Our laboratory has played a central role in establishing a new marine model organism, Oikopleura dioica (see photo http://www.sars.no/personnel/thompsonBio_1.php). The planktonic animal is a tunicate, the closest extant group to vertebrates. It has a vital role in marine ecosystems, forming part of a group that is the second most abundant component of zooplankton. The house with in which the animal lives is repetitively synthesized and discarded (every 4 h), with discarded houses representing a significant contribution to global vertical carbon flux in the oceans. Despite being a complex chordate, the animal has an extremely compact, sequenced genome of only 70Mb, smaller than that of the nematode C. elegans and only 2.5% the size of the human genome.
We study the molecular developmental biology of this organism and also its molecular ecology. Areas of interest include the molecular control of endoreduplicative cell cycle variants that the animal has mastered in its strategy of very rapid growth and chromatin dynamics related to gene expression in a very compact gene regulatory landscape. We also investigate how this group of plankton is likely to respond to predicted changes in ocean temperature and acidity through a combination of laboratory, mesocosm and field studies. In a broader sense we contribute to the development of molecular tools aimed at exploring marine ecosystem interactions and health.
Main collaborations external to the University of Bergen include:
Development of molecular and genomic resources around the Oikopleura model.
Marc Frischer, Skidaway Institute of Oceanography, USA (http://www.skio.usg.edu/people/frischer/)
Ocean acidification, marine trophic interactions, environmental monitoring.
Boris Lenhard, Bergen Centre Computational Science (http://www.sars.no/personnel/lenhard.php)
Bioinformatics of gene regulatory regions in Oikopleura.
John Manak, University of Iowa, USA (http://www.biology.uiowa.edu/faculty_info.php?ID=1441)
Whole genome tiling arrays and the developmental transcriptome of Oikopleura.
Christofer Troedsson, Researcher, also the head of uniEnvironment (http://www.miljo.uni.no/?page_id=879&lang=en)
Jan Inge Øvrebø, PhD student
Katrine Lekang, PhD student
A Department Engineer and additional PhD student are currently being hired.
In addition to our molecular laboratory facilities at the Biology Department and the Sars Centre we maintain year round continuous culture of Oikopleura in wet lab facilities managed by Jean-Marie Bouquet (http://www.sars.no/facilities/appendic.php) and have established a new temperature controlled culture facility for zooplankton at the Espegrend Marine Station (web page under construction) where we conduct mesocosm experiments.
- 2017. Sex-specific chromatin landscapes in an ultra-compact chordate genome. Epigenetics & Chromatin. 10:3: 1-18. doi: 10.1186/s13072-016-0110-4
- 2016. High-throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil-drilling activities. Molecular Ecology. 25: 4392-4406. doi: 10.1111/mec.13761
- 2015. Trans-splicing and operons in metazoans: Translational control in maternally regulated development and recovery from growth arrest. Molecular biology and evolution. 32: 585-599. doi: 10.1093/molbev/msu336
- 2015. Embryonic expression of endogenous retroviral RNAs in somatic tissues adjacent to the Oikopleura germline. Nucleic Acids Research. 43: 3701-3711. doi: 10.1093/nar/gkv169
- 2015. A comparison of DNA extraction methods for biodiversity studies of eukaryotes in marine sediments. Aquatic Microbial Ecology. 75: 15-25. doi: 10.3354/ame01741
- 2015. Oikopleura dioica culturing made easy: A Low-Cost facility for an emerging animal model in EvoDevo. Genesis. 53: 183-193. doi: 10.1002/dvg.22800
- 2015. Co-expressed Cyclin D variants cooperate to regulate proliferation of germline nuclei in a syncytium. Cell Cycle. 14: 2129-2141. doi: 10.1080/15384101.2015.1041690
- 2015. Functional specialization of chordate cdk1 paralogs during oogenic meiosis. Cell Cycle. 14: 880-893. doi: 10.1080/15384101.2015.1006000
- 2014. Future climate scenarios for a coastal productive planktonic food web resulting in microplankton phenology changes and decreased trophic transfer efficiency. PLoS ONE. 9. doi: 10.1371/journal.pone.0094388
