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Brown A, Meiborg AB, Franz-Wachtel M, Macek B, Gordon S, Rog O, Weadick CJ, Werner MS. Characterization of the Pristionchus pacificus "epigenetic toolkit" reveals the evolutionary loss of the histone methyltransferase complex PRC2. Genetics 2024:iyae041. [PMID: 38513719 DOI: 10.1093/genetics/iyae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/04/2023] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
Comparative approaches have revealed both divergent and convergent paths to achieving shared developmental outcomes. Thus, only through assembling multiple case studies can we understand biological principles. Yet, despite appreciating the conservation - or lack thereof - of developmental networks, the conservation of epigenetic mechanisms regulating these networks is poorly understood. The nematode Pristionchus pacificus has emerged as a model system of plasticity and epigenetic regulation as it exhibits a bacterivorous or omnivorous morph depending on its environment. Here, we determined the "epigenetic toolkit" available to P. pacificus as a resource for future functional work on plasticity, and as a comparison with C. elegans to investigate the conservation of epigenetic mechanisms. Broadly, we observed a similar cast of genes with putative epigenetic function between C. elegans and P. pacificus. However, we also found striking differences. Most notably, the histone methyltransferase complex PRC2 appears to be missing in P. pacificus. We described the deletion/pseudogenization of the PRC2 genes mes-2 and mes-6 and concluded that both were lost in the last common ancestor of P. pacificus and a related species P. arcanus. Interestingly, we observed the enzymatic product of PRC2 (H3K27me3) by mass spectrometry and immunofluorescence, suggesting that a currently unknown methyltransferase has been co-opted for heterochromatin silencing. Altogether, we have provided an inventory of epigenetic genes in P. pacificus to compare with C. elegans. This inventory will enable reverse-genetic experiments related to plasticity, and has revealed the first loss of PRC2 in a multicellular organism.
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Affiliation(s)
- Audrey Brown
- School of Biological Sciences, The University of Utah, 257 1400 E, Salt Lake City, UT 84112, USA
| | - Adriaan B Meiborg
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
- Faculty of Biosciences, Collaboration for joint PhD degree between EMBL and Heidelberg University
| | - Mirita Franz-Wachtel
- Proteome Center Tübingen, University of Tübingen, Geschwister-Scholl-Platz, 72074 Tübingen, Germany
| | - Boris Macek
- Proteome Center Tübingen, University of Tübingen, Geschwister-Scholl-Platz, 72074 Tübingen, Germany
| | - Spencer Gordon
- School of Biological Sciences, The University of Utah, 257 1400 E, Salt Lake City, UT 84112, USA
| | - Ofer Rog
- School of Biological Sciences, The University of Utah, 257 1400 E, Salt Lake City, UT 84112, USA
| | - Cameron J Weadick
- Biosciences, University of Exeter, Geoffrey Pope Building, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Michael S Werner
- School of Biological Sciences, The University of Utah, 257 1400 E, Salt Lake City, UT 84112, USA
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2
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Jung J, Loschko T, Reich S, Rassoul-Agha M, Werner MS. Newly identified nematodes from the Great Salt Lake are associated with microbialites and specially adapted to hypersaline conditions. Proc Biol Sci 2024; 291:20232653. [PMID: 38471558 PMCID: PMC10932707 DOI: 10.1098/rspb.2023.2653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/09/2024] [Indexed: 03/14/2024] Open
Abstract
Extreme environments enable the study of simplified food-webs and serve as models for evolutionary bottlenecks and early Earth ecology. We investigated the biodiversity of invertebrate meiofauna in the benthic zone of the Great Salt Lake (GSL), Utah, USA, one of the most hypersaline lake systems in the world. The hypersaline bays within the GSL are currently thought to support only two multicellular animals: brine fly larvae and brine shrimp. Here, we report the presence, habitat, and microbial interactions of novel free-living nematodes. Nematode diversity drops dramatically along a salinity gradient from a freshwater river into the south arm of the lake. In Gilbert Bay, nematodes primarily inhabit reef-like organosedimentary structures built by bacteria called microbialites. These structures likely provide a protective barrier to UV and aridity, and bacterial associations within them may support life in hypersaline environments. Notably, sampling from Owens Lake, another terminal lake in the Great Basin that lacks microbialites, did not recover nematodes from similar salinities. Phylogenetic divergence suggests that GSL nematodes represent previously undescribed members of the family Monhysteridae-one of the dominant fauna of the abyssal zone and deep-sea hydrothermal vents. These findings update our understanding of halophile ecosystems and the habitable limit of animals.
