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Lessenger AT, Swaffer MP, Skotheim JM, Feldman JL. Somatic polyploidy supports biosynthesis and tissue function by increasing transcriptional output. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586714. [PMID: 38585999 PMCID: PMC10996643 DOI: 10.1101/2024.03.25.586714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Cell size and biosynthetic capacity generally increase with increased DNA content. Polyploidy has therefore been proposed to be an adaptive strategy to increase cell size in specialized tissues with high biosynthetic demands. However, if and how DNA concentration limits cellular biosynthesis in vivo is not well understood, and the impacts of polyploidy in non-disease states is not well studied. Here, we show that polyploidy in the C. elegans intestine is critical for cell growth and yolk biosynthesis, a central role of this organ. Artificially lowering the DNA/cytoplasm ratio by reducing polyploidization in the intestine gave rise to smaller cells with more dilute mRNA. Highly-expressed transcripts were more sensitive to this mRNA dilution, whereas lowly-expressed genes were partially compensated - in part by loading more RNA Polymerase II on the remaining genomes. DNA-dilute cells had normal total protein concentration, which we propose is achieved by increasing production of translational machinery at the expense of specialized, cell-type specific proteins.
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2
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Levenson MT, Barrere-Cain R, Truong L, Chen YW, Shuck K, Panter B, Reich E, Yang X, Allard P. Protocol for nuclear dissociation of the adult C. elegans for single-nucleus RNA sequencing and its application for mapping environmental responses. STAR Protoc 2023; 4:102756. [PMID: 38043054 PMCID: PMC10730361 DOI: 10.1016/j.xpro.2023.102756] [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: 08/22/2023] [Revised: 10/17/2023] [Accepted: 11/16/2023] [Indexed: 12/05/2023] Open
Abstract
Caenorhabditis elegans is a valuable model to study organ, tissue, and cell-type responses to external cues. However, the nematode comprises multiple syncytial tissues with spatial coordinates corresponding to distinct nuclear transcriptomes. Here, we present a single-nucleus RNA sequencing (snRNA-seq) protocol that aims to overcome difficulties encountered with single-cell RNA sequencing in C. elegans. We describe steps for isolating C. elegans nuclei for downstream applications including snRNA-seq applied to the context of alcohol exposure. For complete details on the use and execution of this protocol, please refer to Truong et al. (2023).1.
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Affiliation(s)
- Max T Levenson
- Molecular Toxicology Inter-Departmental Program, UCLA, Los Angeles, CA 90095, USA
| | - Rio Barrere-Cain
- Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Lisa Truong
- Human Genetics Graduate Program, UCLA, Los Angeles, CA 90095, USA
| | - Yen-Wei Chen
- Molecular Toxicology Inter-Departmental Program, UCLA, Los Angeles, CA 90095, USA
| | - Karissa Shuck
- Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Blake Panter
- Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Ella Reich
- Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Xia Yang
- Molecular Toxicology Inter-Departmental Program, UCLA, Los Angeles, CA 90095, USA; Integrative Biology and Physiology Department, UCLA, Los Angeles, CA 90095, USA
| | - Patrick Allard
- Molecular Toxicology Inter-Departmental Program, UCLA, Los Angeles, CA 90095, USA; Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA.
