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Jones M, Norman M, Tiet AM, Lee J, Lee MH. C. elegans Germline as Three Distinct Tumor Models. BIOLOGY 2024; 13:425. [PMID: 38927305 PMCID: PMC11200432 DOI: 10.3390/biology13060425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/04/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
Tumor cells display abnormal growth and division, avoiding the natural process of cell death. These cells can be benign (non-cancerous growth) or malignant (cancerous growth). Over the past few decades, numerous in vitro or in vivo tumor models have been employed to understand the molecular mechanisms associated with tumorigenesis in diverse regards. However, our comprehension of how non-tumor cells transform into tumor cells at molecular and cellular levels remains incomplete. The nematode C. elegans has emerged as an excellent model organism for exploring various phenomena, including tumorigenesis. Although C. elegans does not naturally develop cancer, it serves as a valuable platform for identifying oncogenes and the underlying mechanisms within a live organism. In this review, we describe three distinct germline tumor models in C. elegans, highlighting their associated mechanisms and related regulators: (1) ectopic proliferation due to aberrant activation of GLP-1/Notch signaling, (2) meiotic entry failure resulting from the loss of GLD-1/STAR RNA-binding protein, (3) spermatogenic dedifferentiation caused by the loss of PUF-8/PUF RNA-binding protein. Each model requires the mutations of specific genes (glp-1, gld-1, and puf-8) and operates through distinct molecular mechanisms. Despite these differences in the origins of tumorigenesis, the internal regulatory networks within each tumor model display shared features. Given the conservation of many of the regulators implicated in C. elegans tumorigenesis, it is proposed that these unique models hold significant potential for enhancing our comprehension of the broader control mechanisms governing tumorigenesis.
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Affiliation(s)
- Mariah Jones
- Division of Hematology/Oncology, Department of Internal Medicine, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA; (M.J.); (M.N.)
| | - Mina Norman
- Division of Hematology/Oncology, Department of Internal Medicine, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA; (M.J.); (M.N.)
| | - Alex Minh Tiet
- Neuroscience Program, East Carolina University, Greenville, NC 27858, USA;
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Jiwoo Lee
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Myon Hee Lee
- Division of Hematology/Oncology, Department of Internal Medicine, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA; (M.J.); (M.N.)
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
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Zhang P, Xue B, Yang H, Zhang L. Transcriptome Responses to Different Salinity Conditions in Litoditis marina, Revealed by Long-Read Sequencing. Genes (Basel) 2024; 15:317. [PMID: 38540376 PMCID: PMC10970011 DOI: 10.3390/genes15030317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 06/14/2024] Open
Abstract
The marine nematode Litoditis marina is widely distributed in intertidal zones around the globe, yet the mechanisms underlying its broad adaptation to salinity remain elusive. In this study, we applied ONT long-read sequencing technology to unravel the transcriptome responses to different salinity conditions in L. marina. Through ONT sequencing under 3‱, 30‱ and 60‱ salinity environments, we obtained 131.78 G clean data and 26,647 non-redundant long-read transcripts, including 6464 novel transcripts. The DEGs obtained from the current ONT lrRNA-seq were highly correlated with those identified in our previously reported Illumina short-read RNA sequencing data. When we compared the 30‱ to the 3‱ salinity condition, we found that GO terms such as oxidoreductase activity, cation transmembrane transport and ion transmembrane transport were shared between the ONT lrRNA-seq and Illumina data. Similarly, GO terms including extracellular space, structural constituents of cuticle, substrate-specific channel activity, ion transport and substrate-specific transmembrane transporter activity were shared between the ONT and Illumina data under 60‱ compared to 30‱ salinity. In addition, we found that 79 genes significantly increased, while 119 genes significantly decreased, as the salinity increased. Furthermore, through the GO enrichment analysis of 214 genes containing DAS, in 30‱ compared to 3‱ salinity, we found that GO terms such as cellular component assembly and coenzyme biosynthetic process were enriched. Additionally, we observed that GO terms such as cellular component assembly and coenzyme biosynthetic process were also enriched in 60‱ compared to 30‱ salinity. Moreover, we found that 86, 125, and 81 genes that contained DAS were also DEGs, in comparisons between 30‱ and 3‱, 60‱ and 30‱, and 60‱ and 3‱ salinity, respectively. In addition, we demonstrated the landscape of alternative polyadenylation in marine nematode under different salinity conditions This report provides several novel insights for the further study of the mechanisms by which euryhalinity formed and evolved, and it might also contribute to the investigation of salinity dynamics induced by global climate change.
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Affiliation(s)
- Pengchi Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (P.Z.); (B.X.); (H.Y.)
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Beining Xue
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (P.Z.); (B.X.); (H.Y.)
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanwen Yang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (P.Z.); (B.X.); (H.Y.)
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
| | - Liusuo Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (P.Z.); (B.X.); (H.Y.)
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
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Albarqi MMY, Ryder SP. The role of RNA-binding proteins in orchestrating germline development in Caenorhabditis elegans. Front Cell Dev Biol 2023; 10:1094295. [PMID: 36684428 PMCID: PMC9846511 DOI: 10.3389/fcell.2022.1094295] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/19/2022] [Indexed: 01/06/2023] Open
Abstract
RNA passed from parents to progeny controls several aspects of early development. The germline of the free-living nematode Caenorhabditis elegans contains many families of evolutionarily conserved RNA-binding proteins (RBPs) that target the untranslated regions of mRNA transcripts to regulate their translation and stability. In this review, we summarize what is known about the binding specificity of C. elegans germline RNA-binding proteins and the mechanisms of mRNA regulation that contribute to their function. We examine the emerging role of miRNAs in translational regulation of germline and embryo development. We also provide an overview of current technology that can be used to address the gaps in our understanding of RBP regulation of mRNAs. Finally, we present a hypothetical model wherein multiple 3'UTR-mediated regulatory processes contribute to pattern formation in the germline to ensure the proper and timely localization of germline proteins and thus a functional reproductive system.
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Salamon I, Rasin MR. Evolution of the Neocortex Through RNA-Binding Proteins and Post-transcriptional Regulation. Front Neurosci 2022; 15:803107. [PMID: 35082597 PMCID: PMC8784817 DOI: 10.3389/fnins.2021.803107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/16/2021] [Indexed: 12/24/2022] Open
Abstract
The human neocortex is undoubtedly considered a supreme accomplishment in mammalian evolution. It features a prenatally established six-layered structure which remains plastic to the myriad of changes throughout an organism’s lifetime. A fundamental feature of neocortical evolution and development is the abundance and diversity of the progenitor cell population and their neuronal and glial progeny. These evolutionary upgrades are partially enabled due to the progenitors’ higher proliferative capacity, compartmentalization of proliferative regions, and specification of neuronal temporal identities. The driving force of these processes may be explained by temporal molecular patterning, by which progenitors have intrinsic capacity to change their competence as neocortical neurogenesis proceeds. Thus, neurogenesis can be conceptualized along two timescales of progenitors’ capacity to (1) self-renew or differentiate into basal progenitors (BPs) or neurons or (2) specify their fate into distinct neuronal and glial subtypes which participate in the formation of six-layers. Neocortical development then proceeds through sequential phases of proliferation, differentiation, neuronal migration, and maturation. Temporal molecular patterning, therefore, relies on the precise regulation of spatiotemporal gene expression. An extensive transcriptional regulatory network is accompanied by post-transcriptional regulation that is frequently mediated by the regulatory interplay between RNA-binding proteins (RBPs). RBPs exhibit important roles in every step of mRNA life cycle in any system, from splicing, polyadenylation, editing, transport, stability, localization, to translation (protein synthesis). Here, we underscore the importance of RBP functions at multiple time-restricted steps of early neurogenesis, starting from the cell fate transition of transcriptionally primed cortical progenitors. A particular emphasis will be placed on RBPs with mostly conserved but also divergent evolutionary functions in neural progenitors across different species. RBPs, when considered in the context of the fascinating process of neocortical development, deserve to be main protagonists in the story of the evolution and development of the neocortex.
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Albarqi MMY, Ryder SP. The endogenous mex-3 3´UTR is required for germline repression and contributes to optimal fecundity in C. elegans. PLoS Genet 2021; 17:e1009775. [PMID: 34424904 PMCID: PMC8412283 DOI: 10.1371/journal.pgen.1009775] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 09/02/2021] [Accepted: 08/11/2021] [Indexed: 11/18/2022] Open
Abstract
RNA regulation is essential to successful reproduction. Messenger RNAs delivered from parent to progeny govern early embryonic development. RNA-binding proteins (RBPs) are the key effectors of this process, regulating the translation and stability of parental transcripts to control cell fate specification events prior to zygotic gene activation. The KH-domain RBP MEX-3 is conserved from nematode to human. It was first discovered in Caenorhabditis elegans, where it is essential for anterior cell fate and embryo viability. Here, we show that loss of the endogenous mex-3 3´UTR disrupts its germline expression pattern. An allelic series of 3´UTR deletion variants identify repressing regions of the UTR and demonstrate that repression is not precisely coupled to reproductive success. We also show that several RBPs regulate mex-3 mRNA through its 3´UTR to define its unique germline spatiotemporal expression pattern. Additionally, we find that both poly(A) tail length control and the translation initiation factor IFE-3 contribute to its expression pattern. Together, our results establish the importance of the mex-3 3´UTR to reproductive health and its expression in the germline. Our results suggest that additional mechanisms control MEX-3 function when 3´UTR regulation is compromised. In sexually reproducing organisms, germ cells undergo meiosis and differentiate to form oocytes or sperm. Coordination of this process requires a gene regulatory program that acts while the genome is undergoing chromatin condensation. As such, RNA regulatory pathways are an important contributor. The germline of the nematode Caenorhabditis elegans is a suitable model system to study germ cell differentiation. Several RNA-binding proteins (RBPs) coordinate each transition in the germline such as the transition from mitosis to meiosis. MEX-3 is a conserved RNA-binding protein found in most animals including humans. In C. elegans, MEX-3 displays a highly restricted pattern of expression. Here, we define the importance of the 3´UTR in regulating MEX-3 expression pattern in vivo and characterize the RNA-binding proteins involved in this regulation. Our results show that deleting various mex-3 3´UTR regions alter the pattern of expression in the germline in various ways. These mutations also reduced—but did not eliminate—reproductive capacity. Finally, we demonstrate that multiple post-transcriptional mechanisms control MEX-3 levels in different domains of the germline. Our data suggest that coordination of MEX-3 activity requires multiple layers of regulation to ensure reproductive robustness.