- 2014. Characterization of the 18s rRNA gene for designing universal eukaryote specific primers. PLoS ONE. 9. doi: 10.1371/journal.pone.0087624
- 2014. Lifespan extension in a semelparous chordate occurs via developmental growth arrest just prior to meiotic entry. PLoS ONE. 9. doi: 10.1371/journal.pone.0093787
- 2013. OikoBase: a genomics and developmental transcriptomics resource for the urochordate Oikopleura dioica. Nucleic Acids Research. 41: D845-D853. doi: 10.1093/nar/gks1159
- 2013. Response of the pelagic tunicate appendicularian, Oikopleura dioica to controlled simulations of a strong bloom condition: A bottom-up perspective. Limnology and Oceanography. 58: 215-226. doi: 10.4319/lo.2013.58.1.0215
- 2013. Effects of ocean acidification, temperature and nutrient regimes on the appendicularian Oikopleura dioica: a mesocosm study. Marine Biology. 160: 2175-2187. doi: 10.1007/s00227-012-2137-9
- 2012. Expansion of cyclin D and CDK1 paralogs in Oikopleura dioica, a chordate employing diverse cell cycle variants. Molecular biology and evolution. 29: 487-502. doi: 10.1093/molbev/msr136
- 2012. The evolving proteome of a complex extracellular matrix, the Oikopleura House. PLoS ONE. 7. 15 pages. doi: 10.1371/journal.pone.0040172
- 2012. A unified phylogeny-based nomenclature for histone variants. Epigenetics & Chromatin. 5. 19 pages. doi: 10.1186/1756-8935-5-7
- 2012. Conservation and divergence of chemical defense system in the tunicate Oikopleura dioica revealed by genome wide response to two xenobiotics. BMC Genomics. 13. 17 pages. doi: 10.1186/1471-2164-13-55
- 2011. Histone variant innovation in a rapidly evolving chordate lineage. BMC Evolutionary Biology. 11. 18 pages. doi: 10.1186/1471-2148-11-208
- 2011. Cytoskeleton-mediated templating of complex cellulose-scaffolded extracellular structure and its association with oikosins in the urochordate Oikopleura. Cellular and Molecular Life Sciences (CMLS). 68: 1611-1622. doi: 10.1007/s00018-010-0547-8
- 2010. Plasticity of Animal Genome Architecture Unmasked by Rapid Evolution of a Pelagic Tunicate. Science. 330: 1381-1385. doi: 10.1126/science.1194167
- 2010. Functional specialization of cellulose synthase genes of prokaryotic origin in chordate larvaceans. Development. 137: 1483-1492. doi: 10.1242/dev.044503
- 2009. Culture optimization for the emergent zooplanktonic model organism Oikopleura dioica. Journal of Plankton Research. 21: 359-370. doi: 10.1093/plankt/fbn132
- 2009. Regulation of filter-feeding house components in response to varying food regimes in the appendicularian, Oikopleura dioica. Journal of Plankton Research. 31: 1453-1463. doi: 10.1093/plankt/fbp085
- 2008. Altered miRNA repertoire in the simplified chordate, Oikopleura dioica. Molecular biology and evolution. 25: 1067-1080. doi: 10.1093/molbev/msn060
- 2008. Oocyte selection is concurrent with meiosis resumption in the coenocystic oogenesis of Oikopleura. Developmental Biology. 324: 266-276. doi: 10.1016/j.ydbio.2008.09.016
- 2008. Euro chordates: Ascidian community swims ahead. The 4th international tunicate meeting in villefranche sur mer. Developmental Dynamics. 237: 1207-1213. doi: 10.1002/dvdy.21487
- 2007. Rapidly evolving lamins in a chordate, Oikopleura dioica, with unusual nuclear architecture. Gene. 396: 159-169. doi: 10.1016/j.gene.2007.03.006
- 2007. The Oikopleura coenocyst, a unique chordate germ cell permitting rapid, extensive modulation of oocyte production. Developmental Biology. 302: 591-600. doi: 10.1016/j.ydbio.2006.10.021
- 2007. The cytoskeleton organizes germ nuclei with divergent fates and asynchronous cycles in a common cytoplasm during oogenesis in the chordate Oikopleura. Developmental Biology. 302: 577-590. doi: 10.1016/j.ydbio.2006.10.022
- 2007. Phosphorylation of the histone H3.3 variant in mitosis and meiosis of the urochordate Oikopleura dioica. Chromosome Research. 15: 189-201. doi: 10.1007/s10577-006-1112-z
- 2007. Conserved patterns of nuclear compartmentalization are not observed in the chordate Oikopleura. Biology of the Cell. 99: 273-287. doi: 10.1042/BC20060124
- 2007. Molecular quantification of differential ingestion and particle trapping rates by the appendicularian Oikopleura dioica as a function of prey size and shape. Limnology and Oceanography. 52: 416-427.
