1
|
Nandhini S, Thiruppathi G, Ranjani M, Puschmann H, Ravi M, Sundararaj P, Prabhakaran R. Effect of ruthenium(II) complexes on MDA-MB-231 cells and lifespan/tumor growth in gld-1mutant, Daf-16 TF and stress productive genes: A perspective study. J Inorg Biochem 2024; 257:112580. [PMID: 38701694 DOI: 10.1016/j.jinorgbio.2024.112580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/17/2024] [Accepted: 04/26/2024] [Indexed: 05/05/2024]
Abstract
Pincer type coumarin based N-substituted semicarbazone ligands HL1-4 and their corresponding ruthenium(II) complexes (1-4) were synthesized, analyzed and confirmed by various spectro analytical techniques. The molecular structure of the ligand HL3 and complex 3 was confirmed by single crystal X-ray diffraction analysis. The stoichiometry of complexes 1, 2 and 4 was confirmed by high resolution mass spectroscopy (HRMS). The binding affinity of the compounds with CT-DNA (Calf Thymus DNA) and BSA (Bovine Serum Albumin) was established by absorption and emission titration methods. The results of In vitro cytotoxicity showed the significant cytotoxic potential of the complexes against MDA-MB-231 cells (TNBC- Triple-negative breast cancer). Among the complexes, 1 and 4 have shown appreciable results. Further, antimigratory activity against the MDA-MB-231 cells was studied for the complexes 1 and 4. The percentage cell cycle arrest, apoptosis and necrosis were explored by flow cytometry. The in vivo anti-tumor activity of the complexes 1 and 4 using C. elegans as model organism was established by using the tumoral C. elegans strain JK1466 (gld-1(q485)), which bears a mutation in the gld-1 tumor suppressor gene. We have determined the effect of our complexes on tumor gonad reduction and found to be non toxic to the JK1466 worms and they have prolonged their mean lifespan with potential antioxidant ability by overcoming stress responses. Overall, our study reported herein demonstrated that the complexes 1 and 4 could be established as potential metallo-drugs substantiating further exploration.
Collapse
Affiliation(s)
- S Nandhini
- Department of Chemistry, Bharathiar University, Coimbatore 641 046, India
| | - G Thiruppathi
- Department of Zoology, Bharathiar University, Coimbatore 641 046, India
| | - M Ranjani
- Department of Chemistry, Bharathiar University, Coimbatore 641 046, India
| | - Horst Puschmann
- Department of Chemistry, Durham University, Durham DH1 3LE, UK
| | - M Ravi
- Department of Biochemistry, University of Madras, Guindy Campus, Chennai 600025, India
| | - P Sundararaj
- Department of Zoology, Bharathiar University, Coimbatore 641 046, India
| | - R Prabhakaran
- Department of Chemistry, Bharathiar University, Coimbatore 641 046, India.
| |
Collapse
|
2
|
Nandhini S, Ranjani M, Thiruppathi G, Jaithanya YM, Kalaiarasi G, Ravi M, Prabusankar G, Malecki JG, Sundararaj P, Prabhakaran R. Organoruthenium metallocycle induced mutation in gld-1 tumor suppression gene in JK1466 strain and appreciable lifespan expansion. J Inorg Biochem 2024; 257:112593. [PMID: 38754275 DOI: 10.1016/j.jinorgbio.2024.112593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/02/2024] [Accepted: 05/04/2024] [Indexed: 05/18/2024]
Abstract
Four Ru(II) complexes (A2-A5) were synthesized from the reaction of coumarin Schiff base ligands (7da2-tsc, 7da3-mtsc, 7da4-etsc and 7da5-ptsc) with [RuHCl(CO)(PPh3)3]. The compounds were characterized by FT-IR, UV-Vis, 1H, 13C and 31P NMR, mass spectrometry and crystallographic analysis. Calf Thymus DNA (CT-DNA) binding studies revealed the intercalative mode of binding of the complexes with DNA. The results of Bovine serum albumin (BSA) binding studies established the interaction between BSA followed static quenching mechanism. The cytotoxic effects of the complexes and the ligands were evaluated against breast (MCF-7 and MDA-MB-231) and lung carcinoma cell lines (A549 and NCI-H460) using MTT assay. Complex A4 demonstrated potent cytotoxic effects on both breast and lung cancer cells. Furthermore, morphological observations and FACS analysis showed the decrease in cell density by complex A4 by induced morphological changes and apoptotic body formation and cell death in both breast and lung cancer cells. Moreover, the invertebrate model Caenorhabditis elegans was employed to assess the in vivo anticancer activity of compound A4. The findings indicated that the treatment with A4 reduced tumor development and significantly extended organismal lifespan by 64 % in the tumoral strain JK1466 without adversely affecting essential physiological functions of the worm. Additionally, A4 demonstrated an upregulation of two crucial antioxidant defense genes. Overall, these results suggested that the compound A4 can be a potential candidate with novel chemotherapeutic applications.
Collapse
Affiliation(s)
- S Nandhini
- Department of Chemistry, Bharathiar University, Coimbatore 641 046, India
| | - M Ranjani
- Department of Chemistry, Bharathiar University, Coimbatore 641 046, India
| | - G Thiruppathi
- Department of Zoology, Bharathiar University, Coimbatore 641 046, India
| | - Y M Jaithanya
- Department of Biochemistry, University of Madras, Guindy Campus, Chennai 600025, India
| | - G Kalaiarasi
- Department of Chemistry, Bharathiar University, Coimbatore 641 046, India
| | - M Ravi
- Department of Biochemistry, University of Madras, Guindy Campus, Chennai 600025, India.
| | - G Prabusankar
- Department of Chemistry, Indian Institute of Technology, Hyderabad 502285, India
| | - J G Malecki
- Department of Crystallography, Silesia University, Szkolna 9, 40-006 Katowice, Poland
| | - P Sundararaj
- Department of Zoology, Bharathiar University, Coimbatore 641 046, India
| | - R Prabhakaran
- Department of Chemistry, Bharathiar University, Coimbatore 641 046, India.
| |
Collapse
|
3
|
Du Z, Tong D, Chen X, Wu F, Jiang S, Zhang J, Yang Y, Wang R, Gantuya S, Davaajargal T, Lkhagvatseren S, Batsukh Z, Du A, Ma G. Genome-wide RNA interference of the nhr gene family in barber's pole worm identified members crucial for larval viability in vitro. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 122:105609. [PMID: 38806077 DOI: 10.1016/j.meegid.2024.105609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 05/30/2024]
Abstract
Nuclear hormone receptors (NHRs) are emerging target candidates against nematode infection and resistance. However, there is a lack of comprehensive information on NHR-coding genes in parasitic nematodes. In this study, we curated the nhr gene family for 60 major parasitic nematodes from humans and animals. Compared with the free-living model organism Caenorhabditis elegans, a remarkable contraction of the nhr family was revealed in parasitic species, with genetic diversification and conservation unveiled among nematode Clades I (10-13), III (16-42), IV (33-35) and V (25-64). Using an in vitro biosystem, we demonstrated that 40 nhr genes in a blood-feeding nematode Haemonchus contortus (clade V; barber's pole worm) were responsive to host serum and one nhr gene (i.e., nhr-64) was consistently stimulated by anthelmintics (i.e., ivermectin, thiabendazole and levamisole); Using a high-throughput RNA interference platform, we knocked down 43 nhr genes of H. contortus and identified at least two genes that are required for the viability (i.e., nhr-105) and development (i.e., nhr-17) of the infective larvae of this parasitic nematode in vitro. Harnessing this preliminary functional atlas of nhr genes for H. contortus will prime the biological studies of this gene family in nematode genetics, infection, and anthelmintic metabolism within host animals, as well as the promising discovery of novel intervention targets.
Collapse
Affiliation(s)
- Zhendong Du
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Danni Tong
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Xueqiu Chen
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Fei Wu
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Shengjun Jiang
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Jingju Zhang
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Yi Yang
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Rui Wang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia 010018, China
| | - Sambuu Gantuya
- Institute of Veterinary Medicine, Mongolian University of Life Sciences, Ulaanbaatar 17024, Mongolia
| | - Tserennyam Davaajargal
- Institute of Veterinary Medicine, Mongolian University of Life Sciences, Ulaanbaatar 17024, Mongolia
| | - Sukhbaatar Lkhagvatseren
- Institute of Veterinary Medicine, Mongolian University of Life Sciences, Ulaanbaatar 17024, Mongolia.
| | - Zayat Batsukh
- Institute of Veterinary Medicine, Mongolian University of Life Sciences, Ulaanbaatar 17024, Mongolia.
| | - Aifang Du
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Guangxu Ma
- College of Animal Sciences, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Zhejiang University, Hangzhou 310058, China; Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia.
| |
Collapse
|
4
|
Pugsley L, Naineni SK, Amiri M, Yanagiya A, Cencic R, Sonenberg N, Pelletier J. C8ORF88: A Novel eIF4E-Binding Protein. Genes (Basel) 2023; 14:2076. [PMID: 38003019 PMCID: PMC10670996 DOI: 10.3390/genes14112076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Translation initiation in eukaryotes is regulated at several steps, one of which involves the availability of the cap binding protein to participate in cap-dependent protein synthesis. Binding of eIF4E to translational repressors (eIF4E-binding proteins [4E-BPs]) suppresses translation and is used by cells to link extra- and intracellular cues to protein synthetic rates. The best studied of these interactions involves repression of translation by 4E-BP1 upon inhibition of the PI3K/mTOR signaling pathway. Herein, we characterize a novel 4E-BP, C8ORF88, whose expression is predominantly restricted to early spermatids. C8ORF88:eIF4E interaction is dependent on the canonical eIF4E binding motif (4E-BM) present in other 4E-BPs. Whereas 4E-BP1:eIF4E interaction is dependent on the phosphorylation of 4E-BP1, these sites are not conserved in C8ORF88 indicating a different mode of regulation.
Collapse
Affiliation(s)
- Lauren Pugsley
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; (L.P.); (S.K.N.); (M.A.); (N.S.)
| | - Sai Kiran Naineni
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; (L.P.); (S.K.N.); (M.A.); (N.S.)
| | - Mehdi Amiri
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; (L.P.); (S.K.N.); (M.A.); (N.S.)
| | | | - Regina Cencic
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; (L.P.); (S.K.N.); (M.A.); (N.S.)
| | - Nahum Sonenberg
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; (L.P.); (S.K.N.); (M.A.); (N.S.)
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada; (L.P.); (S.K.N.); (M.A.); (N.S.)
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| |
Collapse
|
5
|
Özcan I, Tursun B. Identifying Molecular Roadblocks for Transcription Factor-Induced Cellular Reprogramming In Vivo by Using C. elegans as a Model Organism. J Dev Biol 2023; 11:37. [PMID: 37754839 PMCID: PMC10531806 DOI: 10.3390/jdb11030037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/18/2023] [Accepted: 08/29/2023] [Indexed: 09/28/2023] Open
Abstract
Generating specialized cell types via cellular transcription factor (TF)-mediated reprogramming has gained high interest in regenerative medicine due to its therapeutic potential to repair tissues and organs damaged by diseases or trauma. Organ dysfunction or improper tissue functioning might be restored by producing functional cells via direct reprogramming, also known as transdifferentiation. Regeneration by converting the identity of available cells in vivo to the desired cell fate could be a strategy for future cell replacement therapies. However, the generation of specific cell types via reprogramming is often restricted due to cell fate-safeguarding mechanisms that limit or even block the reprogramming of the starting cell type. Nevertheless, efficient reprogramming to generate homogeneous cell populations with the required cell type's proper molecular and functional identity is critical. Incomplete reprogramming will lack therapeutic potential and can be detrimental as partially reprogrammed cells may acquire undesired properties and develop into tumors. Identifying and evaluating molecular barriers will improve reprogramming efficiency to reliably establish the target cell identity. In this review, we summarize how using the nematode C. elegans as an in vivo model organism identified molecular barriers of TF-mediated reprogramming. Notably, many identified molecular factors have a high degree of conservation and were subsequently shown to block TF-induced reprogramming of mammalian cells.