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Affiliation(s)
- Mennatallah M. Y. Albarqi
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Sean P. Ryder
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
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Flora P, Wong-Deyrup SW, Martin ET, Palumbo RJ, Nasrallah M, Oligney A, Blatt P, Patel D, Fuchs G, Rangan P. Sequential Regulation of Maternal mRNAs through a Conserved cis-Acting Element in Their 3' UTRs. Cell Rep 2019; 25:3828-3843.e9. [PMID: 30590052 PMCID: PMC6328254 DOI: 10.1016/j.celrep.2018.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 10/28/2018] [Accepted: 11/30/2018] [Indexed: 12/31/2022] Open
Abstract
Maternal mRNAs synthesized during oogenesis initiate the development of future generations. Some maternal mRNAs are either somatic or germline determinants and must be translationally repressed until embryogenesis. However, the translational repressors themselves are temporally regulated. We used polar granule component (pgc), a Drosophila maternal mRNA, to ask how maternal transcripts are repressed while the regulatory landscape is shifting. pgc, a germline determinant, is translationally regulated throughout oogenesis. We find that different conserved RNA-binding proteins bind a 10-nt sequence in the 3′ UTR of pgc mRNA to continuously repress translation at different stages of oogenesis. Pumilio binds to this sequence in undifferentiated and early-differentiating oocytes to block Pgc translation. After differentiation, Bruno levels increase, allowing Bruno to bind the same sequence and take over translational repression of pgc mRNA. We have identified a class of maternal mRNAs that are regulated similarly, including zelda, the activator of the zygotic genome. Flora et al. show that pgc, a germline determinant, is translationally regulated throughout oogenesis. Different conserved RBPs bind a 10-nt sequence in the 3′ UTR to continuously repress translation throughout oogenesis. This mode of regulation applies to a class of maternal mRNAs, including zelda, the activator of the zygotic genome.
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Affiliation(s)
- Pooja Flora
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Siu Wah Wong-Deyrup
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Elliot Todd Martin
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Ryan J Palumbo
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Mohamad Nasrallah
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Andrew Oligney
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Patrick Blatt
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Dhruv Patel
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Gabriele Fuchs
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Prashanth Rangan
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12222, USA.
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7
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Rothman J, Jarriault S. Developmental Plasticity and Cellular Reprogramming in Caenorhabditis elegans. Genetics 2019; 213:723-757. [PMID: 31685551 PMCID: PMC6827377 DOI: 10.1534/genetics.119.302333] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/25/2019] [Indexed: 12/28/2022] Open
Abstract
While Caenorhabditis elegans was originally regarded as a model for investigating determinate developmental programs, landmark studies have subsequently shown that the largely invariant pattern of development in the animal does not reflect irreversibility in rigidly fixed cell fates. Rather, cells at all stages of development, in both the soma and germline, have been shown to be capable of changing their fates through mutation or forced expression of fate-determining factors, as well as during the normal course of development. In this chapter, we review the basis for natural and induced cellular plasticity in C. elegans We describe the events that progressively restrict cellular differentiation during embryogenesis, starting with the multipotency-to-commitment transition (MCT) and subsequently through postembryonic development of the animal, and consider the range of molecular processes, including transcriptional and translational control systems, that contribute to cellular plasticity. These findings in the worm are discussed in the context of both classical and recent studies of cellular plasticity in vertebrate systems.
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Affiliation(s)
- Joel Rothman
- Department of MCD Biology and Neuroscience Research Institute, University of California, Santa Barbara, California 93111, and
| | - Sophie Jarriault
- IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire), Department of Development and Stem Cells, CNRS UMR7104, Inserm U1258, Université de Strasbourg, 67404 Illkirch CU Strasbourg, France
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Dynein Light Chain DLC-1 Facilitates the Function of the Germline Cell Fate Regulator GLD-1 in Caenorhabditis elegans. Genetics 2018; 211:665-681. [PMID: 30509955 DOI: 10.1534/genetics.118.301617] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 11/21/2018] [Indexed: 11/18/2022] Open
Abstract
Developmental transitions of germ cells are often regulated at the level of post-transcriptional control of gene expression. In the Caenorhabditis elegans germline, stem and progenitor cells exit the proliferative phase and enter meiotic differentiation to form gametes essential for fertility. The RNA binding protein GLD-1 is a cell fate regulator that promotes meiosis and germ cell differentiation during development by binding to and repressing translation of target messenger RNAs. Here, we discovered that some GLD-1 functions are promoted by binding to DLC-1, a small protein that functions as an allosteric regulator of multisubunit protein complexes. We found that DLC-1 is required to regulate a subset of GLD-1 target messenger RNAs and that DLC-1 binding GLD-1 prevents ectopic germ cell proliferation and facilitates gametogenesis in vivo Additionally, our results reveal a new requirement for GLD-1 in the events of oogenesis leading to ovulation. DLC-1 contributes to GLD-1 function independent of its role as a light chain component of the dynein motor. Instead, we propose that DLC-1 promotes assembly of GLD-1 with other binding partners, which facilitates formation of regulatory ribonucleoprotein complexes and may direct GLD-1 target messenger RNA selectivity.
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Multiple Mechanisms Inactivate the LIN-41 RNA-Binding Protein To Ensure a Robust Oocyte-to-Embryo Transition in Caenorhabditis elegans. Genetics 2018; 210:1011-1037. [PMID: 30206186 PMCID: PMC6218228 DOI: 10.1534/genetics.118.301421] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/10/2018] [Indexed: 12/23/2022] Open
Abstract
In the nematode Caenorhabditis elegans, the conserved LIN-41 RNA-binding protein is a translational repressor that coordinately controls oocyte growth and meiotic maturation. LIN-41 exerts these effects, at least in part, by preventing the premature activation of the cyclin-dependent kinase CDK-1. Here we investigate the mechanism by which LIN-41 is rapidly eliminated upon the onset of meiotic maturation. Elimination of LIN-41 requires the activities of CDK-1 and multiple SCF (Skp1, Cul1, and F-box protein)-type E3 ubiquitin ligase subunits, including the conserved substrate adaptor protein SEL-10/Fbw7/Cdc4, suggesting that LIN-41 is a target of ubiquitin-mediated protein degradation. Within the LIN-41 protein, two nonoverlapping regions, Deg-A and Deg-B, are individually necessary for LIN-41 degradation; both contain several potential phosphodegron sequences, and at least one of these sequences is required for LIN-41 degradation. Finally, Deg-A and Deg-B are sufficient, in combination, to mediate SEL-10-dependent degradation when transplanted into a different oocyte protein. Although LIN-41 is a potent inhibitor of protein translation and M phase entry, the failure to eliminate LIN-41 from early embryos does not result in the continued translational repression of LIN-41 oocyte messenger RNA targets. Based on these observations, we propose a model for the elimination of LIN-41 by the SEL-10 E3 ubiquitin ligase and suggest that LIN-41 is inactivated before it is degraded. Furthermore, we provide evidence that another RNA-binding protein, the GLD-1 tumor suppressor, is regulated similarly. Redundant mechanisms to extinguish translational repression by RNA-binding proteins may both control and provide robustness to irreversible developmental transitions, including meiotic maturation and the oocyte-to-embryo transition.
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Spickard EA, Joshi PM, Rothman JH. The multipotency-to-commitment transition in Caenorhabditis elegans-implications for reprogramming from cells to organs. FEBS Lett 2018; 592:838-851. [PMID: 29334121 DOI: 10.1002/1873-3468.12977] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/22/2017] [Accepted: 01/11/2018] [Indexed: 12/13/2022]
Abstract
In animal embryos, cells transition from a multipotential state, with the capacity to adopt multiple fates, into an irreversible, committed state of differentiation. This multipotency-to-commitment transition (MCT) is evident from experiments in which cell fate is reprogrammed by transcription factors for cell type-specific differentiation, as has been observed extensively in Caenorhabditis elegans. Although factors that direct differentiation into each of the three germ layer types cannot generally reprogram cells after the MCT in this animal, transcription factors for endoderm development are able to do so in multiple differentiated cell types. In one case, these factors can redirect the development of an entire organ in the process of "transorganogenesis". Natural transdifferentiation also occurs in a small number of differentiated cells during normal C. elegans development. We review these reprogramming and transdifferentiation events, highlighting the cellular and developmental contexts in which they occur, and discuss common themes underlying direct cell lineage reprogramming. Although certain aspects may be unique to the model system, growing evidence suggests that some mechanisms are evolutionarily conserved and may shed light on cellular plasticity and disease in humans.
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Affiliation(s)
- Erik A Spickard
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, CA, USA
| | - Pradeep M Joshi
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, CA, USA
| | - Joel H Rothman
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, CA, USA
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LIN-41 and OMA Ribonucleoprotein Complexes Mediate a Translational Repression-to-Activation Switch Controlling Oocyte Meiotic Maturation and the Oocyte-to-Embryo Transition in Caenorhabditis elegans. Genetics 2017; 206:2007-2039. [PMID: 28576864 PMCID: PMC5560804 DOI: 10.1534/genetics.117.203174] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 05/31/2017] [Indexed: 11/30/2022] Open
Abstract
An extended meiotic prophase is a hallmark of oogenesis. Hormonal signaling activates the CDK1/cyclin B kinase to promote oocyte meiotic maturation, which involves nuclear and cytoplasmic events. Nuclear maturation encompasses nuclear envelope breakdown, meiotic spindle assembly, and chromosome segregation. Cytoplasmic maturation involves major changes in oocyte protein translation and cytoplasmic organelles and is poorly understood. In the nematode Caenorhabditis elegans, sperm release the major sperm protein (MSP) hormone to promote oocyte growth and meiotic maturation. Large translational regulatory ribonucleoprotein (RNP) complexes containing the RNA-binding proteins OMA-1, OMA-2, and LIN-41 regulate meiotic maturation downstream of MSP signaling. To understand the control of translation during meiotic maturation, we purified LIN-41-containing RNPs and characterized their protein and RNA components. Protein constituents of LIN-41 RNPs include essential RNA-binding proteins, the GLD-2 cytoplasmic poly(A) polymerase, the CCR4-NOT deadenylase complex, and translation initiation factors. RNA sequencing defined messenger RNAs (mRNAs) associated with both LIN-41 and OMA-1, as well as sets of mRNAs associated with either LIN-41 or OMA-1. Genetic and genomic evidence suggests that GLD-2, which is a component of LIN-41 RNPs, stimulates the efficient translation of many LIN-41-associated transcripts. We analyzed the translational regulation of two transcripts specifically associated with LIN-41 which encode the RNA regulators SPN-4 and MEG-1. We found that LIN-41 represses translation of spn-4 and meg-1, whereas OMA-1 and OMA-2 promote their expression. Upon their synthesis, SPN-4 and MEG-1 assemble into LIN-41 RNPs prior to their functions in the embryo. This study defines a translational repression-to-activation switch as a key element of cytoplasmic maturation.