- 2007. Endostyle cell recruitment as a frame of reference for development and growth in the urochordate Oikopleura dioica. The Biological Bulletin. 213: 325-334.
- 2006. Integrating developmental clocking and growth in a life-history model for the planktonic chordate Oikopleura dioica. Marine Ecology Progress Series. 318: 81-88.
- 2006. A model of developmental time applied to planktonic embryos. Marine Ecology Progress Series. 318: 75-80.
- 2006. Comparative organization of follicle, accessory cells and spawning anlagen in dynamic semelparous clutch manipulators, the urochordate Oikopleuridae. Biology of the Cell. 98: 389-401. doi: 10.1042/BC20060005
- 2005. Histone H4 posttranslational modifications in chordate mitotic and endoreduplicative cell cycles. Journal of Cellular Biochemistry. 95: 885-901.
- 2005. Plasticity of histone modifications across the invertebrate to vertebrate transition: histone H3 lysine 4 trimethylation in heterochromatin. Chromosome Research. 13: 57-72.
- 2005. Variable fatty acid composition of the pelagic appendicularian Oikopleura dioica in response to dietary quality and quantity. Marine Ecology Progress Series. 289: 165-176.
- 2004. Histone mRNAs do not accumulate during S phase of either mitotic or endoreduplicative cycles in the chordate Oikopleura dioica. Molecular and Cellular Biology. 24: 5391-5403.
- 2004. Spliced-leader RNA trans splicing in a chordate, Oikopleura dioica, with a compact genome. Molecular and Cellular Biology. 24. 7795-7805.
- 2002. Histone gene complement, variant expression, and mRNA processing in a urochordate Oikopleura dioica that undergoes extensive polyploidization. Molecular biology and evolution. 19: 2247-2260.
- 2002. Patterning through differential endoreduplication in epithelial organogenesis of the chordate, Oikopleura dioica. Developmental Biology. 252: 59-71.
- 2001. Miniature genome in the marine chordate Oikopleura dioica. Science. 294: 2506.
- 2001. Molecular patterning of the oikoplastic epithelium of the larvacean tunicate Oikopleura dioica. Journal of Biological Chemistry. 276: 20624-20632.
- 2001. Diverse genes expressed in distinct regions of the trunk epithelium define a monolayer cellular template for construction of the Oikopleurid house. Developmental Biology. 238: 260-273.
- 2000. Somatic linker histone H1 is present throughout mouse embryogenesis and is not replaced by variant H1 degrees. Journal of Cell Science. 113: 2897-2907.
- 2004. Patterning and Organisation of the House Secreting Epithelium of Oikopleura dioica. Kapittel, pages 89-112. In:
- 2004. Response of marine ecosystems to global change: Ecological impact of appendicularians. 400 pages.
Sagane Y, Zech K, Bouquet J-M, Schmid M, Bal U, and EM Thompson (2010) Functional specialization of cellulose synthase genes of prokaryotic origin in chordate larvaceans. Development 137, 1483-1492
Troedsson C, Bouquet JM, Skinnes R., Acuña JL, Zech K, Frischer ME and EM Thompson (2009). Regulation of filter-feeding house components in response to varying food regimes in the Appendicularian, Oikopleura dioica. J. Plankton Res. 31, 1453-1463.
Bouquet JM, Spriet E, Troedsson C, Otterå H, Chourrout D and EM Thompson (2009). Culture optimizatin for the emerging zooplanktonic model organism Oikopleura dioica. J. Plankton Res. 31, 359-370. (cover)
Fu X, Adamski M and EM Thompson (2008). Altered miRNA Repertoire in the Simplified Chordate, Oikopleura dioica. Mol. Biol. Evol. 25, 1067-1080.
