USA
| | | | | | - Thine Choi
- University of Florida, Gainesville, FL USA
| | | | | | | | | | | | | | - Keith Patrick Choe
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL USA
,
Correspondence to: Keith Patrick Choe (
)
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34
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Wang SY, Kim K, O'Brown ZK, Levan A, Dodson AE, Kennedy SG, Chernoff C, Greer EL. Hypoxia induces transgenerational epigenetic inheritance of small RNAs. Cell Rep 2022; 41:111800. [PMID: 36516753 PMCID: PMC9847139 DOI: 10.1016/j.celrep.2022.111800] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 09/23/2022] [Accepted: 11/17/2022] [Indexed: 12/15/2022] Open
Abstract
Animals sense and adapt to decreased oxygen availability, but whether and how hypoxia exposure in ancestors can elicit phenotypic consequences in normoxia-reared descendants are unclear. We show that hypoxia educes an intergenerational reduction in lipids and a transgenerational reduction in fertility in the nematode Caenorhabditis elegans. The transmission of these epigenetic phenotypes is dependent on repressive histone-modifying enzymes and the argonaute HRDE-1. Feeding naive C. elegans small RNAs extracted from hypoxia-treated worms is sufficient to induce a fertility defect. Furthermore, the endogenous small interfering RNA F44E5.4/5 is upregulated intergenerationally in response to hypoxia, and soaking naive normoxia-reared C. elegans with F44E5.4/5 double-stranded RNA (dsRNA) is sufficient to induce an intergenerational fertility defect. Finally, we demonstrate that labeled F44E5.4/5 dsRNA is itself transmitted from parents to children. Our results suggest that small RNAs respond to the environment and are sufficient to transmit non-genetic information from parents to their naive children.
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Affiliation(s)
- Simon Yuan Wang
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
| | - Kathleen Kim
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Zach Klapholz O'Brown
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Aileen Levan
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Anne Elizabeth Dodson
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Scott G Kennedy
- Department of Genetics, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Chaim Chernoff
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Eric Lieberman Greer
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
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35
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Kamal M, Tokmakjian L, Knox J, Mastrangelo P, Ji J, Cai H, Wojciechowski JW, Hughes MP, Takács K, Chu X, Pei J, Grolmusz V, Kotulska M, Forman-Kay JD, Roy PJ. A spatiotemporal reconstruction of the C. elegans pharyngeal cuticle reveals a structure rich in phase-separating proteins. eLife 2022; 11:e79396. [PMID: 36259463 PMCID: PMC9629831 DOI: 10.7554/elife.79396] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 10/11/2022] [Indexed: 11/19/2022] Open
Abstract
How the cuticles of the roughly 4.5 million species of ecdysozoan animals are constructed is not well understood. Here, we systematically mine gene expression datasets to uncover the spatiotemporal blueprint for how the chitin-based pharyngeal cuticle of the nematode Caenorhabditis elegans is built. We demonstrate that the blueprint correctly predicts expression patterns and functional relevance to cuticle development. We find that as larvae prepare to molt, catabolic enzymes are upregulated and the genes that encode chitin synthase, chitin cross-linkers, and homologs of amyloid regulators subsequently peak in expression. Forty-eight percent of the gene products secreted during the molt are predicted to be intrinsically disordered proteins (IDPs), many of which belong to four distinct families whose transcripts are expressed in overlapping waves. These include the IDPAs, IDPBs, and IDPCs, which are introduced for the first time here. All four families have sequence properties that drive phase separation and we demonstrate phase separation for one exemplar in vitro. This systematic analysis represents the first blueprint for cuticle construction and highlights the massive contribution that phase-separating materials make to the structure.