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Affiliation(s)
- Julie Jung
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Tobias Loschko
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
- Max Planck Institute for Biology, Tübingen, Germany
| | - Shelley Reich
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Maxim Rassoul-Agha
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Michael S. Werner
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
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3
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Werner MS, Loschko T, King T, Reich S, Theska T, Franz-Wachtel M, Macek B, Sommer RJ. Author Correction: Histone 4 lysine 5/12 acetylation enables developmental plasticity of Pristionchus mouth form. Nat Commun 2023; 14:2837. [PMID: 37202384 DOI: 10.1038/s41467-023-38693-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Affiliation(s)
- Michael S Werner
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, USA
| | - Tobias Loschko
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
| | - Thomas King
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, USA
| | - Shelley Reich
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, USA
| | - Tobias Theska
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
| | | | - Boris Macek
- Proteome Center Tübingen, University of Tübingen, Tübingen, 72076, Germany
| | - Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany.
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4
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Werner MS, Loschko T, King T, Reich S, Theska T, Franz-Wachtel M, Macek B, Sommer RJ. Histone 4 lysine 5/12 acetylation enables developmental plasticity of Pristionchus mouth form. Nat Commun 2023; 14:2095. [PMID: 37055396 PMCID: PMC10102330 DOI: 10.1038/s41467-023-37734-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 03/28/2023] [Indexed: 04/15/2023] Open
Abstract
Development can be altered to match phenotypes with the environment, and the genetic mechanisms that direct such alternative phenotypes are beginning to be elucidated. Yet, the rules that govern environmental sensitivity vs. invariant development, and potential epigenetic memory, remain unknown. Here, we show that plasticity of nematode mouth forms is determined by histone 4 lysine 5 and 12 acetylation (H4K5/12ac). Acetylation in early larval stages provides a permissive chromatin state, which is susceptible to induction during the critical window of environmental sensitivity. As development proceeds deacetylation shuts off switch gene expression to end the critical period. Inhibiting deacetylase enzymes leads to fixation of prior developmental trajectories, demonstrating that histone modifications in juveniles can carry environmental information to adults. Finally, we provide evidence that this regulation was derived from an ancient mechanism of licensing developmental speed. Altogether, our results show that H4K5/12ac enables epigenetic regulation of developmental plasticity that can be stored and erased by acetylation and deacetylation, respectively.
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Affiliation(s)
- Michael S Werner
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, USA
| | - Tobias Loschko
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
| | - Thomas King
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, USA
| | - Shelley Reich
- School of Biological Sciences, The University of Utah, Salt Lake City, UT, USA
| | - Tobias Theska
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
| | | | - Boris Macek
- Proteome Center Tübingen, University of Tübingen, Tübingen, 72076, Germany
| | - Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany.
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5
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Renahan T, Lo WS, Werner MS, Rochat J, Herrmann M, Sommer RJ. Nematode biphasic 'boom and bust' dynamics are dependent on host bacterial load while linking dauer and mouth-form polyphenisms. Environ Microbiol 2021; 23:5102-5113. [PMID: 33587771 DOI: 10.1111/1462-2920.15438] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 01/06/2023]
Abstract
Cross-kingdom interactions involve dynamic processes that shape terrestrial ecosystems and represent striking examples of co-evolution. The multifaceted relationships of entomopathogenic nematodes with their insect hosts and symbiotic bacteria are well-studied cases of co-evolution and pathogenicity. In contrast, microbial interactions in soil after the natural death of insects and other invertebrates are minimally understood. In particular, the turnover and succession of nematodes and bacteria during insect decay have not been well documented - although it represents a rich ecological niche with multiple species interactions. Here, we utilize developmentally plastic nematode Pristionchus pacificus and its associated scarab beetles as models. On La Réunion Island, we collected rhinoceros beetle Oryctes borbonicus, induced death, and placed carcasses in cages both on the island and in a mock-natural environment in the laboratory controlling for high spatial and temporal resolution. Investigating nematode population density and dispersal dynamics, we were able to connect two imperative plasticities, dauer and mouth form. We observed a biphasic 'boom and bust' dispersal dynamic of dauer larvae that corresponds to bacterial load on carcasses but not bacterial type. Strikingly, all post-dauer adults have the predatory mouth form, demonstrating novel intricate interactions on decaying insect hosts. Thus, ecologically relevant survival strategies incorporate critical plastic traits.
