1
|
Sarkies P. The curious case of the disappearing piRNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1849. [PMID: 38629193 DOI: 10.1002/wrna.1849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/19/2024] [Accepted: 03/22/2024] [Indexed: 04/19/2024]
Abstract
Small non-coding RNAs are key regulators of gene expression across eukaryotes. Piwi-interacting small RNAs (piRNAs) are a specific type of small non-coding RNAs, conserved across animals, which are best known as regulators of genome stability through their ability to target transposable elements for silencing. Despite the near ubiquitous presence of piRNAs in animal lineages, there are some examples where the piRNA pathway has been lost completely, most dramatically in nematodes where loss has occurred in at least four independent lineages. In this perspective I will provide an evaluation of the presence of piRNAs across animals, explaining how it is known that piRNAs are missing from certain organisms. I will then consider possible explanations for why the piRNA pathway might have been lost and evaluate the evidence in favor of each possible mechanism. While it is still impossible to provide definitive answers, these theories will prompt further investigations into why such a highly conserved pathway can nevertheless become dispensable in certain lineages. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.
Collapse
Affiliation(s)
- Peter Sarkies
- Department of Biochemistry, University of Oxford, Oxford, UK
| |
Collapse
|
2
|
Dai S, Tang X, Li L, Ishidate T, Ozturk AR, Chen H, Dude AL, Yan YH, Dong MQ, Shen EZ, Mello CC. A family of C. elegans VASA homologs control Argonaute pathway specificity and promote transgenerational silencing. Cell Rep 2022; 40:111265. [PMID: 36070689 PMCID: PMC9887883 DOI: 10.1016/j.celrep.2022.111265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/01/2022] [Accepted: 08/04/2022] [Indexed: 02/02/2023] Open
Abstract
Germline Argonautes direct transcriptome surveillance within perinuclear membraneless organelles called nuage. In C. elegans, a family of Vasa-related Germ Line Helicase (GLH) proteins localize in and promote the formation of nuage. Previous studies have implicated GLH proteins in inherited silencing, but direct roles in small-RNA production, Argonaute binding, or mRNA targeting have not been identified. Here we show that GLH proteins compete with each other to control Argonaute pathway specificity, bind directly to Argonaute target mRNAs, and promote the amplification of small RNAs required for transgenerational inheritance. We show that the ATPase cycle of GLH-1 regulates direct binding to the Argonaute WAGO-1, which engages amplified small RNAs. Our findings support a dynamic and direct role for GLH proteins in inherited silencing beyond their role as structural components of nuage.
Collapse
Affiliation(s)
- Siyuan Dai
- RNA Therapeutic Institute, UMass Chan Medical School, Worcester, MA 01605, USA; Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Xiaoyin Tang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Lili Li
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Takao Ishidate
- RNA Therapeutic Institute, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Ahmet R Ozturk
- RNA Therapeutic Institute, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Hao Chen
- Program in Bioinformatics and Integrative Biology, UMass Chan Medical School, Worcester, MA 01605, USA; Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | - Altair L Dude
- RNA Therapeutic Institute, UMass Chan Medical School, Worcester, MA 01605, USA
| | - Yong-Hong Yan
- National Institute of Biological Sciences, Beijing 102206, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - En-Zhi Shen
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
| | - Craig C Mello
- RNA Therapeutic Institute, UMass Chan Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, Worcester, MA 01605, USA.
| |
Collapse
|
3
|
Zagoskin MV, Wang J, Neff AT, Veronezi GMB, Davis RE. Small RNA pathways in the nematode Ascaris in the absence of piRNAs. Nat Commun 2022; 13:837. [PMID: 35149688 PMCID: PMC8837657 DOI: 10.1038/s41467-022-28482-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/13/2022] [Indexed: 02/07/2023] Open
Abstract
Small RNA pathways play key and diverse regulatory roles in C. elegans, but our understanding of their conservation and contributions in other nematodes is limited. We analyzed small RNA pathways in the divergent parasitic nematode Ascaris. Ascaris has ten Argonautes with five worm-specific Argonautes (WAGOs) that associate with secondary 5’-triphosphate 22-24G-RNAs. These small RNAs target repetitive sequences or mature mRNAs and are similar to the C. elegans mutator, nuclear, and CSR-1 small RNA pathways. Even in the absence of a piRNA pathway, Ascaris CSR-1 may still function to “license” as well as fine-tune or repress gene expression. Ascaris ALG-4 and its associated 26G-RNAs target and likely repress specific mRNAs during testis meiosis. Ascaris WAGO small RNAs demonstrate target plasticity changing their targets between repeats and mRNAs during development. We provide a unique and comprehensive view of mRNA and small RNA expression throughout spermatogenesis. Overall, our study illustrates the conservation, divergence, dynamics, and flexibility of small RNA pathways in nematodes. The parasitic nematode Ascaris lacks piRNAs. Here the authors compare Argonaute proteins and small RNAs from C. elegans and Ascaris, expanding our understanding of the conservation, divergence, and flexibility of Argonautes and small RNA pathways in nematodes.
