1
|
Uebel CJ, Rajeev S, Phillips CM. Caenorhabditis elegans germ granules are present in distinct configurations and assemble in a hierarchical manner. Development 2023; 150:dev202284. [PMID: 38009921 PMCID: PMC10753583 DOI: 10.1242/dev.202284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023]
Abstract
RNA silencing pathways are complex, highly conserved, and perform crucial regulatory roles. In Caenorhabditis elegans germlines, RNA surveillance occurs through a series of perinuclear germ granule compartments - P granules, Z granules, SIMR foci, and Mutator foci - multiple of which form via phase separation. Although the functions of individual germ granule proteins have been extensively studied, the relationships between germ granule compartments (collectively, 'nuage') are less understood. We find that key germ granule proteins assemble into separate but adjacent condensates, and that boundaries between germ granule compartments re-establish after perturbation. We discover a toroidal P granule morphology, which encircles the other germ granule compartments in a consistent exterior-to-interior spatial organization, providing broad implications for the trajectory of an RNA as it exits the nucleus. Moreover, we quantify the stoichiometric relationships between germ granule compartments and RNA to reveal discrete populations of nuage that assemble in a hierarchical manner and differentially associate with RNAi-targeted transcripts, possibly suggesting functional differences between nuage configurations. Our work creates a more accurate model of C. elegans nuage and informs the conceptualization of RNA silencing through the germ granule compartments.
Collapse
Affiliation(s)
- Celja J. Uebel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Sanjana Rajeev
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Carolyn M. Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| |
Collapse
|
2
|
Redl S, de Jesus Domingues AM, Caspani E, Möckel S, Salvenmoser W, Mendez-Lago M, Ketting RF. Extensive nuclear gyration and pervasive non-genic transcription during primordial germ cell development in zebrafish. Development 2021; 148:dev.193060. [PMID: 33298460 PMCID: PMC7847270 DOI: 10.1242/dev.193060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 12/02/2021] [Indexed: 12/02/2022]
Abstract
Primordial germ cells (PGCs) are the precursors of germ cells, which migrate to the genital ridge during early development. Relatively little is known about PGCs after their migration. We studied this post-migratory stage using microscopy and sequencing techniques, and found that many PGC-specific genes, including genes known to induce PGC fate in the mouse, are only activated several days after migration. At this same time point, PGC nuclei become extremely gyrated, displaying general broad opening of chromatin and high levels of intergenic transcription. This is accompanied by changes in nuage morphology, expression of large loci (PGC-expressed non-coding RNA loci, PERLs) that are enriched for retro-transposons and piRNAs, and a rise in piRNA biogenesis signatures. Interestingly, no nuclear Piwi protein could be detected at any time point, indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post-migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation. Highlighted Article: In contrast to common thinking, zebrafish primordial germ cells do not rest after arrival at the genital ridge, but display many morphological changes accompanied by pervasive intergenic transcription and piRNA activation.
Collapse
Affiliation(s)
- Stefan Redl
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
| | | | - Edoardo Caspani
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany.,International PhD Programme on Gene Regulation, Epigenetics & Genome Stability, 55128 Mainz, Germany
| | - Stefanie Möckel
- Flow Cytometry Core Facility, Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - Willi Salvenmoser
- Institute of Zoology, Evolution and Developmental Biology, University of Innsbruck, Technikerstraβe 25, 6020 Innsbruck, Austria
| | - Maria Mendez-Lago
- Genomics Core Facility, Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany
| | - René F Ketting
- Biology of Non-coding RNA Group, Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany .,Institute of Developmental Biology and Neurobiology, Johannes Gutenberg University, 55099 Mainz, Germany
| |
Collapse
|
3
|
Castillejo-López C, Cai X, Fahmy K, Baumgartner S. Drosophila exoribonuclease nibbler is a tumor suppressor, acts within the RNA i machinery and is not enriched in the nuage during early oogenesis. Hereditas 2017; 155:12. [PMID: 28974923 PMCID: PMC5622571 DOI: 10.1186/s41065-017-0047-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 09/11/2017] [Indexed: 01/07/2023] Open
Abstract
Background micro RNAs (miRNAs) are important regulators of many biological pathways. A plethora of steps are required to form, from a precursor, the mature miRNA that eventually acts on its target RNA to repress its expression or to inhibit translation. Recently, Drosophila nibbler (nbr) has been shown to be an important player in the maturation process of miRNA and piRNA. Nbr is an exoribonuclease which helps to shape the 3′ end of miRNAs by trimming the 3′ overhang to a final length. Results In contrast to previous reports on the localization of Nbr, we report that 1) Nbr is expressed only during a short time of oogenesis and appears ubiquitously localized within oocytes, and that 2) Nbr was is not enriched in the nuage where it was shown to be involved in piwi-mediated mechanisms. To date, there is little information available on the function of nbr for cellular and developmental processes. Due to the fact that nbr mutants are viable with minor deleterious effects, we used the GAL4/UAS over-expression system to define novel functions of nbr. We disclose hitherto unknown functions of nbr 1) as a tumor suppressor and 2) as a suppressor of RNAi. Finally, we confirm that nbr is a suppressor of transposon activity. Conclusions Our data suggest that nbr exerts much more widespread functions than previously reported from trimming 3′ ends of miRNAs only.