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Affiliation(s)
- Tess Renahan
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck Ring 9, Tübingen, 720976, Germany
| | - Wen-Sui Lo
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck Ring 9, Tübingen, 720976, Germany
| | - Michael S Werner
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck Ring 9, Tübingen, 720976, Germany.,Department of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Jacques Rochat
- Micropoda, 2 Rue De l'é'toile du Berger, Residence le Jardin des Épices, La Possession, La Réunion, 97419, France
| | - Matthias Herrmann
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck Ring 9, Tübingen, 720976, Germany
| | - Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Max-Planck Ring 9, Tübingen, 720976, Germany
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6
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Theska T, Sieriebriennikov B, Wighard SS, Werner MS, Sommer RJ. Geometric morphometrics of microscopic animals as exemplified by model nematodes. Nat Protoc 2020; 15:2611-2644. [PMID: 32632318 DOI: 10.1038/s41596-020-0347-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 04/27/2020] [Indexed: 12/15/2022]
Abstract
While a host of molecular techniques are utilized by evolutionary developmental (evo-devo) biologists, tools for quantitative evaluation of morphology are still largely underappreciated, especially in studies on microscopic animals. Here, we provide a standardized protocol for geometric morphometric analyses of 2D landmark data sets using a combination of the geomorph and Morpho R packages. Furthermore, we integrate clustering approaches to identify group structures within such datasets. We demonstrate our protocol by performing exemplary analyses on stomatal shapes in the model nematodes Caenorhabditis and Pristionchus. Image acquisition for 80 worms takes 3-4 d, while the entire data analysis requires 10-30 min. In theory, this approach is adaptable to all microscopic model organisms to facilitate a thorough quantification of shape differences within and across species, adding to the methodological toolkit of evo-devo studies on morphological evolution and novelty.
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Affiliation(s)
- Tobias Theska
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Bogdan Sieriebriennikov
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.,Department of Biology, New York University, New York, NY, USA
| | - Sara S Wighard
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Michael S Werner
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.
| | - Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.
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7
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Werner MS, Claaßen MH, Renahan T, Dardiry M, Sommer RJ. Adult Influence on Juvenile Phenotypes by Stage-Specific Pheromone Production. iScience 2018; 10:123-134. [PMID: 30513394 PMCID: PMC6279967 DOI: 10.1016/j.isci.2018.11.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 12/14/2022] Open
Abstract
Many animal and plant species respond to population density by phenotypic plasticity. To investigate if specific age classes and/or cross-generational signaling affect density-dependent plasticity, we developed a dye-based method to differentiate co-existing nematode populations. We applied this method to Pristionchus pacificus, which develops a predatory mouth form to exploit alternative resources and kill competitors in response to high population densities. Remarkably, adult, but not juvenile, crowding induces the predatory morph in other juveniles. High-performance liquid chromatography-mass spectrometry of secreted metabolites combined with genetic mutants traced this result to the production of stage-specific pheromones. In particular, the P. pacificus-specific di-ascaroside#1 that induces the predatory morph is induced in the last juvenile stage and young adults, even though mouth forms are no longer plastic in adults. Cross-generational signaling between adults and juveniles may serve as an indication of rapidly increasing population size, arguing that age classes are an important component of phenotypic plasticity.
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Affiliation(s)
- Michael S Werner
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Marc H Claaßen
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Tess Renahan
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Mohannad Dardiry
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Ralf J Sommer
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany.