Ganot P, Moosmann-Schulmeister A and EM Thompson (2008).Oocyte selection is concurrent with meiosis resumption in the coenocystic oogenesis of Oikopleura. Dev. Biol. 324, 266-276.
Clarke, T, JM Bouquet, X Fu, T Kallesøe, and EM Thompson (2007). Rapidly evolving lamins in a chordate, Oikopleura dioica, with unusual nuclear architecture. Gene 396, 159-169.
Spada F, J Koch, N Sadoni, N Mitchell, P Ganot, U De Boni, D Zink and EM Thompson (2007). Conserved patterns of nuclear compartmentalization are not observed in the chordate Oikopleura. Biol. Cell. 99, 273-287. (cover)
Ganot P, T Kallesøe and EM Thompson (2007).The cytoskeleton organizes germ nuclei with divergent fates and asynchronous cycles in a common cytoplasm during oogenesis in the chordate Oikopleura. Dev. Biol. 302, 577-590.
Schulmeister A, M Schmid and EM Thompson (2007). Phosphorylation of the histone H3.3 variant in mitosis and meiosis of the urochordate Oikopleura dioica. Chrom. Res, 15, 189-201.
Ganot P, JM Bouquet, T Kallesøe and EM Thompson (2007). The Oikopleura coenocyst, a unique chordate germ cell permitting rapid, extensive modulation of oocyte production. Dev. Biol. 302, 591-600.
Troedsson C, ME Frischer, JC Nejstgaard and EM Thompson (2007). Molecular quantification of differential ingestion and particle trapping rates by the Appendicularian Oikopleura dioica as a function of prey size and shape. Limnol. Oceanogr. 52, 416–427.
Ganot P, JM Bouquet and EM Thompson (2006). Comparative organisation of follicle, accessory cells and spawning anlagen in dynamic semelparous clutch manipulators, the urochordate Oikopleuridae. Biol. Cell. 98, 389-401. (cover)
Spada F, M Chioda and EM Thompson (2005). Histone H4 posttranslational modifications in chordate mitotic and endoreduplicative cell cycles. J. Cell. Biochem., 95, 885-901. (cover)
Spada F, M Vincent and EM Thompson (2005). Plasticity of histone modifications across the invertebrate to vertebrate transition: histone H3 lysine 4 trimethylation in heterochromatin. Chrom. Res. 13, 57-72.
Ganot P, T Kallesøe, R Reinhardt, D Chourrout and EM Thompson (2004). Spliced-Leader RNA trans-splicing in a chordate, Oikopleura dioica, with a compact genome. Mol. Cell. Biol., 24, 7795-7805.
Chioda M, F Spada, R Eskeland and EM Thompson (2004). Histone mRNAs do not accumulate during S phase of either mitotic or endoreduplicative cycles in the chordate Oikopleura dioica. Mol. Cell. Biol. 24, 5391-5403.
Chioda M, R Eskeland, and EM Thompson (2002). Histone gene complement, variant expression and processing in a urochordate, Oikopleura dioica, that undergoes extensive polyploidisation. Mol. Biol. Evol. 19, 2247-60.
Ganot P, and EM Thompson (2002). Patterning through differential endoreduplication in epithelial organogenesis of the chordate, Oikopleura dioica. Dev. Biol. 252, 59-71.
Troedsson C, J-M Bouquet, DL Aksnes and EM Thompson (2002). Resource allocation between somatic growth and reproductive output in the pelagic chordate, Oikopleura dioica, allows opportunistic response to nutritional variation. Mar. Ecol. Prog. Ser. 243, 83-91.
Seo HC, M Kube, R Edvardsen, MF Jensen, E Spriet, G Gorsky, EM Thompson, R Reinhardt, H Lehrach, and D Chourrout (2001). The chordate Oikopleura dioica has a miniature genome. Science 294, 2506.
Thompson, EM, T Kallesøe and F Spada (2001). Diverse genes expressed in distinct regions of the trunk epithelium define a monolayer cellular template for construction of the Oikopleurid house. Dev. Biol 238, 260-273. (cover)
Spada, F, H Steen, C Troedsson, T Kallesøe, E Spriet, M Mann and EM Thompson (2001) Molecular patterning of the oikoplastic epithelium of the larvacean tunicate Oikopleura dioica. J. Biol. Chem. 276, 20624-20632.