Collapse
Affiliation(s)
- Casimiro Castillejo-López
- Department of Experimental Medical Science, Lund University, BMC D10, 22184 Lund, Sweden.,Present address: Department of Molecular Epidemiology, Uppsala University, 75185 Uppsala, Sweden
| | - Xiaoli Cai
- Department of Experimental Medical Science, Lund University, BMC D10, 22184 Lund, Sweden
| | - Khalid Fahmy
- Department of Experimental Medical Science, Lund University, BMC D10, 22184 Lund, Sweden.,Present address: Department of Genetics, Ain Shams University, Cairo, Egypt
| | - Stefan Baumgartner
- Department of Experimental Medical Science, Lund University, BMC D10, 22184 Lund, Sweden
| |
Collapse
|
4
|
Ryazansky SS, Kotov AA, Kibanov MV, Akulenko NV, Korbut AP, Lavrov SA, Gvozdev VA, Olenina LV. RNA helicase Spn-E is required to maintain Aub and AGO3 protein levels for piRNA silencing in the germline of Drosophila. Eur J Cell Biol 2016; 95:311-22. [PMID: 27320195 DOI: 10.1016/j.ejcb.2016.06.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 05/14/2016] [Accepted: 06/03/2016] [Indexed: 10/21/2022] Open
Abstract
Germline-specific RNA helicase Spindle-E (Spn-E) is known to be essential for piRNA silencing in Drosophila that takes place mainly in the perinuclear nuage granules. Loss-of-function spn-E mutations lead to tandem Stellate genes derepression in the testes and retrotransposon mobilization in the ovaries. However, Spn-E functions in the piRNA pathway are still obscure. Analysis of total library of short RNAs from the testes of spn-E heterozygous flies revealed the presence of abundant piRNA ping-pong pairs originating from Su(Ste) transcripts. The abundance of these ping-pong pairs were sharply reduced in the library from the testes of spn-E mutants. Thus we found that ping-pong mechanism contributed to Su(Ste) piRNA generation in the testes. The lack of Spn-E caused a significant drop of protein levels of key ping-pong participants, Aubergine (Aub) and AGO3 proteins of PIWI subfamily, in the germline of both males and females, but did not disrupt of their assembly in nuage granules. We found that observed decline of the protein expression was not caused by suppression of aub and ago3 transcription as well as total transcription, indicating possible contribution of Spn-E to post-transcriptional regulation.
Collapse
|
5
|
Abstract
Germ granules are the hallmark of all germ cells. These membrane-less, electron-dense structures were first observed over 100 years ago. Today, their role in regulating and processing transcripts critical for the establishment, maintenance, and protection of germ cells is well established, and pathways outlining the biochemical mechanisms and physical properties associated with their biogenesis are emerging.
Collapse
Affiliation(s)
- Ruth Lehmann
- Howard Hughes Medical Institute (HHMI), Department of Cell Biology, Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, USA.
| |
Collapse
|
6
|
Abstract
Transposable elements (TEs) have the capacity to replicate and insert into new genomic locations. This contributs significantly to evolution of genomes, but can also result in DNA breaks and illegitimate recombination, and therefore poses a significant threat to genomic integrity. Excess damage to the germ cell genome results in sterility. A specific RNA silencing pathway, termed the piRNA pathway operates in germ cells of animals to control TE activity. At the core of the piRNA pathway is a ribonucleoprotein complex consisting of a small RNA, called piRNA, and a protein from the PIWI subfamily of Argonaute nucleases. The piRNA pathway relies on the specificity provided by the piRNA sequence to recognize complementary TE targets, while effector functions are provided by the PIWI protein. PIWI-piRNA complexes silence TEs both at the transcriptional level - by attracting repressive chromatin modifications to genomic targets - and at the posttranscriptional level - by cleaving TE transcripts in the cytoplasm. Impairment of the piRNA pathway leads to overexpression of TEs, significantly compromised genome structure and, invariably, germ cell death and sterility.The piRNA pathway is best understood in the fruit fly, Drosophila melanogaster, and in mouse. This Chapter gives an overview of current knowledge on piRNA biogenesis, and mechanistic details of both transcriptional and posttranscriptional TE silencing by the piRNA pathway. It further focuses on the importance of post-translational modifications and subcellular localization of the piRNA machinery. Finally, it provides a brief description of analogous pathways in other systems.