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8
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Werner MS, Sieriebriennikov B, Prabh N, Loschko T, Lanz C, Sommer RJ. Young genes have distinct gene structure, epigenetic profiles, and transcriptional regulation. Genome Res 2018; 28:1675-1687. [PMID: 30232198 PMCID: PMC6211652 DOI: 10.1101/gr.234872.118] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 09/05/2018] [Indexed: 12/22/2022]
Abstract
Species-specific, new, or "orphan" genes account for 10%-30% of eukaryotic genomes. Although initially considered to have limited function, an increasing number of orphan genes have been shown to provide important phenotypic innovation. How new genes acquire regulatory sequences for proper temporal and spatial expression is unknown. Orphan gene regulation may rely in part on origination in open chromatin adjacent to preexisting promoters, although this has not yet been assessed by genome-wide analysis of chromatin states. Here, we combine taxon-rich nematode phylogenies with Iso-Seq, RNA-seq, ChIP-seq, and ATAC-seq to identify the gene structure and epigenetic signature of orphan genes in the satellite model nematode Pristionchus pacificus Consistent with previous findings, we find young genes are shorter, contain fewer exons, and are on average less strongly expressed than older genes. However, the subset of orphan genes that are expressed exhibit distinct chromatin states from similarly expressed conserved genes. Orphan gene transcription is determined by a lack of repressive histone modifications, confirming long-held hypotheses that open chromatin is important for new gene formation. Yet orphan gene start sites more closely resemble enhancers defined by H3K4me1, H3K27ac, and ATAC-seq peaks, in contrast to conserved genes that exhibit traditional promoters defined by H3K4me3 and H3K27ac. Although the majority of orphan genes are located on chromosome arms that contain high recombination rates and repressive histone marks, strongly expressed orphan genes are more randomly distributed. Our results support a model of new gene origination by rare integration into open chromatin near enhancers.
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Affiliation(s)
- Michael S Werner
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Bogdan Sieriebriennikov
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Neel Prabh
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Tobias Loschko
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Christa Lanz
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Ralf J Sommer
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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9
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Gupta A, Xu J, Lee S, Tsai ST, Zhou B, Kurosawa K, Werner MS, Koide A, Ruthenburg AJ, Dou Y, Koide S. Facile target validation in an animal model with intracellularly expressed monobodies. Nat Chem Biol 2018; 14:895-900. [PMID: 30013062 PMCID: PMC6103845 DOI: 10.1038/s41589-018-0099-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 06/07/2018] [Indexed: 11/16/2022]
Abstract
Rapidly determining the biological effect of perturbing a site within a potential drug target could guide drug discovery efforts but it remains challenging. Here, we describe a facile target validation approach that exploits monobodies, small synthetic binding proteins that can be fully functionally expressed in cells. We developed a potent and selective monobody to WDR5, a core component of the Mixed Lineage Leukemia (MLL) methyltransferase complex. The monobody bound to the MLL-interaction site of WDR5, the same site for small molecule inhibitors whose efficacy has been demonstrated in cells but not in animals. As a genetically encoded reagent, the monobody inhibited proliferation of an MLL-AF9 cell line in vitro, suppressed its leukemogenesis and conferred survival benefit in an in vivo mouse leukemia model. The capacity of this approach to readily bridge biochemical, structural, cellular characterization and tests in animal models may accelerate discovery and validation of druggable sites.
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Affiliation(s)
- Ankit Gupta
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Jing Xu
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Shirley Lee
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Steven T Tsai
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Bo Zhou
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Kohei Kurosawa
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Michael S Werner
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
| | - Akiko Koide
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.,Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Alexander J Ruthenburg
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA
| | - Yali Dou
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA. .,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA. .,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
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10
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Sommer RJ, Dardiry M, Lenuzzi M, Namdeo S, Renahan T, Sieriebriennikov B, Werner MS. The genetics of phenotypic plasticity in nematode feeding structures. Open Biol 2018; 7:rsob.160332. [PMID: 28298309 PMCID: PMC5376706 DOI: 10.1098/rsob.160332] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/10/2017] [Indexed: 12/15/2022] Open
Abstract
Phenotypic plasticity has been proposed as an ecological and evolutionary concept. Ecologically, it can help study how genes and the environment interact to produce robust phenotypes. Evolutionarily, as a facilitator it might contribute to phenotypic novelty and diversification. However, the discussion of phenotypic plasticity remains contentious in parts due to the absence of model systems and rigorous genetic studies. Here, we summarize recent work on the nematode Pristionchus pacificus, which exhibits a feeding plasticity allowing predatory or bacteriovorous feeding. We show feeding plasticity to be controlled by developmental switch genes that are themselves under epigenetic control. Phylogenetic and comparative studies support phenotypic plasticity and its role as a facilitator of morphological novelty and diversity.
