1
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Ow MC, Nishiguchi MA, Dar AR, Butcher RA, Hall SE. RNAi-dependent expression of sperm genes in ADL chemosensory neurons is required for olfactory responses in Caenorhabditis elegans. Front Mol Biosci 2024; 11:1396587. [PMID: 39055986 PMCID: PMC11269235 DOI: 10.3389/fmolb.2024.1396587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 06/11/2024] [Indexed: 07/28/2024] Open
Abstract
Environmental conditions experienced early in the life of an animal can result in gene expression changes later in its life history. We have previously shown that C. elegans animals that experienced the developmentally arrested and stress resistant dauer stage (postdauers) retain a cellular memory of early-life stress that manifests during adulthood as genome-wide changes in gene expression, chromatin states, and altered life history traits. One consequence of developmental reprogramming in C. elegans postdauer adults is the downregulation of osm-9 TRPV channel gene expression in the ADL chemosensory neurons resulting in reduced avoidance to a pheromone component, ascr#3. This altered response to ascr#3 requires the principal effector of the somatic nuclear RNAi pathway, the Argonaute (AGO) NRDE-3. To investigate the role of the somatic nuclear RNAi pathway in regulating the developmental reprogramming of ADL due to early-life stress, we profiled the mRNA transcriptome of control and postdauer ADL in wild-type and nrde-3 mutant adults. We found 711 differentially expressed (DE) genes between control and postdauer ADL neurons, 90% of which are dependent upon NRDE-3. Additionally, we identified a conserved sequence that is enriched in the upstream regulatory sequences of the NRDE-3-dependent differentially expressed genes. Surprisingly, 214 of the ADL DE genes are considered "germline-expressed", including 21 genes encoding the Major Sperm Proteins and two genes encoding the sperm-specific PP1 phosphatases, GSP-3 and GSP-4. Loss of function mutations in gsp-3 resulted in both aberrant avoidance and attraction behaviors. We also show that an AGO pseudogene, Y49F6A.1 (wago-11), is expressed in ADL and is required for ascr#3 avoidance. Overall, our results suggest that small RNAs and reproductive genes program the ADL mRNA transcriptome during their developmental history and highlight a nexus between neuronal and reproductive networks in calibrating animal neuroplasticity.
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Affiliation(s)
- Maria C. Ow
- Biology Department, Syracuse University, Syracuse, NY, United States
| | | | - Abdul Rouf Dar
- Department of Chemistry, University of Florida, Gainesville, FL, United States
| | - Rebecca A. Butcher
- Department of Chemistry, University of Florida, Gainesville, FL, United States
| | - Sarah E. Hall
- Biology Department, Syracuse University, Syracuse, NY, United States
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2
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Kloc M, Halasa M, Kubiak JZ, Ghobrial RM. Invertebrate Immunity, Natural Transplantation Immunity, Somatic and Germ Cell Parasitism, and Transposon Defense. Int J Mol Sci 2024; 25:1072. [PMID: 38256145 PMCID: PMC10815962 DOI: 10.3390/ijms25021072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
While the vertebrate immune system consists of innate and adaptive branches, invertebrates only have innate immunity. This feature makes them an ideal model system for studying the cellular and molecular mechanisms of innate immunity sensu stricto without reciprocal interferences from adaptive immunity. Although invertebrate immunity is evolutionarily older and a precursor of vertebrate immunity, it is far from simple. Despite lacking lymphocytes and functional immunoglobulin, the invertebrate immune system has many sophisticated mechanisms and features, such as long-term immune memory, which, for decades, have been exclusively attributed to adaptive immunity. In this review, we describe the cellular and molecular aspects of invertebrate immunity, including the epigenetic foundation of innate memory, the transgenerational inheritance of immunity, genetic immunity against invading transposons, the mechanisms of self-recognition, natural transplantation, and germ/somatic cell parasitism.
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Affiliation(s)
- Malgorzata Kloc
- Houston Methodist Research Institute, Transplant Immunology, Houston, TX 77030, USA; (M.H.); (R.M.G.)