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3
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Truong L, Chen YW, Barrere-Cain R, Levenson MT, Shuck K, Xiao W, da Veiga Beltrame E, Panter B, Reich E, Sternberg PW, Yang X, Allard P. Single-nucleus resolution mapping of the adult C. elegans and its application to elucidate inter- and trans-generational response to alcohol. Cell Rep 2023; 42:112535. [PMID: 37227821 PMCID: PMC10592506 DOI: 10.1016/j.celrep.2023.112535] [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: 08/05/2022] [Revised: 03/16/2023] [Accepted: 05/03/2023] [Indexed: 05/27/2023] Open
Abstract
Single-cell transcriptomic platforms provide an opportunity to map an organism's response to environmental cues with high resolution. Here, we applied single-nucleus RNA sequencing (snRNA-seq) to establish the tissue and cell type-resolved transcriptome of the adult C. elegans and characterize the inter- and trans-generational transcriptional impact of ethanol. We profiled the transcriptome of 41,749 nuclei resolving into 31 clusters, representing a diverse array of adult cell types including syncytial tissues. Following exposure to human-relevant doses of alcohol, several germline, striated muscle, and neuronal clusters were identified as being the most transcriptionally impacted at the F1 and F3 generations. The effect on germline clusters was confirmed by phenotypic enrichment analysis as well as by functional validation, which revealed a remarkable inter- and trans-generational increase in germline apoptosis, aneuploidy, and embryonic lethality. Together, snRNA-seq represents a valuable approach for the detailed examination of an adult organism's response to environmental exposures.
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Affiliation(s)
- Lisa Truong
- Human Genetics Graduate Program, UCLA, Los Angeles, CA 90095, USA
| | - Yen-Wei Chen
- Molecular Toxicology Inter-Departmental Program, UCLA, Los Angeles, CA 90095, USA
| | - Rio Barrere-Cain
- Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Max T Levenson
- Molecular Toxicology Inter-Departmental Program, UCLA, Los Angeles, CA 90095, USA
| | - Karissa Shuck
- Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Wen Xiao
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | | | - Blake Panter
- Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Ella Reich
- Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Paul W Sternberg
- Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Xia Yang
- Integrative Biology and Physiology Department, UCLA, Los Angeles, CA 90095, USA
| | - Patrick Allard
- Molecular Toxicology Inter-Departmental Program, UCLA, Los Angeles, CA 90095, USA; Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA.
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4
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Crittenden SL, Seidel HS, Kimble J. Analysis of the C. elegans Germline Stem Cell Pool. Methods Mol Biol 2023; 2677:1-36. [PMID: 37464233 DOI: 10.1007/978-1-0716-3259-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
The Caenorhabditis elegans germline is an excellent model for studying the genetic and molecular regulation of stem cell self-renewal and progression of cells from a stem cell state to a differentiated state. The germline tissue is organized in an assembly line with the germline stem cell (GSC) pool at one end and differentiated gametes at the other. A simple mesenchymal niche caps the GSC pool and maintains GSCs in an undifferentiated state by signaling through the conserved Notch pathway. Notch signaling activates transcription of the key GSC regulators lst-1 and sygl-1 proteins in a gradient through the GSC pool. LST-1 and SYGL-1 proteins work with PUF RNA regulators in a self-renewal hub to maintain the GSC pool. In this chapter, we present methods for characterizing the C. elegans GSC pool and early stages of germ cell differentiation. The methods include examination of germlines in living and fixed worms, cell cycle analysis, and analysis of markers. We also discuss assays to separate mutant phenotypes that affect the stem cell vs. differentiation decision from those that affect germ cell processes more generally.
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Affiliation(s)
- Sarah L Crittenden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Hannah S Seidel
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
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5
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Lynch TR, Xue M, Czerniak CW, Lee C, Kimble J. Notch-dependent DNA cis-regulatory elements and their dose-dependent control of C. elegans stem cell self-renewal. Development 2022; 149:274985. [PMID: 35394007 PMCID: PMC9058496 DOI: 10.1242/dev.200332] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/16/2022] [Indexed: 11/20/2022]
Abstract
A long-standing biological question is how DNA cis-regulatory elements shape transcriptional patterns during metazoan development. Reporter constructs, cell culture assays and computational modeling have made major contributions to answering this question, but analysis of elements in their natural context is an important complement. Here, we mutate Notch-dependent LAG-1 binding sites (LBSs) in the endogenous Caenorhabditis elegans sygl-1 gene, which encodes a key stem cell regulator, and analyze the consequences on sygl-1 expression (nascent transcripts, mRNA, protein) and stem cell maintenance. Mutation of one LBS in a three-element cluster approximately halved both expression and stem cell pool size, whereas mutation of two LBSs essentially abolished them. Heterozygous LBS mutant clusters provided intermediate values. Our results lead to two major conclusions. First, both LBS number and configuration impact cluster activity: LBSs act additively in trans and synergistically in cis. Second, the SYGL-1 gradient promotes self-renewal above its functional threshold and triggers differentiation below the threshold. Our approach of coupling CRISPR/Cas9 LBS mutations with effects on both molecular and biological readouts establishes a powerful model for in vivo analyses of DNA cis-regulatory elements. Summary: Notch-dependent DNA cis-regulatory elements work together in their developmental context in C. elegans to shape a transcriptional gradient, control stem cell pool size, and govern differentiation onset.