Collapse
Affiliation(s)
- Maxim V Zagoskin
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA.,RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Jianbin Wang
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA. .,RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA. .,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA. .,UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA.
| | - Ashley T Neff
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Giovana M B Veronezi
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Richard E Davis
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA. .,RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA.
| |
Collapse
|
4
|
Pastore B, Hertz HL, Tang W. Comparative analysis of piRNA sequences, targets and functions in nematodes. RNA Biol 2022; 19:1276-1292. [PMID: 36412988 PMCID: PMC9683057 DOI: 10.1080/15476286.2022.2149170] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Piwi proteins and Piwi-interacting RNAs (piRNAs) are best known for their roles in suppressing transposons and promoting fertility. Yet piRNA biogenesis and its mechanisms of action differ widely between distantly related species. To better understand the evolution of piRNAs, we characterized the piRNA pathway in C. briggsae, a sibling species of the model organism C. elegans. Our analyses define 25,883 piRNA producing-loci in C. briggsae. piRNA sequences in C. briggsae are extremely divergent from their counterparts in C. elegans, yet both species adopt similar genomic organization that drive piRNA expression. By examining production of Piwi-mediated secondary small RNAs, we identified a set of protein-coding genes that are evolutionarily conserved piRNA targets. In contrast to C. elegans, small RNAs targeting ribosomal RNAs or histone transcripts are not hyper-accumulated in C. briggsae Piwi mutants. Instead, we found that transcripts with few introns are prone to small RNA overamplification. Together our work highlights evolutionary conservation and divergence of the nematode piRNA pathway and provides insights into its role in endogenous gene regulation.
Collapse
Affiliation(s)
- Benjamin Pastore
- Department of Biological Chemistry and Pharmacology, The Ohio State University,Department of Biological Chemistry and Pharmacology, Ohio State University, Columbus, OH, USA,Center for RNA Biology, Ohio State University, Columbus, OH, USA
| | - Hannah L. Hertz
- Department of Biological Chemistry and Pharmacology, The Ohio State University,Department of Biological Chemistry and Pharmacology, Ohio State University, Columbus, OH, USA
| | - Wen Tang
- Department of Biological Chemistry and Pharmacology, The Ohio State University,Department of Biological Chemistry and Pharmacology, Ohio State University, Columbus, OH, USA,CONTACT Wen Tang Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
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.
Collapse
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
Collapse
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
| |
Collapse
|
8
|
Barucci G, Cornes E, Singh M, Li B, Ugolini M, Samolygo A, Didier C, Dingli F, Loew D, Quarato P, Cecere G. Small-RNA-mediated transgenerational silencing of histone genes impairs fertility in piRNA mutants. Nat Cell Biol 2020; 22:235-245. [PMID: 32015436 PMCID: PMC7272227 DOI: 10.1038/s41556-020-0462-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 01/05/2020] [Indexed: 11/09/2022]
Abstract
PIWI-interacting RNAs (piRNAs) promote fertility in many animals. However, whether this is due to their conserved role in repressing repetitive elements (REs) remains unclear. Here, we show that the progressive loss of fertility in Caenorhabditis elegans lacking piRNAs is not caused by derepression of REs or other piRNA targets but, rather, is mediated by epigenetic silencing of all of the replicative histone genes. In the absence of piRNAs, downstream components of the piRNA pathway relocalize from germ granules and piRNA targets to histone mRNAs to synthesize antisense small RNAs (sRNAs) and induce transgenerational silencing. Removal of the downstream components of the piRNA pathway restores histone mRNA expression and fertility in piRNA mutants, and the inheritance of histone sRNAs in wild-type worms adversely affects their fertility for multiple generations. We conclude that sRNA-mediated silencing of histone genes impairs the fertility of piRNA mutants and may serve to maintain piRNAs across evolution.