Collapse
Affiliation(s)
- Katalin Fejes Tóth
- Division of Biology and Bioengineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA.
| | - Dubravka Pezic
- Division of Biology and Bioengineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA
| | - Evelyn Stuwe
- Division of Biology and Bioengineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA
| | - Alexandre Webster
- Division of Biology and Bioengineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA
| |
Collapse
|
7
|
Lim RS, Anand A, Nishimiya-Fujisawa C, Kobayashi S, Kai T. Analysis of Hydra PIWI proteins and piRNAs uncover early evolutionary origins of the piRNA pathway. Dev Biol 2014; 386:237-51. [PMID: 24355748 DOI: 10.1016/j.ydbio.2013.12.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 12/03/2013] [Accepted: 12/05/2013] [Indexed: 11/24/2022]
Abstract
To preserve genome integrity, an evolutionarily conserved small RNA-based silencing mechanism involving PIWI proteins and PIWI-interacting RNAs (piRNAs) represses potentially deleterious transposons in animals. Although there has been extensive research into PIWI proteins in bilaterians, these proteins remain to be examined in ancient phyla. Here, we investigated the PIWI proteins Hywi and Hyli in the cnidarian Hydra, and found that both PIWI proteins are enriched in multipotent stem cells, germline stem cells, and in the female germline. Hywi and Hyli localize to the nuage, a perinuclear organelle that has been implicated in piRNA-mediated transposon silencing, together with other conserved nuage and piRNA pathway components. Our findings provide the first report of nuage protein localization patterns in a non-bilaterian. Hydra PIWI proteins possess symmetrical dimethylarginines: modified residues that are known to aid in PIWI protein localization to the nuage and proper piRNA loading. piRNA profiling suggests that transposons are the major targets of the piRNA pathway in Hydra. Our data suggest that piRNA biogenesis through the ping-pong amplification cycle occurs in Hydra and that Hywi and Hyli are likely to preferentially bind primary and secondary piRNAs, respectively. Presumptive piRNA clusters are unidirectionally transcribed and primarily give rise to piRNAs that are antisense to transposons. These results indicate that various conserved features of PIWI proteins, the piRNA pathway, and their associations with the nuage were likely established before the evolution of bilaterians.
Collapse
|
8
|
Lim AK, Lorthongpanich C, Chew TG, Tan CWG, Shue YT, Balu S, Gounko N, Kuramochi-Miyagawa S, Matzuk MM, Chuma S, Messerschmidt DM, Solter D, Knowles BB. The nuage mediates retrotransposon silencing in mouse primordial ovarian follicles. Development 2013; 140:3819-25. [PMID: 23924633 DOI: 10.1242/dev.099184] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mobilization of endogenous retrotransposons can destabilize the genome, an imminent danger during epigenetic reprogramming of cells in the germline. The P-element-induced wimpy testis (PIWI)-interacting RNA (piRNA) pathway is known to silence retrotransposons in the mouse testes. Several piRNA pathway components localize to the unique, germline structure known as the nuage. In this study, we surveyed mouse ovaries and found, for the first time, transient appearance of nuage-like structures in oocytes of primordial follicles. Mouse vasa homolog (MVH), Piwi-like 2 (PIWIL2/MILI) and tudor domain-containing 9 (TDRD9) are present in these structures, whereas aggregates of germ cell protein with ankyrin repeats, sterile alpha motif and leucine zipper (GASZ) localize separately in the cytoplasm. Retrotransposons are silenced in primordial ovarian follicles, and de-repressed upon reduction of piRNA expression in Mvh, Mili or Gasz mutants. However, these null-mutant females, unlike their male counterparts, are fertile, uncoupling retrotransposon activation from sterility.
Collapse
Affiliation(s)
- Ai Khim Lim
- Institute of Medical Biology, A*STAR, 8A Biomedical Grove, Immunos, 138648 Singapore.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|