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Affiliation(s)
- Tina R. Lynch
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Integrated Program in Biochemistry, Madison, WI 53706, USA
| | - Mingyu Xue
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Cazza W. Czerniak
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Joint Department of Biomedical Engineering, Marquette University and Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - ChangHwan Lee
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Integrated Program in Biochemistry, Madison, WI 53706, USA
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6
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Woronik A, Kiontke K, Jallad RS, Herrera RA, Fitch DHA. Laser Microdissection for Species-Agnostic Single-Tissue Applications. J Vis Exp 2022:10.3791/63666. [PMID: 35435919 PMCID: PMC9976942 DOI: 10.3791/63666] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Single-cell methodologies have revolutionized the analysis of the transcriptomes of specific cell types. However, they often require species-specific genetic "toolkits," such as promoters driving tissue-specific expression of fluorescent proteins. Further, protocols that disrupt tissues to isolate individual cells remove cells from their native environment (e.g., signaling from neighbors) and may result in stress responses or other differences from native gene expression states. In the present protocol, laser microdissection (LMD) is optimized to isolate individual nematode tail tips for the study of gene expression during male tail tip morphogenesis. LMD allows the isolation of a portion of the animal without the need for cellular disruption or species-specific toolkits and is thus applicable to any species. Subsequently, single-cell RNA-seq library preparation protocols such as CEL-Seq2 can be applied to LMD-isolated single tissues and analyzed using standard pipelines, given that a well-annotated genome or transcriptome is available for the species. Such data can be used to establish how conserved or different the transcriptomes are that underlie the development of that tissue in different species. Limitations include the ability to cut out the tissue of interest and the sample size. A power analysis shows that as few as 70 tail tips per condition are required for 80% power. Tight synchronization of development is needed to obtain this number of animals at the same developmental stage. Thus, a method to synchronize animals at 1 h intervals is also described.
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Affiliation(s)
- Alyssa Woronik
- Center for Developmental Genetics, New York University,Sacred Heart University
| | - Karin Kiontke
- Center for Developmental Genetics, New York University
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7
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Lee C, Lynch T, Crittenden SL, Kimble J. Image-Based Single-Molecule Analysis of Notch-Dependent Transcription in Its Natural Context. Methods Mol Biol 2022; 2472:131-149. [PMID: 35674897 DOI: 10.1007/978-1-0716-2201-8_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Notch signaling is crucial to animal development and homeostasis. Notch triggers the transcription of its target genes, which produce diverse outcomes depending on context. The high resolution and spatially precise assessment of Notch-dependent transcription is essential for understanding how Notch operates normally in its native context in vivo and how Notch defects lead to pathogenesis. Here we present biological and computational methods to assess Notch-dependent transcriptional activation in stem cells within their niche, focusing on germline stem cells in the nematode Caenorhabditis elegans. Specifically, we describe visualization of single RNAs in fixed gonads using single-molecule RNA fluorescence in situ hybridization (smFISH), live imaging of transcriptional bursting in the intact organism using the MS2 system, and custom-made MATLAB codes, implementing new image processing algorithms to capture the spatiotemporal patterns of Notch-dependent transcriptional activation. These methods allow a powerful analysis of in vivo transcriptional activation and its dynamics in a whole tissue. Our methods can be adapted to essentially any tissue or cell type for any transcript.