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Pushpa K, Kumar GA, Subramaniam K. Translational Control of Germ Cell Decisions. Results Probl Cell Differ 2017; 59:175-200. [PMID: 28247049 DOI: 10.1007/978-3-319-44820-6_6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Germline poses unique challenges to gene expression control at the transcriptional level. While the embryonic germline maintains a global hold on new mRNA transcription, the female adult germline produces transcripts that are not translated into proteins until embryogenesis of subsequent generation. As a consequence, translational control plays a central role in governing various germ cell decisions including the formation of primordial germ cells, self-renewal/differentiation decisions in the adult germline, onset of gametogenesis and oocyte maturation. Mechanistically, several common themes such as asymmetric localization of mRNAs, conserved RNA-binding proteins that control translation by 3' UTR binding, translational activation by the cytoplasmic elongation of the polyA tail and the assembly of mRNA-protein complexes called mRNPs have emerged from the studies on Caenorhabditis elegans, Xenopus and Drosophila. How mRNPs assemble, what influences their dynamics, and how a particular 3' UTR-binding protein turns on the translation of certain mRNAs while turning off other mRNAs at the same time and space are key challenges for future work.
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Affiliation(s)
- Kumari Pushpa
- Regional Centre for Biotechnology, Faridabad, Haryana, India
| | - Ganga Anil Kumar
- Indian Institute of Technology-Kanpur, Kanpur, India.,Indian Institute of Technology-Madras, Chennai, India
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13
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Kaymak E, Farley BM, Hay SA, Li C, Ho S, Hartman DJ, Ryder SP. Efficient generation of transgenic reporter strains and analysis of expression patterns in Caenorhabditis elegans using library MosSCI. Dev Dyn 2016; 245:925-36. [PMID: 27294288 PMCID: PMC4981527 DOI: 10.1002/dvdy.24426] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/09/2016] [Accepted: 06/03/2016] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND In C. elegans, germline development and early embryogenesis rely on posttranscriptional regulation of maternally transcribed mRNAs. In many cases, the 3' untranslated region (UTR) is sufficient to govern the expression patterns of these transcripts. Several RNA-binding proteins are required to regulate maternal mRNAs through the 3'UTR. Despite intensive efforts to map RNA-binding protein-mRNA interactions in vivo, the biological impact of most binding events remains unknown. Reporter studies using single copy integrated transgenes are essential to evaluate the functional consequences of interactions between RNA-binding proteins and their associated mRNAs. RESULTS In this report, we present an efficient method of generating reporter strains with improved throughput by using a library variant of MosSCI transgenesis. Furthermore, using RNA interference, we identify the suite of RNA-binding proteins that control the expression pattern of five different maternal mRNAs. CONCLUSIONS The results provide a generalizable and efficient strategy to assess the functional relevance of protein-RNA interactions in vivo, and reveal new regulatory connections between key RNA-binding proteins and their maternal mRNA targets. Developmental Dynamics 245:925-936, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Ebru Kaymak
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Brian M. Farley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Samantha A. Hay
- Virginia Commonwealth University School of Medicine, VA, USA
| | - Chihua Li
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Samantha Ho
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | | | - Sean P. Ryder
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
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14
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Robert VJ, Garvis S, Palladino F. Repression of somatic cell fate in the germline. Cell Mol Life Sci 2015; 72:3599-620. [PMID: 26043973 PMCID: PMC11113910 DOI: 10.1007/s00018-015-1942-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 01/13/2023]
Abstract
Germ cells must transmit genetic information across generations, and produce gametes while also maintaining the potential to form all cell types after fertilization. Preventing the activation of somatic programs is, therefore, crucial to the maintenance of germ cell identity. Studies in Caenorhabditis elegans, Drosophila melanogaster, and mouse have revealed both similarities and differences in how somatic gene expression is repressed in germ cells, thereby preventing their conversion into somatic tissues. This review will focus on recent developments in our understanding of how global or gene-specific transcriptional repression, chromatin regulation, and translational repression operate in the germline to maintain germ cell identity and repress somatic differentiation programs.
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Affiliation(s)
- Valérie J Robert
- Ecole Normale Supérieure de Lyon, Université de Lyon, 46 allée d'Italie, 69007, Lyon, France
| | - Steve Garvis
- Ecole Normale Supérieure de Lyon, Université de Lyon, 46 allée d'Italie, 69007, Lyon, France
| | - Francesca Palladino
- Ecole Normale Supérieure de Lyon, Université de Lyon, 46 allée d'Italie, 69007, Lyon, France.
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15
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Beadell AV, Haag ES. Evolutionary Dynamics of GLD-1-mRNA complexes in Caenorhabditis nematodes. Genome Biol Evol 2014; 7:314-35. [PMID: 25502909 PMCID: PMC4316625 DOI: 10.1093/gbe/evu272] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2014] [Indexed: 12/17/2022] Open
Abstract
Given the large number of RNA-binding proteins and regulatory RNAs within genomes, posttranscriptional regulation may be an underappreciated aspect of cis-regulatory evolution. Here, we focus on nematode germ cells, which are known to rely heavily upon translational control to regulate meiosis and gametogenesis. GLD-1 belongs to the STAR-domain family of RNA-binding proteins, conserved throughout eukaryotes, and functions in Caenorhabditis elegans as a germline-specific translational repressor. A phylogenetic analysis across opisthokonts shows that GLD-1 is most closely related to Drosophila How and deuterostome Quaking, both implicated in alternative splicing. We identify messenger RNAs associated with C. briggsae GLD-1 on a genome-wide scale and provide evidence that many participate in aspects of germline development. By comparing our results with published C. elegans GLD-1 targets, we detect nearly 100 that are conserved between the two species. We also detected several hundred Cbr-GLD-1 targets whose homologs have not been reported to be associated with C. elegans GLD-1 in either of two independent studies. Low expression in C. elegans may explain the failure to detect most of them, but a highly expressed subset are strong candidates for Cbr-GLD-1-specific targets. We examine GLD-1-binding motifs among targets conserved in C. elegans and C. briggsae and find that most, but not all, display evidence of shared ancestral binding sites. Our work illustrates both the conservative and the dynamic character of evolution at the posttranslational level of gene regulation, even between congeners.
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Affiliation(s)
- Alana V Beadell
- Program in Behavior, Evolution, Ecology, and Systematics, University of Maryland, College Park Present address: Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL
| | - Eric S Haag
- Program in Behavior, Evolution, Ecology, and Systematics, University of Maryland, College Park Department of Biology, University of Maryland, College Park
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16
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Huang NN, Hunter CP. The RNA binding protein MEX-3 retains asymmetric activity in the early Caenorhabditis elegans embryo in the absence of asymmetric protein localization. Gene 2014; 554:160-73. [PMID: 25445286 DOI: 10.1016/j.gene.2014.10.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 10/23/2014] [Accepted: 10/25/2014] [Indexed: 10/24/2022]
Abstract
The RNA binding protein MEX-3 is required to restrict translation of pal-1, the Caenorhabditis elegans caudal homolog, to the posterior of the early embryo. MEX-3 is present uniformly throughout the newly fertilized embryo, but becomes depleted in the posterior by the 4-cell stage. This MEX-3 patterning requires the CCCH zinc-finger protein MEX-5, the RNA Recognition Motif protein SPN-4, and the kinase PAR-4. Genetic and biochemical evidence suggests that MEX-5 binds to MEX-3 in the anterior of the embryo, protecting MEX-3 from degradation and allowing it to bind the pal-1 3'UTR and repress translation. MEX-3 that is not bound to MEX-5 becomes inactivated by par-4, then targeted for spn-4 dependent degradation. After the 4-cell stage, residual MEX-3 is degraded in somatic cells, and only persists in the germline precursors. To better understand regulation of mex-3, GFP was fused to MEX-3 or regions of MEX-3 and expressed in developing oocytes. GFP::MEX-3 expressed in this manner can replace endogenous MEX-3, but surprisingly is not asymmetrically localized at the 4-cell stage. These results indicate that GFP::MEX-3 retains asymmetric activity even in the absence of asymmetric protein localization. Neither the mex-3 3'UTR nor protein degradation at the 4-cell stage is strictly required. A region of MEX-3 containing a glutamine-rich region and potential ubiquitination and phosphorylation sites is sufficient for soma-germline asymmetry. Results from mex-5/6 and spn-4(RNAi) suggest two pathways for MEX-3 degradation, an early spn-4 dependent pathway and a later spn-4 independent pathway. These results indicate that mex-3 activity is regulated at multiple levels, leading to rapid and robust regulation in the quickly developing early embryo.
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Affiliation(s)
- Nancy N Huang
- Molecular Biology Department, Colorado College, Colorado Springs, CO 80903, USA.
| | - Craig P Hunter
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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17
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Tocchini C, Keusch JJ, Miller SB, Finger S, Gut H, Stadler MB, Ciosk R. The TRIM-NHL protein LIN-41 controls the onset of developmental plasticity in Caenorhabditis elegans. PLoS Genet 2014; 10:e1004533. [PMID: 25167051 PMCID: PMC4148191 DOI: 10.1371/journal.pgen.1004533] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 06/11/2014] [Indexed: 12/30/2022] Open
Abstract
The mechanisms controlling cell fate determination and reprogramming are fundamental for development. A profound reprogramming, allowing the production of pluripotent cells in early embryos, takes place during the oocyte-to-embryo transition. To understand how the oocyte reprogramming potential is controlled, we sought Caenorhabditis elegans mutants in which embryonic transcription is initiated precociously in germ cells. This screen identified LIN-41, a TRIM-NHL protein and a component of the somatic heterochronic pathway, as a temporal regulator of pluripotency in the germline. We found that LIN-41 is expressed in the cytoplasm of developing oocytes, which, in lin-41 mutants, acquire pluripotent characteristics of embryonic cells and form teratomas. To understand LIN-41 function in the germline, we conducted structure-function studies. In contrast to other TRIM-NHL proteins, we found that LIN-41 is unlikely to function as an E3 ubiquitin ligase. Similar to other TRIM-NHL proteins, the somatic function of LIN-41 is thought to involve mRNA regulation. Surprisingly, we found that mutations predicted to disrupt the association of LIN-41 with mRNA, which otherwise compromise LIN-41 function in the heterochronic pathway in the soma, have only minor effects in the germline. Similarly, LIN-41-mediated repression of a key somatic mRNA target is dispensable for the germline function. Thus, LIN-41 appears to function in the germline and the soma via different molecular mechanisms. These studies provide the first insight into the mechanism inhibiting the onset of embryonic differentiation in developing oocytes, which is required to ensure a successful transition between generations. Reprogramming into a naïve, pluripotent state during the oocyte-to-embryo transition is directed by the oocyte cytoplasm. To understand how this reprogramming is controlled, we searched for C. elegans mutants in which the activation of embryonic genome, a landmark event demarcating the switch from a germline- to embryo-specific transcription, is initiated precociously in germ cells. This screen identified a novel function for LIN-41, a member of the TRIM-NHL protein family, in preventing a premature onset of embryonic-like differentiation and teratoma formation in developing oocytes, thus ensuring a successful passage between generations. This is the first example of such a regulator in cells that are poised for embryonic development. Interestingly, the majority of molecular “roadblocks” to reprograming that have been identified so far are epigenetic regulators. However, we propose that, at least in germ cells, LIN-41-like regulators may fulfill an analogous role in the cytoplasm, which has possible implications for the generation of human pluripotent stem cells.