Collapse
Affiliation(s)
- Ismail Özcan
- Department of Biology, Institute of Cell and Systems Biology of Animals, University of Hamburg, 20146 Hamburg, Germany
| | - Baris Tursun
- Department of Biology, Institute of Cell and Systems Biology of Animals, University of Hamburg, 20146 Hamburg, Germany
| |
Collapse
|
6
|
Ruthig VA, Hatkevich T, Hardy J, Friedersdorf MB, Mayère C, Nef S, Keene JD, Capel B. The RNA binding protein DND1 is elevated in a subpopulation of pro-spermatogonia and targets chromatin modifiers and translational machinery during late gestation. PLoS Genet 2023; 19:e1010656. [PMID: 36857387 PMCID: PMC10010562 DOI: 10.1371/journal.pgen.1010656] [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] [Received: 07/01/2022] [Revised: 03/13/2023] [Accepted: 02/06/2023] [Indexed: 03/02/2023] Open
Abstract
DND1 is essential to maintain germ cell identity. Loss of Dnd1 function results in germ cell differentiation to teratomas in some inbred strains of mice or to somatic fates in zebrafish. Using our knock-in mouse line in which a functional fusion protein between DND1 and GFP is expressed from the endogenous locus (Dnd1GFP), we distinguished two male germ cell (MGC) populations during late gestation cell cycle arrest (G0), consistent with recent reports of heterogeneity among MGCs. Most MGCs express lower levels of DND1-GFP (DND1-GFP-lo), but some MGCs express elevated levels of DND1-GFP (DND1-GFP-hi). A RNA-seq time course confirmed high Dnd1 transcript levels in DND1-GFP-hi cells along with 5-10-fold higher levels for multiple epigenetic regulators. Using antibodies against DND1-GFP for RNA immunoprecipitation (RIP)-sequencing, we identified multiple epigenetic and translational regulators that are binding targets of DND1 during G0 including DNA methyltransferases (Dnmts), histone deacetylases (Hdacs), Tudor domain proteins (Tdrds), actin dependent regulators (Smarcs), and a group of ribosomal and Golgi proteins. These data suggest that in DND1-GFP-hi cells, DND1 hosts coordinating mRNA regulons that consist of functionally related and localized groups of epigenetic enzymes and translational components.
Collapse
Affiliation(s)
- Victor A. Ruthig
- Sexual Medicine Lab, Department of Urology, Weill Cornell Medicine, New York, New York, United States of America
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Talia Hatkevich
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Josiah Hardy
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Matthew B. Friedersdorf
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Chloé Mayère
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
- iGE3, Institute of Genetics and Genomics of Geneva, University of Geneva, Geneva, Switzerland
| | - Serge Nef
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
- iGE3, Institute of Genetics and Genomics of Geneva, University of Geneva, Geneva, Switzerland
| | - Jack D. Keene
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Blanche Capel
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| |
Collapse
|
7
|
Domingo-Muelas A, Duart-Abadia P, Morante-Redolat JM, Jordán-Pla A, Belenguer G, Fabra-Beser J, Paniagua-Herranz L, Pérez-Villalba A, Álvarez-Varela A, Barriga FM, Gil-Sanz C, Ortega F, Batlle E, Fariñas I. Post-transcriptional control of a stemness signature by RNA-binding protein MEX3A regulates murine adult neurogenesis. Nat Commun 2023; 14:373. [PMID: 36690670 PMCID: PMC9871011 DOI: 10.1038/s41467-023-36054-6] [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: 08/01/2022] [Accepted: 01/12/2023] [Indexed: 01/25/2023] Open
Abstract
Neural stem cells (NSCs) in the adult murine subependymal zone balance their self-renewal capacity and glial identity with the potential to generate neurons during the lifetime. Adult NSCs exhibit lineage priming via pro-neurogenic fate determinants. However, the protein levels of the neural fate determinants are not sufficient to drive direct differentiation of adult NSCs, which raises the question of how cells along the neurogenic lineage avoid different conflicting fate choices, such as self-renewal and differentiation. Here, we identify RNA-binding protein MEX3A as a post-transcriptional regulator of a set of stemness associated transcripts at critical transitions in the subependymal neurogenic lineage. MEX3A regulates a quiescence-related RNA signature in activated NSCs that is needed for their return to quiescence, playing a role in the long-term maintenance of the NSC pool. Furthermore, it is required for the repression of the same program at the onset of neuronal differentiation. Our data indicate that MEX3A is a pivotal regulator of adult murine neurogenesis acting as a translational remodeller.
Collapse
Grants
- EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
- Ministerio de Ciencia e Innovación (MICINN, Spain) - PID2020-119917RB-I00.
- Regional Government of Valencia | Conselleria d'Educació, Investigació, Cultura i Esport (Conselleria d'Educació, Investigació, Cultura i Esport de la Generalitat Valenciana)
- Ministerio de Ciencia e Innovación (MICINN, Spain) - PID2020-117937GB-I00, PID2020-119917RB-I00, PID 2019-109155RB-I00, PID2020-114227RB-I00, RyC-2015-19058, PRE2018-084838. Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED, Spain) - MICINN- CB06/05/0086.
Collapse
Affiliation(s)
- Ana Domingo-Muelas
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Pere Duart-Abadia
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Jose Manuel Morante-Redolat
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Antonio Jordán-Pla
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
| | - Germán Belenguer
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Jaime Fabra-Beser
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
| | - Lucía Paniagua-Herranz
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense de Madrid (UCM), Madrid, Spain
- Instituto Universitario de Investigación en Neuroquímica (IUIN), Madrid, Spain
- Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Ana Pérez-Villalba
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Adrián Álvarez-Varela
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Francisco M Barriga
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Cristina Gil-Sanz
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain
| | - Felipe Ortega
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense de Madrid (UCM), Madrid, Spain
- Instituto Universitario de Investigación en Neuroquímica (IUIN), Madrid, Spain
- Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Isabel Fariñas
- Departamento de Biología Celular, Biología Funcional y Antropología Física, Universidad de Valencia, Valencia, Spain.
- Instituto de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, Valencia, Spain.
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Valencia, Spain.
| |
Collapse
|
8
|
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.
Collapse
|
9
|
Rochester JD, Min H, Gajjar GA, Sharp CS, Maki NJ, Rollins JA, Keiper BD, Graber JH, Updike DL. GLH-1/Vasa represses neuropeptide expression and drives spermiogenesis in the C. elegans germline. Dev Biol 2022; 492:200-211. [PMID: 36273621 PMCID: PMC9677334 DOI: 10.1016/j.ydbio.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/26/2022] [Accepted: 10/07/2022] [Indexed: 01/09/2023]
Abstract
Germ granules harbor processes that maintain germline integrity and germline stem cell capacity. Depleting core germ granule components in C. elegans leads to the reprogramming of germ cells, causing them to express markers of somatic differentiation in day-two adults. Somatic reprogramming is associated with complete sterility at this stage. The resulting germ cell atrophy and other pleiotropic defects complicate our understanding of the initiation of reprogramming and how processes within germ granules safeguard the totipotency and immortal potential of germline stem cells. To better understand the initial events of somatic reprogramming, we examined total mRNA (transcriptome) and polysome-associated mRNA (translatome) changes in a precision full-length deletion of glh-1, which encodes a homolog of the germline-specific Vasa/DDX4 DEAD-box RNA helicase. Fertile animals at a permissive temperature were analyzed as young adults, a stage that precedes by 24 h the previously determined onset of somatic reporter-gene expression in the germline. Two significant changes are observed at this early stage. First, the majority of neuropeptide-encoding transcripts increase in both the total and polysomal mRNA fractions, suggesting that GLH-1 or its effectors suppress this expression. Second, there is a significant decrease in Major Sperm Protein (MSP)-domain mRNAs when glh-1 is deleted. We find that the presence of GLH-1 helps repress spermatogenic expression during oogenesis, but boosts MSP expression to drive spermiogenesis and sperm motility. These insights define an early role for GLH-1 in repressing somatic reprogramming to maintain germline integrity.
Collapse
Affiliation(s)
- Jesse D Rochester
- Kathryn W. Davis Center for Regenerative Biology and Aging, The Mount Desert Island Biological Laboratory, Bar Harbor, ME, United States; Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, United States
| | - Hyemin Min
- Kathryn W. Davis Center for Regenerative Biology and Aging, The Mount Desert Island Biological Laboratory, Bar Harbor, ME, United States
| | - Gita A Gajjar
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC, United States
| | - Catherine S Sharp
- Kathryn W. Davis Center for Regenerative Biology and Aging, The Mount Desert Island Biological Laboratory, Bar Harbor, ME, United States
| | - Nathaniel J Maki
- Kathryn W. Davis Center for Regenerative Biology and Aging, The Mount Desert Island Biological Laboratory, Bar Harbor, ME, United States
| | - Jarod A Rollins
- Kathryn W. Davis Center for Regenerative Biology and Aging, The Mount Desert Island Biological Laboratory, Bar Harbor, ME, United States
| | - Brett D Keiper
- Department of Biochemistry and Molecular Biology, Brody School of Medicine, East Carolina University, Greenville, NC, United States
| | - Joel H Graber
- Kathryn W. Davis Center for Regenerative Biology and Aging, The Mount Desert Island Biological Laboratory, Bar Harbor, ME, United States
| | - Dustin L Updike
- Kathryn W. Davis Center for Regenerative Biology and Aging, The Mount Desert Island Biological Laboratory, Bar Harbor, ME, United States.
| |
Collapse
|
10
|
Phillips CM, Updike DL. Germ granules and gene regulation in the Caenorhabditis elegans germline. Genetics 2022; 220:6541922. [PMID: 35239965 PMCID: PMC8893257 DOI: 10.1093/genetics/iyab195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 10/10/2021] [Indexed: 01/27/2023] Open
Abstract
The transparency of Caenorhabditis elegans provides a unique window to observe and study the function of germ granules. Germ granules are specialized ribonucleoprotein (RNP) assemblies specific to the germline cytoplasm, and they are largely conserved across Metazoa. Within the germline cytoplasm, they are positioned to regulate mRNA abundance, translation, small RNA production, and cytoplasmic inheritance to help specify and maintain germline identity across generations. Here we provide an overview of germ granules and focus on the significance of more recent observations that describe how they further demix into sub-granules, each with unique compositions and functions.
Collapse
Affiliation(s)
- Carolyn M Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA,Corresponding author: (C.M.P.); (D.L.U.)
| | - Dustin L Updike
- The Mount Desert Island Biological Laboratory, Bar Harbor, ME 04672, USA,Corresponding author: (C.M.P.); (D.L.U.)
| |
Collapse
|
11
|
The great small organisms of developmental genetics: Caenorhabditis elegans and Drosophila melanogaster. Dev Biol 2022; 485:93-122. [PMID: 35247454 PMCID: PMC9092520 DOI: 10.1016/j.ydbio.2022.02.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/25/2022] [Accepted: 02/27/2022] [Indexed: 12/30/2022]
Abstract
Experimental embryologists working at the turn of the 19th century suggested fundamental mechanisms of development, such as localized cytoplasmic determinants and tissue induction. However, the molecular basis underlying these processes proved intractable for a long time, despite concerted efforts in many developmental systems to isolate factors with a biological role. That road block was overcome by combining developmental biology with genetics. This powerful approach used unbiased genome-wide screens to isolate mutants with developmental defects and to thereby identify genes encoding key determinants and regulatory pathways that govern development. Two small invertebrates were the pioneers: the fruit fly Drosophila melanogaster and the nematode Caenorhabditis elegans. Their modes of development differ in many ways, but the two together led the way to unraveling the molecular mechanisms of many fundamental developmental processes. The discovery of the grand homologies between key players in development throughout the animal kingdom underscored the usefulness of studying these small invertebrate models for animal development and even human disease. We describe developmental genetics in Drosophila and C. elegans up to the rise of genomics at the beginning of the 21st Century. Finally, we discuss themes that emerge from the histories of such distinct organisms and prospects of this approach for the future.
