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Chen S, Phillips CM. Nuclear Argonaute protein NRDE-3 switches small RNA binding partners during embryogenesis coincident with the formation of SIMR granules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.29.605686. [PMID: 39131395 PMCID: PMC11312606 DOI: 10.1101/2024.07.29.605686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
RNA interference (RNAi) is a conserved gene regulation mechanism that utilizes the Argonaute protein and their associated small RNAs to exert regulatory function on complementary transcripts. While the majority of germline-expressed RNAi pathway components reside in perinuclear germ granules, it is unknown whether and how RNAi pathways are spatially organized in other cell types. Here we find that the small RNA biogenesis machinery is spatially and temporally organized during embryogenesis. Specifically, the RNAi factor, SIMR-1, forms visible concentrates during mid-embryogenesis that contain an RNA-dependent RNA polymerase, a poly-UG polymerase, and the unloaded nuclear Argonaute protein, NRDE-3. Further, we observe that many other RNAi factors form foci in embryonic cells distinct from SIMR granules, including the Argonaute protein CSR-1, underscoring a potential role for cytoplasmic concentrates of RNAi factors to promote gene regulation in embryos. Curiously, coincident with the appearance of the "SIMR granules", the small RNAs bound to NRDE-3 switch from predominantly CSR-class 22G-RNAs to ERGO-dependent 22G-RNAs. Thus, our study defines two separable roles for NRDE-3, targeting germline-expressed genes during early embryogenesis and switching later in embryogenesis to repress recently duplicated genes and retrotransposons in somatic cells, highlighting the plasticity of Argonaute proteins and the need for more precise temporal characterization of Argonaute-small RNA interactions.
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Affiliation(s)
- Shihui Chen
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Carolyn M Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
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2
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Zeng W, Lin J, Xie J, Fu Y, Lin Y, Chen T, Li B, Yu X, Chen W, Jiang D, Cheng J. RNA-dependent RNA polymerases regulate ascospore discharge through the exonic-sRNA-mediated RNAi pathway. mBio 2024; 15:e0037724. [PMID: 38752738 PMCID: PMC11237814 DOI: 10.1128/mbio.00377-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/10/2024] [Indexed: 06/13/2024] Open
Abstract
Ascospores, forcibly released into the air from perithecia, are the primary inoculum for Fusarium head blight. In Fusarium graminearum, the biological functions of four RNA-dependent RNA polymerases (RdRPs) (Fgrdrp1-4) have been reported, but their regulatory mechanisms are poorly understood and the function of Fgrdrp5 is still unknown. In this study, we found that in addition to Fgrdrp1 and Fgrdrp2, Fgrdrp5 also plays an important role in ascospore discharge, and they all participate in the generation of turgor pressure in a polyol-dependent manner. Moreover, these three genes all affect the maturation of ascospores. Deep sequencing and co-analysis of small RNA and mRNA certified that Fgrdrp1, Fgrdrp2, and Fgrdrp5 partly share their functions in the biogenesis and accumulation of exonic small interference RNA (ex-siRNA), and these three RdRPs negatively regulate the expression levels of ex-siRNA corresponding genes, including certain genes associated with ascospore development or discharge. Furthermore, the differentially expressed genes of deletion mutants, those involved in lipid and sugar metabolism or transport as well as sexual development-related transcription factors, may also contribute to the defects in ascospore maturation or ascospore discharge. In conclusion, our study suggested that the components of the dicer-dependent ex-siRNA-mediated RNA interference pathway include at least Fgrdrp1, Fgrdrp2, and Fgrdrp5. IMPORTANCE We found that in addition to Fgrdrp1 and Fgrdrp2, Fgrdrp5 also plays important roles in ascospore maturation and ascospore discharge of Fusarium graminearum. These three RNA-dependent RNA polymerases participate in the biogenesis and accumulation of exonic small interference RNA and then regulate ascospore discharge.