Collapse
Affiliation(s)
- Giorgia Barucci
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR 3738, CNRS, Paris, France
- Sorbonne Université, Collège doctoral, Paris, France
| | - Eric Cornes
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR 3738, CNRS, Paris, France
| | - Meetali Singh
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR 3738, CNRS, Paris, France
| | - Blaise Li
- Bioinformatics and Biostatistics Hub, C3BI, Institut Pasteur, USR 3756, CNRS, Paris, France
| | - Martino Ugolini
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR 3738, CNRS, Paris, France
- Scuola Normale Superiore, Pisa, Italy
| | - Aleksei Samolygo
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR 3738, CNRS, Paris, France
- Moscow Institute of Physics and Technology, Moscow, Russia
| | - Celine Didier
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR 3738, CNRS, Paris, France
| | - Florent Dingli
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie, PSL Research University, Paris, France
| | - Damarys Loew
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie, PSL Research University, Paris, France
| | - Piergiuseppe Quarato
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR 3738, CNRS, Paris, France
- Sorbonne Université, Collège doctoral, Paris, France
| | - Germano Cecere
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR 3738, CNRS, Paris, France.
| |
Collapse
|
9
|
Xu F, Feng X, Chen X, Weng C, Yan Q, Xu T, Hong M, Guang S. A Cytoplasmic Argonaute Protein Promotes the Inheritance of RNAi. Cell Rep 2019; 23:2482-2494. [PMID: 29791857 DOI: 10.1016/j.celrep.2018.04.072] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 03/24/2018] [Accepted: 04/16/2018] [Indexed: 01/02/2023] Open
Abstract
RNAi-elicited gene silencing is heritable and can persist for multiple generations after its initial induction in C. elegans. However, the mechanism by which parental-acquired trait-specific information from RNAi is inherited by the progenies is not fully understood. Here, we identified a cytoplasmic Argonaute protein, WAGO-4, necessary for the inheritance of RNAi. WAGO-4 exhibits asymmetrical translocation to the germline during early embryogenesis, accumulates at the perinuclear foci in the germline, and is required for the inheritance of exogenous RNAi targeting both germline- and soma-expressed genes. WAGO-4 binds to 22G-RNAs and their mRNA targets. Interestingly, WAGO-4-associated endogenous 22G-RNAs target the same cohort of germline genes as CSR-1 and contain untemplated addition of uracil at the 3' ends. The poly(U) polymerase CDE-1 is required for the untemplated uridylation of 22G-RNAs and inheritance of RNAi. Therefore, we conclude that, in addition to the nuclear RNAi pathway, the cytoplasmic RNAi machinery also promotes RNAi inheritance.
Collapse
Affiliation(s)
- Fei Xu
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Xuezhu Feng
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Xiangyang Chen
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Chenchun Weng
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Qi Yan
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Ting Xu
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Minjie Hong
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Shouhong Guang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China; CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
10
|
Cutter AD, Garrett RH, Mark S, Wang W, Sun L. Molecular evolution across developmental time reveals rapid divergence in early embryogenesis. Evol Lett 2019; 3:359-373. [PMID: 31388446 PMCID: PMC6675142 DOI: 10.1002/evl3.122] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 05/30/2019] [Indexed: 12/16/2022] Open
Abstract
Ontogenetic development hinges on the changes in gene expression in time and space within an organism, suggesting that the demands of ontogenetic growth can impose or reveal predictable pattern in the molecular evolution of genes expressed dynamically across development. Here, we characterize coexpression modules of the Caenorhabditis elegans transcriptome, using a time series of 30 points from early embryo to adult. By capturing the functional form of expression profiles with quantitative metrics, we find fastest evolution in the distinctive set of genes with transcript abundance that declines through development from a peak in young embryos. These genes are highly enriched for oogenic function and transient early zygotic expression, are nonrandomly distributed in the genome, and correspond to a life stage especially prone to inviability in interspecies hybrids. These observations conflict with the "early conservation model" for the evolution of development, although expression-weighted sequence divergence analysis provides some support for the "hourglass model." Genes in coexpression modules that peak toward adulthood also evolve fast, being hyper-enriched for roles in spermatogenesis, implicating a history of sexual selection and relaxation of selection on sperm as key factors driving rapid change to ontogenetically distinguishable coexpression modules of genes. We propose that these predictable trends of molecular evolution for dynamically expressed genes across ontogeny predispose particular life stages, early embryogenesis in particular, to hybrid dysfunction in the speciation process.