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Affiliation(s)
- ChangHwan Lee
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA.
| | - Tina Lynch
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Sarah L Crittenden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
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8
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Doenier J, Lynch TR, Kimble J, Aoki ST. An improved in vivo tethering assay with single molecule FISH reveals that a nematode Nanos enhances reporter expression and mRNA stability. RNA (NEW YORK, N.Y.) 2021; 27:643-652. [PMID: 33727224 PMCID: PMC8127996 DOI: 10.1261/rna.078693.121] [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] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/08/2021] [Indexed: 06/12/2023]
Abstract
Robust methods are critical for testing the in vivo regulatory mechanism of RNA binding proteins. Here we report improvement of a protein-mRNA tethering assay to probe the function of an RNA binding protein in its natural context within the C. elegans adult germline. The assay relies on a dual reporter expressing two mRNAs from a single promoter and resolved by trans-splicing. The gfp reporter 3'UTR harbors functional binding elements for λN22 peptide, while the mCherry reporter 3'UTR carries mutated nonfunctional elements. This strategy enables internally controlled quantitation of reporter protein by immunofluorescence and mRNA by smFISH. To test the new system, we analyzed a C. elegans Nanos protein, NOS-3, which serves as a post-transcriptional regulator of germ cell fate. Unexpectedly, tethered NOS-3 enhanced reporter expression. We confirmed this enhancement activity with a second reporter engineered at an endogenous germline gene. NOS-3 enhancement of reporter expression was associated with its amino-terminal intrinsically disordered region, not its carboxy-terminal zinc fingers. RNA quantitation revealed that tethered NOS-3 enhances stability of the reporter mRNA. We suggest that this direct NOS-3 enhancement activity may explain a paradox: Classically Nanos proteins are expected to repress RNA, but nos-3 had been found to promote gld-1 expression, an effect that could be direct. Regardless, the new dual reporter dramatically improves in situ quantitation of reporter expression after RNA binding protein tethering to determine its molecular mechanism in a multicellular tissue.
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Affiliation(s)
- Jonathan Doenier
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Tina R Lynch
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Scott T Aoki
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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9
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Feng L, Zhang J, Lee C, Kim G, Liu F, Petersen AJ, Lim E, Anderson CL, Orland KM, Robertson GA, Eckhardt LL, January CT, Kamp TJ. Long QT Syndrome KCNH2 Variant Induces hERG1a/1b Subunit Imbalance in Patient-Specific Induced Pluripotent Stem Cell-Derived Cardiomyocytes. Circ Arrhythm Electrophysiol 2021; 14:e009343. [PMID: 33729832 PMCID: PMC8058932 DOI: 10.1161/circep.120.009343] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Li Feng
- Cellular and Molecular Arrhythmia Research Program, Department of Medicine, Division of Cardiovascular Medicine, University of Wisconsin-Madison, Madison, WI
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, National Clinical Research Center for Cardiovascular Diseases, Beijing, China
| | - Jianhua Zhang
- Cellular and Molecular Arrhythmia Research Program, Department of Medicine, Division of Cardiovascular Medicine, University of Wisconsin-Madison, Madison, WI
| | - ChangHwan Lee
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY
| | - Gina Kim
- Cellular and Molecular Arrhythmia Research Program, Department of Medicine, Division of Cardiovascular Medicine, University of Wisconsin-Madison, Madison, WI
| | - Fang Liu
- Department of Neuroscience, Wisconsin Institutes for Medical Research, University of Wisconsin-Madison, Madison, WI
| | | | - Evi Lim
- Cellular and Molecular Arrhythmia Research Program, Department of Medicine, Division of Cardiovascular Medicine, University of Wisconsin-Madison, Madison, WI
| | - Corey L. Anderson
- Cellular and Molecular Arrhythmia Research Program, Department of Medicine, Division of Cardiovascular Medicine, University of Wisconsin-Madison, Madison, WI
| | - Kate M. Orland
- Cellular and Molecular Arrhythmia Research Program, Department of Medicine, Division of Cardiovascular Medicine, University of Wisconsin-Madison, Madison, WI
| | - Gail A. Robertson
- Department of Neuroscience, Wisconsin Institutes for Medical Research, University of Wisconsin-Madison, Madison, WI
| | - Lee L. Eckhardt
- Cellular and Molecular Arrhythmia Research Program, Department of Medicine, Division of Cardiovascular Medicine, University of Wisconsin-Madison, Madison, WI
| | - Craig T. January