- Department of Surgery, Houston Methodist Hospital, Houston, TX 77030, USA
- Department of Genetics, MD Anderson Cancer Center, University of Texas, Houston, TX 77030, USA
| | - Marta Halasa
- Houston Methodist Research Institute, Transplant Immunology, Houston, TX 77030, USA; (M.H.); (R.M.G.)
- Department of Surgery, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Jacek Z. Kubiak
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine-National Research Institute (WIM-PIB), Szaserow 128, 04-141 Warsaw, Poland;
- Dynamics and Mechanics of Epithelia Group, Faculty of Medicine, Institute of Genetics and Development of Rennes, University of Rennes, CNRS, UMR 6290, 35043 Rennes, France
| | - Rafik M. Ghobrial
- Houston Methodist Research Institute, Transplant Immunology, Houston, TX 77030, USA; (M.H.); (R.M.G.)
- Department of Surgery, Houston Methodist Hospital, Houston, TX 77030, USA
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3
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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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4
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Carro MDLM, Grimson A, Cohen PE. Small RNAs and their protein partners in animal meiosis. Curr Top Dev Biol 2022; 151:245-279. [PMID: 36681472 DOI: 10.1016/bs.ctdb.2022.06.001] [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: 01/25/2023]
Abstract
Meiosis is characterized by highly regulated transitions in gene expression that require diverse mechanisms of gene regulation. For example, in male mammals, transcription undergoes a global shut-down in early prophase I of meiosis, followed by increasing transcriptional activity into pachynema. Later, as spermiogenesis proceeds, the histones bound to DNA are replaced with transition proteins, which are themselves replaced with protamines, resulting in a highly condensed nucleus with repressed transcriptional activity. In addition, two specialized gene silencing events take place during prophase I: meiotic silencing of unsynapsed chromatin (MSUC), and the sex chromatin specific mechanism, meiotic sex chromosome inactivation (MSCI). Notably, conserved roles for the RNA binding protein (RBP) machinery that functions with small non-coding RNAs have been described as participating in these meiosis-specific mechanisms, suggesting that RNA-mediated gene regulation is critical for fertility in many species. Here, we review roles of small RNAs and their associated RBPs in meiosis-related processes such as centromere function, silencing of unpaired chromatin and meiotic recombination. We will discuss the emerging evidence of non-canonical functions of these components in meiosis.
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Affiliation(s)
- María de Las Mercedes Carro
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States; Cornell Reproductive Sciences Center (CoRe), Cornell University, Ithaca, NY, United States
| | - Andrew Grimson
- Cornell Reproductive Sciences Center (CoRe), Cornell University, Ithaca, NY, United States; Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, United States.
| | - Paula E Cohen
- Department of Biomedical Sciences, Cornell University, Ithaca, NY, United States; Cornell Reproductive Sciences Center (CoRe), Cornell University, Ithaca, NY, United States.
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5
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Campos TL, Korhonen PK, Hofmann A, Gasser RB, Young ND. Harnessing model organism genomics to underpin the machine learning-based prediction of essential genes in eukaryotes - Biotechnological implications. Biotechnol Adv 2021; 54:107822. [PMID: 34461202 DOI: 10.1016/j.biotechadv.2021.107822] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 08/17/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022]
Abstract
The availability of high-quality genomes and advances in functional genomics have enabled large-scale studies of essential genes in model eukaryotes, including the 'elegant worm' (Caenorhabditis elegans; Nematoda) and the 'vinegar fly' (Drosophila melanogaster; Arthropoda). However, this is not the case for other, much less-studied organisms, such as socioeconomically important parasites, for which functional genomic platforms usually do not exist. Thus, there is a need to develop innovative techniques or approaches for the prediction, identification and investigation of essential genes. A key approach that could enable the prediction of such genes is machine learning (ML). Here, we undertake an historical review of experimental and computational approaches employed for the characterisation of essential genes in eukaryotes, with a particular focus on model ecdysozoans (C. elegans and D. melanogaster), and discuss the possible applicability of ML-approaches to organisms such as socioeconomically important parasites. We highlight some recent results showing that high-performance ML, combined with feature engineering, allows a reliable prediction of essential genes from extensive, publicly available 'omic data sets, with major potential to prioritise such genes (with statistical confidence) for subsequent functional genomic validation. These findings could 'open the door' to fundamental and applied research areas. Evidence of some commonality in the essential gene-complement between these two organisms indicates that an ML-engineering approach could find broader applicability to ecdysozoans such as parasitic nematodes or arthropods, provided that suitably large and informative data sets become/are available for proper feature engineering, and for the robust training and validation of algorithms. This area warrants detailed exploration to, for example, facilitate the identification and characterisation of essential molecules as novel targets for drugs and vaccines against parasitic diseases. This focus is particularly important, given the substantial impact that such diseases have worldwide, and the current challenges associated with their prevention and control and with drug resistance in parasite populations.