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Affiliation(s)
- Wenping Zeng
- Key Laboratory of Environment Change and Resources Use in Beibu Gulf, Ministry of Education, Nanning Normal University, Nanning, China
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Jing Lin
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiatao Xie
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yanping Fu
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yang Lin
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tao Chen
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Bo Li
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiao Yu
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Weidong Chen
- USA Department of Agriculture, Agricultural Research Service, Washington State University, Pullman, Washington, USA
| | - Daohong Jiang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiasen Cheng
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- The Provincial Key Lab of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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Naim D, Ahsan A, Imtiaj A, Mollah NH. Genome-wide identification and in silico characterization of major RNAi gene families in date palm (Phoenix dactylifera). BMC Genom Data 2024; 25:31. [PMID: 38491426 PMCID: PMC10943882 DOI: 10.1186/s12863-024-01217-x] [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: 05/13/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Dates contain various minerals that are essential for good health. The major RNA interference (RNAi) gene families play a vital role in plant growth and development by controlling the expression of protein-coding genes against different biotic and abiotic stresses. However, these gene families for date palm are not yet studied. Therefore, this study has explored major RNAi genes and their characteristics in date palm. RESULTS We have identified 4 PdDCLs, 7 PdAGOs, and 3 PdRDRs as RNAi proteins from the date palm genome by using AtRNAi genes as query sequences in BLASTp search. Domain analysis of predicted RNAi genes has revealed the Helicase_C, Dicer_dimer, PAZ, RNase III, and Piwi domains that are associated with the gene silencing mechanisms. Most PdRNAi proteins have been found in the nucleus and cytosol associated with the gene silencing actions. The gene ontology (GO) enrichment analysis has revealed some important GO terms including RNA interference, dsRNA fragmentation, and ribonuclease_III activity that are related to the protein-coding gene silencing mechanisms. Gene regulatory network (GRN) analysis has identified PAZ and SNF2 as the transcriptional regulators of PdRNAi genes. Top-ranked 10 microRNAs including Pda-miR156b, Pda-miR396a, Pda-miR166a, Pda-miR167d, and Pda-miR529a have been identified as the key post-transcriptional regulators of PdRNAi genes that are associated with different biotic/abiotic stresses. The cis-acting regulatory element analysis of PdRNAi genes has detected some vital cis-acting elements including ABRE, MBS, MYB, MYC, Box-4, G-box, I-box, and STRE that are linked with different abiotic stresses. CONCLUSION The results of this study might be valuable resources for the improvement of different characteristics in date palm by further studies in wet-lab.
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Affiliation(s)
- Darun Naim
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, 6205, Rajshahi, Bangladesh
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, 6205, Rajshahi, Bangladesh
| | - Asif Ahsan
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, 6205, Rajshahi, Bangladesh
| | - Ahmed Imtiaj
- Department of Botany, Faculty of Biological Sciences, University of Rajshahi, 6205, Rajshahi, Bangladesh
| | - Nurul Haque Mollah
- Bioinformatics Lab, Department of Statistics, Faculty of Science, University of Rajshahi, 6205, Rajshahi, Bangladesh.
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Bhatia S, Hunter CP. SID-4/NCK-1 is important for dsRNA import in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2022; 12:6722623. [PMID: 36165710 PMCID: PMC9635667 DOI: 10.1093/g3journal/jkac252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/25/2022] [Indexed: 12/24/2022]
Abstract
RNA interference is sequence-specific gene silencing triggered by double-stranded RNA. Systemic RNA interference is where double-stranded RNA, expressed or introduced into 1 cell, is transported to and initiates RNA interference in other cells. Systemic RNA interference is very efficient in Caenorhabditis elegans and genetic screens for systemic RNA interference-defective mutants have identified RNA transporters (SID-1, SID-2, and SID-5) and a signaling protein (SID-3). Here, we report that SID-4 is nck-1, a C. elegans NCK-like adaptor protein. sid-4 null mutations cause a weak, dose-sensitive, systemic RNA interference defect and can be effectively rescued by SID-4 expression in target tissues only, implying a role in double-stranded RNA import. SID-4 and SID-3 (ACK-1 kinase) homologs interact in mammals and insects, suggesting that they may function in a common signaling pathway; however, a sid-3; sid-4 double mutants showed additive resistance to RNA interference, suggesting that these proteins likely interact with other signaling pathways as well. A bioinformatic screen coupled to RNA interference sensitivity tests identified 23 additional signaling components with weak RNA interference-defective phenotypes. These observations suggest that environmental conditions may modulate systemic RNA interference efficacy, and indeed, sid-3 and sid-4 are required for growth temperature effects on systemic RNA interference silencing efficiency.
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Affiliation(s)
- Sonya Bhatia
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138, USA
| | - Craig P Hunter
- Corresponding author: Department of Molecular and Cellular Biology, 16 Divinity Avenue, Harvard University, Cambridge MA, 02138 USA.
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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.
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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.
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Phillips CM, Updike DL. Germ granules and gene regulation in the Caenorhabditis elegans germline. Genetics 2022; 220:6541922. [PMID: 35239965 PMCID: PMC8893257 DOI: 10.1093/genetics/iyab195] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 10/10/2021] [Indexed: 01/27/2023] Open
Abstract
The transparency of Caenorhabditis elegans provides a unique window to observe and study the function of germ granules. Germ granules are specialized ribonucleoprotein (RNP) assemblies specific to the germline cytoplasm, and they are largely conserved across Metazoa. Within the germline cytoplasm, they are positioned to regulate mRNA abundance, translation, small RNA production, and cytoplasmic inheritance to help specify and maintain germline identity across generations. Here we provide an overview of germ granules and focus on the significance of more recent observations that describe how they further demix into sub-granules, each with unique compositions and functions.
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Affiliation(s)
- Carolyn M Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA,Corresponding author: (C.M.P.); (D.L.U.)
| | - Dustin L Updike
- The Mount Desert Island Biological Laboratory, Bar Harbor, ME 04672, USA,Corresponding author: (C.M.P.); (D.L.U.)