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Affiliation(s)
- Cristina Tocchini
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Jeremy J. Keusch
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Sarah B. Miller
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Susanne Finger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Heinz Gut
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Michael B. Stadler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Rafal Ciosk
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- * E-mail:
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18
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Doh JH, Jung Y, Reinke V, Lee MH. C. elegans RNA-binding protein GLD-1 recognizes its multiple targets using sequence, context, and structural information to repress translation. WORM 2014; 2:e26548. [PMID: 24744981 DOI: 10.4161/worm.26548] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Revised: 09/12/2013] [Accepted: 09/19/2013] [Indexed: 11/19/2022]
Abstract
Caenorhabditis elegans GLD-1, a maxi-KH motif containing RNA-binding protein, has various functions mainly during female germ cell development, suggesting that it likely controls the expression of a selective group of maternal mRNAs. To gain an insight into how GLD-1 specifically recognizes these mRNA targets, we identified 38 biochemically proven GLD-1 binding regions from multiple mRNA targets that are among over 100 putative targets co-immunoprecipitated with GLD-1. The sequence information of these regions revealed three over-represented and phylogenetically conserved sequence motifs. We found that two of the motifs, one of which is novel, are important for GLD-1 binding in several GLD-1 binding regions but not in other regions. Further analyses indicate that the importance of one of the sequence motifs is dependent on two aspects: (1) surrounding sequence information, likely acting as an accessory feature for GLD-1 to efficiently select the sequence motif and (2) RNA secondary structural environment where the sequence motif resides, which likely provides "binding-site accessibility" for GLD-1 to effectively recognize its targets. Our data suggest some mRNAs recruit GLD-1 by a distinct mechanism, which involves more than one sequence motif that needs to be embedded in the correct context and structural environment.
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Affiliation(s)
- Jung H Doh
- Department of Biological Sciences; University at Albany; SUNY; Albany, NY USA
| | - Yuchae Jung
- Department of Biological Sciences; University at Albany; SUNY; Albany, NY USA
| | - Valerie Reinke
- Department of Genetics; Yale University School of Medicine; New Haven, CT USA
| | - Min-Ho Lee
- Department of Biological Sciences; University at Albany; SUNY; Albany, NY USA
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19
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Elramah S, Landry M, Favereaux A. MicroRNAs regulate neuronal plasticity and are involved in pain mechanisms. Front Cell Neurosci 2014; 8:31. [PMID: 24574967 PMCID: PMC3920573 DOI: 10.3389/fncel.2014.00031] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 01/22/2014] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) are emerging as master regulators of gene expression in the nervous system where they contribute not only to brain development but also to neuronal network homeostasis and plasticity. Their function is the result of a cascade of events including miRNA biogenesis, target recognition, and translation inhibition. It has been suggested that miRNAs are major switches of the genome owing to their ability to regulate multiple genes at the same time. This regulation is essential for normal neuronal activity and, when affected, can lead to drastic pathological conditions. As an example, we illustrate how deregulation of miRNAs can affect neuronal plasticity leading to chronic pain. The origin of pain and its dual role as a key physiological function and a debilitating disease has been highly debated until now. The incidence of chronic pain is estimated to be 20-25% worldwide, thus making it a public health problem. Chronic pain can be considered as a form of maladaptive plasticity. Long-lasting modifications develop as a result of global changes in gene expression, and are thus likely to be controlled by miRNAs. Here, we review the literature on miRNAs and their targets responsible for maladaptive plasticity in chronic pain conditions. In addition, we conduct a retrospective analysis of miRNA expression data published for different pain models, taking into account recent progress in our understanding of the role of miRNAs in neuronal plasticity.
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Affiliation(s)
- Sara Elramah
- Interdisciplinary Institute for Neuroscience, UMR 5297, University of Bordeaux Bordeaux, France ; Interdisciplinary Institute for Neuroscience, UMR 5297, Centre National de la Recherche Scientifique Bordeaux, France
| | - Marc Landry
- Interdisciplinary Institute for Neuroscience, UMR 5297, University of Bordeaux Bordeaux, France ; Interdisciplinary Institute for Neuroscience, UMR 5297, Centre National de la Recherche Scientifique Bordeaux, France
| | - Alexandre Favereaux
- Interdisciplinary Institute for Neuroscience, UMR 5297, University of Bordeaux Bordeaux, France ; Interdisciplinary Institute for Neuroscience, UMR 5297, Centre National de la Recherche Scientifique Bordeaux, France
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20
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Akay A, Craig A, Lehrbach N, Larance M, Pourkarimi E, Wright JE, Lamond A, Miska E, Gartner A. RNA-binding protein GLD-1/quaking genetically interacts with the mir-35 and the let-7 miRNA pathways in Caenorhabditis elegans. Open Biol 2013; 3:130151. [PMID: 24258276 PMCID: PMC3843822 DOI: 10.1098/rsob.130151] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Messenger RNA translation is regulated by RNA-binding proteins and small non-coding RNAs called microRNAs. Even though we know the majority of RNA-binding proteins and microRNAs that regulate messenger RNA expression, evidence of interactions between the two remain elusive. The role of the RNA-binding protein GLD-1 as a translational repressor is well studied during Caenorhabditis elegans germline development and maintenance. Possible functions of GLD-1 during somatic development and the mechanism of how GLD-1 acts as a translational repressor are not known. Its human homologue, quaking (QKI), is essential for embryonic development. Here, we report that the RNA-binding protein GLD-1 in C. elegans affects multiple microRNA pathways and interacts with proteins required for microRNA function. Using genome-wide RNAi screening, we found that nhl-2 and vig-1, two known modulators of miRNA function, genetically interact with GLD-1. gld-1 mutations enhance multiple phenotypes conferred by mir-35 and let-7 family mutants during somatic development. We used stable isotope labelling with amino acids in cell culture to globally analyse the changes in the proteome conferred by let-7 and gld-1 during animal development. We identified the histone mRNA-binding protein CDL-1 to be, in part, responsible for the phenotypes observed in let-7 and gld-1 mutants. The link between GLD-1 and miRNA-mediated gene regulation is further supported by its biochemical interaction with ALG-1, CGH-1 and PAB-1, proteins implicated in miRNA regulation. Overall, we have uncovered genetic and biochemical interactions between GLD-1 and miRNA pathways.
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Affiliation(s)
- Alper Akay
- Centre for Gene Regulation and Expression, University of Dundee, Dundee DD1 5EH, UK
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21
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Brümmer A, Kishore S, Subasic D, Hengartner M, Zavolan M. Modeling the binding specificity of the RNA-binding protein GLD-1 suggests a function of coding region-located sites in translational repression. RNA (NEW YORK, N.Y.) 2013; 19:1317-1326. [PMID: 23974436 PMCID: PMC3854522 DOI: 10.1261/rna.037531.112] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 06/25/2013] [Indexed: 06/02/2023]
Abstract
To understand the function of the hundreds of RNA-binding proteins (RBPs) that are encoded in animal genomes it is important to identify their target RNAs. Although it is generally accepted that the binding specificity of an RBP is well described in terms of the nucleotide sequence of its binding sites, other factors such as the structural accessibility of binding sites or their clustering, to enable binding of RBP multimers, are also believed to play a role. Here we focus on GLD-1, a translational regulator of Caenorhabditis elegans, whose binding specificity and targets have been studied with a variety of methods such as CLIP (cross-linking and immunoprecipitation), RIP-Chip (microarray measurement of RNAs associated with an immunoprecipitated protein), profiling of polysome-associated mRNAs and biophysical determination of binding affinities of GLD-1 for short nucleotide sequences. We show that a simple biophysical model explains the binding of GLD-1 to mRNA targets to a large extent, and that taking into account the accessibility of putative target sites significantly improves the prediction of GLD-1 binding, particularly due to a more accurate prediction of binding in transcript coding regions. Relating GLD-1 binding to translational repression and stabilization of its target transcripts we find that binding sites along the entire transcripts contribute to functional responses, and that CDS-located sites contribute most to translational repression. Finally, biophysical measurements of GLD-1 affinity for a small number of oligonucleotides appear to allow an accurate reconstruction of the sequence specificity of the protein. This approach can be applied to uncover the specificity and function of other RBPs.
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Affiliation(s)
- Anneke Brümmer
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | - Deni Subasic
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Michael Hengartner
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
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22
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Hansen D, Schedl T. Stem cell proliferation versus meiotic fate decision in Caenorhabditis elegans. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 757:71-99. [PMID: 22872475 PMCID: PMC3786863 DOI: 10.1007/978-1-4614-4015-4_4] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The C. elegans germ line has emerged as an important model for -understanding how a stem cell population is maintained throughout the life of the animal while still producing the gametes necessary for propagation of the species. The stem cell population in the adult hermaphrodite is relatively large, with stem cells giving rise to daughters that appear intrinsically equivalent; however, some of the daughters retain the proliferative fate while others enter meiotic prophase. While machinery exists for cells to progress through the mitotic cell cycle and machinery exists for cells to progress through meiotic prophase, central to understanding germ line development is identifying the genes and regulatory processes that determine whether the mitotic cell cycle or meiotic prophase machinery will be utilized; in other words, the genes that regulate the switch of germ cells from the proliferative stem cell fate to the meiotic development fate. Whether a germ cell self-renews or enters meiotic prophase is largely determined by its proximity to the distal tip cell (DTC), which is the somatic niche cell that caps the distal end of the gonad. Germ cells close to the DTC have high levels of GLP-1 Notch signaling, which promotes the proliferative fate, while cells further from the DTC have high activity levels of the GLD-1 and GLD-2 redundant RNA regulatory pathways, as well as a third uncharacterized pathway, each of which direct cells to enter meiotic prophase. Other factors and pathways modulate this core genetic pathway, or work in parallel to it, presumably to ensure that a tight balance is maintained between proliferation and meiotic entry.