Collapse
|
12
|
Marchal I, Tursun B. Induced Neurons From Germ Cells in Caenorhabditis elegans. Front Neurosci 2021; 15:771687. [PMID: 34924939 PMCID: PMC8678065 DOI: 10.3389/fnins.2021.771687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/08/2021] [Indexed: 11/28/2022] Open
Abstract
Cell fate conversion by the forced overexpression of transcription factors (TFs) is a process known as reprogramming. It leads to de-differentiation or trans-differentiation of mature cells, which could then be used for regenerative medicine applications to replenish patients suffering from, e.g., neurodegenerative diseases, with healthy neurons. However, TF-induced reprogramming is often restricted due to cell fate safeguarding mechanisms, which require a better understanding to increase reprogramming efficiency and achieve higher fidelity. The germline of the nematode Caenorhabditis elegans has been a powerful model to investigate the impediments of generating neurons from germ cells by reprogramming. A number of conserved factors have been identified that act as a barrier for TF-induced direct reprogramming of germ cells to neurons. In this review, we will first summarize our current knowledge regarding cell fate safeguarding mechanisms in the germline. Then, we will focus on the molecular mechanisms underlying neuronal induction from germ cells upon TF-mediated reprogramming. We will shortly discuss the specific characteristics that might make germ cells especially fit to change cellular fate and become neurons. For future perspectives, we will look at the potential of C. elegans research in advancing our knowledge of the mechanisms that regulate cellular identity, and what implications this has for therapeutic approaches such as regenerative medicine.
Collapse
Affiliation(s)
- Iris Marchal
- Berlin Institute for Medical Systems Biology, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Baris Tursun
- Berlin Institute for Medical Systems Biology, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Biology, Institute of Zoology, University of Hamburg, Hamburg, Germany
| |
Collapse
|
13
|
Levi-Ferber M, Shalash R, Le-Thomas A, Salzberg Y, Shurgi M, Benichou JI, Ashkenazi A, Henis-Korenblit S. Neuronal regulated ire- 1-dependent mRNA decay controls germline differentiation in Caenorhabditis elegans. eLife 2021; 10:65644. [PMID: 34477553 PMCID: PMC8416019 DOI: 10.7554/elife.65644] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 08/13/2021] [Indexed: 12/17/2022] Open
Abstract
Understanding the molecular events that regulate cell pluripotency versus acquisition of differentiated somatic cell fate is fundamentally important. Studies in Caenorhabditis elegans demonstrate that knockout of the germline-specific translation repressor gld-1 causes germ cells within tumorous gonads to form germline-derived teratoma. Previously we demonstrated that endoplasmic reticulum (ER) stress enhances this phenotype to suppress germline tumor progression(Levi-Ferber et al., 2015). Here, we identify a neuronal circuit that non-autonomously suppresses germline differentiation and show that it communicates with the gonad via the neurotransmitter serotonin to limit somatic differentiation of the tumorous germline. ER stress controls this circuit through regulated inositol requiring enzyme-1 (IRE-1)-dependent mRNA decay of transcripts encoding the neuropeptide FLP-6. Depletion of FLP-6 disrupts the circuit’s integrity and hence its ability to prevent somatic-fate acquisition by germline tumor cells. Our findings reveal mechanistically how ER stress enhances ectopic germline differentiation and demonstrate that regulated Ire1-dependent decay can affect animal physiology by controlling a specific neuronal circuit.
Collapse
Affiliation(s)
- Mor Levi-Ferber
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Rewayd Shalash
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Adrien Le-Thomas
- Cancer Immunology, Genentech, South San Francisco, United States
| | - Yehuda Salzberg
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Maor Shurgi
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Jennifer Ic Benichou
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Avi Ashkenazi
- Cancer Immunology, Genentech, South San Francisco, United States
| | - Sivan Henis-Korenblit
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| |
Collapse
|
14
|
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.
Collapse
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:
| |
Collapse
|
15
|
Pham K, Masoudi N, Leyva-Díaz E, Hobert O. A nervous system-specific subnuclear organelle in Caenorhabditis elegans. Genetics 2021; 217:1-17. [PMID: 33683371 DOI: 10.1093/genetics/iyaa016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/12/2020] [Indexed: 12/26/2022] Open
Abstract
We describe here phase-separated subnuclear organelles in the nematode Caenorhabditis elegans, which we term NUN (NUclear Nervous system-specific) bodies. Unlike other previously described subnuclear organelles, NUN bodies are highly cell type specific. In fully mature animals, 4-10 NUN bodies are observed exclusively in the nucleus of neuronal, glial and neuron-like cells, but not in other somatic cell types. Based on co-localization and genetic loss of function studies, NUN bodies are not related to other previously described subnuclear organelles, such as nucleoli, splicing speckles, paraspeckles, Polycomb bodies, promyelocytic leukemia bodies, gems, stress-induced nuclear bodies, or clastosomes. NUN bodies form immediately after cell cycle exit, before other signs of overt neuronal differentiation and are unaffected by the genetic elimination of transcription factors that control many other aspects of neuronal identity. In one unusual neuron class, the canal-associated neurons, NUN bodies remodel during larval development, and this remodeling depends on the Prd-type homeobox gene ceh-10. In conclusion, we have characterized here a novel subnuclear organelle whose cell type specificity poses the intriguing question of what biochemical process in the nucleus makes all nervous system-associated cells different from cells outside the nervous system.
Collapse
Affiliation(s)
- Kenneth Pham
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
| | - Neda Masoudi
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
| | - Eduardo Leyva-Díaz
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
| | - Oliver Hobert
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, NY 10027, USA
| |
Collapse
|
16
|
Fry AL, Webster AK, Burnett J, Chitrakar R, Baugh LR, Hubbard EJA. DAF-18/PTEN inhibits germline zygotic gene activation during primordial germ cell quiescence. PLoS Genet 2021; 17:e1009650. [PMID: 34288923 PMCID: PMC8294487 DOI: 10.1371/journal.pgen.1009650] [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: 12/29/2020] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
Quiescence, an actively-maintained reversible state of cell cycle arrest, is not well understood. PTEN is one of the most frequently lost tumor suppressors in human cancers and regulates quiescence of stem cells and cancer cells. The sole PTEN ortholog in Caenorhabditis elegans is daf-18. In a C. elegans loss-of-function mutant for daf-18, primordial germ cells (PGCs) divide inappropriately in L1 larvae hatched into starvation conditions, in a TOR-dependent manner. Here, we further investigated the role of daf-18 in maintaining PGC quiescence in L1 starvation. We found that maternal or zygotic daf-18 is sufficient to maintain cell cycle quiescence, that daf-18 acts in the germ line and soma, and that daf-18 affects timing of PGC divisions in fed animals. Importantly, our results also implicate daf-18 in repression of germline zygotic gene activation, though not in germline fate specification. However, TOR is less important to germline zygotic gene expression, suggesting that in the absence of food, daf-18/PTEN prevents inappropriate germline zygotic gene activation and cell division by distinct mechanisms.
Collapse
Affiliation(s)
- Amanda L. Fry
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Grossman School of Medicine, New York, New York, United States of America
| | - Amy K. Webster
- Department of Biology, Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - Julia Burnett
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Grossman School of Medicine, New York, New York, United States of America
| | - Rojin Chitrakar
- Department of Biology, Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - L. Ryan Baugh
- Department of Biology, Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, United States of America
| | - E. Jane Albert Hubbard
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU Grossman School of Medicine, New York, New York, United States of America
| |
Collapse
|
17
|
Lederer M, Müller S, Glaß M, Bley N, Ihling C, Sinz A, Hüttelmaier S. Oncogenic Potential of the Dual-Function Protein MEX3A. BIOLOGY 2021; 10:415. [PMID: 34067172 PMCID: PMC8151450 DOI: 10.3390/biology10050415] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/26/2021] [Accepted: 05/05/2021] [Indexed: 12/23/2022]
Abstract
MEX3A belongs to the MEX3 (Muscle EXcess) protein family consisting of four members (MEX3A-D) in humans. Characteristic for MEX3 proteins is their domain structure with 2 HNRNPK homology (KH) domains mediating RNA binding and a C-terminal really interesting new gene (RING) domain that harbors E3 ligase function. In agreement with their domain composition, MEX3 proteins were reported to modulate both RNA fate and protein ubiquitination. MEX3 paralogs exhibit an oncofetal expression pattern, they are severely downregulated postnatally, and re-expression is observed in various malignancies. Enforced expression of MEX3 proteins in various cancers correlates with poor prognosis, emphasizing their oncogenic potential. The latter is supported by MEX3A's impact on proliferation, self-renewal as well as migration of tumor cells in vitro and tumor growth in xenograft studies.
Collapse
Affiliation(s)
- Marcell Lederer
- Charles Tanford Protein Center, Faculty of Medicine, Institute of Molecular Medicine, Section for Molecular Cell Biology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle, Germany; (S.M.).; (M.G.).; (N.B.); (S.H.)
| | - Simon Müller
- Charles Tanford Protein Center, Faculty of Medicine, Institute of Molecular Medicine, Section for Molecular Cell Biology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle, Germany; (S.M.).; (M.G.).; (N.B.); (S.H.)
| | - Markus Glaß
- Charles Tanford Protein Center, Faculty of Medicine, Institute of Molecular Medicine, Section for Molecular Cell Biology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle, Germany; (S.M.).; (M.G.).; (N.B.); (S.H.)
| | - Nadine Bley
- Charles Tanford Protein Center, Faculty of Medicine, Institute of Molecular Medicine, Section for Molecular Cell Biology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle, Germany; (S.M.).; (M.G.).; (N.B.); (S.H.)
| | - Christian Ihling
- Center for Structural Mass Spectrometry, Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany; (C.I.); (A.S.)
| | - Andrea Sinz
- Center for Structural Mass Spectrometry, Department of Pharmaceutical Chemistry & Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany; (C.I.); (A.S.)
| | - Stefan Hüttelmaier
- Charles Tanford Protein Center, Faculty of Medicine, Institute of Molecular Medicine, Section for Molecular Cell Biology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle, Germany; (S.M.).; (M.G.).; (N.B.); (S.H.)
| |
Collapse
|
18
|
Kazmierczak M, Farré i Díaz C, Ofenbauer A, Herzog S, Tursun B. The CONJUDOR pipeline for multiplexed knockdown of gene pairs identifies RBBP-5 as a germ cell reprogramming barrier in C. elegans. Nucleic Acids Res 2021; 49:e22. [PMID: 33290523 PMCID: PMC7913679 DOI: 10.1093/nar/gkaa1171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/12/2020] [Accepted: 11/17/2020] [Indexed: 12/05/2022] Open
Abstract
Multiple gene activities control complex biological processes such as cell fate specification during development and cellular reprogramming. Investigating the manifold gene functions in biological systems requires also simultaneous depletion of two or more gene activities. RNA interference-mediated knockdown (RNAi) is commonly used in Caenorhabditis elegans to assess essential genes, which otherwise lead to lethality or developmental arrest upon full knockout. RNAi application is straightforward by feeding worms with RNAi plasmid-containing bacteria. However, the general approach of mixing bacterial RNAi clones to deplete two genes simultaneously often yields poor results. To address this issue, we developed a bacterial conjugation-mediated double RNAi technique 'CONJUDOR'. It allows combining RNAi bacteria for robust double RNAi with high-throughput. To demonstrate the power of CONJUDOR for large scale double RNAi screens we conjugated RNAi against the histone chaperone gene lin-53 with more than 700 other chromatin factor genes. Thereby, we identified the Set1/MLL methyltransferase complex member RBBP-5 as a novel germ cell reprogramming barrier. Our findings demonstrate that CONJUDOR increases efficiency and versatility of RNAi screens to examine interconnected biological processes in C. elegans with high-throughput.