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7
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Hu Y, Hu X, Li D, Du Z, Shi K, He C, Zhang Y, Zhang D. The APC/C FZY-1/Cdc20 Complex Coordinates With OMA-1 to Regulate the Oocyte-to-Embryo Transition in Caenorhabditis elegans. Front Cell Dev Biol 2021; 9:749654. [PMID: 34722532 PMCID: PMC8554129 DOI: 10.3389/fcell.2021.749654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
During oocyte maturation and the oocyte-to-embryo transition, key developmental regulators such as RNA-binding proteins coordinate translation of particular messenger RNA (mRNAs) and related developmental processes by binding to their cognate maternal mRNAs. In the nematode Caenorhabditis elegans, these processes are regulated by a set of CCCH zinc finger proteins. Oocyte maturation defective-1 (OMA-1) and OMA-2 are two functionally redundant CCCH zinc finger proteins that turnover rapidly during the first embryonic cell division. These turnovers are required for proper transition from oogenesis to embryogenesis. A gain-of-function mutant of OMA-1, oma-1(zu405), stabilizes and delays degradation of OMA-1, resulting in delayed turnover and mis-segregation of other cell fate determinants, which eventually causes embryonic lethality. We performed a large-scale forward genetic screen to identify suppressors of the oma-1(zu405) mutant. We show here that multiple alleles affecting functions of various anaphase promoting complex/cyclosome (APC/C) subunits, including MAT-1, MAT-2, MAT-3, EMB-30, and FZY-1, suppress the gain-of-function mutant of OMA-1. Transcriptome analysis suggested that overall transcription in early embryos occurred after introducing mutations in APC/C genes into the oma-1(zu405) mutant. Mutations in APC/C genes prevent OMA-1 enrichment in P granules and correct delayed degradation of downstream cell fate determinants including pharynx and intestine in excess-1 (PIE-1), posterior segregation-1 (POS-1), muscle excess-3 (MEX-3), and maternal effect germ-cell defective-1 (MEG-1). We demonstrated that only the activator FZY-1, but not FZR-1, is incorporated in the APC/C complex to regulate the oocyte-to-embryo transition. Our findings suggested a genetic relationship linking the APC/C complex and OMA-1, and support a model in which the APC/C complex promotes P granule accumulation and modifies RNA binding of OMA-1 to regulate the oocyte-to-embryo transition process.
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Affiliation(s)
- Yabing Hu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuewen Hu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dongchen Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhenzhen Du
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kun Shi
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chenxia He
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Donglei Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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8
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Toudji-Zouaz A, Bertrand V, Barrière A. Imaging of native transcription and transcriptional dynamics in vivo using a tagged Argonaute protein. Nucleic Acids Res 2021; 49:e86. [PMID: 34107044 PMCID: PMC8421136 DOI: 10.1093/nar/gkab469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 04/16/2021] [Accepted: 05/18/2021] [Indexed: 12/26/2022] Open
Abstract
A flexible method to image unmodified transcripts and transcription in vivo would be a valuable tool to understand the regulation and dynamics of transcription. Here, we present a novel approach to follow native transcription, with fluorescence microscopy, in live C. elegans. By using the fluorescently tagged Argonaute protein NRDE-3, programmed by exposure to defined dsRNA to bind to nascent transcripts of the gene of interest, we demonstrate transcript labelling of multiple genes, at the transcription site and in the cytoplasm. This flexible approach does not require genetic manipulation, and can be easily scaled up by relying on whole-genome dsRNA libraries. We apply this method to image the transcriptional dynamics of the heat-shock inducible gene hsp-4 (a member of the hsp70 family), as well as two transcription factors: ttx-3 (a LHX2/9 orthologue) in embryos, and hlh-1 (a MyoD orthologue) in larvae, respectively involved in neuronal and muscle development.
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Affiliation(s)
- Amel Toudji-Zouaz
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Vincent Bertrand
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
| | - Antoine Barrière
- Aix Marseille University, CNRS, IBDM, Turing Centre for Living Systems, Marseille, France
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9
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Sundby AE, Molnar RI, Claycomb JM. Connecting the Dots: Linking Caenorhabditis elegans Small RNA Pathways and Germ Granules. Trends Cell Biol 2021; 31:387-401. [PMID: 33526340 DOI: 10.1016/j.tcb.2020.12.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 12/15/2022]
Abstract
Germ granules are non-membrane bound, phase-separated organelles, composed of RNAs and proteins. Germ granules are present only within the germ cells of animals, including model systems such as Caenorhabditis elegans, Drosophila, mice, and zebrafish, where they play critical roles in specifying the germ lineage, the inheritance of epigenetic information, and post-transcriptional gene regulation. Across species, conserved germ granule proteins reflect these essential functions. A significant proportion of proteins that localize to germ granules are components of RNA metabolism and small RNA (sRNA) gene regulatory pathways. Here we synthesize our current knowledge of the roles that germ granules and their components play in sRNA pathway functions, transgenerational inheritance, and fertility in the C. elegans germline.