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Affiliation(s)
- Tulio L Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia; Bioinformatics Core Facility, Instituto Aggeu Magalhães, Fundação Oswaldo Cruz (IAM-Fiocruz), Recife, Pernambuco, Brazil
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
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6
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Charlesworth AG, Seroussi U, Lehrbach NJ, Renaud MS, Sundby AE, Molnar RI, Lao RX, Willis AR, Woock JR, Aber MJ, Diao AJ, Reinke AW, Ruvkun G, Claycomb JM. Two isoforms of the essential C. elegans Argonaute CSR-1 differentially regulate sperm and oocyte fertility. Nucleic Acids Res 2021; 49:8836-8865. [PMID: 34329465 PMCID: PMC8421154 DOI: 10.1093/nar/gkab619] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 07/01/2021] [Accepted: 07/19/2021] [Indexed: 01/09/2023] Open
Abstract
The Caenorhabditis elegans genome encodes nineteen functional Argonaute proteins that use 22G-RNAs, 26G-RNAs, miRNAs or piRNAs to regulate target transcripts. Only one Argonaute is essential under normal laboratory conditions: CSR-1. While CSR-1 has been studied widely, nearly all studies have overlooked the fact that the csr-1 locus encodes two isoforms. These isoforms differ by an additional 163 amino acids present in the N-terminus of CSR-1a. Using CRISPR-Cas9 genome editing to introduce GFP::3xFLAG into the long (CSR-1a) and short (CSR-1b) isoforms, we found that CSR-1a is expressed during spermatogenesis and in several somatic tissues, including the intestine. CSR-1b is expressed constitutively in the germline. small RNA sequencing of CSR-1 complexes shows that they interact with partly overlapping sets of 22G-RNAs. Phenotypic analyses reveal that the essential functions of csr-1 described in the literature coincide with CSR-1b, while CSR-1a plays tissue specific functions. During spermatogenesis, CSR-1a integrates into an sRNA regulatory network including ALG-3, ALG-4 and WAGO-10 that is necessary for fertility at 25°C. In the intestine, CSR-1a silences immunity and pathogen-responsive genes, and its loss results in improved survival from the pathogen Pseudomonas aeruginosa. Our findings functionally distinguish the CSR-1 isoforms and highlight the importance of studying each AGO isoform independently.