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Affiliation(s)
- Dave Hansen
- Department of Biological Sciences, 2500 University Drive, University of Calgary, Calgary, Alberta, Canada
| | - Tim Schedl
- Department of Genetics, Campus Box 8232, Washington University School of Medicine, 4566 Scott Ave, St Louis MO
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23
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Translational control in the Caenorhabditis elegans germ line. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 757:205-47. [PMID: 22872479 DOI: 10.1007/978-1-4614-4015-4_8] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Translational control is a prevalent form of gene expression regulation in the Caenorhabditis elegans germ line. Linking the amount of protein synthesis to mRNA quantity and translational accessibility in the cell cytoplasm provides unique advantages over DNA-based controls for developing germ cells. This mode of gene expression is especially exploited in germ cell fate decisions and during oogenesis, when the developing oocytes stockpile hundreds of different mRNAs required for early embryogenesis. Consequently, a dense web of RNA regulators, consisting of diverse RNA-binding proteins and RNA-modifying enzymes, control the translatability of entire mRNA expression programs. These RNA regulatory networks are tightly coupled to germ cell developmental progression and are themselves under translational control. The underlying molecular mechanisms and RNA codes embedded in the mRNA molecules are beginning to be understood. Hence, the C. elegans germ line offers fertile grounds for discovering post-transcriptional mRNA regulatory mechanisms and emerges as great model for a systems level understanding of translational control during development.
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24
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Cai C, Liu J, Wang C, Shen J. KHDC1A, a novel translational repressor, induces endoplasmic reticulum-dependent apoptosis. DNA Cell Biol 2012; 31:1447-57. [PMID: 22731819 DOI: 10.1089/dna.2012.1682] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
RNA binding proteins are characterized as a new family of apoptosis inducers; however, the mechanism by which they induce apoptosis is poorly understood. KHDC1 family members were recently identified as K-homology (KH)-domain containing RNA binding proteins that are unique to eutherian mammals and highly expressed in oocytes. In this study, we report that the expression of KHDC1A induces caspase-3 dependent apoptosis and inhibits mRNA translation, and the translational repression is independent of apoptosis. We demonstrate that both the N-terminus and C-terminus of KHDC1A are required for its pro-apoptotic and translational repression activities. Furthermore, in the C-terminus of KHDC1A, a putative trans-membrane motif (TMM) is critical for these activities. In addition, the ectopically expressed KHDC1A is localized to the endoplasmic reticulum (ER) and changes the morphology of the ER. The inhibition of ER-specific caspase-12 successfully rescues KHDC1A-induced apoptosis, but not Fas-induced apoptosis. Taken together, we conclude that KHDC1A functions as a global translational repressor and induces apoptosis through an ER-dependent signaling pathway.
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Affiliation(s)
- Congli Cai
- Institute for Medical Biology, College of Life Sciences, South-Central University for Nationalities, Wuhan, China
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25
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Hubstenberger A, Cameron C, Shtofman R, Gutman S, Evans TC. A network of PUF proteins and Ras signaling promote mRNA repression and oogenesis in C. elegans. Dev Biol 2012; 366:218-31. [PMID: 22542599 PMCID: PMC3361503 DOI: 10.1016/j.ydbio.2012.03.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 02/21/2012] [Accepted: 03/19/2012] [Indexed: 11/16/2022]
Abstract
Cell differentiation requires integration of gene expression controls with dynamic changes in cell morphology, function, and control. Post-transcriptional mRNA regulation and signaling systems are important to this process but their mechanisms and connections are unclear. During C. elegans oogenesis, we find that two groups of PUF RNA binding proteins (RNABPs), PUF-3/11 and PUF-5/6/7, control different specific aspects of oocyte formation. PUF-3/11 limits oocyte growth, while PUF-5/6/7 promotes oocyte organization and formation. These two PUF groups repress mRNA translation through overlapping but distinct sets of 3' untranslated regions (3'UTRs). Several PUF-dependent mRNAs encode other mRNA regulators suggesting both PUF groups control developmental patterning of mRNA regulation circuits. Furthermore, we find that the Ras-MapKinase/ERK pathway functions with PUF-5/6/7 to repress specific mRNAs and control oocyte organization and growth. These results suggest that diversification of PUF proteins and their integration with Ras-MAPK signaling modulates oocyte differentiation. Together with other studies, these findings suggest positive and negative interactions between the Ras-MAPK system and PUF RNA-binding proteins likely occur at multiple levels. Changes in these interactions over time can influence spatiotemporal patterning of tissue development.
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Affiliation(s)
- Arnaud Hubstenberger
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora CO 80045
| | - Cristiana Cameron
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora CO 80045
| | - Rebecca Shtofman
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora CO 80045
| | - Shiri Gutman
- Program in Cell biology, Stem Cells, and Development, University of Colorado Anschutz Medical Campus, Aurora CO 80045
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora CO 80045
| | - Thomas C. Evans
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora CO 80045
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26
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Genome-wide analysis of GLD-1-mediated mRNA regulation suggests a role in mRNA storage. PLoS Genet 2012; 8:e1002742. [PMID: 22693456 PMCID: PMC3364957 DOI: 10.1371/journal.pgen.1002742] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 04/18/2012] [Indexed: 11/28/2022] Open
Abstract
Translational repression is often accompanied by mRNA degradation. In contrast, many mRNAs in germ cells and neurons are “stored" in the cytoplasm in a repressed but stable form. Unlike repression, the stabilization of these mRNAs is surprisingly little understood. A key player in Caenorhabditis elegans germ cell development is the STAR domain protein GLD-1. By genome-wide analysis of mRNA regulation in the germ line, we observed that GLD-1 has a widespread role in repressing translation but, importantly, also in stabilizing a sub-population of its mRNA targets. Additionally, these mRNAs appear to be stabilized by the DDX6-like RNA helicase CGH-1, which is a conserved component of germ granules and processing bodies. Because many GLD-1 and CGH-1 stabilized mRNAs encode factors important for the oocyte-to-embryo transition (OET), our findings suggest that the regulation by GLD-1 and CGH-1 serves two purposes. Firstly, GLD-1–dependent repression prevents precocious translation of OET–promoting mRNAs. Secondly, GLD-1– and CGH-1–dependent stabilization ensures that these mRNAs are sufficiently abundant for robust translation when activated during OET. In the absence of this protective mechanism, the accumulation of OET–promoting mRNAs, and consequently the oocyte-to-embryo transition, might be compromised. One of the most striking developmental events is the oocyte-to-embryo transition that, in the absence of Pol II–dependent transcription, depends on regulated translation of maternal mRNAs. Prior to their activation, these maternal mRNAs need to be “stored" in the egg cytoplasm in a repressed but stable form. Surprisingly little is known about how the stored mRNAs are stabilized. The STAR family of RNA–binding proteins includes the C. elegans GLD-1, which controls many aspects of germ cell development. To obtain a comprehensive picture of GLD-1–dependent mRNA regulation, we performed a genome-wide survey of translational repression and mRNA stability of GLD-1 targets. This uncovered a potential role of GLD-1 in mRNA storage, as we found that GLD-1 both represses and stabilizes a subpopulation of its targets. The stabilization also involves a DDX6-like RNA helicase, CGH-1, which is a component of repressive germ granules and processing bodies. Remarkably, the GLD-1 and CGH-1 stabilized mRNAs encode regulators of the oocyte-to-embryo transition, providing an insight into how these functionally related mRNAs are specifically stabilized during germ cell formation. These findings have potential implications for oocyte quality and reproductive fitness, and for mRNA storage in other cell types such as neurons.
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Goldfless SJ, Belmont BJ, de Paz AM, Liu JF, Niles JC. Direct and specific chemical control of eukaryotic translation with a synthetic RNA-protein interaction. Nucleic Acids Res 2012; 40:e64. [PMID: 22275521 PMCID: PMC3351163 DOI: 10.1093/nar/gks028] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Sequence-specific RNA–protein interactions, though commonly used in biological systems to regulate translation, are challenging to selectively modulate. Here, we demonstrate the use of a chemically-inducible RNA–protein interaction to regulate eukaryotic translation. By genetically encoding Tet Repressor protein (TetR)-binding RNA elements into the 5′-untranslated region (5′-UTR) of an mRNA, translation of a downstream coding sequence is directly controlled by TetR and tetracycline analogs. In endogenous and synthetic 5′-UTR contexts, this system efficiently regulates the expression of multiple target genes, and is sufficiently stringent to distinguish functional from non-functional RNA–TetR interactions. Using a reverse TetR variant, we illustrate the potential for expanding the regulatory properties of the system through protein engineering strategies.
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Affiliation(s)
- Stephen J Goldfless
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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28
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Mainpal R, Priti A, Subramaniam K. PUF-8 suppresses the somatic transcription factor PAL-1 expression in C. elegans germline stem cells. Dev Biol 2011; 360:195-207. [PMID: 21968099 PMCID: PMC3736097 DOI: 10.1016/j.ydbio.2011.09.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Revised: 08/30/2011] [Accepted: 09/18/2011] [Indexed: 10/17/2022]
Abstract
RNA-binding proteins of the PUF family are well conserved post-transcriptional regulators that control a variety of developmental processes. The C. elegans protein PUF-8 is essential for several aspects of germ cell development including the maintenance of germline stem cells (GSCs). To explore the molecular mechanisms underlying its function, we have identified 160 germline-expressed mRNAs as potential targets of PUF-8. We generated GFP::H2B-3' UTR fusions for 17 mRNAs to assay their post-transcriptional regulation in germ cells. Twelve transgenes were not expressed in the mitotic germ cells, and depletion of PUF-8 led to misexpression of six of them in these cells. In contrast, the expression of 3' UTR fusion of hip-1, which encodes the HSP-70 interacting protein, was dependent on PUF-8. These results indicate that PUF-8 may regulate the expression of its targets both negatively as well as positively. We investigated the PUF-8-mediated post-transcriptional control of one mRNA, namely pal-1, which encodes a homeodomain transcription factor responsible for muscle development. Our results show that PUF-8 binds in vitro to specific sequences within pal-1 3' UTR that are critical for post-transcriptional suppression in GSCs. Removal of PUF-8 resulted in PAL-1 misexpression, and PAL-1-dependent misexpression of the myogenic promoter HLH-1 in germ cells. We propose that PUF-8 protects GSCs from the influence of somatic differentiation factors such as PAL-1, which are produced in the maternal germline but meant for embryogenesis.