Adenot, PG, E Campion, E Legouy, CD Allis, S Dimitrov, J-P Renard and EM Thompson (2000). Somatic linker histone H1 is present throughout mouse embryogenesis and is not replaced by variant H1°. J. Cell Sci., 113, 2897-2907.
Thompson, EM, E Legouy and JP Renard (1998). Mouse embryos do not wait for the MBT: Chromatin and RNA polymerase remodeling in genome activation at the onset of development. Develop. Genetics 22, 31-42.
Rees, JF, B de Wergifosse, O Noiset, M Dubuisson, B Janssens and EM Thompson (1998). The origins of marine bioluminescence: turning oxygen defence mechanisms into deep-sea communication tools. J. Exp. Biol. 201, 1211-1221.
Legouy, E., EM Thompson, C Murchardt and JP Renard (1998). Differential preimplantation regulation of two mouse homologues of the yeast SWI2 protein. Develop. Dynamics 212, 38-48.
Spada, F, A Brunet, Y Mercier, JP Renard, ME Bianchi and EM Thompson (1998). High mobility group 1 (HMG1) protein in mouse preimplantation embryos. Mech. of Development, 76, 57-66.
Dvorak, P,. JE Flechon, EM Thompson, V Horak, P Adenot and JP Renard (1997). Embryoglycans regulate FGF-2-mediated mesoderm induction in the rabbit embryo. J. Cell Sci.110, 1-10.
Adenot, P, Y Mercier, JP Renard and EM Thompson (1997). Differential H4 acetylation of paternal and maternal chromatin precedes DNA replication and differential transcriptional activity in pronuclei of 1-cell mouse embryos. Development 124, 4615-4625.
Thompson, EM, P Adenot, FI Tsuji, and JP Renard (1995). Real time imaging of transcriptional activity in live mouse preimplantation embryos using a secreted luciferase. Proc. Natl. Acad. Sci. USA 92, 1317-1321.
Christians, E, E Campion, EM Thompson and JP Renard (1995). Expression of the HSP70.1 gene, a landmark of early zygotic activity in the mouse embryo is restricted to the first burst of transcription. Development 121, 113-122.
Thompson, EM, E Legouy, E Christians and JP Renard (1995). Progressive maturation of chromatin structure regulates HSP70.1 gene expression in the preimplantation mouse embryo. Development 121, 3425-3437.
Thompson, EM, E Christians, MG Stinnakre, and JP Renard (1994). Scaffold-attachment regions stimulate HSP70.1 expression in mouse preimplantation embryos but not in differentiated tissues. Mol. Cell. Biol. 14, 4694-4703.
Thompson, EM, S Nagata and FI Tsuji (1990). Vargula hilgendorfii luciferase: a secreted reporter enzyme for monitoring gene expression in mammalian cells. Gene 96, 257-262.
Thompson, EM, S Nagata and FI Tsuji (1989). Cloning and expression of cDNA for the luciferase from the marine ostracod Vargula hilgendorfii. Proc. Natl. Acad. Sci. USA 86, 6567-6571.
See also: Publications in Frida
In addition Eric Thompson is the author of two Patents as well as chapters and articles in popular and technical science forums.
Eric Thompson holds a BSc in Biochemistry from the University of Toronto, Canada and a PhD in Biology from the University of Southern California, USA (1987). He held postdoctoral fellowships at the Osaka Bioscience Institute, Japan and INRA, Jouy-en-Josas, France. He has teaching experience in biology, physiology, ecology, molecular cell biology, comparative genomics, gene technology, protein structure and function, and epigenetics in both lecture and practical courses through the Molecular Biology Institute, University of Bergen, the Oslo Biotechnology Centre, University of Oslo, the Høgskolen in Bodø, INSERM, France and the University of Southern California. He has been the primary supervisor of 8 postdoctoral fellows, 6 PhD students and 7 Masters students.
2010 – 2012 NFR-KMB 190265/S40 (partner), 10 M NOK: ” Pylogenetic microarrays and high throughput sequencing: a new tool for biodiversity assessment in Northern Norway”
The primary objective is to improve the resolution of current environmental monitoring programs (EMP). We aim to develop and evaluate the potential of using genomic-based technologies (environomics). This project is in collaboration with Statoil.