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Affiliation(s)
- 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
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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10
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Stage-specific protein regulation during somatic embryo development of Carica papaya L. 'Golden'. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140561. [PMID: 33161157 DOI: 10.1016/j.bbapap.2020.140561] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/13/2020] [Accepted: 10/27/2020] [Indexed: 11/20/2022]
Abstract
Somatic embryogenesis is an important biotechnological technique for large-scale propagation of elite genotypes. Identifying stage-specific compounds associated with somatic embryo development can help elucidate the ontogenesis of Carica papaya L. somatic embryos and improve tissue culture protocols. To identify the stage-specific proteins that are present during the differentiation of C. papaya somatic embryos, proteomic analyses of embryos at the globular, heart, torpedo and cotyledonary developmental stages were performed. Mass spectrometry data have been deposited in the ProteomeXchange with the dataset identifier PXD021107. Comparative proteomic analyses revealed a total of 801 proteins, with 392 classified as differentially accumulated proteins in at least one of the developmental stages. The globular-staged presented a higher number of unique proteins (16), and 7 were isoforms of 60S ribosomal proteins, suggesting high translational activity at the beginning of somatic embryogenesis. Proteins related to mitochondrial metabolism accumulated to a high degree at the early developmental stages and then decreased with increasing development, and they contributed to cell homeostasis in early somatic embryos. A progressive increase in the accumulation of vicilin, late embryogenesis abundant proteins and chloroplastic proteins that lead to somatic embryo maturation was also observed. The differential accumulation of acetylornithine deacetylase and S-adenosylmethionine synthase 2 proteins was correlated with increases in putrescine and spermidine contents, which suggests that both polyamines should be tested to determine whether they increase the conversion rates of globular- to cotyledonary-staged somatic embryos. Taken together, the results showed that somatic embryo development in C. papaya is regulated by the differential accumulation of proteins, with ribosomal and mitochondrial proteins more abundant during the early somatic embryo stages and seed maturation proteins more abundant during the late stages.
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11
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Manage KI, Rogers AK, Wallis DC, Uebel CJ, Anderson DC, Nguyen DAH, Arca K, Brown KC, Cordeiro Rodrigues RJ, de Albuquerque BF, Ketting RF, Montgomery TA, Phillips CM. A tudor domain protein, SIMR-1, promotes siRNA production at piRNA-targeted mRNAs in C. elegans. eLife 2020; 9:56731. [PMID: 32338603 PMCID: PMC7255803 DOI: 10.7554/elife.56731] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 04/24/2020] [Indexed: 02/06/2023] Open
Abstract
piRNAs play a critical role in the regulation of transposons and other germline genes. In Caenorhabditis elegans, regulation of piRNA target genes is mediated by the mutator complex, which synthesizes high levels of siRNAs through the activity of an RNA-dependent RNA polymerase. However, the steps between mRNA recognition by the piRNA pathway and siRNA amplification by the mutator complex are unknown. Here, we identify the Tudor domain protein, SIMR-1, as acting downstream of piRNA production and upstream of mutator complex-dependent siRNA biogenesis. Interestingly, SIMR-1 also localizes to distinct subcellular foci adjacent to P granules and Mutator foci, two phase-separated condensates that are the sites of piRNA-dependent mRNA recognition and mutator complex-dependent siRNA amplification, respectively. Thus, our data suggests a role for multiple perinuclear condensates in organizing the piRNA pathway and promoting mRNA regulation by the mutator complex. In the biological world, a process known as RNA interference helps cells to switch genes on and off and to defend themselves against harmful genetic material. This mechanism works by deactivating RNA sequences, the molecular templates cells can use to create proteins. Overall, RNA interference relies on the cell creating small RNA molecules that can target and inhibit the harmful RNA sequences that need to be silenced. More precisely, in round worms such as Caenorhabditis elegans, RNA interference happens in two steps. First, primary small RNAs identify the target sequences, which are then combatted by newly synthetised, secondary small RNAs. A number of proteins are also involved in both steps of the process. RNA interference is particularly important to preserve fertility, guarding sex cells against ‘rogue’ segments of genetic information that could be passed on to the next generation. In future sex cells, the proteins involved in RNA interference cluster together, forming a structure called a germ granule. Yet, little is known about the roles and identity of these proteins. To fill this knowledge gap, Manage et al. focused on the second stage of the RNA interference pathway in the germ granules of C. elegans, examining the molecules that physically interact with a key protein. This work revealed a new protein called SIMR-1. Looking into the role of SIMR-1 showed that the protein is required to amplify secondary small RNAs, but not to identify target sequences. However, it only promotes the creation of secondary small RNAs if a specific subtype of primary small RNAs have recognized the target RNAs for silencing. Further experiments also showed that within the germ granule, SIMR-1 is present in a separate substructure different from any compartment previously identified. This suggests that each substep of the RNA interference process takes place at a different location in the granule. In both C. elegans and humans, disruptions in the RNA interference pathway can lead to conditions such as cancer or infertility. Dissecting the roles of the proteins involved in this process in roundworms may help to better grasp how this process unfolds in mammals, and how it could be corrected in the case of disease.