Collapse
Affiliation(s)
- Asher D. Cutter
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONM6G1W3Canada
| | - Rose H. Garrett
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONM6G1W3Canada
- Division of Biostatistics, Dalla Lana School of Public HealthUniversity of TorontoTorontoONM6G1W3Canada
- Department of Statistical SciencesUniversity of TorontoTorontoONM6G1W3Canada
| | - Stephanie Mark
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONM6G1W3Canada
| | - Wei Wang
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONM6G1W3Canada
| | - Lei Sun
- Division of Biostatistics, Dalla Lana School of Public HealthUniversity of TorontoTorontoONM6G1W3Canada
- Department of Statistical SciencesUniversity of TorontoTorontoONM6G1W3Canada
| |
Collapse
|
11
|
Mark S, Weiss J, Sharma E, Liu T, Wang W, Claycomb JM, Cutter AD. Genome structure predicts modular transcriptome responses to genetic and environmental conditions. Mol Ecol 2019; 28:3681-3697. [PMID: 31325381 DOI: 10.1111/mec.15185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 07/05/2019] [Accepted: 07/10/2019] [Indexed: 12/13/2022]
Abstract
Understanding the plasticity, robustness and modularity of transcriptome expression to genetic and environmental conditions is crucial to deciphering how organisms adapt in nature. To test how genome architecture influences transcriptome profiles, we quantified expression responses for distinct temperature-adapted genotypes of the nematode Caenorhabditis briggsae when exposed to chronic temperature stresses throughout development. We found that 56% of the 8,795 differentially expressed genes show genotype-specific changes in expression in response to temperature (genotype-by-environment interactions, GxE). Most genotype-specific responses occur under heat stress, indicating that cold vs. heat stress responses involve distinct genomic architectures. The 22 co-expression modules that we identified differ in their enrichment of genes with genetic vs. environmental vs. interaction effects, as well as their genomic spatial distributions, functional attributes and rates of molecular evolution at the sequence level. Genes in modules enriched for simple effects of either genotype or temperature alone tend to evolve especially rapidly, consistent with disproportionate influence of adaptation or weaker constraint on these subsets of loci. Chromosome-scale heterogeneity in nucleotide polymorphism, however, rather than the scale of individual genes predominates as the source of genetic differences among expression profiles, and natural selection regimes are largely decoupled between coding sequences and noncoding flanking sequences that contain cis-regulatory elements. These results illustrate how the form of transcriptome modularity and genome structure contribute to predictable profiles of evolutionary change.
Collapse
Affiliation(s)
- Stephanie Mark
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Joerg Weiss
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Eesha Sharma
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Ting Liu
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Wei Wang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Asher D Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
12
|
Weiser NE, Kim JK. Multigenerational Regulation of the Caenorhabditis elegans Chromatin Landscape by Germline Small RNAs. Annu Rev Genet 2019; 53:289-311. [PMID: 31150586 DOI: 10.1146/annurev-genet-112618-043505] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In animals, small noncoding RNAs that are expressed in the germline and transmitted to progeny control gene expression to promote fertility. Germline-expressed small RNAs, including endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs), drive the repression of deleterious transcripts such as transposons, repetitive elements, and pseudogenes. Recent studies have highlighted an important role for small RNAs in transgenerational epigenetic inheritance via regulation of heritable chromatin marks; therefore, small RNAs are thought to convey an epigenetic memory of genomic self and nonself elements. Small RNA pathways are highly conserved in metazoans and have been best described for the model organism Caenorhabditis elegans. In this review, we describe the biogenesis, regulation, and function of C. elegans endo-siRNAs and piRNAs, along with recent insights into how these distinct pathways are integrated to collectively regulate germline gene expression, transgenerational epigenetic inheritance, and ultimately, animal fertility.