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Affiliation(s)
| | - Uri Seroussi
- Department of Molecular Genetics, University of Toronto Toronto, ON M5S 1A8 Canada
| | - Nicolas J Lehrbach
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Mathias S Renaud
- Department of Molecular Genetics, University of Toronto Toronto, ON M5S 1A8 Canada
| | - Adam E Sundby
- Department of Molecular Genetics, University of Toronto Toronto, ON M5S 1A8 Canada
| | - Ruxandra I Molnar
- Department of Molecular Genetics, University of Toronto Toronto, ON M5S 1A8 Canada
| | - Robert X Lao
- Department of Molecular Genetics, University of Toronto Toronto, ON M5S 1A8 Canada
| | - Alexandra R Willis
- Department of Molecular Genetics, University of Toronto Toronto, ON M5S 1A8 Canada
| | - Jenna R Woock
- Department of Molecular Genetics, University of Toronto Toronto, ON M5S 1A8 Canada
| | - Matthew J Aber
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Annette J Diao
- Department of Molecular Genetics, University of Toronto Toronto, ON M5S 1A8 Canada
| | - Aaron W Reinke
- Department of Molecular Genetics, University of Toronto Toronto, ON M5S 1A8 Canada
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto Toronto, ON M5S 1A8 Canada
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7
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Campos TL, Korhonen PK, Sternberg PW, Gasser RB, Young ND. Predicting gene essentiality in Caenorhabditis elegans by feature engineering and machine-learning. Comput Struct Biotechnol J 2020; 18:1093-1102. [PMID: 32489524 PMCID: PMC7251299 DOI: 10.1016/j.csbj.2020.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/01/2020] [Accepted: 05/06/2020] [Indexed: 02/08/2023] Open
Abstract
Defining genes that are essential for life has major implications for understanding critical biological processes and mechanisms. Although essential genes have been identified and characterised experimentally using functional genomic tools, it is challenging to predict with confidence such genes from molecular and phenomic data sets using computational methods. Using extensive data sets available for the model organism Caenorhabditis elegans, we constructed here a machine-learning (ML)-based workflow for the prediction of essential genes on a genome-wide scale. We identified strong predictors for such genes and showed that trained ML models consistently achieve highly-accurate classifications. Complementary analyses revealed an association between essential genes and chromosomal location. Our findings reveal that essential genes in C. elegans tend to be located in or near the centre of autosomal chromosomes; are positively correlated with low single nucleotide polymorphim (SNP) densities and epigenetic markers in promoter regions; are involved in protein and nucleotide processing; are transcribed in most cells; are enriched in reproductive tissues or are targets for small RNAs bound to the argonaut CSR-1. Based on these results, we hypothesise an interplay between epigenetic markers and small RNA pathways in the germline, with transcription-based memory; this hypothesis warrants testing. From a technical perspective, further work is needed to evaluate whether the present ML-based approach will be applicable to other metazoans (including Drosophila melanogaster) for which comprehensive data sets (i.e. genomic, transcriptomic, proteomic, variomic, epigenetic and phenomic) are available.
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Key Words
- CDS, coding sequence
- CRISPR, Clustered Regularly Interspaced Short Palindromic Repeats
- Caenorhabditis elegans
- ES, Essentiality Score
- EST, expressed sequence tag
- Essential genes
- Essentiality predictions
- GBM, Gradient Boosting Method
- GFF, general feature format
- GLM, Generalised Linear Model
- GO, gene ontology
- ML, machine-learning
- Machine-learning
- NN, Artificial Neural Network
- PPI, protein-protein interaction
- PR-AUC, Area Under the Precision-Recall Curve
- RF, Random Forest
- RNAi, RNA interference
- ROC-AUC, Area Under the Receiver Operating Characteristic Curve
- SNP, single nucleotide polymorphism
- SPLS, Sparse Partial Least Squares
- SVM, Support-Vector Machine
- TEA, Tissue Enrichment Analysis tool (WormBase)
- TSS, transcription start site
- VCF, variant call file
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Affiliation(s)
- Tulio L Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.,Instituto Aggeu Magalhães, Fundação Oswaldo Cruz (IAM-Fiocruz), Recife, Pernambuco, Brazil
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
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8
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Davis GM, Tu S, Anderson JW, Colson RN, Gunzburg MJ, Francisco MA, Ray D, Shrubsole SP, Sobotka JA, Seroussi U, Lao RX, Maity T, Wu MZ, McJunkin K, Morris QD, Hughes TR, Wilce JA, Claycomb JM, Weng Z, Boag PR. The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in C. e legans. eLife 2018; 7:35478. [PMID: 30575518 PMCID: PMC6351104 DOI: 10.7554/elife.35478] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 12/20/2018] [Indexed: 12/26/2022] Open
Abstract
Proper regulation of germline gene expression is essential for fertility and maintaining species integrity. In the C. elegans germline, a diverse repertoire of regulatory pathways promote the expression of endogenous germline genes and limit the expression of deleterious transcripts to maintain genome homeostasis. Here we show that the conserved TRIM-NHL protein, NHL-2, plays an essential role in the C. elegans germline, modulating germline chromatin and meiotic chromosome organization. We uncover a role for NHL-2 as a co-factor in both positively (CSR-1) and negatively (HRDE-1) acting germline 22G-small RNA pathways and the somatic nuclear RNAi pathway. Furthermore, we demonstrate that NHL-2 is a bona fide RNA binding protein and, along with RNA-seq data point to a small RNA independent role for NHL-2 in regulating transcripts at the level of RNA stability. Collectively, our data implicate NHL-2 as an essential hub of gene regulatory activity in both the germline and soma.