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Affiliation(s)
- Kevin I Manage
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Alicia K Rogers
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Dylan C Wallis
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Celja J Uebel
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Dorian C Anderson
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Dieu An H Nguyen
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Katerina Arca
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Kristen C Brown
- Department of Biology, Colorado State University, Fort Collins, United States.,Cell and Molecular Biology Program, Colorado State University, Fort Collins, United States
| | - Ricardo J Cordeiro Rodrigues
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Mainz, Germany.,International PhD Programme on Gene Regulation, Epigenetics, and Genome Stability, Mainz, Germany
| | | | - René F Ketting
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Mainz, Germany
| | - Taiowa A Montgomery
- Department of Biology, Colorado State University, Fort Collins, United States
| | - Carolyn Marie Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
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12
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Fabrizio JJ, Rollins J, Bazinet CW, Wegener S, Koziy I, Daniel R, Lombardo V, Pryce D, Bharrat K, Innabi E, Villanobos M, Mendoza G, Ferrara E, Rodway S, Vicioso M, Siracusa V, Dailey E, Pronovost J, Innabi S, Patel V, DeSouza N, Quaranto D, Niknejad A. Tubulin-binding cofactor E-like (TBCEL), the protein product of the mulet gene, is required in the germline for the regulation of inter-flagellar microtubule dynamics during spermatid individualization. Biol Open 2020; 9:bio049080. [PMID: 32033965 PMCID: PMC7055396 DOI: 10.1242/bio.049080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/22/2020] [Indexed: 11/14/2022] Open
Abstract
Individual sperm cells are resolved from a syncytium during late step of spermiogenesis known as individualization, which is accomplished by an Individualization Complex (IC) composed of 64 investment cones. mulet encodes Tubulin-binding cofactor E-like (TBCEL), suggesting a role for microtubule dynamics in individualization. Indeed, a population of ∼100 cytoplasmic microtubules fails to disappear in mulet mutant testes during spermatogenesis. This persistence, detected using epi-fluorescence and electron microscopy, suggests that removal of these microtubules by TBCEL is a prerequisite for individualization. Immunofluorescence reveals TBCEL expression in elongated spermatid cysts. In addition, testes from mulet mutant males were rescued to wild type using tubulin-Gal4 to drive TBCEL expression, indicating that the mutant phenotype is caused by the lack of TBCEL. Finally, RNAi driven by bam-GAL4 successfully phenocopied mulet, confirming that mulet is required in the germline for individualization. We propose a model in which the cytoplasmic microtubules serve as alternate tracks for investment cones in mulet mutant testes.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- James J Fabrizio
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Janet Rollins
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | | | - Stephanie Wegener
- Leibniz Institute for Neurobiology Magdeburg, Department Genetics of Learning and Memory, 39118 Magdeburg, Germany
| | - Iryna Koziy
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Rachel Daniel
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Vincent Lombardo
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Dwaine Pryce
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Kavita Bharrat
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Elissa Innabi
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Marielle Villanobos
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Gabriela Mendoza
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Elisa Ferrara
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Stephanie Rodway
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Matthew Vicioso
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Victoria Siracusa
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Erin Dailey
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Justin Pronovost
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Simon Innabi
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Vrutant Patel
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Nicole DeSouza
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Danielle Quaranto
- Division of Natural Sciences, College of Mt St Vincent, Bronx, NY 10471, USA
| | - Amir Niknejad
- Department of Mathematics, College of Mt St Vincent, Bronx, NY 10471, USA
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13
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Wang J, Zhang X, Deng S, Ma E, Zhang J, Xing S. Molecular characterization and RNA interference analysis of the DEAD-box gene family in Locusta migratoria. Gene 2020; 728:144297. [DOI: 10.1016/j.gene.2019.144297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 12/13/2019] [Accepted: 12/13/2019] [Indexed: 12/17/2022]
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14
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Marnik EA, Fuqua JH, Sharp CS, Rochester JD, Xu EL, Holbrook SE, Updike DL. Germline Maintenance Through the Multifaceted Activities of GLH/Vasa in Caenorhabditis elegans P Granules. Genetics 2019; 213:923-939. [PMID: 31506335 PMCID: PMC6827368 DOI: 10.1534/genetics.119.302670] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/03/2019] [Indexed: 02/07/2023] Open
Abstract
Vasa homologs are ATP-dependent DEAD-box helicases, multipotency factors, and critical components that specify and protect the germline. They regulate translation, amplify piwi-interacting RNAs (piRNAs), and act as RNA solvents; however, the limited availability of mutagenesis-derived alleles and their wide range of phenotypes have complicated their analysis. Now, with clustered regularly interspaced short palindromic repeats (CRISPR/Cas9), these limitations can be mitigated to determine why protein domains have been lost or retained throughout evolution. Here, we define the functional motifs of GLH-1/Vasa in Caenorhabditis elegans using 28 endogenous, mutant alleles. We show that GLH-1's helicase activity is required to retain its association with P granules. GLH-1 remains in P granules when changes are made outside of the helicase and flanking domains, but fertility is still compromised. Removal of the glycine-rich repeats from GLH proteins progressively diminishes P-granule wetting-like interactions at the nuclear periphery. Mass spectrometry of GLH-1-associated proteins implies conservation of a transient piRNA-amplifying complex, and reveals a novel affinity between GLH-1 and three structurally conserved PCI (26S Proteasome Lid, COP9, and eIF3) complexes or "zomes," along with a reciprocal aversion for assembled ribosomes and the 26S proteasome. These results suggest that P granules compartmentalize the cytoplasm to exclude large protein assemblies, effectively shielding associated transcripts from translation and associated proteins from turnover. Within germ granules, Vasa homologs may act as solvents, ensuring mRNA accessibility by small RNA surveillance and amplification pathways, and facilitating mRNA export through germ granules to initiate translation.