- Cellular and Molecular Arrhythmia Research Program, Department of Medicine, Division of Cardiovascular Medicine, University of Wisconsin-Madison, Madison, WI
| | - Timothy J. Kamp
- Cellular and Molecular Arrhythmia Research Program, Department of Medicine, Division of Cardiovascular Medicine, University of Wisconsin-Madison, Madison, WI
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI
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10
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Robert VJ, Knutson AK, Rechtsteiner A, Garvis S, Yvert G, Strome S, Palladino F. Caenorhabditis elegans SET1/COMPASS Maintains Germline Identity by Preventing Transcriptional Deregulation Across Generations. Front Cell Dev Biol 2020; 8:561791. [PMID: 33072747 PMCID: PMC7536326 DOI: 10.3389/fcell.2020.561791] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 08/18/2020] [Indexed: 12/11/2022] Open
Abstract
Chromatin regulators contribute to the maintenance of the germline transcriptional program. In the absence of SET-2, the Caenorhabditis elegans homolog of the SET1/COMPASS H3 Lys4 (H3K4) methyltransferase, animals show transgenerational loss of germline identity, leading to sterility. To identify transcriptional signatures associated with progressive loss of fertility, we performed expression profiling of set-2 mutant germlines across generations. We identify a subset of genes whose misexpression is first observed in early generations, a step we refer to as priming; their misexpression then further progresses in late generations, as animals reach sterility. Analysis of misregulated genes shows that down-regulation of germline genes, expression of somatic transcriptional programs, and desilencing of the X-chromosome are concurrent events leading to loss of germline identity in both early and late generations. Upregulation of transcription factor LIN-15B, the C/EBP homolog CEBP-1, and TGF-β pathway components strongly contribute to loss of fertility, and RNAi inactivation of cebp-1 and TGF-β/Smad signaling delays the onset of sterility, showing they individually contribute to maintenance of germ cell identity. Our approach therefore identifies genes and pathways whose misexpression actively contributes to the loss of germ cell fate. More generally, our data shows how loss of a chromatin regulator in one generation leads to transcriptional changes that are amplified over subsequent generations, ultimately leading to loss of appropriate cell fate.
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Affiliation(s)
- Valérie J Robert
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard de Lyon, Université de Lyon, Lyon, France
| | - Andrew K Knutson
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Andreas Rechtsteiner
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Steven Garvis
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard de Lyon, Université de Lyon, Lyon, France
| | - Gaël Yvert
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard de Lyon, Université de Lyon, Lyon, France
| | - Susan Strome
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Francesca Palladino
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard de Lyon, Université de Lyon, Lyon, France
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11
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Ravikumar S, Devanapally S, Jose AM. Gene silencing by double-stranded RNA from C. elegans neurons reveals functional mosaicism of RNA interference. Nucleic Acids Res 2019; 47:10059-10071. [PMID: 31501873 PMCID: PMC6821342 DOI: 10.1093/nar/gkz748] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/12/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022] Open
Abstract
Delivery of double-stranded RNA (dsRNA) into animals can silence genes of matching sequence in diverse cell types through mechanisms that have been collectively called RNA interference. In the nematode Caenorhabditis elegans, dsRNA from multiple sources can trigger the amplification of silencing signals. Amplification occurs through the production of small RNAs by two RNA-dependent RNA polymerases (RdRPs) that are thought to be tissue-specific - EGO-1 in the germline and RRF-1 in somatic cells. Here we demonstrate that EGO-1 can compensate for the lack of RRF-1 when dsRNA from neurons is used to silence genes in intestinal cells. However, the lineal origins of cells that can use EGO-1 varies. This variability could be because random sets of cells can either receive different amounts of dsRNA from the same source or use different RdRPs to perform the same function. Variability is masked in wild-type animals, which show extensive silencing by neuronal dsRNA. As a result, cells appear similarly functional despite underlying differences that vary from animal to animal. This functional mosaicism cautions against inferring uniformity of mechanism based on uniformity of outcome. We speculate that functional mosaicism could contribute to escape from targeted therapies and could allow developmental systems to drift over evolutionary time.