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Affiliation(s)
- Gregory M Davis
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia.,School of Health and Life Sciences, Federation University, Victoria, Australia
| | - Shikui Tu
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States
| | - Joshua Wt Anderson
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Rhys N Colson
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Menachem J Gunzburg
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | | | - Debashish Ray
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Sean P Shrubsole
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Julia A Sobotka
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Uri Seroussi
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Robert X Lao
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Tuhin Maity
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Monica Z Wu
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Katherine McJunkin
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| | - Quaid D Morris
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Timothy R Hughes
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Jacqueline A Wilce
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, United States
| | - Peter R Boag
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
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9
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Quintana JF, Babayan SA, Buck AH. Small RNAs and extracellular vesicles in filarial nematodes: From nematode development to diagnostics. Parasite Immunol 2017; 39. [PMID: 27748953 DOI: 10.1111/pim.12395] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/08/2016] [Accepted: 10/12/2016] [Indexed: 02/06/2023]
Abstract
Parasitic nematodes have evolved sophisticated mechanisms to communicate with their hosts in order to survive and successfully establish an infection. The transfer of RNA within extracellular vesicles (EVs) has recently been described as a mechanism that could contribute to this communication in filarial nematodes. It has been shown that these EVs are loaded with several types of RNAs, including microRNAs, leading to the hypothesis that parasites could actively use these molecules to manipulate host gene expression and to the exciting prospect that these pathways could result in new diagnostic and therapeutic strategies. Here, we review the literature on the diverse RNAi pathways that operate in nematodes and more specifically our current knowledge of extracellular RNA (exRNA) and EVs derived from filarial nematodes in vitro and within their hosts. We further detail some of the issues and questions related to the capacity of RNA-mediated communication to function in parasite-host interactions and the ability of exRNA to enable us to distinguish and detect different nematode parasites in their hosts.
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Affiliation(s)
- J F Quintana
- Institute of Immunology and Infection Research and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - S A Babayan
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - A H Buck
- Institute of Immunology and Infection Research and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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10
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Paces J, Nic M, Novotny T, Svoboda P. Literature review of baseline information to support the risk assessment of RNAi‐based GM plants. ACTA ACUST UNITED AC 2017. [PMCID: PMC7163844 DOI: 10.2903/sp.efsa.2017.en-1246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Paces
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
| | | | | | - Petr Svoboda
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic (IMG)
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11
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Abstract
The Caenorhabditis elegans germline is an excellent model for studying the regulation of a pool of stem cells and progression of cells from a stem cell state to a differentiated state. At the tissue level, the germline is organized in an assembly line with the germline stem cell (GSC) pool at one end and differentiated cells at the other. A simple mesenchymal niche caps the GSC region of the germline and maintains GSCs in an undifferentiated state by signaling through the conserved Notch pathway. Downstream of Notch signaling, key regulators include novel LST-1 and SYGL-1 proteins and a network of RNA regulatory proteins. In this chapter we present methods for characterizing the C. elegans GSC pool and early germ cell differentiation. The methods include examination of the germline in living and fixed worms, cell cycle analysis, and analysis of markers. We also discuss assays to separate mutants 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
- HHMI/Department of Biochemistry, Howard Hughes Medical Institute and University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706-1544, USA.