Collapse
Affiliation(s)
- Natasha E Weiser
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - John K Kim
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA;
| |
Collapse
|
13
|
Almeida MV, Andrade-Navarro MA, Ketting RF. Function and Evolution of Nematode RNAi Pathways. Noncoding RNA 2019; 5:E8. [PMID: 30650636 PMCID: PMC6468775 DOI: 10.3390/ncrna5010008] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/07/2019] [Accepted: 01/08/2019] [Indexed: 12/11/2022] Open
Abstract
Selfish genetic elements, like transposable elements or viruses, are a threat to genomic stability. A variety of processes, including small RNA-based RNA interference (RNAi)-like pathways, has evolved to counteract these elements. Amongst these, endogenous small interfering RNA and Piwi-interacting RNA (piRNA) pathways were implicated in silencing selfish genetic elements in a variety of organisms. Nematodes have several incredibly specialized, rapidly evolving endogenous RNAi-like pathways serving such purposes. Here, we review recent research regarding the RNAi-like pathways of Caenorhabditis elegans as well as those of other nematodes, to provide an evolutionary perspective. We argue that multiple nematode RNAi-like pathways share piRNA-like properties and together form a broad nematode toolkit that allows for silencing of foreign genetic elements.
Collapse
Affiliation(s)
| | - Miguel A Andrade-Navarro
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany.
- Faculty of Biology, Johannes Gutenberg Universität, 55122 Mainz, Germany.
| | - René F Ketting
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany.
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Ow MC, Borziak K, Nichitean AM, Dorus S, Hall SE. Early experiences mediate distinct adult gene expression and reproductive programs in Caenorhabditis elegans. PLoS Genet 2018; 14:e1007219. [PMID: 29447162 PMCID: PMC5831748 DOI: 10.1371/journal.pgen.1007219] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 02/28/2018] [Accepted: 01/24/2018] [Indexed: 01/16/2023] Open
Abstract
Environmental stress during early development in animals can have profound effects on adult phenotypes via programmed changes in gene expression. Using the nematode C. elegans, we demonstrated previously that adults retain a cellular memory of their developmental experience that is manifested by differences in gene expression and life history traits; however, the sophistication of this system in response to different environmental stresses, and how it dictates phenotypic plasticity in adults that contribute to increased fitness in response to distinct environmental challenges, was unknown. Using transcriptional profiling, we show here that C. elegans adults indeed retain distinct cellular memories of different environmental conditions. We identified approximately 500 genes in adults that entered dauer due to starvation that exhibit significant opposite (“seesaw”) transcriptional phenotypes compared to adults that entered dauer due to crowding, and are distinct from animals that bypassed dauer. Moreover, we show that two-thirds of the genes in the genome experience a 2-fold or greater seesaw trend in gene expression, and based upon the direction of change, are enriched in large, tightly linked regions on different chromosomes. Importantly, these transcriptional programs correspond to significant changes in brood size depending on the experienced stress. In addition, we demonstrate that while the observed seesaw gene expression changes occur in both somatic and germline tissue, only starvation-induced changes require a functional GLP-4 protein necessary for germline development, and both programs require the Argonaute CSR-1. Thus, our results suggest that signaling between the soma and the germ line can generate phenotypic plasticity as a result of early environmental experience, and likely contribute to increased fitness in adverse conditions and the evolution of the C. elegans genome. Environmental stress during early development in animals can have profound effects on adult behavior and physiology due to programmed changes in gene expression. However, whether different stresses result in distinct changes in traits that allow stressed animals to better survive and reproduce in future adverse conditions is largely unknown. Using the animal model system, C. elegans, we show that adults that experienced starvation exhibit opposite (“seesaw”) genome-wide gene expression changes compared to adults that experienced crowding, and are distinct from animals that experienced favorable conditions. Genes that are similarly up- or downregulated due to either starvation or crowding are located in clusters on the same chromosomes. Importantly, these gene expression changes of differently-stressed animals result in corresponding changes in progeny number, a life history trait of evolutionary significance. These distinct gene expression programs require different signaling pathways that communicate across somatic and germline tissue types. Thus, different environmental stresses experienced early in development induce distinct signaling mechanisms to result in changes in gene expression and reproduction in adults, and likely contribute to increased survival in future adverse conditions.