Collapse
Affiliation(s)
- Marlon Kazmierczak
- Berlin Institute for Medical Systems Biology, Berlin 10115, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Carlota Farré i Díaz
- Berlin Institute for Medical Systems Biology, Berlin 10115, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Andreas Ofenbauer
- Berlin Institute for Medical Systems Biology, Berlin 10115, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Sergej Herzog
- Berlin Institute for Medical Systems Biology, Berlin 10115, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Baris Tursun
- Berlin Institute for Medical Systems Biology, Berlin 10115, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| |
Collapse
|
19
|
Robert VJ, Knutson AK, Rechtsteiner A, Garvis S, Yvert G, Strome S, Palladino F. Caenorhabditis elegans SET1/COMPASS Maintains Germline Identity by Preventing Transcriptional Deregulation Across Generations. Front Cell Dev Biol 2020; 8:561791. [PMID: 33072747 PMCID: PMC7536326 DOI: 10.3389/fcell.2020.561791] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 08/18/2020] [Indexed: 12/11/2022] Open
Abstract
Chromatin regulators contribute to the maintenance of the germline transcriptional program. In the absence of SET-2, the Caenorhabditis elegans homolog of the SET1/COMPASS H3 Lys4 (H3K4) methyltransferase, animals show transgenerational loss of germline identity, leading to sterility. To identify transcriptional signatures associated with progressive loss of fertility, we performed expression profiling of set-2 mutant germlines across generations. We identify a subset of genes whose misexpression is first observed in early generations, a step we refer to as priming; their misexpression then further progresses in late generations, as animals reach sterility. Analysis of misregulated genes shows that down-regulation of germline genes, expression of somatic transcriptional programs, and desilencing of the X-chromosome are concurrent events leading to loss of germline identity in both early and late generations. Upregulation of transcription factor LIN-15B, the C/EBP homolog CEBP-1, and TGF-β pathway components strongly contribute to loss of fertility, and RNAi inactivation of cebp-1 and TGF-β/Smad signaling delays the onset of sterility, showing they individually contribute to maintenance of germ cell identity. Our approach therefore identifies genes and pathways whose misexpression actively contributes to the loss of germ cell fate. More generally, our data shows how loss of a chromatin regulator in one generation leads to transcriptional changes that are amplified over subsequent generations, ultimately leading to loss of appropriate cell fate.
Collapse
Affiliation(s)
- Valérie J Robert
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard de Lyon, Université de Lyon, Lyon, France
| | - Andrew K Knutson
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Andreas Rechtsteiner
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Steven Garvis
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard de Lyon, Université de Lyon, Lyon, France
| | - Gaël Yvert
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard de Lyon, Université de Lyon, Lyon, France
| | - Susan Strome
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, United States
| | - Francesca Palladino
- Laboratory of Biology and Modeling of the Cell, Ecole Normale Supérieure de Lyon, CNRS, Université Claude Bernard de Lyon, Université de Lyon, Lyon, France
| |
Collapse
|
20
|
Naef V, De Sarlo M, Testa G, Corsinovi D, Azzarelli R, Borello U, Ori M. The Stemness Gene Mex3A Is a Key Regulator of Neuroblast Proliferation During Neurogenesis. Front Cell Dev Biol 2020; 8:549533. [PMID: 33072742 PMCID: PMC7536324 DOI: 10.3389/fcell.2020.549533] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/31/2020] [Indexed: 01/31/2023] Open
Abstract
Mex3A is an RNA binding protein that can also act as an E3 ubiquitin ligase to control gene expression at the post-transcriptional level. In intestinal adult stem cells, MEX3A is required for cell self-renewal and when overexpressed, MEX3A can contribute to support the proliferation of different cancer cell types. In a completely different context, we found mex3A among the genes expressed in neurogenic niches of the embryonic and adult fish brain and, notably, its expression was downregulated during brain aging. The role of mex3A during embryonic and adult neurogenesis in tetrapods is still unknown. Here, we showed that mex3A is expressed in the proliferative region of the developing brain in both Xenopus and mouse embryos. Using gain and loss of gene function approaches, we showed that, in Xenopus embryos, mex3A is required for neuroblast proliferation and its depletion reduced the neuroblast pool, leading to microcephaly. The tissue-specific overexpression of mex3A in the developing neural plate enhanced the expression of sox2 and msi-1 keeping neuroblasts into a proliferative state. It is now clear that the stemness property of mex3A, already demonstrated in adult intestinal stem cells and cancer cells, is a key feature of mex3a also in developing brain, opening new lines of investigation to better understand its role during brain aging and brain cancer development.
Collapse
Affiliation(s)
- Valentina Naef
- Unità di Biologia Cellulare e dello Sviluppo, Dipartimento di Biologia, Università di Pisa, Pisa, Italy.,Molecular Medicine, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Miriam De Sarlo
- Unità di Biologia Cellulare e dello Sviluppo, Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Giovanna Testa
- Unità di Biologia Cellulare e dello Sviluppo, Dipartimento di Biologia, Università di Pisa, Pisa, Italy.,Scuola Normale Superiore di Pisa, Pisa, Italy
| | - Debora Corsinovi
- Unità di Biologia Cellulare e dello Sviluppo, Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Roberta Azzarelli
- Unità di Biologia Cellulare e dello Sviluppo, Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Ugo Borello
- Unità di Biologia Cellulare e dello Sviluppo, Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Michela Ori
- Unità di Biologia Cellulare e dello Sviluppo, Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| |
Collapse
|
21
|
ul Fatima N, Tursun B. Conversion of Germ Cells to Somatic Cell Types in C. elegans. J Dev Biol 2020; 8:E24. [PMID: 33036439 PMCID: PMC7712076 DOI: 10.3390/jdb8040024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 12/11/2022] Open
Abstract
The potential of a cell to produce all types of differentiated cells in an organism is termed totipotency. Totipotency is an essential property of germ cells, which constitute the germline and pass on the parental genetic material to the progeny. The potential of germ cells to give rise to a whole organism has been the subject of intense research for decades and remains important in order to better understand the molecular mechanisms underlying totipotency. A better understanding of the principles of totipotency in germ cells could also help to generate this potential in somatic cell lineages. Strategies such as transcription factor-mediated reprogramming of differentiated cells to stem cell-like states could benefit from this knowledge. Ensuring pluripotency or even totipotency of reprogrammed stem cells are critical improvements for future regenerative medicine applications. The C. elegans germline provides a unique possibility to study molecular mechanisms that maintain totipotency and the germ cell fate with its unique property of giving rise to meiotic cells Studies that focused on these aspects led to the identification of prominent chromatin-repressing factors such as the C. elegans members of the Polycomb Repressive Complex 2 (PRC2). In this review, we summarize different factors that were recently identified, which use molecular mechanisms such as control of protein translation or chromatin repression to ensure maintenance of totipotency and the germline fate. Additionally, we focus on recently identified factors involved in preventing transcription-factor-mediated conversion of germ cells to somatic lineages. These so-called reprogramming barriers have been shown in some instances to be conserved with regard to their function as a cell fate safeguarding factor in mammals. Overall, continued studies assessing the different aspects of molecular pathways involved in maintaining the germ cell fate in C. elegans may provide more insight into cell fate safeguarding mechanisms also in other species.
Collapse
Affiliation(s)
- Nida ul Fatima
- Berlin Institute of Medical Systems Biology, 10115 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Baris Tursun
- Berlin Institute of Medical Systems Biology, 10115 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| |
Collapse
|
22
|
Rogers AK, Phillips CM. RNAi pathways repress reprogramming of C. elegans germ cells during heat stress. Nucleic Acids Res 2020; 48:4256-4273. [PMID: 32187370 PMCID: PMC7192617 DOI: 10.1093/nar/gkaa174] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 03/02/2020] [Accepted: 03/10/2020] [Indexed: 01/08/2023] Open
Abstract
Repression of cellular reprogramming in germ cells is critical to maintaining cell fate and fertility. When germ cells mis-express somatic genes they can be directly converted into other cell types, resulting in loss of totipotency and reproductive potential. Identifying the molecular mechanisms that coordinate these cell fate decisions is an active area of investigation. Here we show that RNAi pathways play a key role in maintaining germline gene expression and totipotency after heat stress. By examining transcriptional changes that occur in mut-16 mutants, lacking a key protein in the RNAi pathway, at elevated temperature we found that genes normally expressed in the soma are mis-expressed in germ cells. Furthermore, these genes displayed increased chromatin accessibility in the germlines of mut-16 mutants at elevated temperature. These findings indicate that the RNAi pathway plays a key role in preventing aberrant expression of somatic genes in the germline during heat stress. This regulation occurs in part through the maintenance of germline chromatin, likely acting through the nuclear RNAi pathway. Identification of new pathways governing germ cell reprogramming is critical to understanding how cells maintain proper gene expression and may provide key insights into how cell identity is lost in some germ cell tumors.
Collapse
Affiliation(s)
- Alicia K Rogers
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Carolyn M Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| |
Collapse
|
23
|
Henarejos-Escudero P, Hernández-García S, Guerrero-Rubio MA, García-Carmona F, Gandía-Herrero F. Antitumoral Drug Potential of Tryptophan-Betaxanthin and Related Plant Betalains in the Caenorhabditis elegans Tumoral Model. Antioxidants (Basel) 2020; 9:antiox9080646. [PMID: 32707947 PMCID: PMC7465535 DOI: 10.3390/antiox9080646] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/14/2020] [Accepted: 07/17/2020] [Indexed: 12/18/2022] Open
Abstract
Betalains are plants pigments identified as potent antioxidant molecules, naturally present in foods like beetroot and prickly pears. Although activities described for betalain-containing formulations include cancer prevention and treatment, the use of extracts instead of purified pigments has avoided the investigation of the real chemopreventive and chemotherapeutic potential of these phytochemicals. Three betalain-rich extracts and six individual pure betalains were used in this work to characterize the activity and to explore possible molecular mechanisms. The animal model Caenorhabditis elegans (tumoral strain JK1466) was used to evaluate the effect of betalains as chemotherapeutics drugs. An objective evaluation method of tumor growth in C. elegans has been developed to assess the possible antitumoral activity of the different treatments. This protocol allowed a fast and reliable screening of possible antitumoral drugs. Among the betalains tested, tryptophan-betaxanthin reduced tumor size by 56.4% and prolonged the animal’s lifespan by 9.3%, indicating high effectiveness and low toxicity. Structure–activity relationships are considered. Assays with mutant strains of C. elegans showed that the mechanism underlying these effects was the modulation of the DAF-16 transcription factor and the insulin signaling pathway. Our results indicate that tryptophan-betaxanthin and related betalains are strong candidates as antitumoral molecules in cancer treatment.