| | - Hannah S Seidel
- HHMI/Department of Biochemistry, Howard Hughes Medical Institute and University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706-1544, USA
| | - Judith Kimble
- HHMI/Department of Biochemistry, Howard Hughes Medical Institute and University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI, 53706-1544, USA
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12
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Ow MC, Hall SE. A Method for Obtaining Large Populations of Synchronized Caenorhabditis elegans Dauer Larvae. Methods Mol Biol 2016; 1327:209-19. [PMID: 26423977 DOI: 10.1007/978-1-4939-2842-2_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The C. elegans dauer is an attractive model with which to investigate fundamental biological questions, such as how environmental cues are sensed and are translated into developmental decisions through a series of signaling cascades that ultimately result in a transformed animal. Here we describe a simple method of using egg white plates to obtain highly synchronized purified dauers that can be used in downstream applications requiring large quantities of dauers or postdauer animals.
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Affiliation(s)
- Maria C Ow
- Department of Biology, Syracuse University, 107 College Place, Room 110, Syracuse, NY, 13244, USA
| | - Sarah E Hall
- Department of Biology, Syracuse University, 107 College Place, Room 110, Syracuse, NY, 13244, USA.
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13
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Arur S. Context-dependent regulation of Dicer activity and small RNA production: Implications to oocyte-to-embryo transition. WORM 2016; 4:e1086062. [PMID: 27123367 PMCID: PMC4826148 DOI: 10.1080/21624054.2015.1086062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 08/05/2015] [Accepted: 08/17/2015] [Indexed: 12/26/2022]
Abstract
Cellular and molecular mechanisms that suppress small RNAs in oocytes while maintaining them in zygotes remain unknown. Signal-mediated regulation of small RNA biogenesis pathway is emerging as a theme for regulating small RNA production. We recently reported that ERK-mediated phosphorylation of Dicer, a central player in small RNA biogenesis, induced Dicer to move from the cytoplasm to the nucleus. Dicer phosphorylation inhibited its function, e.g., the production of 26G endo-siRNAs in the female germline. Moreover, our findings showed that the inhibition of Dicer function was necessary for normal progression of meiosis I and oogenesis, and that Dicer function had to be restored before fertilization for normal progression of embryogenesis. Thus, extracellular signal-dependent inhibition and then reactivation of Dicer is essential for oocyte-to-embryo transition. Strikingly, signal-induced Dicer translocation from the cytoplasm to nucleus is evolutionarily conserved from worm, flies, mice to humans thereby suggesting the ERK-mediated control of Dicer activity may be a generalized mechanism for regulating small RNA biogenesis.
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Affiliation(s)
- Swathi Arur
- Department of Genetics; UT MD Anderson Cancer Center ; Houston, TX USA
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14
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Tu S, Wu MZ, Wang J, Cutter AD, Weng Z, Claycomb JM. Comparative functional characterization of the CSR-1 22G-RNA pathway in Caenorhabditis nematodes. Nucleic Acids Res 2014; 43:208-24. [PMID: 25510497 PMCID: PMC4288196 DOI: 10.1093/nar/gku1308] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
As a champion of small RNA research for two decades, Caenorhabditis elegans has revealed the essential Argonaute CSR-1 to play key nuclear roles in modulating chromatin, chromosome segregation and germline gene expression via 22G-small RNAs. Despite CSR-1 being preserved among diverse nematodes, the conservation and divergence in function of the targets of small RNA pathways remains poorly resolved. Here we apply comparative functional genomic analysis between C. elegans and Caenorhabditis briggsae to characterize the CSR-1 pathway, its targets and their evolution. C. briggsae CSR-1-associated small RNAs that we identified by immunoprecipitation-small RNA sequencing overlap with 22G-RNAs depleted in cbr-csr-1 RNAi-treated worms. By comparing 22G-RNAs and target genes between species, we defined a set of CSR-1 target genes with conserved germline expression, enrichment in operons and more slowly evolving coding sequences than other genes, along with a small group of evolutionarily labile targets. We demonstrate that the association of CSR-1 with chromatin is preserved, and show that depletion of cbr-csr-1 leads to chromosome segregation defects and embryonic lethality. This first comparative characterization of a small RNA pathway in Caenorhabditis establishes a conserved nuclear role for CSR-1 and highlights its key role in germline gene regulation across multiple animal species.