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Affiliation(s)
- Muntasir Kamal
- Department of Molecular Genetics, University of TorontoTorontoCanada
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
| | - Levon Tokmakjian
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
- Department of Pharmacology and Toxicology, University of TorontoTorontoCanada
| | - Jessica Knox
- Department of Molecular Genetics, University of TorontoTorontoCanada
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
| | - Peter Mastrangelo
- Department of Molecular Genetics, University of TorontoTorontoCanada
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
| | - Jingxiu Ji
- Department of Molecular Genetics, University of TorontoTorontoCanada
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
| | - Hao Cai
- Molecular Medicine Program, The Hospital for Sick ChildrenTorontoCanada
| | - Jakub W Wojciechowski
- Wroclaw University of Science and Technology, Faculty of Fundamental Problems of Technology, Department of Biomedical EngineeringWroclawPoland
| | - Michael P Hughes
- Department of Cell and Molecular Biology, St. Jude Children’s Research HospitalMemphisUnited States
| | - Kristóf Takács
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös UniversityBudapestHungary
| | - Xiaoquan Chu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking UniversityBeijingChina
| | - Jianfeng Pei
- Department of Computer Science and Technology, Tsinghua UniversityBeijingChina
| | - Vince Grolmusz
- PIT Bioinformatics Group, Institute of Mathematics, Eötvös UniversityBudapestHungary
| | - Malgorzata Kotulska
- Wroclaw University of Science and Technology, Faculty of Fundamental Problems of Technology, Department of Biomedical EngineeringWroclawPoland
| | - Julie Deborah Forman-Kay
- Molecular Medicine Program, The Hospital for Sick ChildrenTorontoCanada
- Department of Biochemistry, University of TorontoTorontoCanada
| | - Peter J Roy
- Department of Molecular Genetics, University of TorontoTorontoCanada
- The Donnelly Centre for Cellular and Biomolecular Research, University of TorontoTorontoCanada
- Department of Pharmacology and Toxicology, University of TorontoTorontoCanada
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36
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Change of motifs in C. elegans reveals developmental principle of neural network. Biochem Biophys Res Commun 2022; 624:112-119. [PMID: 35940123 DOI: 10.1016/j.bbrc.2022.07.108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 07/28/2022] [Indexed: 11/23/2022]
Abstract
Revealing the organizing principles of developing neural networks is a difficult but significant task in neuroscience. As a creature with a rather compact and well-studied neural network, C. elegans is an ideal subject for neuroscience study. However, the researches on its developing neural network remain challenging. The changes in specific properties of neural network across development may uncover part of its principles. Motif is a typical structure property that can be well applied to various complex networks. Here, we study the motif changes in C. elegans neural network across development. By counting the occurrence number of all three-node subgraph motif structures in its neural network at different stages of C. elegans development, along with those in corresponding random networks, we determine which of these structures are motifs for C. elegans, finding out the regular changes of motifs during its development. Combined with the potential function of these subgraph motifs and synaptic information, we gain insight into the organizing principle of neural network during development, which may increase our understanding of neuroscience and inspire the construction of artificial neural network.
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37
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Pekec T, Lewandowski J, Komur AA, Sobańska D, Guo Y, Świtońska-Kurkowska K, Małecki JM, Dubey AA, Pokrzywa W, Frankowski M, Figiel M, Ciosk R. Ferritin-mediated iron detoxification promotes hypothermia survival in Caenorhabditis elegans and murine neurons. Nat Commun 2022; 13:4883. [PMID: 35986016 PMCID: PMC9391379 DOI: 10.1038/s41467-022-32500-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 08/02/2022] [Indexed: 11/22/2022] Open
Abstract
How animals rewire cellular programs to survive cold is a fascinating problem with potential biomedical implications, ranging from emergency medicine to space travel. Studying a hibernation-like response in the free-living nematode Caenorhabditis elegans, we uncovered a regulatory axis that enhances the natural resistance of nematodes to severe cold. This axis involves conserved transcription factors, DAF-16/FoxO and PQM-1, which jointly promote cold survival by upregulating FTN-1, a protein related to mammalian ferritin heavy chain (FTH1). Moreover, we show that inducing expression of FTH1 also promotes cold survival of mammalian neurons, a cell type particularly sensitive to deterioration in hypothermia. Our findings in both animals and cells suggest that FTN-1/FTH1 facilitates cold survival by detoxifying ROS-generating iron species. We finally show that mimicking the effects of FTN-1/FTH1 with drugs protects neurons from cold-induced degeneration, opening a potential avenue to improved treatments of hypothermia. Strategies to improve cold resistance are of potential biomedical interest. Here the authors demonstrate that ferritin-mediated detoxification of iron, preventing the generation of reactive oxygen species, promotes cold survival in both Caenorhabditis elegans and cultured mammalian neurons.