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Affiliation(s)
- Ralf J Sommer
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Developmental Biology, Spemannstrasse 37, 72076 Tübingen, Germany
| | - Mohannad Dardiry
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Developmental Biology, Spemannstrasse 37, 72076 Tübingen, Germany
| | - Masa Lenuzzi
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Developmental Biology, Spemannstrasse 37, 72076 Tübingen, Germany
| | - Suryesh Namdeo
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Developmental Biology, Spemannstrasse 37, 72076 Tübingen, Germany
| | - Tess Renahan
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Developmental Biology, Spemannstrasse 37, 72076 Tübingen, Germany
| | - Bogdan Sieriebriennikov
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Developmental Biology, Spemannstrasse 37, 72076 Tübingen, Germany
| | - Michael S Werner
- Department for Integrative Evolutionary Biology, Max-Planck Institute for Developmental Biology, Spemannstrasse 37, 72076 Tübingen, Germany
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11
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Werner MS, Sieriebriennikov B, Loschko T, Namdeo S, Lenuzzi M, Dardiry M, Renahan T, Sharma DR, Sommer RJ. Environmental influence on Pristionchus pacificus mouth form through different culture methods. Sci Rep 2017; 7:7207. [PMID: 28775277 PMCID: PMC5543044 DOI: 10.1038/s41598-017-07455-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 06/28/2017] [Indexed: 12/29/2022] Open
Abstract
Environmental cues can impact development to elicit distinct phenotypes in the adult. The consequences of phenotypic plasticity can have profound effects on morphology, life cycle, and behavior to increase the fitness of the organism. The molecular mechanisms governing these interactions are beginning to be elucidated in a few cases, such as social insects. Nevertheless, there is a paucity of systems that are amenable to rigorous experimentation, preventing both detailed mechanistic insight and the establishment of a generalizable conceptual framework. The mouth dimorphism of the model nematode Pristionchus pacificus offers the rare opportunity to examine the genetics, genomics, and epigenetics of environmental influence on developmental plasticity. Yet there are currently no easily tunable environmental factors that affect mouth-form ratios and are scalable to large cultures required for molecular biology. Here we present a suite of culture conditions to toggle the mouth-form phenotype of P. pacificus. The effects are reversible, do not require the costly or labor-intensive synthesis of chemicals, and proceed through the same pathways previously examined from forward genetic screens. Different species of Pristionchus exhibit different responses to culture conditions, demonstrating unique gene-environment interactions, and providing an opportunity to study environmental influence on a macroevolutionary scale.
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Affiliation(s)
- Michael S Werner
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Bogdan Sieriebriennikov
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Tobias Loschko
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Suryesh Namdeo
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Masa Lenuzzi
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Mohannad Dardiry
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Tess Renahan
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Devansh Raj Sharma
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Ralf J Sommer
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany.