Collapse
|
24
|
Zheng T, Nakamoto A, Kumano G. H3K27me3 suppresses sister-lineage somatic gene expression in late embryonic germline cells of the ascidian, Halocynthia roretzi. Dev Biol 2020; 460:200-214. [PMID: 31904374 DOI: 10.1016/j.ydbio.2019.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/21/2019] [Accepted: 12/29/2019] [Indexed: 10/25/2022]
Abstract
Protection of the germline from somatic differentiation programs is crucial for germ cell development. In many animals, whose germline development relies on the maternally inherited germ plasm, such protection in particular at early stages of embryogenesis is achieved by maternally localized global transcriptional repressors, such as PIE-1 of Caenorhabditis elegans, Pgc of Drosophila melanogaster and Pem of ascidians. However, zygotic gene expression starts in later germline cells eventually and mechanisms by which somatic gene expression is selectively kept under repression in the transcriptionally active cells are poorly understood. By using the ascidian species Halocynthia roretzi, we found that H3K27me3, a repressive transcription-related chromatin mark, became enriched in germline cells starting at the 64-cell stage when Pem protein level and its contribution to transcriptional repression decrease. Interestingly, inhibition of H3K27me3 together with Pem knockdown resulted in ectopic expression in germline cells of muscle developmental genes Muscle actin (MA4) and Snail, and of Clone 22 (which is expressed in all somatic but not germline cells), but not of other tissue-specific genes such as the notochord gene Brachyury, the nerve cord marker ETR-1 and a heart precursor gene Mesp, at the 110-cell stage. Importantly, these ectopically expressed genes are normally expressed in the germline sister cells (B7.5), the last somatic lineage separated from the germline. Also, the ectopic expression of MA4 was dependent on a maternally localized muscle determinant Macho-1. Taken together, we propose that H3K27me3 may be responsible for selective transcriptional repression for somatic genes in later germline cells in Halocynthia embryos and that the preferential repression of germline sister-lineage genes may be related to the mechanism of germline segregation in ascidian embryos, where the germline is segregated progressively by successive asymmetric cell divisions during cell cleavage stages. Together with findings from C. elegans and D. melanogaster, our data for this urochordate animal support the proposal for a mechanism, conserved widely throughout the animal kingdom, where germline transcriptional repression is mediated initially by maternally localized factors and subsequently by a chromatin-based mechanism.
Collapse
Affiliation(s)
- Tao Zheng
- Asamushi Research Center for Marine Biology, Graduate School of Life Sciences, Tohoku University, Japan.
| | - Ayaki Nakamoto
- Asamushi Research Center for Marine Biology, Graduate School of Life Sciences, Tohoku University, Japan
| | - Gaku Kumano
- Asamushi Research Center for Marine Biology, Graduate School of Life Sciences, Tohoku University, Japan
| |
Collapse
|
25
|
Huggins HP, Subash JS, Stoffel H, Henderson MA, Hoffman JL, Buckner DS, Sengupta MS, Boag PR, Lee MH, Keiper BD. Distinct roles of two eIF4E isoforms in the germline of Caenorhabditis elegans. J Cell Sci 2020; 133:jcs237990. [PMID: 32079657 PMCID: PMC7132772 DOI: 10.1242/jcs.237990] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/10/2020] [Indexed: 01/15/2023] Open
Abstract
Germ cells use both positive and negative mRNA translational control to regulate gene expression that drives their differentiation into gametes. mRNA translational control is mediated by RNA-binding proteins, miRNAs and translation initiation factors. We have uncovered the discrete roles of two translation initiation factor eIF4E isoforms (IFE-1, IFE-3) that bind 7-methylguanosine (m7G) mRNA caps during Caenorhabditiselegans germline development. IFE-3 plays important roles in germline sex determination (GSD), where it promotes oocyte cell fate and is dispensable for spermatogenesis. IFE-3 is expressed throughout the germline and localizes to germ granules, but is distinct from IFE-1 and PGL-1, and facilitates oocyte growth and viability. This contrasts with the robust expression in spermatocytes of IFE-1, the isoform that resides within P granules in spermatocytes and oocytes, and promotes late spermatogenesis. Each eIF4E is localized by its cognate eIF4E-binding protein (IFE-1:PGL-1 and IFE-3:IFET-1). IFE-3 and IFET-1 regulate translation of several GSD mRNAs, but not those under control of IFE-1. Distinct mutant phenotypes, in vivo localization and differential mRNA translation suggest independent dormant and active periods for each eIF4E isoform in the germline.
Collapse
Affiliation(s)
- Hayden P Huggins
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
| | - Jacob S Subash
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
| | - Hamilton Stoffel
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
| | - Melissa A Henderson
- Department of Molecular Sciences, DeBusk College of Osteopathic Medicine, Lincoln Memorial University, Harrogate, TN 37752, USA
| | - Jenna L Hoffman
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
| | - David S Buckner
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
| | - Madhu S Sengupta
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Peter R Boag
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Myon-Hee Lee
- Department of Internal Medicine, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
| | - Brett D Keiper
- Department of Biochemistry and Molecular Biology, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
| |
Collapse
|
26
|
Pereira B, Amaral AL, Dias A, Mendes N, Muncan V, Silva AR, Thibert C, Radu AG, David L, Máximo V, van den Brink GR, Billaud M, Almeida R. MEX3A regulates Lgr5 + stem cell maintenance in the developing intestinal epithelium. EMBO Rep 2020; 21:e48938. [PMID: 32052574 PMCID: PMC7132344 DOI: 10.15252/embr.201948938] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 12/12/2022] Open
Abstract
Intestinal stem cells (ISCs) fuel the lifelong self‐renewal of the intestinal tract and are paramount for epithelial repair. In this context, the Wnt pathway component LGR5 is the most consensual ISC marker to date. Still, the effort to better understand ISC identity and regulation remains a challenge. We have generated a Mex3a knockout mouse model and show that this RNA‐binding protein is crucial for the maintenance of the Lgr5+ISC pool, as its absence disrupts epithelial turnover during postnatal development and stereotypical organoid maturation ex vivo. Transcriptomic profiling of intestinal crypts reveals that Mex3a deletion induces the peroxisome proliferator‐activated receptor (PPAR) pathway, along with a decrease in Wnt signalling and loss of the Lgr5+ stem cell signature. Furthermore, we identify PPARγ activity as a molecular intermediate of MEX3A‐mediated regulation. We also show that high PPARγ signalling impairs Lgr5+ISC function, thus uncovering a new layer of post‐transcriptional regulation that critically contributes to intestinal homeostasis.
Collapse
Affiliation(s)
- Bruno Pereira
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Ana L Amaral
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Alexandre Dias
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Nuno Mendes
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Vanesa Muncan
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Tytgat Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - Ana R Silva
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Chantal Thibert
- Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, University Grenoble Alpes, Grenoble, France
| | - Anca G Radu
- Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, University Grenoble Alpes, Grenoble, France
| | - Leonor David
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,FMUP-Faculty of Medicine, University of Porto, Porto, Portugal
| | - Valdemar Máximo
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,FMUP-Faculty of Medicine, University of Porto, Porto, Portugal
| | - Gijs R van den Brink
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Tytgat Institute, University of Amsterdam, Amsterdam, The Netherlands.,Medicines Research Center, GSK, Stevenage, UK
| | - Marc Billaud
- Clinical and Experimental Model of Lymphomagenesis, INSERM U1052, CNRS UMR5286, Centre Léon Bérard, Université Claude Bernard Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Raquel Almeida
- i3S - Institute for Research and Innovation in Health (Instituto de Investigação e Inovação em Saúde), University of Porto, Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,FMUP-Faculty of Medicine, University of Porto, Porto, Portugal.,Biology Department, Faculty of Sciences, University of Porto, Porto, Portugal
| |
Collapse
|
27
|
Yang D, Jiao Y, Li Y, Fang X. Clinical characteristics and prognostic value of MEX3A mRNA in liver cancer. PeerJ 2020; 8:e8252. [PMID: 31998552 PMCID: PMC6979405 DOI: 10.7717/peerj.8252] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 11/20/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND MEX3A is an RNA-binding proteins (RBPs) that promotes the proliferation, invasion, migration and viability of cancer cells. The aim of this study was to explore the clinicopathological characteristics and prognostic significance of MEX3A mRNA expression in liver cancer. METHODS RNA-Seq and clinical data were collected from The Cancer Genome Atlas (TCGA). Boxplots were used to represent discrete variables of MEX3A. Chi-square tests were used to analyze the correlation between clinical features and MEX3A expression. Receiver operating characteristic (ROC) curves were used to confirm diagnostic ability. Independent prognostic ability and values were assessed using Kaplan-Meier curves and Cox analysis. RESULTS We acquired MEX3A RNA-Seq from 50 normal liver tissues and 373 liver cancer patients along with clinical data. We found that MEX3A was up-regulated in liver cancer which increased according to histological grade (p < 0.001). MEX3A showed moderate diagnostic ability for liver cancer (AUC = 0.837). Kaplan-Meier curves and Cox analysis revealed that the high expression of MEX3A was significantly associated with poor survival (OS and RFS) (p < 0.001). Moreover, MEX3A was identified as an independent prognostic factor of liver cancer (p < 0.001). CONCLUSIONS MEX3A expression shows promise as an independent predictor of liver cancer prognosis.
Collapse
Affiliation(s)
- Dingquan Yang
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Yan Jiao
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Yanqing Li
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Xuedong Fang
- Department of Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| |
Collapse
|
28
|
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.
Collapse
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.
| |
Collapse
|
29
|
Hubbard EJA, Schedl T. Biology of the Caenorhabditis elegans Germline Stem Cell System. Genetics 2019; 213:1145-1188. [PMID: 31796552 PMCID: PMC6893382 DOI: 10.1534/genetics.119.300238] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 09/09/2019] [Indexed: 12/14/2022] Open
Abstract
Stem cell systems regulate tissue development and maintenance. The germline stem cell system is essential for animal reproduction, controlling both the timing and number of progeny through its influence on gamete production. In this review, we first draw general comparisons to stem cell systems in other organisms, and then present our current understanding of the germline stem cell system in Caenorhabditis elegans In contrast to stereotypic somatic development and cell number stasis of adult somatic cells in C. elegans, the germline stem cell system has a variable division pattern, and the system differs between larval development, early adult peak reproduction and age-related decline. We discuss the cell and developmental biology of the stem cell system and the Notch regulated genetic network that controls the key decision between the stem cell fate and meiotic development, as it occurs under optimal laboratory conditions in adult and larval stages. We then discuss alterations of the stem cell system in response to environmental perturbations and aging. A recurring distinction is between processes that control stem cell fate and those that control cell cycle regulation. C. elegans is a powerful model for understanding germline stem cells and stem cell biology.
Collapse
Affiliation(s)
- E Jane Albert Hubbard
- Skirball Institute of Biomolecular Medicine, Departments of Cell Biology and Pathology, New York University School of Medicine, New York 10016
| | - Tim Schedl
- and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
Ruthig VA, Friedersdorf MB, Garness JA, Munger SC, Bunce C, Keene JD, Capel B. The RNA-binding protein DND1 acts sequentially as a negative regulator of pluripotency and a positive regulator of epigenetic modifiers required for germ cell reprogramming. Development 2019; 146:dev175950. [PMID: 31253634 PMCID: PMC6803376 DOI: 10.1242/dev.175950] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 06/20/2019] [Indexed: 12/18/2022]
Abstract
The adult spermatogonial stem cell population arises from pluripotent primordial germ cells (PGCs) that enter the fetal testis around embryonic day (E)10.5. PGCs undergo rapid mitotic proliferation, then enter prolonged cell cycle arrest (G1/G0), during which they transition to pro-spermatogonia. In mice homozygous for the Ter mutation in the RNA-binding protein Dnd1 (Dnd1Ter/Ter ), many male germ cells (MGCs) fail to enter G1/G0 and instead form teratomas: tumors containing many embryonic cell types. To investigate the origin of these tumors, we sequenced the MGC transcriptome in Dnd1Ter/Ter mutants at E12.5, E13.5 and E14.5, immediately prior to teratoma formation, and correlated this information with DO-RIP-Seq-identified DND1 direct targets. Consistent with previous results, we found DND1 controls downregulation of many genes associated with pluripotency and active cell cycle, including mTor, Hippo and Bmp/Nodal signaling pathway elements. However, DND1 targets also include genes associated with male differentiation, including a large group of chromatin regulators activated in wild-type but not mutant MGCs during the E13.5 and E14.5 transition. Results suggest multiple DND1 functions and link DND1 to initiation of epigenetic modifications in MGCs.