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Affiliation(s)
- Rana Mainpal
- Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Agarwal Priti
- Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur 208016, India
| | - Kuppuswamy Subramaniam
- Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur 208016, India
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29
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Zuryn S, Daniele T, Jarriault S. Direct cellular reprogramming in Caenorhabditis elegans: facts, models, and promises for regenerative medicine. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2011; 1:138-52. [PMID: 23801672 DOI: 10.1002/wdev.7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In vitro systems of cellular reprogramming [induced pluripotent stem (iPS) cells and direct reprogramming or transdifferentiation] are rapidly improving our repertoire of molecular techniques that can force cells in culture to change into a desired identity. However, the new frontier for regenerative medicine is in vivo cellular reprogramming, which in light of concerns about the safety of in vitro cell manipulations, is an increasingly attractive approach for regenerative medicine. Powerful in vivo approaches are currently being undertaken in the genetic model Caenorhabditis elegans. Several very distinct cell types have been induced to change or have been discovered to transform naturally, into altogether different cell types. These examples have improved our understanding of the fundamental molecular and cellular mechanisms that permit cell identity changes in live animals. In addition, the combination of a stereotyped lineage with single cell analyses allows dissection of the early and intermediate mechanisms of reprogramming, as well as their kinetics. As a result, several important concepts on in vivo cellular reprogramming have been recently developed.
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Affiliation(s)
- Steven Zuryn
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U964, Université de Strasbourg, Illkirch Cu Strasbourg, France
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Hajduskova M, Ahier A, Daniele T, Jarriault S. Cell plasticity in Caenorhabditis elegans: from induced to natural cell reprogramming. Genesis 2011; 50:1-17. [PMID: 21932439 DOI: 10.1002/dvg.20806] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 08/29/2011] [Accepted: 08/30/2011] [Indexed: 01/17/2023]
Abstract
Achieving controlled reprogramming of differentiated cells into a desired cell type would open new opportunities in stem-cell biology and regenerative medicine. Experimentation on cell reprogramming requires a model in which cell conversion can be induced and tracked individually. The tiny nematode, Caenorhabditis elegans, owing to its known cellular lineage, allows the study of direct cell type conversion with a single-cell resolution. Indeed, recent advances have shown that despite its invariant cell lineage, cellular identities can be reprogrammed, leading to cell conversion in vivo. In addition, natural transdifferentiation events occur in the worm, providing a powerful model for the study of cellular plasticity in a physiological cellular microenvironment. Here, we review pioneer studies on induced and naturally occurring reprogramming events in C. elegans and the new notions that have emerged.
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Affiliation(s)
- Martina Hajduskova
- Development and Stem Cells Programme, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U964, Université de Strasbourg, 67404 Illkirch CU Strasbourg, France
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31
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Wright JE, Gaidatzis D, Senften M, Farley BM, Westhof E, Ryder SP, Ciosk R. A quantitative RNA code for mRNA target selection by the germline fate determinant GLD-1. EMBO J 2010; 30:533-45. [PMID: 21169991 DOI: 10.1038/emboj.2010.334] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Accepted: 11/22/2010] [Indexed: 01/21/2023] Open
Abstract
RNA-binding proteins (RBPs) are critical regulators of gene expression. To understand and predict the outcome of RBP-mediated regulation a comprehensive analysis of their interaction with RNA is necessary. The signal transduction and activation of RNA (STAR) family of RBPs includes developmental regulators and tumour suppressors such as Caenorhabditis elegans GLD-1, which is a key regulator of germ cell development. To obtain a comprehensive picture of GLD-1 interactions with the transcriptome, we identified GLD-1-associated mRNAs by RNA immunoprecipitation followed by microarray detection. Based on the computational analysis of these mRNAs we generated a predictive model, where GLD-1 association with mRNA is determined by the strength and number of 7-mer GLD-1-binding motifs (GBMs) within UTRs. We verified this quantitative model both in vitro, by competition GLD-1/GBM-binding experiments to determine relative affinity, and in vivo, by 'transplantation' experiments, where 'weak' and 'strong' GBMs imposed translational repression of increasing strength on a non-target mRNA. This study demonstrates that transcriptome-wide identification of RBP mRNA targets combined with quantitative computational analysis can generate highly predictive models of post-transcriptional regulatory networks.
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Affiliation(s)
- Jane E Wright
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
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32
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Sun W, Julie Li YS, Huang HD, Shyy JYJ, Chien S. microRNA: a master regulator of cellular processes for bioengineering systems. Annu Rev Biomed Eng 2010; 12:1-27. [PMID: 20415587 DOI: 10.1146/annurev-bioeng-070909-105314] [Citation(s) in RCA: 179] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
microRNAs (miRNAs) are small RNAs 18 to 24 nucleotides in length that serve the pivotal function of regulating gene expression. Instead of being translated into proteins, the mature single-stranded miRNA binds to messenger RNAs (mRNAs) to interfere with the translational process. It is estimated that whereas only 1% of the genomic transcripts in mammalian cells encode miRNA, nearly one-third of the encoded genes are regulated by miRNA. Various bioinformatics databases, tools, and algorithms have been developed to predict the sequences of miRNAs and their target genes. In combination with the in silico approaches in systems biology, experimental studies on miRNA provide a new bioengineering approach for understanding the mechanism of fine-tuning gene regulation. This review aims to provide state-of-the-art information on this important mechanism of gene regulation for researchers working in biomedical engineering and related fields. Particular emphases are placed on summarizing the current tools and strategies for miRNA study from a bioengineering perspective and the possible applications of miRNAs (such as antagomirs and miRNA sponges) in biomedical engineering research.
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Affiliation(s)
- Wei Sun
- Division of Biomedical Sciences, University of California, Riverside, California 92521, USA
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33
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Guven-Ozkan T, Robertson SM, Nishi Y, Lin R. zif-1 translational repression defines a second, mutually exclusive OMA function in germline transcriptional repression. Development 2010; 137:3373-82. [PMID: 20826530 PMCID: PMC2947753 DOI: 10.1242/dev.055327] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2010] [Indexed: 02/03/2023]
Abstract
Specification of primordial germ cells requires global repression of transcription. In C. elegans, primordial germ cells are generated through four rounds of asymmetric divisions, starting from the zygote P0, each producing a transcriptionally repressed germline blastomere (P1-P4). Repression in P2-P4 requires PIE-1, which is provided maternally in oocytes and segregated to all germline blastomeres. We have shown previously that OMA-1 and OMA-2 repress global transcription in P0 and P1 by sequestering TAF-4, an essential component of TFIID. Soon after the first mitotic cycle, OMA proteins undergo developmentally regulated degradation. Here, we show that OMA proteins also repress transcription in P2-P4 indirectly, through a completely different mechanism that operates in oocytes. OMA proteins bind to both the 3' UTR of the zif-1 transcript and the eIF4E-binding protein, SPN-2, repressing translation of zif-1 mRNA in oocytes. zif-1 encodes the substrate-binding subunit of the E3 ligase for PIE-1 degradation. Inhibition of zif-1 translation in oocytes ensures high PIE-1 levels in oocytes and germline blastomeres. The two OMA protein functions are strictly regulated in both space and time by MBK-2, a kinase activated following fertilization. Phosphorylation by MBK-2 facilitates the binding of OMA proteins to TAF-4 and simultaneously inactivates their function in repressing zif-1 translation. Phosphorylation of OMA proteins displaces SPN-2 from the zif-1 3' UTR, releasing translational repression. We propose that MBK-2 phosphorylation serves as a developmental switch, converting OMA proteins from specific translational repressors in oocytes to global transcriptional repressors in embryos, together effectively repressing transcription in all germline blastomeres.
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Affiliation(s)
| | | | - Yuichi Nishi
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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34
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Hwang SY, Rose LS. Control of asymmetric cell division in early C. elegans embryogenesis: teaming-up translational repression and protein degradation. BMB Rep 2010; 43:69-78. [PMID: 20193124 DOI: 10.5483/bmbrep.2010.43.2.069] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Asymmetric cell division is a fundamental mechanism for the generation of body axes and cell diversity during early embryogenesis in many organisms. During intrinsically asymmetric divisions, an axis of polarity is established within the cell and the division plane is oriented to ensure the differential segregation of developmental determinants to the daughter cells. Studies in the nematode Caenorhabditis elegans have contributed greatly to our understanding of the regulatory mechanisms underlying cell polarity and asymmetric division. However, much remains to be elucidated about the molecular machinery controlling the spatiotemporal distribution of key components. In this review we discuss recent findings that reveal intricate interactions between translational control and targeted proteolysis. These two mechanisms of regulation serve to carefully modulate protein levels and reinforce asymmetries, or to eliminate proteins from certain cells.
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Affiliation(s)
- Sue-Yun Hwang
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
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35
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Racher H, Hansen D. Translational control in the C. elegans hermaphrodite germ line. Genome 2010; 53:83-102. [DOI: 10.1139/g09-090] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The formation of a fully developed gamete from an undifferentiated germ cell requires progression through numerous developmental stages and cell fate decisions. The precise timing and level of gene expression guides cells through these stages. Translational regulation is highly utilized in the germ line of many species, including Caenorhabditis elegans , to regulate gene expression and ensure the proper formation of gametes. In this review, we discuss some of the developmental stages and cell fate decisions involved in the formation of functional gametes in the C. elegans germ line in which translational control has been implicated. These stages include the mitosis versus meiosis decision, the sperm/oocyte decision, and gamete maturation. We also discuss some of the techniques used to identify mRNA targets; the identification of these targets is necessary to clearly understand the role each RNA-binding protein plays in these decisions. Relatively few mRNA targets have been identified, thus providing a major focus for future research. Finally, we propose some reasons why translational control may be utilized so heavily in the germ line. Given that many species have this substantial reliance on translational regulation for the control of gene expression in the germ line, an understanding of translational regulation in the C. elegans germ line is likely to increase our understanding of gamete formation in general.
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Affiliation(s)
- Hilary Racher
- University of Calgary, 2500 University Drive, Department of Biological Sciences, Calgary, AB T2N 1N4, Canada
| | - Dave Hansen
- University of Calgary, 2500 University Drive, Department of Biological Sciences, Calgary, AB T2N 1N4, Canada
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36
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Lee MH, Schedl T. C. elegans star proteins, GLD-1 and ASD-2, regulate specific RNA targets to control development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2010; 693:106-22. [PMID: 21189689 DOI: 10.1007/978-1-4419-7005-3_8] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
A comprehensive understanding of the C. elegans STAR proteins GLD-1 and ASD-2 is emerging from a combination of studies. Those employing genetic analysis reveal in vivo function, others involving biochemical approaches pursue the identification of mRNA targets through which these proteins act. Lastly, mechanistic studies provide the molecular pathway of target mRNA regulation.
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Affiliation(s)
- Min-Ho Lee
- Department of Biological Sciences, University at Albany, SUNY, Albany, New York 12222, USA.