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Affiliation(s)
| | - J Heath Fuqua
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine 04672
- The College of the Atlantic, Bar Harbor, Maine 04609
| | - Catherine S Sharp
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine 04672
| | - Jesse D Rochester
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine 04672
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, Maine 04469
| | - Emily L Xu
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine 04672
- The College of William and Mary, Williamsburg, Virginia 23185
| | - Sarah E Holbrook
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine 04672
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, Maine 04469
- The Jackson Laboratory, Bar Harbor, Maine 04609
| | - Dustin L Updike
- The Mount Desert Island Biological Laboratory, Bar Harbor, Maine 04672
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15
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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.
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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;
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16
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A secondary structure within a human piRNA modulates its functionality. Biochimie 2018; 157:72-80. [PMID: 30414834 DOI: 10.1016/j.biochi.2018.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 11/04/2018] [Indexed: 01/30/2023]
Abstract
The piwi-interacting RNAs (piRNAs) are small non-coding RNAs, mostly 24-32 nucleotides in length. The piRNAs are not known to have any conserved secondary structure or sequence motifs. Using bioinformatics analysis, we discovered the presence of putative G-quadruplex (GQ) forming sequences in human piRNAs. We studied human piR-48164/piR-GQ containing a potential GQ forming sequence and using biochemical and biophysical techniques confirmed its ability to form a GQ. Using EMSA, we discovered that the formation of GQ structure led to inhibition of the piRNA binding to the HIWI-PAZ domain as well as the complementary base pairing to a target RNA. The inability of the piR-GQ to interact with the PIWI protein might be detrimental to the function of the piRNA. To investigate if the formation of a GQ structure in piRNA prevents its target gene silencing in vivo, we used a reporter assay. The piR-GQ failed to inhibit the reporter gene expression while a mutated version that lacked the ability to form GQ inhibited reporter gene expression indicating that the presence of GQ in piRNA is detrimental to its function. These studies unraveled the dependence of a piRNA's functionality on an RNA secondary structure and added a new layer of regulation to their function.
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17
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Reich DP, Tyc KM, Bass BL. C. elegans ADARs antagonize silencing of cellular dsRNAs by the antiviral RNAi pathway. Genes Dev 2018; 32:271-282. [PMID: 29483152 PMCID: PMC5859968 DOI: 10.1101/gad.310672.117] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 01/26/2018] [Indexed: 12/03/2022]
Abstract
In this study, Reich et al. researched the functions of Caenorhabditis elegans adenosine deaminases that act on RNA (ADARs), which catalyze A-to-I RNA editing in dsRNA. Using dsRNA immunoprecipitation (dsRIP) and RNA-seq, they identified 1523 regions of clustered A-to-I editing, termed editing-enriched regions (EERs), in four stages of C. elegans development, often with highest expression in embryos. Cellular dsRNAs are edited by adenosine deaminases that act on RNA (ADARs). While editing can alter mRNA-coding potential, most editing occurs in noncoding sequences, the function of which is poorly understood. Using dsRNA immunoprecipitation (dsRIP) and RNA sequencing (RNA-seq), we identified 1523 regions of clustered A-to-I editing, termed editing-enriched regions (EERs), in four stages of Caenorhabditis elegans development, often with highest expression in embryos. Analyses of small RNA-seq data revealed 22- to 23-nucleotide (nt) siRNAs, reminiscent of viral siRNAs, that mapped to EERs and were abundant in adr-1;adr-2 mutant animals. Consistent with roles for these siRNAs in silencing, EER-associated genes (EAGs) were down-regulated in adr-1;adr-2 embryos, and this was dependent on associated EERs and the RNAi factor RDE-4. We observed that ADARs genetically interact with the 26G endogenous siRNA (endo-siRNA) pathway, which likely competes for RNAi components; deletion of factors required for this pathway (rrf-3 or ergo-1) in adr-1;adr-2 mutant strains caused a synthetic phenotype that was rescued by deleting antiviral RNAi factors. Poly(A)+ RNA-seq revealed EAG down-regulation and antiviral gene induction in adr-1;adr-2;rrf-3 embryos, and these expression changes were dependent on rde-1 and rde-4. Our data suggest that ADARs restrict antiviral silencing of cellular dsRNAs.