2007 – 2010 NFR-FUGE 183690/S10 (partner), 5.3M NOK: ”Systems Biology in the marine tunicate Oikopleura Dioica”
Gene regulatory modules are central to the coordination of an organism’s developmental program and responses to its environment and understanding of them is a key objective of modern molecular biology and medicine. In this project we will systematically identify gene regulatory modules and compare them to other chordate genomes. We will establish a comprehensive temporal transcriptome database and assess alternative promoter usage in different splice variants using whole genome tiling arrays. Through this approach we plan to evaluate the contribution of histone variants and their post-translational modifications to the epigenetic regulation of gene expression in a context where promoters often occupy sub-nucleosomal regions of chromatin. We will also begin to characterize male and female specific transcriptional networks, and gain insight into regulatory shifts that modulate cell cycle variants.
2006 – 2009 NFR-FUGE 17541/S10 (PI), 4.9M NOK: “Cellular mechanisms templating complex extracellular structures via cellulose scaffolds: the Oikopleura house”
Cellulose is the most abundant natural product in the biosphere, but among metazoans, only urochordate tunicates, the closest extant group to the vertebrates, can synthesize cellulose. The main objective is to elucidate mechanisms used by animal cells to template cellulose microfibrils into scaffolds for building complex 3-dimensional extracellular structures. 2003 - 2006 NFR-FUGE 152073/150 (partner), 21.4M NOK: ”Bergen MIC”The goal was to establish a National Molecular Imaging Platform through the FUGE program.
2002 - 2006 NFR-BIOTEK (PI), 6.2M NOK: “Developmental Genomics of Oikopleura,
a marine architect at the invertebrate/vertebrate transition. (OIKOGEN)”
Marine functional genomics will be instrumental in understanding the evolution of animal development and in exploiting rich oceanic biodiversity. This proposal addresses the acute need to develop marine model organisms and focuses on a chordate offering key advantages for genome-based studies. The tunicate, Oikopleura, has a miniature genome size (70 Mb), with a high gene density of 1 gene every 4 kb. Occupying a key phylogenetic position at the invertebrate/vertebrate transition, it has an extraordinarily short generation time of 6 days at 15 C. The animal is transparent throughout its life cycle, greatly facilitating molecular in situ and in vivo studies. Using genes that act in concert to build the Oikopleurid house, we will dissect coordination of their expression, and study how temporal changes in the spatial organisation of these genes in the nucleus generate differential expression patterns.
2001 – 2004 NFR-NT 145326/432 (PI), 1.5M NOK: “Molecular analysis of trade-offs in growth and reproductive allotment in a vital component of marine zooplankton”
Understanding factors that are critical determinants in life history strategies is a fundamental challenge of modern ecology. The principal objective is to test the controversial hypothesis that organsims will tend to a strategy of maximum net benefit in trade-offs between different life history characteristics. The focus of the study will be on a vital component of marine ecosystems, the appendicularian, O. dioica. The analysis will not only include morphological and detailed biochemical analysis of the problem but will provide innovative measurements at the molecular level, where primary responses to changes in environmental conditions are taking place.
2002 - 2003 EJ/hsmISAur02-36 NFR (PI) Aurora 26K NOK: “Molecular analysis of trade-offs in growth and reproductive allotment in a vital component of marine zooplankton”
A grant facilitating exchange with French collaborators at the Oceanic Observatory In Villefranche-sur-mer.
1998 – 2012 NFR 133335/V40 (PI), 48.7M NOK: “Sars Group Core Budget”
Subcontracted from the NFR to run a group studying chromatin and gene expression in developing a new marine chordate model organism Oikopleura dioica.
1995 – 1996 DGA/DRET N°94/060 (PI), 350K FF
A grant to develop technology to read out gene expression from living preimplantation mammalian embryos using a secreted luciferase cloned and patented by Eric Thompson.
1995 – 1996 UE DG XIII EC – VALUE (PI), 250K FF
A grant funded by the European Union to enable collaboration with the Berthold company in the development and testing of a highly sensitive CCD camera system in applications for in vivo monitoring of gene expression and for the pre-selection of transgenic bovine embryos prior to embryo transfer.