Collapse
Affiliation(s)
- Maria C. Ow
- Department of Biology, Syracuse University, Syracuse, NY, United States of America
| | - Kirill Borziak
- Department of Biology, Syracuse University, Syracuse, NY, United States of America
- Center for Reproductive Evolution, Department of Biology, Syracuse University, Syracuse, NY, United States of America
| | | | - Steve Dorus
- Department of Biology, Syracuse University, Syracuse, NY, United States of America
- Center for Reproductive Evolution, Department of Biology, Syracuse University, Syracuse, NY, United States of America
| | - Sarah E. Hall
- Department of Biology, Syracuse University, Syracuse, NY, United States of America
- * E-mail:
| |
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Tyc KM, Nabih A, Wu MZ, Wedeles CJ, Sobotka JA, Claycomb JM. The Conserved Intron Binding Protein EMB-4 Plays Differential Roles in Germline Small RNA Pathways of C. elegans. Dev Cell 2017; 42:256-270.e6. [DOI: 10.1016/j.devcel.2017.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 05/15/2017] [Accepted: 07/05/2017] [Indexed: 02/08/2023]
|
18
|
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)
| |
Collapse
|
19
|
Andralojc KM, Campbell AC, Kelly AL, Terrey M, Tanner PC, Gans IM, Senter-Zapata MJ, Khokhar ES, Updike DL. ELLI-1, a novel germline protein, modulates RNAi activity and P-granule accumulation in Caenorhabditis elegans. PLoS Genet 2017; 13:e1006611. [PMID: 28182654 PMCID: PMC5325599 DOI: 10.1371/journal.pgen.1006611] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 02/24/2017] [Accepted: 01/31/2017] [Indexed: 12/13/2022] Open
Abstract
Germ cells contain non-membrane bound cytoplasmic organelles that help maintain germline integrity. In C. elegans they are called P granules; without them, the germline undergoes partial masculinization and aberrant differentiation. One key P-granule component is the Argonaute CSR-1, a small-RNA binding protein that antagonizes accumulation of sperm-specific transcripts in developing oocytes and fine-tunes expression of proteins critical to early embryogenesis. Loss of CSR-1 complex components results in a very specific, enlarged P-granule phenotype. In a forward screen to identify mutants with abnormal P granules, ten alleles were recovered with a csr-1 P-granule phenotype, eight of which contain mutations in known components of the CSR-1 complex (csr-1, ego-1, ekl-1, and drh-3). The remaining two alleles are in a novel gene now called elli-1 (enlarged germline granules). ELLI-1 is first expressed in primordial germ cells during mid-embryogenesis, and continues to be expressed in the adult germline. While ELLI-1 forms cytoplasmic aggregates, they occasionally dock, but do not co-localize with P granules. Instead, the majority of ELLI-1 aggregates accumulate in the shared germline cytoplasm. In elli-1 mutants, several genes that promote RNAi and P-granule accumulation are upregulated, and embryonic lethality, sterility, and RNAi resistance in a hypomorphic drh-3 allele is enhanced, suggesting that ELLI-1 functions with CSR-1 to modulate RNAi activity, P-granule accumulation, and post-transcriptional expression in the germline.