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38
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Patel R, Galagali H, Kim JK, Frand AR. Feedback between a retinoid-related nuclear receptor and the let-7 microRNAs controls the pace and number of molting cycles in C. elegans. eLife 2022; 11:e80010. [PMID: 35968765 PMCID: PMC9377799 DOI: 10.7554/elife.80010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Animal development requires coordination among cyclic processes, sequential cell fate specifications, and once-a-lifetime morphogenic events, but the underlying timing mechanisms are not well understood. Caenorhabditis elegans undergoes four molts at regular 8 to 10 hour intervals. The pace of the cycle is governed by PERIOD/lin-42 and other as-yet unknown factors. Cessation of the cycle in young adults is controlled by the let-7 family of microRNAs and downstream transcription factors in the heterochronic pathway. Here, we characterize a negative feedback loop between NHR-23, the worm homolog of mammalian retinoid-related orphan receptors (RORs), and the let-7 family of microRNAs that regulates both the frequency and finite number of molts. The molting cycle is decelerated in nhr-23 knockdowns and accelerated in let-7(-) mutants, but timed similarly in let-7(-) nhr-23(-) double mutants and wild-type animals. NHR-23 binds response elements (ROREs) in the let-7 promoter and activates transcription. In turn, let-7 dampens nhr-23 expression across development via a complementary let-7-binding site (LCS) in the nhr-23 3' UTR. The molecular interactions between NHR-23 and let-7 hold true for other let-7 family microRNAs. Either derepression of nhr-23 transcripts by LCS deletion or high gene dosage of nhr-23 leads to protracted behavioral quiescence and extra molts in adults. NHR-23 and let-7 also coregulate scores of genes required for execution of the molts, including lin-42. In addition, ROREs and LCSs isolated from mammalian ROR and let-7 genes function in C. elegans, suggesting conservation of this feedback mechanism. We propose that this feedback loop unites the molting timer and the heterochronic gene regulatory network, possibly by functioning as a cycle counter.
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Affiliation(s)
- Ruhi Patel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Himani Galagali
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - John K Kim
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Alison R Frand
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
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39
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Real age prediction from the transcriptome with RAPToR. Nat Methods 2022; 19:969-975. [PMID: 35817937 DOI: 10.1038/s41592-022-01540-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 05/25/2022] [Indexed: 11/08/2022]
Abstract
Transcriptomic data is often affected by uncontrolled variation among samples that can obscure and confound the effects of interest. This variation is frequently due to unintended differences in developmental stages between samples. The transcriptome itself can be used to estimate developmental progression, but existing methods require many samples and do not estimate a specimen's real age. Here we present real-age prediction from transcriptome staging on reference (RAPToR), a computational method that precisely estimates the real age of a sample from its transcriptome, exploiting existing time-series data as reference. RAPToR works with whole animal, dissected tissue and single-cell data for the most common animal models, humans and even for non-model organisms lacking reference data. We show that RAPToR can be used to remove age as a confounding factor and allow recovery of a signal of interest in differential expression analysis. RAPToR will be especially useful in large-scale single-organism profiling because it eliminates the need for accurate staging or synchronisation before profiling.
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40
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Roy PJ. Temporal Regulation of Gene Expression in Post-Mitotic Cells is Revealed from a Synchronized Population of C. elegans Larvae. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000587. [PMID: 35783576 PMCID: PMC9242692 DOI: 10.17912/micropub.biology.000587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 11/08/2022]
Abstract
Unsupervised Uniform Manifold Approximation and Projection (UMAP) plots of single cell sequencing data from synchronized Caenorhabditis elegans larvae yield tissue-specific data clusters, some of which are plotted as elongated archipelagos. These archipelagos likely represent a single cell type. I show that the pharyngeal archipelagos express a myriad of asynchronous temporally regulated genes, which likely accounts for their elongated topology. With one archipelago, I show that there is a high correlation between a) the base pair distance between the binding sites of an archipelago-specific transcription factor (HLH-6) and the transcriptional start site of the targeted genes and b) the timing of peak gene expression of those genes that are expressed in an archipelago-specific manner. Despite the correlation being made with only four genes, it prompts the hypothesis that the physical distance between a transcription factor and the relevant transcription start site may be an important factor in determining the temporal onset of transcription and transcript abundance.