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Affiliation(s)
- Shikui Tu
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA 01605
| | - Monica Z Wu
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Jie Wang
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA 01605
| | - Asher D Cutter
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, USA 01605
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8
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15
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Youngman EM, Claycomb JM. From early lessons to new frontiers: the worm as a treasure trove of small RNA biology. Front Genet 2014; 5:416. [PMID: 25505902 PMCID: PMC4245922 DOI: 10.3389/fgene.2014.00416] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 11/07/2014] [Indexed: 02/02/2023] Open
Abstract
In the past 20 years, the tiny soil nematode Caenorhabditis elegans has provided critical insights into our understanding of the breadth of small RNA-mediated gene regulatory activities. The first microRNA was identified in C. elegans in 1993, and the understanding that dsRNA was the driving force behind RNA-mediated gene silencing came from experiments performed in C. elegans in 1998. Likewise, early genetic screens in C. elegans for factors involved in RNA interference pointed to conserved mechanisms for small RNA-mediated gene silencing pathways, placing the worm squarely among the founding fathers of a now extensive field of molecular biology. Today, the worm continues to be at the forefront of ground-breaking insight into small RNA-mediated biology. Recent studies have revealed with increasing mechanistic clarity that C. elegans possesses an extensive nuclear small RNA regulatory network that encompasses not only gene silencing but also gene activating roles. Further, a portrait is emerging whereby small RNA pathways play key roles in integrating responses to environmental stimuli and transmitting epigenetic information about such responses from one generation to the next. Here we discuss endogenous small RNA pathways in C. elegans and the insight worm biology has provided into the mechanisms employed by these pathways. We touch on the increasingly spectacular diversity of small RNA biogenesis and function, and discuss the relevance of lessons learned in the worm for human biology.
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Affiliation(s)
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto Toronto, ON, Canada
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16
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Weidmann CA, Raynard NA, Blewett NH, Van Etten J, Goldstrohm AC. The RNA binding domain of Pumilio antagonizes poly-adenosine binding protein and accelerates deadenylation. RNA (NEW YORK, N.Y.) 2014; 20:1298-319. [PMID: 24942623 PMCID: PMC4105754 DOI: 10.1261/rna.046029.114] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 05/20/2014] [Indexed: 05/24/2023]
Abstract
PUF proteins are potent repressors that serve important roles in stem cell maintenance, neurological processes, and embryonic development. These functions are driven by PUF protein recognition of specific binding sites within the 3' untranslated regions of target mRNAs. In this study, we investigated mechanisms of repression by the founding PUF, Drosophila Pumilio, and its human orthologs. Here, we evaluated a previously proposed model wherein the Pumilio RNA binding domain (RBD) binds Argonaute, which in turn blocks the translational activity of the eukaryotic elongation factor 1A. Surprisingly, we found that Argonautes are not necessary for repression elicited by Drosophila and human PUFs in vivo. A second model proposed that the RBD of Pumilio represses by recruiting deadenylases to shorten the mRNA's polyadenosine tail. Indeed, the RBD binds to the Pop2 deadenylase and accelerates deadenylation; however, this activity is not crucial for regulation. Rather, we determined that the poly(A) is necessary for repression by the RBD. Our results reveal that poly(A)-dependent repression by the RBD requires the poly(A) binding protein, pAbp. Furthermore, we show that repression by the human PUM2 RBD requires the pAbp ortholog, PABPC1. Pumilio associates with pAbp but does not disrupt binding of pAbp to the mRNA. Taken together, our data support a model wherein the Pumilio RBD antagonizes the ability of pAbp to promote translation. Thus, the conserved function of the PUF RBD is to bind specific mRNAs, antagonize pAbp function, and promote deadenylation.