Collapse
Affiliation(s)
- Victor A Ruthig
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Matthew B Friedersdorf
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Jason A Garness
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Corey Bunce
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Jack D Keene
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Blanche Capel
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| |
Collapse
|
32
|
Han M, Wei G, McManus CE, Hillier LW, Reinke V. Isolated C. elegans germ nuclei exhibit distinct genomic profiles of histone modification and gene expression. BMC Genomics 2019; 20:500. [PMID: 31208332 PMCID: PMC6580472 DOI: 10.1186/s12864-019-5893-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/10/2019] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND The wide variety of specialized permissive and repressive mechanisms by which germ cells regulate developmental gene expression are not well understood genome-wide. Isolation of germ cells with high integrity and purity from living animals is necessary to address these open questions, but no straightforward methods are currently available. RESULTS Here we present an experimental paradigm that permits the isolation of nuclei from C. elegans germ cells at quantities sufficient for genomic analyses. We demonstrate that these nuclei represent a very pure population and are suitable for both transcriptome analysis (RNA-seq) and chromatin immunoprecipitation (ChIP-seq) of histone modifications. From these data, we find unexpected germline- and soma-specific patterns of gene regulation. CONCLUSIONS This new capacity removes a major barrier in the field to dissect gene expression mechanisms in the germ line of C. elegans. Consequent discoveries using this technology will be relevant to conserved regulatory mechanisms across species.
Collapse
Affiliation(s)
- Mei Han
- Department of Genetics, Yale University, New Haven, CT 06520 USA
| | - Guifeng Wei
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, OX1 3QU UK
| | | | - LaDeana W. Hillier
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, 98195 USA
| | - Valerie Reinke
- Department of Genetics, Yale University, New Haven, CT 06520 USA
| |
Collapse
|
33
|
Delaney K, Strobino M, Wenda JM, Pankowski A, Steiner FA. H3.3K27M-induced chromatin changes drive ectopic replication through misregulation of the JNK pathway in C. elegans. Nat Commun 2019; 10:2529. [PMID: 31175278 PMCID: PMC6555832 DOI: 10.1038/s41467-019-10404-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 05/10/2019] [Indexed: 12/20/2022] Open
Abstract
Substitution of lysine 27 with methionine in histone H3.3 is a recently discovered driver mutation of pediatric high-grade gliomas. Mutant cells show decreased levels and altered distribution of H3K27 trimethylation (H3K27me3). How these chromatin changes are established genome-wide and lead to tumorigenesis remains unclear. Here we show that H3.3K27M-mediated alterations in H3K27me3 distribution result in ectopic DNA replication and cell cycle progression of germ cells in Caenorhabditis elegans. By genetically inducing changes in the H3.3 distribution, we demonstrate that both H3.3K27M and pre-existing H3K27me3 act locally and antagonistically on Polycomb Repressive Complex 2 (PRC2) in a concentration-dependent manner. The heterochromatin changes result in extensive gene misregulation, and genetic screening identified upregulation of JNK as an underlying cause of the germcell aberrations. Moreover, JNK inhibition suppresses the replicative fate in human tumor-derived H3.3K27M cells, thus establishing C. elegans as a powerful model for the identification of potential drug targets for treatment of H3.3K27M tumors. Substitution of lysine 27 with methionine in histone H3.3 (H3.3K27M) is a driver mutation of pediatric high-grade gliomas. Here the authors show that H3.3K27M-mediated alterations in H3K27me3 distribution result in ectopic DNA replication and cell cycle progression of germ cells in Caenorhabditis elegans, through JNK pathway misregulation.
Collapse
Affiliation(s)
- Kamila Delaney
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva, University of Geneva, 1211, Geneva, Switzerland
| | - Maude Strobino
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva, University of Geneva, 1211, Geneva, Switzerland
| | - Joanna M Wenda
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva, University of Geneva, 1211, Geneva, Switzerland
| | - Andrzej Pankowski
- Team of Mathematics and Physics, Faculty of Civil Engineering, Mechanics and Petrochemistry, Warsaw University of Technology, 09-400, Płock, Poland
| | - Florian A Steiner
- Department of Molecular Biology and Institute for Genetics and Genomics in Geneva, University of Geneva, 1211, Geneva, Switzerland.
| |
Collapse
|
34
|
MINA-1 and WAGO-4 are part of regulatory network coordinating germ cell death and RNAi in C. elegans. Cell Death Differ 2019; 26:2157-2178. [PMID: 30728462 DOI: 10.1038/s41418-019-0291-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/23/2018] [Accepted: 11/26/2018] [Indexed: 01/22/2023] Open
Abstract
Post-transcriptional control of mRNAs by RNA-binding proteins (RBPs) has a prominent role in the regulation of gene expression. RBPs interact with mRNAs to control their biogenesis, splicing, transport, localization, translation, and stability. Defects in such regulation can lead to a wide range of human diseases from neurological disorders to cancer. Many RBPs are conserved between Caenorhabditis elegans and humans, and several are known to regulate apoptosis in the adult C. elegans germ line. How these RBPs control apoptosis is, however, largely unknown. Here, we identify mina-1(C41G7.3) in a RNA interference-based screen as a novel regulator of apoptosis, which is exclusively expressed in the adult germ line. The absence of MINA-1 causes a dramatic increase in germ cell apoptosis, a reduction in brood size, and an impaired P granules organization and structure. In vivo crosslinking immunoprecipitation experiments revealed that MINA-1 binds a set of mRNAs coding for RBPs associated with germ cell development. Additionally, a system-wide analysis of a mina-1 deletion mutant compared with wild type, including quantitative proteome and transcriptome data, hints to a post-transcriptional regulatory RBP network driven by MINA-1 during germ cell development in C. elegans. In particular, we found that the germline-specific Argonaute WAGO-4 protein levels are increased in mina-1 mutant background. Phenotypic analysis of double mutant mina-1;wago-4 revealed that contemporary loss of MINA-1 and WAGO-4 strongly rescues the phenotypes observed in mina-1 mutant background. To strengthen this functional interaction, we found that upregulation of WAGO-4 in mina-1 mutant animals causes hypersensitivity to exogenous RNAi. Our comprehensive experimental approach allowed us to describe a phenocritical interaction between two RBPs controlling germ cell apoptosis and exogenous RNAi. These findings broaden our understanding of how RBPs can orchestrate different cellular events such as differentiation and death in C. elegans.
Collapse
|
35
|
Hajduskova M, Baytek G, Kolundzic E, Gosdschan A, Kazmierczak M, Ofenbauer A, Beato Del Rosal ML, Herzog S, Ul Fatima N, Mertins P, Seelk-Müthel S, Tursun B. MRG-1/MRG15 Is a Barrier for Germ Cell to Neuron Reprogramming in Caenorhabditis elegans. Genetics 2019; 211:121-139. [PMID: 30425042 PMCID: PMC6325694 DOI: 10.1534/genetics.118.301674] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 11/09/2018] [Indexed: 12/13/2022] Open
Abstract
Chromatin regulators play important roles in the safeguarding of cell identities by opposing the induction of ectopic cell fates and, thereby, preventing forced conversion of cell identities by reprogramming approaches. Our knowledge of chromatin regulators acting as reprogramming barriers in living organisms needs improvement as most studies use tissue culture. We used Caenorhabditis elegans as an in vivo gene discovery model and automated solid-phase RNA interference screening, by which we identified 10 chromatin-regulating factors that protect cells against ectopic fate induction. Specifically, the chromodomain protein MRG-1 safeguards germ cells against conversion into neurons. MRG-1 is the ortholog of mammalian MRG15 (MORF-related gene on chromosome 15) and is required during germline development in C. elegans However, MRG-1's function as a barrier for germ cell reprogramming has not been revealed previously. Here, we further provide protein-protein and genome interactions of MRG-1 to characterize its molecular functions. Conserved chromatin regulators may have similar functions in higher organisms, and therefore, understanding cell fate protection in C. elegans may also help to facilitate reprogramming of human cells.
Collapse
Affiliation(s)
- Martina Hajduskova
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Gülkiz Baytek
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Ena Kolundzic
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Alexander Gosdschan
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Marlon Kazmierczak
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Andreas Ofenbauer
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Maria Lena Beato Del Rosal
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Sergej Herzog
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Nida Ul Fatima
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Stefanie Seelk-Müthel
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| | - Baris Tursun
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute for Medical Systems Biology, 13125 Berlin, Germany
| |
Collapse
|
36
|
3′-UTRs and the Control of Protein Expression in Space and Time. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1203:133-148. [DOI: 10.1007/978-3-030-31434-7_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
37
|
Li Y, Maine EM. The balance of poly(U) polymerase activity ensures germline identity, survival and development in Caenorhabditis elegans. Development 2018; 145:145/19/dev165944. [PMID: 30305273 DOI: 10.1242/dev.165944] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/29/2018] [Indexed: 12/21/2022]
Abstract
Poly(U) polymerases (PUPs) catalyze 3' uridylation of mRNAs and small RNAs, a modification often correlating with decreased RNA stability. We have investigated the importance of three proteins with in vitro PUP activity, PUP-1/CDE-1, PUP-2 and PUP-3, in C. elegans germline development. Genetic analysis indicates that PUP-1/CDE-1 and PUP-2 are developmentally redundant under conditions of temperature stress during which they ensure germline viability and development. Multiple lines of evidence indicate that pup-1/-2 double mutant germ cells fail to maintain their identity as distinct from soma. Consistent with phenotypic data, PUP-1 and PUP-2 are expressed in embryonic germ cell precursors and throughout germline development. The developmental importance of PUP activity is presumably in regulating gene expression as both a direct and indirect consequence of modifying target RNAs. PUP-3 is significantly overexpressed in the pup-1/-2 germline, and loss of pup-3 function partially suppresses pup-1/-2 germline defects. We conclude that one major function of PUP-1/-2 is to limit PUP-3 expression. Overall, the balance of PUP-1, PUP-2 and PUP-3 activities appears to ensure proper germline development.
Collapse
Affiliation(s)
- Yini Li
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA
| | - Eleanor M Maine
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA
| |
Collapse
|
38
|
Wang H, Zhao Y, Ezcurra M, Benedetto A, Gilliat AF, Hellberg J, Ren Z, Galimov ER, Athigapanich T, Girstmair J, Telford MJ, Dolphin CT, Zhang Z, Gems D. A parthenogenetic quasi-program causes teratoma-like tumors during aging in wild-type C. elegans. NPJ Aging Mech Dis 2018; 4:6. [PMID: 29928508 PMCID: PMC5998035 DOI: 10.1038/s41514-018-0025-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 05/10/2018] [Accepted: 05/21/2018] [Indexed: 01/02/2023] Open
Abstract
A long-standing belief is that aging (senescence) is the result of stochastic damage accumulation. Alternatively, senescent pathology may also result from late-life, wild-type gene action (i.e., antagonistic pleiotropy, as argued by Williams) leading to non-adaptive run-on of developmental programs (or quasi-programs) (as suggested more recently by Blagosklonny). In this study, we use existing and new data to show how uterine tumors, a prominent form of senescent pathology in the nematode Caenorhabditis elegans, likely result from quasi-programs. Such tumors develop from unfertilized oocytes which enter the uterus and become hypertrophic and replete with endoreduplicated chromatin masses. Tumor formation begins with ovulation of unfertilized oocytes immediately after exhaustion of sperm stocks. We show that the timing of this transition between program and quasi-program (i.e., the onset of senescence), and the onset of tumor formation, depends upon the timing of sperm depletion. We identify homology between uterine tumors and mammalian ovarian teratomas, which both develop from oocytes that fail to mature after meiosis I. In teratomas, futile activation of developmental programs leads to the formation of differentiated structures within the tumor. We report that older uterine tumors express markers of later embryogenesis, consistent with teratoma-like activation of developmental programs. We also present evidence of coupling of distal gonad atrophy to oocyte hypertrophy. This study shows how the Williams Blagosklonny model can provide a mechanistic explanation of this component of C. elegans aging. It also suggests etiological similarity between teratoma and some forms of senescent pathology, insofar as both are caused by quasi-programs.