Collapse
Affiliation(s)
- Karolina M. Andralojc
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine, United States of America
| | - Anne C. Campbell
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine, United States of America
| | - Ashley L. Kelly
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine, United States of America
| | - Markus Terrey
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine, United States of America
| | - Paige C. Tanner
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine, United States of America
| | - Ian M. Gans
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine, United States of America
| | | | - Eraj S. Khokhar
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine, United States of America
| | - Dustin L. Updike
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine, United States of America
| |
Collapse
|
20
|
Cook DE, Zdraljevic S, Roberts JP, Andersen EC. CeNDR, the Caenorhabditis elegans natural diversity resource. Nucleic Acids Res 2016; 45:D650-D657. [PMID: 27701074 PMCID: PMC5210618 DOI: 10.1093/nar/gkw893] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/20/2016] [Accepted: 09/26/2016] [Indexed: 01/06/2023] Open
Abstract
Studies in model organisms have yielded considerable insights into the etiology of disease and our understanding of evolutionary processes. Caenorhabditis elegans is among the most powerful model organisms used to understand biology. However, C. elegans is not used as extensively as other model organisms to investigate how natural variation shapes traits, especially through the use of genome-wide association (GWA) analyses. Here, we introduce a new platform, the C. elegans Natural Diversity Resource (CeNDR) to enable statistical genetics and genomics studies of C. elegans and to connect the results to human disease. CeNDR provides the research community with wild strains, genome-wide sequence and variant data for every strain, and a GWA mapping portal for studying natural variation in C. elegans. Additionally, researchers outside of the C. elegans community can benefit from public mappings and integrated tools for comparative analyses. CeNDR uses several databases that are continually updated through the addition of new strains, sequencing data, and association mapping results. The CeNDR data are accessible through a freely available web portal located at http://www.elegansvariation.org or through an application programming interface.
Collapse
Affiliation(s)
- Daniel E Cook
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA.,Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Stefan Zdraljevic
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, IL 60208, USA.,Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Joshua P Roberts
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| |
Collapse
|
21
|
Li R, Ren X, Bi Y, Ho VWS, Hsieh CL, Young A, Zhang Z, Lin T, Zhao Y, Miao L, Sarkies P, Zhao Z. Specific down-regulation of spermatogenesis genes targeted by 22G RNAs in hybrid sterile males associated with an X-Chromosome introgression. Genome Res 2016; 26:1219-32. [PMID: 27197225 PMCID: PMC5052035 DOI: 10.1101/gr.204479.116] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 05/16/2016] [Indexed: 12/23/2022]
Abstract
Hybrid incompatibility (HI) prevents gene flow between species, thus lying at the heart of speciation genetics. One of the most common HIs is male sterility. Two superficially contradictory observations exist for hybrid male sterility. First, an introgression on the X Chromosome is more likely to produce male sterility than on autosome (so-called large-X theory); second, spermatogenesis genes are enriched on the autosomes but depleted on the X Chromosome (demasculinization of X Chromosome). Analysis of gene expression in Drosophila hybrids suggests a genetic interaction between the X Chromosome and autosomes that is essential for male fertility. However, the prevalence of such an interaction and its underlying mechanism remain largely unknown. Here we examine the interaction in nematode species by contrasting the expression of both coding genes and transposable elements (TEs) between hybrid sterile males and its parental nematode males. We use two lines of hybrid sterile males, each carrying an independent introgression fragment from Caenorhabditis briggsae X Chromosome in an otherwise Caenorhabditis nigoni background, which demonstrate similar defects in spermatogenesis. We observe a similar pattern of down-regulated genes that are specific for spermatogenesis between the two hybrids. Importantly, the down-regulated genes caused by the X Chromosome introgressions show a significant enrichment on the autosomes, supporting an epistatic interaction between the X Chromosome and autosomes. We investigate the underlying mechanism of the interaction by measuring small RNAs and find that a subset of 22G RNAs specifically targeting the down-regulated spermatogenesis genes is significantly up-regulated in hybrids, suggesting that perturbation of small RNA-mediated regulation may contribute to the X-autosome interaction.