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37
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38
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Translational control during early development. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2009; 90:211-54. [PMID: 20374743 DOI: 10.1016/s1877-1173(09)90006-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Translational control of specific messenger RNAs, which themselves are often asymmetrically localized within the cytoplasm of a cell, underlies many events in germline development, and in embryonic axis specification. This comprehensive, but by no means exhaustive, review attempts to present a picture of the present state of knowledge about mechanisms underlying mRNA localization and translational control of specific mRNAs that are mediated by trans-acting protein factors. While RNA localization and translational control are widespread in evolution and have been studied in many experimental systems, this article will focus mainly on three particularly well-characterized systems: Drosophila, Caenorhabditis elegans, and Xenopus. In keeping with the overall theme of this volume, instances in which translational control factors have been linked to human disease states will also be discussed.
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39
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Biedermann B, Wright J, Senften M, Kalchhauser I, Sarathy G, Lee MH, Ciosk R. Translational repression of cyclin E prevents precocious mitosis and embryonic gene activation during C. elegans meiosis. Dev Cell 2009; 17:355-64. [PMID: 19758560 DOI: 10.1016/j.devcel.2009.08.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Revised: 06/15/2009] [Accepted: 08/11/2009] [Indexed: 12/21/2022]
Abstract
Germ cells, the cells that give rise to sperm and egg, maintain the potential to recreate all cell types in a new individual. This wide developmental potential, or totipotency, is manifested in unusual tumors called teratomas, in which germ cells undergo somatic differentiation. Although recent studies have implicated RNA regulation, the mechanism that normally prevents the loss of germ cell identity remains unexplained. In C. elegans, a teratoma is induced in the absence of the conserved RNA-binding protein GLD-1. Here, we demonstrate that GLD-1 represses translation of CYE-1/cyclin E during meiotic prophase, which prevents germ cells from re-entering mitosis and inducing embryonic-like transcription. We describe a mechanism that prevents precocious mitosis in germ cells undergoing meiosis, propose that this mechanism maintains germ cell identity by delaying the onset of embryonic gene activation until after fertilization, and provide a paradigm for the possible origin of human teratomas.
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Affiliation(s)
- Bjoern Biedermann
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
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40
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41
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Ariz M, Mainpal R, Subramaniam K. C. elegans RNA-binding proteins PUF-8 and MEX-3 function redundantly to promote germline stem cell mitosis. Dev Biol 2008; 326:295-304. [PMID: 19100255 PMCID: PMC2680957 DOI: 10.1016/j.ydbio.2008.11.024] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Revised: 11/24/2008] [Accepted: 11/25/2008] [Indexed: 11/21/2022]
Abstract
Maintenance of mitotically cycling germline stem cells (GSCs) is vital for continuous production of gametes. In worms and insects, signaling from surrounding somatic cells play an essential role in the maintenance of GSCs by preventing premature differentiation. In addition, germ cell proteins such as the Drosophila Pumilio and Caenorhabditis elegans FBF, both members of the PUF family translational regulators, contribute to GSC maintenance. FBF functions by suppressing GLD-1, which promotes meiotic entry. However, factors that directly promote GSC proliferation, rather than prevent differentiation, are not known. Here we show that PUF-8, another C. elegans member of the PUF family and MEX-3, a KH domain translational regulator, function redundantly to promote GSC mitosis. We find that PUF-8 protein is highly enriched in mitotic germ cells, which is similar to the expression pattern of MEX-3 described earlier. The puf-8(−) mex-3(−) double mutant gonads contain far fewer germ cells than both single mutants and wild-type. While these cells lack mitotic, meiotic and sperm markers, they retain the germ cell-specific P granules, and are capable of gametogenesis if GLP-1, which normally blocks meiotic entry, is removed. Significantly, we find that at least one of these two proteins is essential for germ cell proliferation even in meiotic entry-defective mutants, which otherwise produce germ cell tumors. We conclude PUF-8 and MEX-3 contribute to GSC maintenance by promoting mitotic proliferation rather than by blocking meiotic entry.
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Affiliation(s)
- Mohd Ariz
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
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42
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Merritt C, Rasoloson D, Ko D, Seydoux G. 3' UTRs are the primary regulators of gene expression in the C. elegans germline. Curr Biol 2008; 18:1476-82. [PMID: 18818082 DOI: 10.1016/j.cub.2008.08.013] [Citation(s) in RCA: 275] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Revised: 07/25/2008] [Accepted: 08/05/2008] [Indexed: 11/16/2022]
Abstract
How genes are regulated to produce the correct assortment of proteins for every cell type is a fundamental question in biology. For many genes, regulation begins at the DNA level with the use of promoter sequences to control transcription. Regulation can also occur after transcription using sequences in the 3' untranslated region (UTR) of the mRNA to affect mRNA stability and/or translation [1]. The C. elegans gonad is an excellent tissue to study gene regulation during development: In the adult, germ cells are arranged in order of differentiation, with undifferentiated progenitors at one end of the gonad, cells in meiotic prophase in the middle, and gametes at the other end [2]. Using a transgenic assay, we have compared the contribution of promoters and 3' UTRs to gene regulation during germline development. We find that for most genes tested, 3' UTRs are sufficient for regulation. With the exception of promoters activated during spermatogenesis, promoters are permissive for expression in all germ cell types (from progenitors to oocytes and sperm). In progenitors, 3' UTRs inhibit the production of meiotic and oocyte proteins by posttranscriptional mechanisms involving PUF- and KH-domain RNA-binding proteins. Our findings indicate that many genes rely primarily on 3' UTRs, not promoters, for regulation during germline development.
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Affiliation(s)
- Christopher Merritt
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Center for Cell Dynamics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
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43
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Noble SL, Allen BL, Goh LK, Nordick K, Evans TC. Maternal mRNAs are regulated by diverse P body-related mRNP granules during early Caenorhabditis elegans development. J Cell Biol 2008; 182:559-72. [PMID: 18695046 PMCID: PMC2500140 DOI: 10.1083/jcb.200802128] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2008] [Accepted: 07/08/2008] [Indexed: 01/15/2023] Open
Abstract
Processing bodies (P bodies) are conserved mRNA-protein (mRNP) granules that are thought to be cytoplasmic centers for mRNA repression and degradation. However, their specific functions in vivo remain poorly understood. We find that repressed maternal mRNAs and their regulators localize to P body-like mRNP granules in the Caenorhabditis elegans germ line. Surprisingly, several distinct types of regulated granules form during oocyte and embryo development. 3' untranslated region elements direct mRNA targeting to one of these granule classes. The P body factor CAR-1/Rap55 promotes association of repressed mRNA with granules and contributes to repression of Notch/glp-1 mRNA. However, CAR-1 controls Notch/glp-1 only during late oogenesis, where it functions with the RNA-binding regulators PUF-5, PUF-6, and PUF-7. The P body protein CGH-1/Rck/Dhh1 differs from CAR-1 in control of granule morphology and promotes mRNP stability in arrested oocytes. Therefore, a system of diverse and regulated RNP granules elicits stage-specific functions that ensure proper mRNA control during early development.
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Affiliation(s)
- Scott L Noble
- Program in Molecular Biology, University of Colorado, Denver Health Sciences Center, Aurora, CO 80045, USA
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44
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Glisovic T, Bachorik JL, Yong J, Dreyfuss G. RNA-binding proteins and post-transcriptional gene regulation. FEBS Lett 2008; 582:1977-86. [PMID: 18342629 PMCID: PMC2858862 DOI: 10.1016/j.febslet.2008.03.004] [Citation(s) in RCA: 979] [Impact Index Per Article: 61.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2008] [Accepted: 03/03/2008] [Indexed: 01/11/2023]
Abstract
RNAs in cells are associated with RNA-binding proteins (RBPs) to form ribonucleoprotein (RNP) complexes. The RBPs influence the structure and interactions of the RNAs and play critical roles in their biogenesis, stability, function, transport and cellular localization. Eukaryotic cells encode a large number of RBPs (thousands in vertebrates), each of which has unique RNA-binding activity and protein-protein interaction characteristics. The remarkable diversity of RBPs, which appears to have increased during evolution in parallel to the increase in the number of introns, allows eukaryotic cells to utilize them in an enormous array of combinations giving rise to a unique RNP for each RNA. In this short review, we focus on the RBPs that interact with pre-mRNAs and mRNAs and discuss their roles in the regulation of post-transcriptional gene expression.
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Affiliation(s)
- Tina Glisovic
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6148, United States
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45
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Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet 2008; 9:102-14. [PMID: 18197166 DOI: 10.1038/nrg2290] [Citation(s) in RCA: 3864] [Impact Index Per Article: 241.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
MicroRNAs constitute a large family of small, approximately 21-nucleotide-long, non-coding RNAs that have emerged as key post-transcriptional regulators of gene expression in metazoans and plants. In mammals, microRNAs are predicted to control the activity of approximately 30% of all protein-coding genes, and have been shown to participate in the regulation of almost every cellular process investigated so far. By base pairing to mRNAs, microRNAs mediate translational repression or mRNA degradation. This Review summarizes the current understanding of the mechanistic aspects of microRNA-induced repression of translation and discusses some of the controversies regarding different modes of microRNA function.
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Tissue development and RNA control: “HOW” is it coordinated? Trends Genet 2008; 24:94-101. [DOI: 10.1016/j.tig.2007.11.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Revised: 11/22/2007] [Accepted: 11/22/2007] [Indexed: 11/20/2022]
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Abstract
Sexual identity is one of the most important factors that determine how an animal will develop. Although it controls many dimorphic tissues in the body, its most ancient role is in the germ line, where it species that some cells become sperm, and others become eggs. In most animals, these two fates occur in distinct sexes. However, certain nematodes like C. elegans produce XX hermaphrodites, which make both types of gametes. In these animals, a core sex-determination pathway regulates the development of both the body and the germ line. However, modifier genes alter the activity of this pathway in germ cells, and these changes are critical for allowing XX animals to produce oocytes and sperm in an otherwise female body. In this review, I focus on (1) the core sex-determination pathway, (2) the activity of the transcription factor TRA-1 and its immediate targets fog-1 and fog-3 in germ cells, (3) how the regulation of tra-2 activity allows XX spermatogenesis, and (4) how the regulation of fem-3 activity maintains the appropriate balance between TRA-2 and FEM-3 in the germ line. Finally, I consider the major questions in this field that are driving new research.