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Affiliation(s)
- Snusha Ravikumar
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Sindhuja Devanapally
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA
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12
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Lee C, Shin H, Kimble J. Dynamics of Notch-Dependent Transcriptional Bursting in Its Native Context. Dev Cell 2019; 50:426-435.e4. [PMID: 31378588 PMCID: PMC6724715 DOI: 10.1016/j.devcel.2019.07.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 05/23/2019] [Accepted: 07/01/2019] [Indexed: 12/16/2022]
Abstract
Transcription is well known to be inherently stochastic and episodic, but the regulation of transcriptional dynamics is not well understood. Here, we analyze how Notch signaling modulates transcriptional bursting during animal development. Our focus is Notch regulation of transcription in germline stem cells of the nematode C. elegans. Using the MS2 system to visualize nascent transcripts and live imaging to record dynamics, we analyze bursting as a function of position within the intact animal. We find that Notch-dependent transcriptional activation is indeed "bursty"; that wild-type Notch modulates burst duration (ON-time) rather than duration of pauses between bursts (OFF-time) or mean burst intensity; and that a mutant Notch receptor, which is compromised for assembly into the Notch transcription factor complex, primarily modifies burst size (duration × intensity). These analyses thus visualize the effect of a canonical signaling pathway on metazoan transcriptional bursting in its native context.
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Affiliation(s)
- ChangHwan Lee
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Heaji Shin
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, WI 53706, USA.
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13
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Breimann L, Preusser F, Preibisch S. Light-microscopy methods in C. elegans research. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.coisb.2018.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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14
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Lee C, Sorensen EB, Lynch TR, Kimble J. C. elegans GLP-1/Notch activates transcription in a probability gradient across the germline stem cell pool. eLife 2016; 5:e18370. [PMID: 27705743 PMCID: PMC5094854 DOI: 10.7554/elife.18370] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 10/04/2016] [Indexed: 12/26/2022] Open
Abstract
C. elegans Notch signaling maintains a pool of germline stem cells within their single-celled mesenchymal niche. Here we investigate the Notch transcriptional response in germline stem cells using single-molecule fluorescence in situ hybridization coupled with automated, high-throughput quantitation. This approach allows us to distinguish Notch-dependent nascent transcripts in the nucleus from mature mRNAs in the cytoplasm. We find that Notch-dependent active transcription sites occur in a probabilistic fashion and, unexpectedly, do so in a steep gradient across the stem cell pool. Yet these graded nuclear sites create a nearly uniform field of mRNAs that extends beyond the region of transcriptional activation. Therefore, active transcription sites provide a precise view of where the Notch-dependent transcriptional complex is productively engaged. Our findings offer a new window into the Notch transcriptional response and demonstrate the importance of assaying nascent transcripts at active transcription sites as a readout for canonical signaling.
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Affiliation(s)
- ChangHwan Lee
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, United States
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Erika B Sorensen
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, United States
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Tina R Lynch
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Judith Kimble
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, United States
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
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