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Affiliation(s)
- Peter J. Roy
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
,
Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
,
The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
,
Correspondence to: Peter J. Roy (
)
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41
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Stojanovski K, Großhans H, Towbin BD. Coupling of growth rate and developmental tempo reduces body size heterogeneity in C. elegans. Nat Commun 2022; 13:3132. [PMID: 35668054 PMCID: PMC9170734 DOI: 10.1038/s41467-022-29720-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 03/24/2022] [Indexed: 11/15/2022] Open
Abstract
Animals increase by orders of magnitude in volume during development. Therefore, small variations in growth rates among individuals could amplify to a large heterogeneity in size. By live imaging of C. elegans, we show that amplification of size heterogeneity is prevented by an inverse coupling of the volume growth rate to the duration of larval stages and does not involve strict size thresholds for larval moulting. We perturb this coupling by changing the developmental tempo through manipulation of a transcriptional oscillator that controls the duration of larval development. As predicted by a mathematical model, this perturbation alters the body volume. Model analysis shows that an inverse relation between the period length and the growth rate is an intrinsic property of genetic oscillators and can occur independently of additional complex regulation. This property of genetic oscillators suggests a parsimonious mechanism that counteracts the amplification of size differences among individuals during development. Animals must reach the correct size during development, despite stochastic differences in their growth rate. Here, Stojanovski et al. show that a coupling of growth and development by an oscillatory timer buffers fluctuations in the growth of the nematode C. elegans to ensure its correct size.
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Affiliation(s)
| | - Helge Großhans
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| | - Benjamin D Towbin
- University of Bern, Bern, Switzerland. .,Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland.
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42
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Joseph BB, Edeen PT, Meadows S, Binti S, Fay DS. An unexpected role for the conserved ADAM-family metalloprotease ADM-2 in Caenorhabditis elegans molting. PLoS Genet 2022; 18:e1010249. [PMID: 35639786 PMCID: PMC9187072 DOI: 10.1371/journal.pgen.1010249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 06/10/2022] [Accepted: 05/11/2022] [Indexed: 11/18/2022] Open
Abstract
Molting is a widespread developmental process in which the external extracellular matrix (ECM), the cuticle, is remodeled to allow for organismal growth and environmental adaptation. Studies in the nematode Caenorhabditis elegans have identified a diverse set of molting-associated factors including signaling molecules, intracellular trafficking regulators, ECM components, and ECM-modifying enzymes such as matrix metalloproteases. C. elegans NEKL-2 and NEKL-3, two conserved members of the NEK family of protein kinases, are essential for molting and promote the endocytosis of environmental steroid-hormone precursors by the epidermis. Steroids in turn drive the cyclic induction of many genes required for molting. Here we report a role for the sole C. elegans ADAM–meltrin metalloprotease family member, ADM-2, as a mediator of molting. Loss of adm-2, including mutations that disrupt the metalloprotease domain, led to the strong suppression of molting defects in partial loss-of-function nekl mutants. ADM-2 is expressed in the epidermis, and its trafficking through the endo-lysosomal network was disrupted after NEKL depletion. We identified the epidermally expressed low-density lipoprotein receptor–related protein, LRP-1, as a candidate target of ADM-2 regulation. Whereas loss of ADM-2 activity led to the upregulation of apical epidermal LRP-1, ADM-2 overexpression caused a reduction in LRP-1 levels. Consistent with this, several mammalian ADAMs, including the meltrin ADAM12, have been shown to regulate mammalian LRP1 via proteolysis. In contrast to mammalian homologs, however, the regulation of LRP-1 by ADM-2 does not appear to involve the metalloprotease function of ADM-2, nor is proteolytic processing of LRP-1 strongly affected in adm-2 mutants. Our findings suggest a noncanonical role for an ADAM family member in the regulation of a lipoprotein-like receptor and lead us to propose that endocytic trafficking may be important for both the internalization of factors that promote molting as well as the removal of proteins that can inhibit the process. The molecular and cellular features of molting in nematodes share many similarities with cellular and developmental processes that occur in mammals. This includes the degradation and reorganization of extracellular matrix materials that surround cells, as well as the intracellular machineries that allow cells to sample and modify their environments. In the current study, we found an unexpected function for a conserved protein that cleaves other proteins on the external surface of cells. Rather than promoting molting through extracellular matrix reorganization, however, the ADM-2 protease appears to function as a negative regulator of molting. This observation can be explained in part by data showing that ADM-2 negatively regulates a cell surface receptor required for molting. Surprisingly, it appears to do so through a mechanism that does not involve proteolysis. Our data provide insights into the mechanisms controlling molting and link several conserved proteins to show how they function together during development.