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Affiliation(s)
- Ronald E Ellis
- Department of Molecular Biology, School of Osteopathic Medicine, B303 Science Center, The University of Medicine and Dentistry of New Jersey, Stratford, NJ 08084, USA
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Buchet-Poyau K, Courchet J, Hir HL, Séraphin B, Scoazec JY, Duret L, Domon-Dell C, Freund JN, Billaud M. Identification and characterization of human Mex-3 proteins, a novel family of evolutionarily conserved RNA-binding proteins differentially localized to processing bodies. Nucleic Acids Res 2007; 35:1289-300. [PMID: 17267406 PMCID: PMC1851655 DOI: 10.1093/nar/gkm016] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In Caenorhabditis elegans, the Mex-3 protein is a translational regulator that specifies the posterior blastomere identity in the early embryo and contributes to the maintenance of the germline totipotency. We have now identified a family of four homologous human Mex-3 genes, called hMex-3A to -3D that encode proteins containing two heterogeneous nuclear ribonucleoprotein K homology (KH) domains and one carboxy-terminal RING finger module. The hMex-3 are phosphoproteins that bind RNA through their KH domains and shuttle between the nucleus and the cytoplasm via the CRM1-dependent export pathway. Our analysis further revealed that hMex-3A and hMex-3B, but not hMex-3C, colocalize with both the hDcp1a decapping factor and Argonaute (Ago) proteins in processing bodies (P bodies), recently characterized as centers of mRNA turnover. Taken together, these findings indicate that hMex-3 proteins constitute a novel family of evolutionarily conserved RNA-binding proteins, differentially recruited to P bodies and potentially involved in post-transcriptional regulatory mechanisms.
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Affiliation(s)
- Karine Buchet-Poyau
- Université de Lyon, Lyon, F-69003, France; université Lyon 1, Domaine Rockefeller, Lyon, F-69003, France; CNRS UMR 5201, Laboratoire de Génétique Moléculaire, Signalisation et Cancer, Lyon, F-69003, France, CNRS UPR 2167, 6 avenue de la Terrasse, 91198 Gif sur Yvette, France, Service Central d’Anatomie et Cytologie Pathologiques, Hôpital Edouard Herriot, 69437 Lyon, France, CNRS UMR 5558, 16 rue Dubois, 69622 Villeurbanne Cedex, France and INSERM U682, 3 avenue Molière, 67200 Strasbourg, France
| | - Julien Courchet
- Université de Lyon, Lyon, F-69003, France; université Lyon 1, Domaine Rockefeller, Lyon, F-69003, France; CNRS UMR 5201, Laboratoire de Génétique Moléculaire, Signalisation et Cancer, Lyon, F-69003, France, CNRS UPR 2167, 6 avenue de la Terrasse, 91198 Gif sur Yvette, France, Service Central d’Anatomie et Cytologie Pathologiques, Hôpital Edouard Herriot, 69437 Lyon, France, CNRS UMR 5558, 16 rue Dubois, 69622 Villeurbanne Cedex, France and INSERM U682, 3 avenue Molière, 67200 Strasbourg, France
| | - Hervé Le Hir
- Université de Lyon, Lyon, F-69003, France; université Lyon 1, Domaine Rockefeller, Lyon, F-69003, France; CNRS UMR 5201, Laboratoire de Génétique Moléculaire, Signalisation et Cancer, Lyon, F-69003, France, CNRS UPR 2167, 6 avenue de la Terrasse, 91198 Gif sur Yvette, France, Service Central d’Anatomie et Cytologie Pathologiques, Hôpital Edouard Herriot, 69437 Lyon, France, CNRS UMR 5558, 16 rue Dubois, 69622 Villeurbanne Cedex, France and INSERM U682, 3 avenue Molière, 67200 Strasbourg, France
| | - Bertrand Séraphin
- Université de Lyon, Lyon, F-69003, France; université Lyon 1, Domaine Rockefeller, Lyon, F-69003, France; CNRS UMR 5201, Laboratoire de Génétique Moléculaire, Signalisation et Cancer, Lyon, F-69003, France, CNRS UPR 2167, 6 avenue de la Terrasse, 91198 Gif sur Yvette, France, Service Central d’Anatomie et Cytologie Pathologiques, Hôpital Edouard Herriot, 69437 Lyon, France, CNRS UMR 5558, 16 rue Dubois, 69622 Villeurbanne Cedex, France and INSERM U682, 3 avenue Molière, 67200 Strasbourg, France
| | - Jean-Yves Scoazec
- Université de Lyon, Lyon, F-69003, France; université Lyon 1, Domaine Rockefeller, Lyon, F-69003, France; CNRS UMR 5201, Laboratoire de Génétique Moléculaire, Signalisation et Cancer, Lyon, F-69003, France, CNRS UPR 2167, 6 avenue de la Terrasse, 91198 Gif sur Yvette, France, Service Central d’Anatomie et Cytologie Pathologiques, Hôpital Edouard Herriot, 69437 Lyon, France, CNRS UMR 5558, 16 rue Dubois, 69622 Villeurbanne Cedex, France and INSERM U682, 3 avenue Molière, 67200 Strasbourg, France
| | - Laurent Duret
- Université de Lyon, Lyon, F-69003, France; université Lyon 1, Domaine Rockefeller, Lyon, F-69003, France; CNRS UMR 5201, Laboratoire de Génétique Moléculaire, Signalisation et Cancer, Lyon, F-69003, France, CNRS UPR 2167, 6 avenue de la Terrasse, 91198 Gif sur Yvette, France, Service Central d’Anatomie et Cytologie Pathologiques, Hôpital Edouard Herriot, 69437 Lyon, France, CNRS UMR 5558, 16 rue Dubois, 69622 Villeurbanne Cedex, France and INSERM U682, 3 avenue Molière, 67200 Strasbourg, France
| | - Claire Domon-Dell
- Université de Lyon, Lyon, F-69003, France; université Lyon 1, Domaine Rockefeller, Lyon, F-69003, France; CNRS UMR 5201, Laboratoire de Génétique Moléculaire, Signalisation et Cancer, Lyon, F-69003, France, CNRS UPR 2167, 6 avenue de la Terrasse, 91198 Gif sur Yvette, France, Service Central d’Anatomie et Cytologie Pathologiques, Hôpital Edouard Herriot, 69437 Lyon, France, CNRS UMR 5558, 16 rue Dubois, 69622 Villeurbanne Cedex, France and INSERM U682, 3 avenue Molière, 67200 Strasbourg, France
| | - Jean-Noël Freund
- Université de Lyon, Lyon, F-69003, France; université Lyon 1, Domaine Rockefeller, Lyon, F-69003, France; CNRS UMR 5201, Laboratoire de Génétique Moléculaire, Signalisation et Cancer, Lyon, F-69003, France, CNRS UPR 2167, 6 avenue de la Terrasse, 91198 Gif sur Yvette, France, Service Central d’Anatomie et Cytologie Pathologiques, Hôpital Edouard Herriot, 69437 Lyon, France, CNRS UMR 5558, 16 rue Dubois, 69622 Villeurbanne Cedex, France and INSERM U682, 3 avenue Molière, 67200 Strasbourg, France
| | - Marc Billaud
- Université de Lyon, Lyon, F-69003, France; université Lyon 1, Domaine Rockefeller, Lyon, F-69003, France; CNRS UMR 5201, Laboratoire de Génétique Moléculaire, Signalisation et Cancer, Lyon, F-69003, France, CNRS UPR 2167, 6 avenue de la Terrasse, 91198 Gif sur Yvette, France, Service Central d’Anatomie et Cytologie Pathologiques, Hôpital Edouard Herriot, 69437 Lyon, France, CNRS UMR 5558, 16 rue Dubois, 69622 Villeurbanne Cedex, France and INSERM U682, 3 avenue Molière, 67200 Strasbourg, France
- *To whom correspondence should be addressed. Tel: (+33) 478 77 72 14; Fax: (+33) 478 77 72 20; E-mail:
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Lublin AL, Evans TC. The RNA-binding proteins PUF-5, PUF-6, and PUF-7 reveal multiple systems for maternal mRNA regulation during C. elegans oogenesis. Dev Biol 2006; 303:635-49. [PMID: 17234175 DOI: 10.1016/j.ydbio.2006.12.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2006] [Revised: 11/25/2006] [Accepted: 12/02/2006] [Indexed: 02/04/2023]
Abstract
In metazoans, many mRNAs needed for embryogenesis are produced during oogenesis and must be tightly regulated during the complex events of oocyte development. In C. elegans, translation of the Notch receptor GLP-1 is repressed during oogenesis and is then activated specifically in anterior cells of the early embryo. The KH domain protein GLD-1 represses glp-1 translation during early stages of meiosis, but the factors that repress glp-1 during late oogenesis are not known. Here, we provide evidence that the PUF domain protein PUF-5 and two nearly identical PUF proteins PUF-6 and PUF-7 function during a specific period of oocyte differentiation to repress glp-1 and other maternal mRNAs. Depletion of PUF-5 and PUF-6/7 together caused defects in oocyte formation and early embryonic cell divisions. Loss of PUF-5 and PUF-6/7 also caused inappropriate expression of GLP-1 protein in oocytes, but GLP-1 remained repressed in meiotic germ cells. PUF-5 and PUF-6/7 function was required directly or indirectly for translational repression through elements of the glp-1 3' untranslated region. Oogenesis and embryonic defects could not be rescued by loss of GLP-1 activity, suggesting that PUF-5 and PUF-6/7 regulate other mRNAs in addition to glp-1. PUF-5 and PUF-6/7 depletion, however, did not perturb repression of the maternal factors GLD-1 and POS-1, suggesting that subsets of maternal gene products may be regulated by distinct pathways. Interestingly, PUF-5 protein was detected exclusively during mid to late oogenesis but became undetectable prior to completion of oocyte differentiation. These results reveal a previously unknown maternal mRNA control system that is specific to late stages of oogenesis and suggest new functions for PUF family proteins in post-mitotic differentiation. Multiple sets of RNA-binding complexes function in different domains of the C. elegans germ line to maintain silencing of Notch/glp-1 and other mRNAs.
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Affiliation(s)
- Alex L Lublin
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Mail Stop 8108, P.O. Box 6511, Aurora, CO 80045, USA
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50
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Gallo CM, Seydoux G. Toti "potent" repressors. Bioessays 2006; 28:865-7. [PMID: 16937341 DOI: 10.1002/bies.20454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A fascinating property of germ cells is their ability to maintain totipotency throughout development. At fertilization, this totipotency is unleashed and the egg generates all the cell types needed to make a brand new organism. Occasionally, germ cells differentiate precociously in the embryo or in the gonads and form teratomas, tumors containing many differentiated somatic cell types. Until recently, the genetic basis for teratoma formation was not known. The unexpected discovery of a teratoma in a C. elegans double mutant points to translational control as a key mechanism to maintain totipotency in developing germ cells.
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Affiliation(s)
- Christopher M Gallo
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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