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Affiliation(s)
- Daniel P Reich
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Katarzyna M Tyc
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Brenda L Bass
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, USA
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18
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Shiu PK, Hunter CP. Early Developmental Exposure to dsRNA Is Critical for Initiating Efficient Nuclear RNAi in C. elegans. Cell Rep 2017; 18:2969-2978. [PMID: 28329688 DOI: 10.1016/j.celrep.2017.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 12/21/2016] [Accepted: 02/28/2017] [Indexed: 11/17/2022] Open
Abstract
RNAi has enabled researchers to study the function of many genes. However, it is not understood why some RNAi experiments succeed while others do not. Here, we show in C. elegans that pharyngeal muscle is resistant to RNAi when initially exposed to double-stranded RNA (dsRNA) by feeding but sensitive to RNAi in the next generation. Investigating this observation, we find that pharyngeal muscle cells as well as vulval muscle cells require nuclear rather than cytoplasmic RNAi. Further, we find in these cell types that nuclear RNAi silencing is most efficiently triggered during early development, defining a critical period for initiating nuclear RNAi. Finally, using heat-shock-induced dsRNA expression, we show that synMuv B class mutants act in part to extend this critical window. The synMuv-B-dependent early-development-associated critical period for initiating nuclear RNAi suggests that mechanisms that restrict developmental plasticity may also restrict the initiation of nuclear RNAi.
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Affiliation(s)
- Philip K Shiu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Craig P Hunter
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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19
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The RNAi Inheritance Machinery of Caenorhabditis elegans. Genetics 2017; 206:1403-1416. [PMID: 28533440 DOI: 10.1534/genetics.116.198812] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 04/17/2017] [Indexed: 12/30/2022] Open
Abstract
Gene silencing mediated by dsRNA (RNAi) can persist for multiple generations in Caenorhabditis elegans (termed RNAi inheritance). Here we describe the results of a forward genetic screen in C. elegans that has identified six factors required for RNAi inheritance: GLH-1/VASA, PUP-1/CDE-1, MORC-1, SET-32, and two novel nematode-specific factors that we term here (heritable RNAi defective) HRDE-2 and HRDE-4 The new RNAi inheritance factors exhibit mortal germline (Mrt) phenotypes, which we show is likely caused by epigenetic deregulation in germ cells. We also show that HRDE-2 contributes to RNAi inheritance by facilitating the binding of small RNAs to the inheritance Argonaute (Ago) HRDE-1 Together, our results identify additional components of the RNAi inheritance machinery whose conservation provides insights into the molecular mechanism of RNAi inheritance, further our understanding of how the RNAi inheritance machinery promotes germline immortality, and show that HRDE-2 couples the inheritance Ago HRDE-1 with the small RNAs it needs to direct RNAi inheritance and germline immortality.
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20
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Zhou X, Feng X, Mao H, Li M, Xu F, Hu K, Guang S. RdRP-synthesized antisense ribosomal siRNAs silence pre-rRNA via the nuclear RNAi pathway. Nat Struct Mol Biol 2017; 24:258-269. [DOI: 10.1038/nsmb.3376] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 01/10/2017] [Indexed: 12/27/2022]
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21
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Chen X, Li M, Feng X, Guang S. Targeted Chromosomal Translocations and Essential Gene Knockout Using CRISPR/Cas9 Technology in Caenorhabditis elegans. Genetics 2015; 201:1295-306. [PMID: 26482793 PMCID: PMC4676527 DOI: 10.1534/genetics.115.181883] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/09/2015] [Indexed: 11/18/2022] Open
Abstract
Many genes play essential roles in development and fertility; their disruption leads to growth arrest or sterility. Genetic balancers have been widely used to study essential genes in many organisms. However, it is technically challenging and laborious to generate and maintain the loss-of-function mutations of essential genes. The CRISPR/Cas9 technology has been successfully applied for gene editing and chromosome engineering. Here, we have developed a method to induce chromosomal translocations and produce genetic balancers using the CRISPR/Cas9 technology and have applied this approach to edit essential genes in Caenorhabditis elegans. The co-injection of dual small guide RNA targeting genes on different chromosomes resulted in reciprocal translocation between nonhomologous chromosomes. These animals with chromosomal translocations were subsequently crossed with animals that contain normal sets of chromosomes. The F1 progeny were subjected to a second round of Cas9-mediated gene editing. Through this method, we successfully produced nematode strains with specified chromosomal translocations and generated a number of loss-of-function alleles of two essential genes (csr-1 and mes-6). Therefore, our method provides an easy and efficient approach to generate and maintain loss-of-function alleles of essential genes with detailed genetic background information.