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Affiliation(s)
- Braveen B. Joseph
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Phillip T. Edeen
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Sarina Meadows
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - Shaonil Binti
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
| | - David S. Fay
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming, United States of America
- * E-mail:
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43
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Deviations from temporal scaling support a stage-specific regulation for C. elegans postembryonic development. BMC Biol 2022; 20:94. [PMID: 35477393 PMCID: PMC9047341 DOI: 10.1186/s12915-022-01295-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 04/12/2022] [Indexed: 12/04/2022] Open
Abstract
Background After embryonic development, Caenorhabditis elegans progress through for larval stages, each of them finishing with molting. The repetitive nature of C. elegans postembryonic development is considered an oscillatory process, a concept that has gained traction from regulation by a circadian clock gene homologue. Nevertheless, each larval stage has a defined duration and entails specific events. Since the overall duration of development is controlled by numerous factors, we have asked whether different rate-limiting interventions impact all stages equally. Results We have measured the duration of each stage of development for over 2500 larvae, under varied environmental conditions known to alter overall developmental rate. We applied changes in temperature and in the quantity and quality of nutrition and analysed the effect of genetically reduced insulin signalling. Our results show that the distinct developmental stages respond differently to these perturbations. The changes in the duration of specific larval stages seem to depend on stage-specific events. Furthermore, our high-resolution measurement of the effect of temperature on the stage-specific duration of development has unveiled novel features of temperature dependence in C. elegans postembryonic development. Conclusions Altogether, our results show that multiple factors fine tune developmental timing, impacting larval stages independently. Further understanding of the regulation of this process will allow modelling the mechanisms that control developmental timing. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01295-2.
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44
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Koks S, Pfaff AL, Bubb VJ, Quinn JP. Longitudinal intronic RNA-Seq analysis of Parkinson's disease patients reveals disease-specific nascent transcription. Exp Biol Med (Maywood) 2022; 247:945-957. [PMID: 35289213 DOI: 10.1177/15353702221081027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Transcriptomic studies usually focus on either gene or exon-based annotations, and only limited experiments have reported changes in reads mapping to introns. The analysis of intronic reads allows the detection of nascent transcription that is not influenced by steady-state RNA levels and provides information on actively transcribed genes. Here, we describe substantial intronic transcriptional changes in Parkinson's disease (PD) patients compared to healthy controls (CO) at two different timepoints; at the time of diagnosis (BL) and three years later (V08). We used blood RNA-Seq data from the Parkinson's Progression Markers Initiative (PPMI) cohort and identified significantly changed transcription of intronic reads only in PD patients during this follow-up period. In CO subjects, only nine transcripts demonstrated differentially expressed introns between visits. However, in PD patients, 4873 transcripts had differentially expressed introns at visit V08 compared to BL, many of them in genes previously associated with neurodegenerative diseases, such as LRRK2, C9orf72, LGALS3, KANSL1AS1, and ALS2. In addition, at the time of diagnosis (BL visit), we identified 836 transcripts (e.g. SNCA, DNAJC19, PRRG4) and at visit V08, 2184 transcripts (e.g. PINK1, GBA, ALS2, PLEKHM1) with differential intronic expression specific to PD patients. In contrast, reads mapping to exonic regions demonstrated little variation indicating highly specific changes only in intronic transcription. Our study demonstrated that PD is characterized by substantial changes in the nascent transcription, and description of these changes could help to understand the molecular pathology underpinning this disease.