Collapse
Affiliation(s)
- Hongyuan Wang
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001 China
- Institute of Healthy Ageing, University College London, London, UK
| | - Yuan Zhao
- Institute of Healthy Ageing, University College London, London, UK
| | - Marina Ezcurra
- Institute of Healthy Ageing, University College London, London, UK
- School of Biological & Chemical Sciences, Queen Mary University of London, London, UK
| | - Alexandre Benedetto
- Institute of Healthy Ageing, University College London, London, UK
- Division of Biochemical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, UK
| | - Ann F. Gilliat
- Institute of Healthy Ageing, University College London, London, UK
| | | | - Ziyu Ren
- Institute of Healthy Ageing, University College London, London, UK
| | | | | | - Johannes Girstmair
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Maximilian J. Telford
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Colin T. Dolphin
- Institute of Pharmaceutical Science, King’s College London, London, UK
| | - Zhizhou Zhang
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001 China
| | - David Gems
- Institute of Healthy Ageing, University College London, London, UK
| |
Collapse
|
39
|
Fassnacht C, Tocchini C, Kumari P, Gaidatzis D, Stadler MB, Ciosk R. The CSR-1 endogenous RNAi pathway ensures accurate transcriptional reprogramming during the oocyte-to-embryo transition in Caenorhabditis elegans. PLoS Genet 2018; 14:e1007252. [PMID: 29579041 PMCID: PMC5886687 DOI: 10.1371/journal.pgen.1007252] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 04/05/2018] [Accepted: 02/13/2018] [Indexed: 12/30/2022] Open
Abstract
Endogenous RNAi (endoRNAi) is a conserved mechanism for fine-tuning gene expression. In the nematode Caenorhabditis elegans, several endoRNAi pathways are required for the successful development of reproductive cells. The CSR-1 endoRNAi pathway promotes germ cell development, primarily by facilitating the expression of germline genes. In this study, we report a novel function for the CSR-1 pathway in preventing premature activation of embryonic transcription in the developing oocytes, which is accompanied by a general Pol II activation. This CSR-1 function requires its RNase activity, suggesting that, by controlling the levels of maternal mRNAs, CSR-1-dependent endoRNAi contributes to an orderly reprogramming of transcription during the oocyte-to-embryo transition. During the oocyte-to-embryo transition, the control of development is transferred from the mother to the embryo. A key event during this transition is the transcriptional activation of the embryonic genome, which is tightly controlled. Here, by using the nematode C. elegans, we uncover a role for endogenous RNA interference in this process. We demonstrate that a specific endoRNAi pathway, employing the Argonaute protein CSR-1, functions as a break on gene-specific, and potentially global, activation of embryonic transcription in the developing oocytes. Our findings reveal a new layer of control over the transcriptional reprogramming during the oocyte-to-embryo transition, raising questions about its potential conservation in mammalian development.
Collapse
Affiliation(s)
- Christina Fassnacht
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Cristina Tocchini
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Pooja Kumari
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Dimos Gaidatzis
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Swiss Institute of Bioinformatics, 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
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- * E-mail: ,
| |
Collapse
|
40
|
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.
Collapse
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
| |
Collapse
|
41
|
Rink JC. Stem Cells, Patterning and Regeneration in Planarians: Self-Organization at the Organismal Scale. Methods Mol Biol 2018; 1774:57-172. [PMID: 29916155 DOI: 10.1007/978-1-4939-7802-1_2] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The establishment of size and shape remains a fundamental challenge in biological research that planarian flatworms uniquely epitomize. Planarians can regenerate complete and perfectly proportioned animals from tiny and arbitrarily shaped tissue pieces; they continuously renew all organismal cell types from abundant pluripotent stem cells, yet maintain shape and anatomy in the face of constant turnover; they grow when feeding and literally degrow when starving, while scaling form and function over as much as a 40-fold range in body length or an 800-fold change in total cell numbers. This review provides a broad overview of the current understanding of the planarian stem cell system, the mechanisms that pattern the planarian body plan and how the interplay between patterning signals and cell fate choices orchestrates regeneration. What emerges is a conceptual framework for the maintenance and regeneration of the planarian body plan on basis of the interplay between pluripotent stem cells and self-organizing patterns and further, the general utility of planarians as model system for the mechanistic basis of size and shape.
Collapse
Affiliation(s)
- Jochen C Rink
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| |
Collapse
|
42
|
Kolundzic E, Seelk S, Tursun B. Application of RNAi and Heat-shock-induced Transcription Factor Expression to Reprogram Germ Cells to Neurons in C. elegans. J Vis Exp 2018. [PMID: 29364230 PMCID: PMC5908413 DOI: 10.3791/56889] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Studying the cell biological processes during converting the identities of specific cell types provides important insights into mechanism that maintain and protect cellular identities. The conversion of germ cells into specific neurons in the nematode Caenorhabditis elegans (C. elegans) is a powerful tool for performing genetic screens in order to dissect regulatory pathways that safeguard established cell identities. Reprogramming of germ cells to a specific type of neurons termed ASE requires transgenic animals that allow broad over-expression of the Zn-finger transcription factor (TF) CHE-1. Endogenous CHE-1 is expressed exclusively in two head neurons and is required to specify the glutamatergic ASE neurons fate, which can easily be visualized by the gcy-5prom::gfp reporter. A trans gene containing the heat-shock promoter-driven che-1 gene expression construct allows broad mis-expression of CHE-1 in the entire animal upon heat-shock treatment. The combination of RNAi against the chromatin-regulating factor LIN-53 and heat-shock-induced che-1 over-expression leads to reprogramming of germ cell into ASE neuron-like cells. We describe here the specific RNAi procedure and appropriate conditions for heat-shock treatment of transgenic animals in order to successfully induce germ cell to neuron conversion.
Collapse
Affiliation(s)
- Ena Kolundzic
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association
| | - Stefanie Seelk
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association
| | - Baris Tursun
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association;
| |
Collapse
|
43
|
The Vertebrate Protein Dead End Maintains Primordial Germ Cell Fate by Inhibiting Somatic Differentiation. Dev Cell 2017; 43:704-715.e5. [DOI: 10.1016/j.devcel.2017.11.019] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/14/2017] [Accepted: 11/20/2017] [Indexed: 12/14/2022]
|
44
|
Yang L, Wang C, Li F, Zhang J, Nayab A, Wu J, Shi Y, Gong Q. The human RNA-binding protein and E3 ligase MEX-3C binds the MEX-3-recognition element (MRE) motif with high affinity. J Biol Chem 2017; 292:16221-16234. [PMID: 28808060 DOI: 10.1074/jbc.m117.797746] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/05/2017] [Indexed: 11/06/2022] Open
Abstract
MEX-3 is a K-homology (KH) domain-containing RNA-binding protein first identified as a translational repressor in Caenorhabditis elegans, and its four orthologs (MEX-3A-D) in human and mouse were subsequently found to have E3 ubiquitin ligase activity mediated by a RING domain and critical for RNA degradation. Current evidence implicates human MEX-3C in many essential biological processes and suggests a strong connection with immune diseases and carcinogenesis. The highly conserved dual KH domains in MEX-3 proteins enable RNA binding and are essential for the recognition of the 3'-UTR and post-transcriptional regulation of MEX-3 target transcripts. However, the molecular mechanisms of translational repression and the consensus RNA sequence recognized by the MEX-3C KH domain are unknown. Here, using X-ray crystallography and isothermal titration calorimetry, we investigated the RNA-binding activity and selectivity of human MEX-3C dual KH domains. Our high-resolution crystal structures of individual KH domains complexed with a noncanonical U-rich and a GA-rich RNA sequence revealed that the KH1/2 domains of human MEX-3C bound MRE10, a 10-mer RNA (5'-CAGAGUUUAG-3') consisting of an eight-nucleotide MEX-3-recognition element (MRE) motif, with high affinity. Of note, we also identified a consensus RNA motif recognized by human MEX-3C. The potential RNA-binding sites in the 3'-UTR of the human leukocyte antigen serotype (HLA-A2) mRNA were mapped with this RNA-binding motif and further confirmed by fluorescence polarization. The binding motif identified here will provide valuable information for future investigations of the functional pathways controlled by human MEX-3C and for predicting potential mRNAs regulated by this enzyme.
Collapse
Affiliation(s)
- Lingna Yang
- From the Hefei National Laboratory for Physical Science at Microscale, Collaborative Innovation Center of Chemistry for Life Sciences and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China and
| | - Chongyuan Wang
- From the Hefei National Laboratory for Physical Science at Microscale, Collaborative Innovation Center of Chemistry for Life Sciences and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China and
| | - Fudong Li
- From the Hefei National Laboratory for Physical Science at Microscale, Collaborative Innovation Center of Chemistry for Life Sciences and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China and
| | - Jiahai Zhang
- From the Hefei National Laboratory for Physical Science at Microscale, Collaborative Innovation Center of Chemistry for Life Sciences and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China and
| | - Anam Nayab
- From the Hefei National Laboratory for Physical Science at Microscale, Collaborative Innovation Center of Chemistry for Life Sciences and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China and
| | - Jihui Wu
- From the Hefei National Laboratory for Physical Science at Microscale, Collaborative Innovation Center of Chemistry for Life Sciences and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China and
| | - Yunyu Shi
- From the Hefei National Laboratory for Physical Science at Microscale, Collaborative Innovation Center of Chemistry for Life Sciences and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China and.,CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing 100101, China
| | - Qingguo Gong
- From the Hefei National Laboratory for Physical Science at Microscale, Collaborative Innovation Center of Chemistry for Life Sciences and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China and
| |
Collapse
|
45
|
Pereira B, Billaud M, Almeida R. RNA-Binding Proteins in Cancer: Old Players and New Actors. Trends Cancer 2017; 3:506-528. [PMID: 28718405 DOI: 10.1016/j.trecan.2017.05.003] [Citation(s) in RCA: 451] [Impact Index Per Article: 64.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/04/2017] [Accepted: 05/05/2017] [Indexed: 12/15/2022]
Abstract
RNA-binding proteins (RBPs) are key players in post-transcriptional events. The combination of versatility of their RNA-binding domains with structural flexibility enables RBPs to control the metabolism of a large array of transcripts. Perturbations in RBP-RNA networks activity have been causally associated with cancer development, but the rational framework describing these contributions remains fragmented. We review here the evidence that RBPs modulate multiple cancer traits, emphasize their functional diversity, and assess future trends in the study of RBPs in cancer.
Collapse
Affiliation(s)
- Bruno Pereira
- i3S - Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-465 Porto, Portugal.
| | - Marc Billaud
- Clinical and Experimental Model of Lymphomagenesis, Institut National de la Santé et de la Recherche Médicale (INSERM) Unité 1052, Centre National de la Recherche Scientifique (CNRS) Unité 5286, Centre Léon Bérard, Université Claude Bernard Lyon 1, Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | - Raquel Almeida
- i3S - Institute for Research and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), 4200-465 Porto, Portugal; Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; Biology Department, Faculty of Sciences of the University of Porto, 4169-007 Porto, Portugal
| |
Collapse
|
46
|
Cell Fate Maintenance and Reprogramming During the Oocyte-to-Embryo Transition. Results Probl Cell Differ 2017; 59:269-286. [PMID: 28247053 DOI: 10.1007/978-3-319-44820-6_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
This chapter reviews our current understanding of the mechanisms that regulate reprogramming during the oocyte-to-embryo transition (OET). There are two major events reshaping the transcriptome during OET. One is the clearance of maternal transcripts in the early embryo, extensively reviewed by others. The other event, which is the focus of this chapter, is the embryonic (or zygotic) genome activation (EGA). The mechanisms controlling EGA can be broadly divided into transcriptional and posttranscriptional. The former includes the regulation of the basal transcription machinery, the regulation by specific transcription factors and chromatin modifications. The latter is performed mostly via specific RNA-binding proteins (RBPs). Different animal models have been used to decipher the regulation of EGA. These models are often biased for the specific type of regulation, which is why we discuss the models ranging from invertebrates to mammals. Whether these biases stem from incomplete understanding of EGA in these models, or reflect evolutionarily distinct solutions to EGA regulation, is a key unresolved problem in developmental biology. As the mechanisms controlling developmental reprogramming can, and in some cases have been shown to, function in differentiated cells subjected to induced reprogramming, our understanding of EGA regulation may have implications for the efficiency of induced reprogramming and, thus, for regenerative medicine.