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Affiliation(s)
- Xiangyang Chen
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China
| | - Mu Li
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China
| | - Xuezhu Feng
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China
| | - Shouhong Guang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China
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22
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23
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Jose AM. Movement of regulatory RNA between animal cells. Genesis 2015; 53:395-416. [PMID: 26138457 PMCID: PMC4915348 DOI: 10.1002/dvg.22871] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 06/28/2015] [Accepted: 06/29/2015] [Indexed: 12/12/2022]
Abstract
Recent studies suggest that RNA can move from one cell to another and regulate genes through specific base-pairing. Mechanisms that modify or select RNA for secretion from a cell are unclear. Secreted RNA can be stable enough to be detected in the extracellular environment and can enter the cytosol of distant cells to regulate genes. Mechanisms that import RNA into the cytosol of an animal cell can enable uptake of RNA from many sources including other organisms. This role of RNA is akin to that of steroid hormones, which cross cell membranes to regulate genes. The potential diagnostic use of RNA in human extracellular fluids has ignited interest in understanding mechanisms that enable the movement of RNA between animal cells. Genetic model systems will be essential to gain more confidence in proposed mechanisms of RNA transport and to connect an extracellular RNA with a specific biological function. Studies in the worm C. elegans and in other animals have begun to reveal parts of this novel mechanism of cell-to-cell communication. Here, I summarize the current state of this nascent field, highlight the many unknowns, and suggest future directions.
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Affiliation(s)
- Antony M Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland
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24
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Tsai HY, Chen CCG, Conte D, Moresco JJ, Chaves DA, Mitani S, Yates JR, Tsai MD, Mello CC. A ribonuclease coordinates siRNA amplification and mRNA cleavage during RNAi. Cell 2015; 160:407-19. [PMID: 25635455 DOI: 10.1016/j.cell.2015.01.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 10/21/2014] [Accepted: 12/23/2014] [Indexed: 11/29/2022]
Abstract
Effective silencing by RNA-interference (RNAi) depends on mechanisms that amplify and propagate the silencing signal. In some organisms, small-interfering RNAs (siRNAs) are amplified from target mRNAs by RNA-dependent RNA polymerase (RdRP). Both RdRP recruitment and mRNA silencing require Argonaute proteins, which are generally thought to degrade RNAi targets by directly cleaving them. However, in C. elegans, the enzymatic activity of the primary Argonaute, RDE-1, is not required for silencing activity. We show that RDE-1 can instead recruit an endoribonuclease, RDE-8, to target RNA. RDE-8 can cleave RNA in vitro and is needed for the production of 3' uridylated fragments of target mRNA in vivo. We also find that RDE-8 promotes RdRP activity, thereby ensuring amplification of siRNAs. Together, our findings suggest a model in which RDE-8 cleaves target mRNAs to mediate silencing, while generating 3' uridylated mRNA fragments to serve as templates for the RdRP-directed amplification of the silencing signal.
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Affiliation(s)
- Hsin-Yue Tsai
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Chun-Chieh G Chen
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Darryl Conte
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - James J Moresco
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel A Chaves
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Shohei Mitani
- CREST, Japan Science and Technology Agency and Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo 162-8666, Japan
| | - John R Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Craig C Mello
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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25
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Dual sgRNA-directed gene knockout using CRISPR/Cas9 technology in Caenorhabditis elegans. Sci Rep 2014; 4:7581. [PMID: 25531445 PMCID: PMC4273605 DOI: 10.1038/srep07581] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/03/2014] [Indexed: 01/06/2023] Open
Abstract
The CRISPR RNA-guided Cas9 nuclease gene-targeting system has been successfully used for genome editing in a variety of organisms. Here, we report the use of dual sgRNA-guided Cas9 nuclease to generate knockout mutants of protein coding genes, noncoding genes, and repetitive sequences in C. elegans. Co-injection of C. elegans with dual sgRNAs results in the removal of the interval between two sgRNAs and the loss-of-function phenotype of targeted genes. We sought to determine how large an interval can be eliminated and found that at least a 24 kb chromosome segment can be deleted using this dual sgRNA/Cas9 strategy. The deletion of large chromosome segments facilitates mutant screening by PCR and agarose electrophoresis. Thus, the use of the CRISPR/Cas9 system in combination with dual sgRNAs provides a powerful platform with which to easily generate gene knockout mutants in C. elegans. Our data also suggest that encoding multiple sgRNA sequences into a single CRISPR array to simultaneously edit several sites within the genome may cause the off-target deletion of chromosome sequences.
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26
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