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Affiliation(s)
- Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Abigail L Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
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45
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Abstract
An enduring mystery of development is how its timing is controlled, particularly for development after birth, where timing is highly flexible and depends on environmental conditions, such as food availability and diet. We followed timing of cell- and organism-level events in individual Caenorhabditis elegans larvae developing from hatching to adulthood, uncovering widespread variations in event timing, both between isogenic individuals in the same environment and when changing conditions and genotypes. However, in almost all cases, we found that events occurred at the same time, when time was rescaled by the duration of development measured in each individual. This observation of “temporal scaling” poses strong constraints on models to explain timing of larval development. It is essential that correct temporal order of cellular events is maintained during animal development. During postembryonic development, the rate of development depends on external conditions, such as food availability, diet, and temperature. How timing of cellular events is impacted when the rate of development is changed at the organism level is not known. We used a unique time-lapse microscopy approach to simultaneously measure timing of oscillatory gene expression, hypodermal stem cell divisions, and cuticle shedding in individual Caenorhabditis elegans larvae, as they developed from hatching to adulthood. This revealed strong variability in timing between isogenic individuals under the same conditions. However, this variability obeyed “temporal scaling,” meaning that events occurred at the same time when measured relative to the total duration of development in each individual. We also observed pervasive changes in timing when temperature, diet, or genotype were varied, but with larval development divided in “epochs” that differed in how event timing was impacted. Yet, these variations in timing were still explained by temporal scaling when time was rescaled by the duration of the respective epochs in each individual. Surprisingly, timing obeyed temporal scaling even in mutants lacking lin-42/Period, presumed a core regulator of timing of larval development, that exhibited strongly delayed, heterogeneous timing. However, shifting conditions middevelopment perturbed temporal scaling and changed event order in a highly condition-specific manner, indicating that a complex machinery is responsible for temporal scaling under constant conditions.
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46
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Li JR, Tang M, Li Y, Amos CI, Cheng C. Genetic variants associated mRNA stability in lung. BMC Genomics 2022; 23:196. [PMID: 35272635 PMCID: PMC8915503 DOI: 10.1186/s12864-022-08405-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 02/21/2022] [Indexed: 12/04/2022] Open
Abstract
Background Expression quantitative trait loci (eQTLs) analyses have been widely used to identify genetic variants associated with gene expression levels to understand what molecular mechanisms underlie genetic traits. The resultant eQTLs might affect the expression of associated genes through transcriptional or post-transcriptional regulation. In this study, we attempt to distinguish these two types of regulation by identifying genetic variants associated with mRNA stability of genes (stQTLs). Results Here, we presented a computational framework that takes advantage of recently developed methods to infer the mRNA stability of genes based on RNA-seq data and performed association analysis to identify stQTLs. Using the Genotype-Tissue Expression (GTEx) lung RNA-Seq data, we identified a total of 142,801 stQTLs for 3942 genes and 186,132 eQTLs for 4751 genes from 15,122,700 genetic variants for 13,476 genes on the autosomes, respectively. Interestingly, our results indicated that stQTLs were enriched in the CDS and 3’UTR regions, while eQTLs are enriched in the CDS, 3’UTR, 5’UTR, and upstream regions. We also found that stQTLs are more likely than eQTLs to overlap with RNA binding protein (RBP) and microRNA (miRNA) binding sites. Our analyses demonstrate that simultaneous identification of stQTLs and eQTLs can provide more mechanistic insight on the association between genetic variants and gene expression levels. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08405-y.
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Affiliation(s)
- Jian-Rong Li
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.,Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Mabel Tang
- Department of BioSciences, Biochemistry and Cell Biology, Rice University, Houston, TX, USA
| | - Yafang Li
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.,Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Christopher I Amos
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.,Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA. .,Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA. .,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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47
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Binti S, Melinda RV, Joseph BB, Edeen PT, Miller SD, Fay DS. A life cycle alteration can correct molting defects in Caenorhabditis elegans. Dev Biol 2022; 483:143-156. [PMID: 35038442 PMCID: PMC8867747 DOI: 10.1016/j.ydbio.2022.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/21/2021] [Accepted: 01/03/2022] [Indexed: 11/28/2022]
Abstract
Molting is a widespread feature in the development of many invertebrates, including nematodes and arthropods. In Caenorhabditis elegans, the highly conserved protein kinases NEKL-2/NEK8/9 and NEKL-3/NEK6/7 (NEKLs) promote molting through their involvement in the uptake and intracellular trafficking of epidermal cargos. We found that the relative requirements for NEKL-2 and NEKL-3 differed at different life-cycle stages and under different environmental conditions. Most notably, the transition from the second to the third larval stage (L2→L3 molt) required a higher level of NEKL function than during several other life stages or when animals had experienced starvation at the L1 stage. Specifically, larvae that entered the pre-dauer L2d stage could escape molting defects when transiting to the (non-dauer) L3 stage. Consistent with this, mutations that promote entry into L2d suppressed nekl-associated molting defects, whereas mutations that inhibit L2d entry reduced starvation-mediated suppression. We further showed that loss or reduction of NEKL functions led to defects in the transcription of cyclically expressed molting genes, many of which are under the control of systemic steroid hormone regulation. Moreover, the timing and severity of these transcriptional defects correlated closely with the strength of nekl alleles and with their stage of arrest. Interestingly, transit through L2d rescued nekl-associated expression defects in suppressed worms, providing an example of how life-cycle decisions can impact subsequent developmental events. Given that NEKLs are implicated in the uptake of sterols by the epidermis, we propose that loss of NEKLs leads to a physiological reduction in steroid-hormone signaling and consequent defects in the transcription of genes required for molting.