Collapse
|
47
|
Jeremias WDJ, Araújo FMG, Queiroz FR, Pais FSM, de Mattos ACA, Salim ACDM, Coelho PMZ, Oliveira GC, Kusel JR, Guerra-Sá R, Coimbra RS, Babá ÉH. Comparative sequence analysis reveals regulation of genes in developing schistosomula of Schistosoma mansoni exposed to host portal serum. PLoS One 2017. [PMID: 28622369 PMCID: PMC5473564 DOI: 10.1371/journal.pone.0178829] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Once inside a vertebrate host after infection, individual schistosomula of the parasite Schistosoma mansoni find a new and complex environment, which requires quick adjustments for survival, such as those that allow it to avoid the innate immune response of the host. Thus, it is very important for the parasite to remain within the skin after entering the host for a period of about 3 days, at which time it can then reach the venous system, migrate to the lungs and, by the end of eighth day post-infection, it reach the portal venous system, while undergoing minimal changes in morphology. However, after just a few days in the portal blood system, the parasite experiences an extraordinary increase in biomass and significant morphological alterations. Therefore, determining the constituents of the portal venous system that may trigger these changes that causes the parasite to consolidate its development inside the vertebrate host, thus causing the disease schistosomiasis, is essential. The present work simulated the conditions found in the portal venous system of the vertebrate host by exposing schistosomula of S. mansoni to in vitro culture in the presence of portal serum of the hamster, Mesocricetus auratus. Two different incubation periods were evaluated, one of 3 hours and one of 12 hours. These time periods were used to mimic the early contact of the parasite with portal serum during the course of natural infection. As a control, parasites were incubated in presence of hamster peripheral serum, in order to compare gene expression signatures between the two conditions. The mRNA obtained from parasites cultured under both conditions were submitted to a whole transcriptome library preparation and sequenced with a next generation platform. On average, nearly 15 million reads were produced per sample and, for the purpose of gene expression quantification, only reads mapped to one location of the transcriptome were considered. After statistical analysis, we found 103 genes differentially expressed by schistosomula cultured for 3 hours and 12 hours in the presence of hamster portal serum. After the subtraction of a second list of genes, also differentially expressed between schistosomula cultured for 3 hours and 12 hours in presence of peripheral serum, a set of 58 genes was finally established. This pattern was further validated for a subset of 17 genes, by measuring gene expression through quantitative real time polymerase chain reaction (qPCR). Processes that were activated by the portal serum stimulus include response to stress, membrane transport, protein synthesis and folding/degradation, signaling, cytoskeleton arrangement, cell adhesion and nucleotide synthesis. Additionally, a smaller number of genes down-regulated under the same condition act on cholinergic signaling, inorganic cation and organic anion membrane transport, cell adhesion and cytoskeleton arrangement. Considering the role of these genes in triggering processes that allow the parasite to quickly adapt, escape the immune response of the host and start maturation into an adult worm after contact with the portal serum, this work may point to unexplored molecular targets for drug discovery and vaccine development against schistosomiasis.
Collapse
Affiliation(s)
- Wander de Jesus Jeremias
- René Rachou, Oswaldo Cruz Foundation – FIOCRUZ-MG, Belo Horizonte, Minas Gerais, Brazil
- Centro Universitário de Belo Horizonte – UNIBH, Belo Horizonte, Minas Gerais, Brazil
- * E-mail:
| | | | - Fábio Ribeiro Queiroz
- René Rachou, Oswaldo Cruz Foundation – FIOCRUZ-MG, Belo Horizonte, Minas Gerais, Brazil
| | | | | | | | | | - Guilherme Correa Oliveira
- René Rachou, Oswaldo Cruz Foundation – FIOCRUZ-MG, Belo Horizonte, Minas Gerais, Brazil
- Instituto Tecnológico Vale, Belém, Pará, Brazil
| | - John Robert Kusel
- Glasgow University, Centre for Open Studies, Glasgow, United Kingdom
| | - Renata Guerra-Sá
- Federal University of Ouro Preto, Institute of Exact and Biological Sciences, Ouro Preto, Minas Gerais, Brazil
| | - Roney Santos Coimbra
- René Rachou, Oswaldo Cruz Foundation – FIOCRUZ-MG, Belo Horizonte, Minas Gerais, Brazil
| | - Élio Hideo Babá
- René Rachou, Oswaldo Cruz Foundation – FIOCRUZ-MG, Belo Horizonte, Minas Gerais, Brazil
| |
Collapse
|
48
|
Subasic D, Stoeger T, Eisenring S, Matia-González AM, Imig J, Zheng X, Xiong L, Gisler P, Eberhard R, Holtackers R, Gerber AP, Pelkmans L, Hengartner MO. Post-transcriptional control of executioner caspases by RNA-binding proteins. Genes Dev 2017; 30:2213-2225. [PMID: 27798844 PMCID: PMC5088569 DOI: 10.1101/gad.285726.116] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/16/2016] [Indexed: 12/03/2022]
Abstract
In this study, Subasic et al. investigated the post-transcriptional control of caspases. The authors describe four conserved RNA-binding proteins (RBPs) that sequentially repress the CED-3 caspase in distinct regions of the C. elegans germline and identify seven RBPs that regulate human caspase-3 expression and/or activation, suggesting that translational inhibition of executioner caspases by RBPs might be a general strategy used widely across the animal kingdom to control apoptosis. Caspases are key components of apoptotic pathways. Regulation of caspases occurs at several levels, including transcription, proteolytic processing, inhibition of enzymatic function, and protein degradation. In contrast, little is known about the extent of post-transcriptional control of caspases. Here, we describe four conserved RNA-binding proteins (RBPs)—PUF-8, MEX-3, GLD-1, and CGH-1—that sequentially repress the CED-3 caspase in distinct regions of the Caenorhabditis elegans germline. We demonstrate that GLD-1 represses ced-3 mRNA translation via two binding sites in its 3′ untranslated region (UTR), thereby ensuring a dual control of unwanted cell death: at the level of p53/CEP-1 and at the executioner caspase level. Moreover, we identified seven RBPs that regulate human caspase-3 expression and/or activation, including human PUF-8, GLD-1, and CGH-1 homologs PUM1, QKI, and DDX6. Given the presence of unusually long executioner caspase 3′ UTRs in many metazoans, translational control of executioner caspases by RBPs might be a strategy used widely across the animal kingdom to control apoptosis.
Collapse
Affiliation(s)
- Deni Subasic
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland.,Molecular Life Sciences PhD Program, Swiss Federal Institute of Technology, University of Zurich, 8057 Zurich, Switzerland
| | - Thomas Stoeger
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland.,Systems Biology PhD Program, Swiss Federal Institute of Technology, University of Zurich, 8057 Zurich, Switzerland
| | - Seline Eisenring
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Ana M Matia-González
- Faculty of Health and Medical Sciences, Department of Microbial and Cellular Sciences, University of Surrey, Stag Hill Campus, GU2 7XH Guildford, United Kingdom
| | - Jochen Imig
- Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Xue Zheng
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Lei Xiong
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Pascal Gisler
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Ralf Eberhard
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - René Holtackers
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - André P Gerber
- Faculty of Health and Medical Sciences, Department of Microbial and Cellular Sciences, University of Surrey, Stag Hill Campus, GU2 7XH Guildford, United Kingdom
| | - Lucas Pelkmans
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Michael O Hengartner
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| |
Collapse
|
49
|
Barriga FM, Montagni E, Mana M, Mendez-Lago M, Hernando-Momblona X, Sevillano M, Guillaumet-Adkins A, Rodriguez-Esteban G, Buczacki SJA, Gut M, Heyn H, Winton DJ, Yilmaz OH, Attolini CSO, Gut I, Batlle E. Mex3a Marks a Slowly Dividing Subpopulation of Lgr5+ Intestinal Stem Cells. Cell Stem Cell 2017; 20:801-816.e7. [PMID: 28285904 PMCID: PMC5774992 DOI: 10.1016/j.stem.2017.02.007] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 11/05/2016] [Accepted: 02/10/2017] [Indexed: 12/15/2022]
Abstract
Highly proliferative Lgr5+ stem cells maintain the intestinal epithelium and are thought to be largely homogeneous. Although quiescent intestinal stem cell (ISC) populations have been described, the identity and features of such a population remain controversial. Here we report unanticipated heterogeneity within the Lgr5+ ISC pool. We found that expression of the RNA-binding protein Mex3a labels a slowly cycling subpopulation of Lgr5+ ISCs that contribute to all intestinal lineages with distinct kinetics. Single-cell transcriptome profiling revealed that Lgr5+ cells adopt two discrete states, one of which is defined by a Mex3a expression program and relatively low levels of proliferation genes. During homeostasis, Mex3a+ cells continually shift into the rapidly dividing, self-renewing ISC pool. Chemotherapy and radiation preferentially target rapidly dividing Lgr5+ cells but spare the Mex3a-high/Lgr5+ population, helping to promote regeneration of the intestinal epithelium following toxic insults. Thus, Mex3a defines a reserve-like ISC population within the Lgr5+ compartment.
Collapse
Affiliation(s)
- Francisco M Barriga
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Elisa Montagni
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Miyeko Mana
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Maria Mendez-Lago
- CNAG-CRG-Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Xavier Hernando-Momblona
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Marta Sevillano
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Amy Guillaumet-Adkins
- CNAG-CRG-Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Gustavo Rodriguez-Esteban
- CNAG-CRG-Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Simon J A Buczacki
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Marta Gut
- CNAG-CRG-Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Holger Heyn
- CNAG-CRG-Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Douglas J Winton
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK
| | - Omer H Yilmaz
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA; Department of Biology, MIT, Cambridge, MA 02139, USA
| | - Camille Stephan-Otto Attolini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Ivo Gut
- CNAG-CRG-Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
| |
Collapse
|
50
|
Hsu HJ, Drummond-Barbosa D. A visual screen for diet-regulated proteins in the Drosophila ovary using GFP protein trap lines. Gene Expr Patterns 2017; 23-24:13-21. [PMID: 28093350 DOI: 10.1016/j.gep.2017.01.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/06/2017] [Accepted: 01/12/2017] [Indexed: 02/06/2023]
Abstract
The effect of diet on reproduction is well documented in a large number of organisms; however, much remains to be learned about the molecular mechanisms underlying this connection. The Drosophila ovary has a well described, fast and largely reversible response to diet. Ovarian stem cells and their progeny proliferate and grow faster on a yeast-rich diet than on a yeast-free (poor) diet, and death of early germline cysts, degeneration of early vitellogenic follicles and partial block in ovulation further contribute to the ∼60-fold decrease in egg laying observed on a poor diet. Multiple diet-dependent factors, including insulin-like peptides, the steroid ecdysone, the nutrient sensor Target of Rapamycin, AMP-dependent kinase, and adipocyte factors mediate this complex response. Here, we describe the results of a visual screen using a collection of green fluorescent protein (GFP) protein trap lines to identify additional factors potentially involved in this response. In each GFP protein trap line, an artificial GFP exon is fused in frame to an endogenous protein, such that the GFP fusion pattern parallels the levels and subcellular localization of the corresponding native protein. We identified 53 GFP-tagged proteins that exhibit changes in levels and/or subcellular localization in the ovary at 12-16 hours after switching females from rich to poor diets, suggesting them as potential candidates for future functional studies.
Collapse
Affiliation(s)
- Hwei-Jan Hsu
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Daniela Drummond-Barbosa
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA.
| |
Collapse
|