Collapse
Affiliation(s)
- Runsheng Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Xiaoliang Ren
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yu Bi
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Vincy Wing Sze Ho
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | | | - Amanda Young
- Illumina Incorporated, San Diego, California 92122, USA
| | - Zhihong Zhang
- Illumina Incorporated, San Diego, California 92122, USA
| | - Tingting Lin
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100190, China
| | - Yanmei Zhao
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100190, China
| | - Long Miao
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100190, China
| | - Peter Sarkies
- MRC Clinical Sciences Centre, London W12 0NN, United Kingdom; Institute of Clinical Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong, China; State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, China
| |
Collapse
|
22
|
Houri-Ze’evi L, Korem Y, Sheftel H, Faigenbloom L, Toker IA, Dagan Y, Awad L, Degani L, Alon U, Rechavi O. A Tunable Mechanism Determines the Duration of the Transgenerational Small RNA Inheritance in C. elegans. Cell 2016; 165:88-99. [DOI: 10.1016/j.cell.2016.02.057] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/19/2016] [Accepted: 02/24/2016] [Indexed: 01/13/2023]
|
23
|
Blumenfeld AL, Jose AM. Reproducible features of small RNAs in C. elegans reveal NU RNAs and provide insights into 22G RNAs and 26G RNAs. RNA (NEW YORK, N.Y.) 2016; 22:184-192. [PMID: 26647462 PMCID: PMC4712669 DOI: 10.1261/rna.054551.115] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/02/2015] [Indexed: 06/05/2023]
Abstract
Small RNAs regulate gene expression and most genes in the worm Caenorhabditis elegans are subject to their regulation. Here, we analyze small RNA data sets and use reproducible features of RNAs present in multiple data sets to discover a new class of small RNAs and to reveal insights into two known classes of small RNAs--22G RNAs and 26G RNAs. We found that reproducibly detected 22-nt RNAs, although are predominantly RNAs with a G at the 5' end, also include RNAs with A, C, or U at the 5' end. These RNAs are synthesized downstream from characteristic sequence motifs on mRNA and have U-tailed derivatives. Analysis of 26G RNAs revealed that they are processed from a blunt end of double-stranded RNAs and that production of one 26G RNA generates a hotspot immediately downstream for production of another. To our surprise, analysis of RNAs shorter than 18 nt revealed a new class of RNAs, which we call NU RNAs (pronounced "new RNAs") because they have a NU bias at the 5' end, where N is any nucleotide. NU RNAs are antisense to genes and originate downstream from U bases on mRNA. Although many genes have complementary NU RNAs, their genome-wide distribution is distinct from that of previously known classes of small RNAs. Our results suggest that current approaches underestimate reproducibly detected RNAs that are shorter than 18 nt, and theoretical considerations suggest that such shorter RNAs could be used for sequence-specific gene regulation in organisms like C. elegans that have small genomes.
Collapse
Affiliation(s)
- Andrew L Blumenfeld
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA
| | - Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742, USA
| |
Collapse
|
24
|
Mao H, Zhu C, Zong D, Weng C, Yang X, Huang H, Liu D, Feng X, Guang S. The Nrde Pathway Mediates Small-RNA-Directed Histone H3 Lysine 27 Trimethylation in Caenorhabditis elegans. Curr Biol 2015; 25:2398-403. [PMID: 26365259 DOI: 10.1016/j.cub.2015.07.051] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 06/13/2015] [Accepted: 07/20/2015] [Indexed: 11/29/2022]
Abstract
Small-RNA-mediated chromatin modifications have been widely studied in plants and S. pombe. However, direct evidence of small-RNA-guided sequence-specific chromatin alterations is scarce in animals. In C. elegans, the nuclear RNAi defective (Nrde) pathway functions to transport siRNA from the cytoplasm to the nucleus, modulate transcription elongation, induce histone H3 lysine 9 (H3K9) trimethylation, and mediate transgenerational inheritance of RNAi. Here, we show that both exogenous RNAi and NRDE-bound endogenous 22G RNAs can direct sequence-specific histone H3 lysine 27 (H3K27) trimethylation at targeted loci through the Nrde pathway. The resulting H3K27me3 status can be inherited by progeny for multiple generations. piRNAs and WAGO-1-associated siRNAs induce H3K27 methylation as well. Interestingly, CSR-1-associated endogenous siRNAs fail to trigger H3K27 methylation, whereas exogenous provision of dsRNAs can induce H3K27 methylation at the CSR-1-targeted loci via the Nrde pathway. We further observed distinct genetic requirements of H3K9 and H3K27 trimethylation. Whereas set-25 and met-2 are required for K9 methylation, mes-2 is required for K27 methylation. The depletion of mes-2 leads to a nuclear RNAi defective phenotype. These results indicate that dsRNA-triggered chromatin modification is a sequence-specific response that engages the Nrde pathway in C. elegans.
Collapse
Affiliation(s)
- Hui Mao
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Chengming Zhu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Dandan Zong
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Chenchun Weng
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Xiangwei Yang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Hui Huang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Dun Liu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Xuezhu Feng
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.
| | - Shouhong Guang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.
| |
Collapse
|