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Affiliation(s)
- Shaonil Binti
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, 82071, USA
| | - Rosa V Melinda
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, 82071, USA
| | - Braveen B Joseph
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, 82071, USA
| | - Phillip T Edeen
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, 82071, USA
| | - Sam D Miller
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, 82071, USA
| | - David S Fay
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, WY, 82071, USA.
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48
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Gupta A, Shamsi F, Altemose N, Dorlhiac GF, Cypess AM, White AP, Yosef N, Patti ME, Tseng YH, Streets A. Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages. Genome Res 2022; 32:242-257. [PMID: 35042723 PMCID: PMC8805720 DOI: 10.1101/gr.275509.121] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 12/10/2021] [Indexed: 02/02/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) enables molecular characterization of complex biological tissues at high resolution. The requirement of single-cell extraction, however, makes it challenging for profiling tissues such as adipose tissue, for which collection of intact single adipocytes is complicated by their fragile nature. For such tissues, single-nucleus extraction is often much more efficient and therefore single-nucleus RNA sequencing (snRNA-seq) presents an alternative to scRNA-seq. However, nuclear transcripts represent only a fraction of the transcriptome in a single cell, with snRNA-seq marked with inherent transcript enrichment and detection biases. Therefore, snRNA-seq may be inadequate for mapping important transcriptional signatures in adipose tissue. In this study, we compare the transcriptomic landscape of single nuclei isolated from preadipocytes and mature adipocytes across human white and brown adipocyte lineages, with whole-cell transcriptome. We show that snRNA-seq is capable of identifying the broad cell types present in scRNA-seq at all states of adipogenesis. However, we also explore how and why the nuclear transcriptome is biased and limited, as well as how it can be advantageous. We robustly characterize the enrichment of nuclear-localized transcripts and adipogenic regulatory lncRNAs in snRNA-seq, while also providing a detailed understanding for the preferential detection of long genes upon using this technique. To remove such technical detection biases, we propose a normalization strategy for a more accurate comparison of nuclear and cellular data. Finally, we show successful integration of scRNA-seq and snRNA-seq data sets with existing bioinformatic tools. Overall, our results illustrate the applicability of snRNA-seq for the characterization of cellular diversity in the adipose tissue.