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Affiliation(s)
- Chase A Weidmann
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA Genetics Training Program, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Nathan A Raynard
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA Genetics Training Program, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Nathan H Blewett
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Jamie Van Etten
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Aaron C Goldstrohm
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA Genetics Training Program, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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17
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Wang JJ, Cui DY, Xiao T, Sun X, Zhang P, Chen R, He S, Huang DW. The influences of PRG-1 on the expression of small RNAs and mRNAs. BMC Genomics 2014; 15:321. [PMID: 24884413 PMCID: PMC4035053 DOI: 10.1186/1471-2164-15-321] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 04/24/2014] [Indexed: 12/16/2022] Open
Abstract
Background In metazoans, Piwi-related Argonaute proteins play important roles in maintaining germline integrity and fertility and have been linked to a class of germline-enriched small RNAs termed piRNAs. Caenorhabditis elegans encodes two Piwi family proteins called PRG-1 and PRG-2, and PRG-1 interacts with the C. elegans piRNAs (21U-RNAs). Previous studies found that mutation of prg-1 causes a marked reduction in the expression of 21U-RNAs, temperature-sensitive defects in fertility and other phenotypic defects. Results In this study, we wanted to systematically demonstrate the function of PRG-1 in the regulation of small RNAs and their targets. By analyzing small RNAs and mRNAs with and without a mutation in prg-1 during C. elegans development, we demonstrated that (1) mutation of prg-1 leads to a decrease in the expression of 21U-RNAs, and causes 35 ~ 40% of miRNAs to be down-regulated; (2) in C. elegans, approximately 3% (6% in L4) of protein-coding genes are differentially expressed after mutating prg-1, and 60 ~ 70% of these substantially altered protein-coding genes are up-regulated; (3) the target genes of the down-regulated miRNAs and the candidate target genes of the down-regulated 21U-RNAs are enriched in the up-regulated protein-coding genes; and (4) PRG-1 regulates protein-coding genes by down-regulating small RNAs (miRNAs and 21U-RNAs) that target genes that participate in the development of C. elegans. Conclusions In prg-1-mutated C. elegans, the expression of miRNAs and 21U-RNAs was reduced, and the protein-coding targets, which were associated with the development of C. elegans, were up-regulated. This may be the mechanism underlying PRG-1 function. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-321) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Runsheng Chen
- School of Life Science, Hebei University, Hebei 071002, People's Republic of China.
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18
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Wedeles CJ, Wu MZ, Claycomb JM. Protection of germline gene expression by the C. elegans Argonaute CSR-1. Dev Cell 2014; 27:664-71. [PMID: 24360783 DOI: 10.1016/j.devcel.2013.11.016] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 11/10/2013] [Accepted: 11/19/2013] [Indexed: 10/25/2022]
Abstract
In Caenorhabditis elegans, the Piwi-interacting small RNA (piRNA)-mediated germline surveillance system encodes more than 30,000 unique 21-nucleotide piRNAs, which silence a variety of foreign nucleic acids. What mechanisms allow endogenous germline-expressed transcripts to evade silencing by the piRNA pathway? One likely candidate in a protective mechanism is the Argonaute CSR-1, which interacts with 22G-small RNAs that are antisense to nearly all germline-expressed genes. Here, we use an in vivo RNA tethering assay to demonstrate that the recruitment of CSR-1 to a transcript licenses expression of the transcript, protecting it from piRNA-mediated silencing. Licensing occurs mainly at the level of transcription, as we observe changes in pre-mRNA levels consistent with transcriptional activation when CSR-1 is tethered. Furthermore, the recruitment of CSR-1 to a previously silenced locus transcriptionally activates its expression. Together, these results demonstrate a rare positive role for an endogenous Argonaute pathway in heritably licensing and protecting germline transcripts.
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