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Affiliation(s)
- Anushka Gupta
- University of California at Berkeley-University of California at San Francisco Graduate Program in Bioengineering, Berkeley, California 94720, USA
| | - Farnaz Shamsi
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nicolas Altemose
- University of California at Berkeley-University of California at San Francisco Graduate Program in Bioengineering, Berkeley, California 94720, USA
| | - Gabriel F Dorlhiac
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California 94720, USA
| | - Aaron M Cypess
- Diabetes, Endocrinology, and Obesity Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Andrew P White
- Department of Orthopedic Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nir Yosef
- Center for Computational Biology, University of California, Berkeley, Berkeley, California 94720, USA
- Department of Electrical Engineering and Computer Sciences, University of California at Berkeley, Berkeley, California 94720, USA
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts 02139, USA
| | | | - Yu-Hua Tseng
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, Massachusetts 02115, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Aaron Streets
- University of California at Berkeley-University of California at San Francisco Graduate Program in Bioengineering, Berkeley, California 94720, USA
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, California 94720, USA
- Chan Zuckerberg Biohub, San Francisco, California 94158, USA
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49
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Cohen JD, Cadena del Castillo CE, Serra ND, Kaech A, Spang A, Sundaram MV. The Caenorhabditis elegans Patched domain protein PTR-4 is required for proper organization of the precuticular apical extracellular matrix. Genetics 2021; 219:iyab132. [PMID: 34740248 PMCID: PMC8570789 DOI: 10.1093/genetics/iyab132] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 08/04/2021] [Indexed: 12/30/2022] Open
Abstract
The Patched-related superfamily of transmembrane proteins can transport lipids or other hydrophobic molecules across cell membranes. While the Hedgehog receptor Patched has been intensively studied, much less is known about the biological roles of other Patched-related family members. Caenorhabditis elegans has a large number of Patched-related proteins, despite lacking a canonical Hedgehog pathway. Here, we show that PTR-4 promotes the assembly of the precuticle apical extracellular matrix, a transient and molecularly distinct matrix that precedes and patterns the later collagenous cuticle or exoskeleton. ptr-4 mutants share many phenotypes with precuticle mutants, including defects in eggshell dissolution, tube shaping, alae (cuticle ridge) structure, molting, and cuticle barrier function. PTR-4 localizes to the apical side of a subset of outward-facing epithelia, in a cyclical manner that peaks when precuticle matrix is present. Finally, PTR-4 is required to limit the accumulation of the lipocalin LPR-3 and to properly localize the Zona Pellucida domain protein LET-653 within the precuticle. We propose that PTR-4 transports lipids or other hydrophobic components that help to organize the precuticle and that the cuticle and molting defects seen in ptr-4 mutants result at least in part from earlier disorganization of the precuticle.
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Affiliation(s)
- Jennifer D Cohen
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | | | - Nicholas D Serra
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Andres Kaech
- Center for Microscopy and Image Analysis, University of Zürich, 8006 Zürich, Switzerland
| | - Anne Spang
- Biozentrum, University of Basel, 4001 Basel, Switzerland
| | - Meera V Sundaram
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
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50
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Parmar BS, Peeters MKR, Boonen K, Clark EC, Baggerman G, Menschaert G, Temmerman L. Identification of Non-Canonical Translation Products in C. elegans Using Tandem Mass Spectrometry. Front Genet 2021; 12:728900. [PMID: 34759956 PMCID: PMC8575065 DOI: 10.3389/fgene.2021.728900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/16/2021] [Indexed: 11/22/2022] Open
Abstract
Transcriptome and ribosome sequencing have revealed the existence of many non-canonical transcripts, mainly containing splice variants, ncRNA, sORFs and altORFs. However, identification and characterization of products that may be translated out of these remains a challenge. Addressing this, we here report on 552 non-canonical proteins and splice variants in the model organism C. elegans using tandem mass spectrometry. Aided by sequencing-based prediction, we generated a custom proteome database tailored to search for non-canonical translation products of C. elegans. Using this database, we mined available mass spectrometric resources of C. elegans, from which 51 novel, non-canonical proteins could be identified. Furthermore, we utilized diverse proteomic and peptidomic strategies to detect 40 novel non-canonical proteins in C. elegans by LC-TIMS-MS/MS, of which 6 were common with our meta-analysis of existing resources. Together, this permits us to provide a resource with detailed annotation of 467 splice variants and 85 novel proteins mapped onto UTRs, non-coding regions and alternative open reading frames of the C. elegans genome.
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Affiliation(s)
- Bhavesh S. Parmar
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Marlies K. R. Peeters
- Laboratory of Bioinformatics and Computational Genomics (BioBix), Department of Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Kurt Boonen
- Centre for Proteomics (CFP), University of Antwerp, Antwerp, Belgium
| | - Ellie C. Clark
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Geert Baggerman
- Centre for Proteomics (CFP), University of Antwerp, Antwerp, Belgium
| | - Gerben Menschaert
- Laboratory of Bioinformatics and Computational Genomics (BioBix), Department of Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Liesbet Temmerman
- Animal Physiology and Neurobiology, University of Leuven (KU Leuven), Leuven, Belgium
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