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12
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Werner MS, Ruthenburg AJ. Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes. Cell Rep 2015; 12:1089-98. [PMID: 26257179 DOI: 10.1016/j.celrep.2015.07.033] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 07/02/2015] [Accepted: 07/14/2015] [Indexed: 01/09/2023] Open
Abstract
A number of long noncoding RNAs (lncRNAs) have been reported to regulate transcription via recruitment of chromatin modifiers or bridging distal enhancer elements to gene promoters. However, the generality of these modes of regulation and the mechanisms of chromatin attachment for thousands of unstudied human lncRNAs remain unclear. To address these questions, we performed stringent nuclear fractionation coupled to RNA sequencing. We provide genome-wide identification of human chromatin-associated lncRNAs and demonstrate tethering of RNA to chromatin by RNAPII is a pervasive mechanism of attachment. We also uncovered thousands of chromatin-enriched RNAs (cheRNAs) that share molecular properties with known lncRNAs. Although distinct from eRNAs derived from active prototypical enhancers, the production of cheRNAs is strongly correlated with the expression of neighboring protein-coding genes. This work provides an updated framework for nuclear RNA organization that includes a large chromatin-associated transcript population correlated with active genes and may prove useful in de novo enhancer annotation.
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Affiliation(s)
- Michael S Werner
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Alexander J Ruthenburg
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.
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Werner MS, Hornblass A, Reifler DM, Dresner SC, Harrison W. Intravascular papillary endothelial hyperplasia: collection of four cases and a review of the literature. Ophthalmic Plast Reconstr Surg 1997; 13:48-56. [PMID: 9076784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Intravascular papillary endothelial hyperplasia is a benign tumor that rarely presents in the orbit and ocular adnexa. Generally, it occurs as an isolated eyelid mass, not associated with systemic or local disease. Histopathologically, it can be easily confused with angiosarcoma or Kimura's disease. We present our experience with four cases of this tumor in the ocular adnexa, along with a literature review.
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Affiliation(s)
- M S Werner
- Department of Ophthalmology, Manhattan Eye, Ear, and Throat Hospital, New York, New York 10021, USA
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Abstract
A 78-year-old woman with recurrent chalazia of the upper eyelid was found to have mucinous eccrine carcinoma. This rare pathologic entity, with low metastatic potential, nevertheless has a significant recurrence rate. This case underscores the importance of considering this tumor in recalcitrant eyelid lesions and highlights the pathology of this tumor. A summary of previous cases is also presented.
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Affiliation(s)
- M S Werner
- Department of Ophthalmology, Manhattan Eye, Ear & Throat Hospital, New York, New York, USA
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Raza ST, Mukherjee SK, Danias PG, Abraham J, Johnson KM, Sands MJ, Werner MS, Silverman DI. Hemodynamically significant extrinsic left atrial compression by gastric structures in the mediastinum. Ann Intern Med 1995; 123:114-6. [PMID: 7778823 DOI: 10.7326/0003-4819-123-2-199507150-00006] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- S T Raza
- New Britain General Hospital, Connecticut, USA
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Abstract
PURPOSE To determine which signs are sensitive and specific in the setting of trauma to establish the diagnosis of an occult scleral rupture. METHODS The charts of patients with presumed scleral rupture were identified retrospectively. The ocular findings among the patients who had a rupture based on findings at surgery were compared with those patients who were noted to have normal findings at surgery. RESULTS Visual acuity worse than 20/400, decreased intraocular pressure, intraocular pressure less than that in the nontraumatized eye, and an afferent pupillary defect were all significant indicators of an open globe. CONCLUSION Determining the likelihood of an occult rupture can be facilitated by noting the presence or absence of those indicators that are significant and carry a high specificity.
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Affiliation(s)
- M S Werner
- Department of Ophthalmology and Visual Science, University of Illinois, Chicago College of Medicine 60612
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Abstract
PURPOSE The authors sought to provide relevant data regarding the demographic and clinical aspects of spontaneous and traumatic vitreous hemorrhages to guide clinicians in better delineating the expected etiologic patterns of these hemorrhages in an urban environment. METHODS The records of 253 consecutive patients with newly diagnosed vitreous hemorrhage seen in a general eye clinic were selected for retrospective analysis. To minimize selection bias of a tertiary care center, patients who were referred to the clinic by outside ophthalmologists for vitreoretinal consultation or those with a history of recent intraocular surgery, postoperative complications, or loss to follow-up were excluded from study. Demographic, ocular, and general medical variables were tabulated for the 200 patients (230 eyes) who met our inclusion criteria. RESULTS Fifty percent of the patients were black, 26% were white, 23% were Hispanic, and 1% was Oriental. The causes of vitreous hemorrhage were proliferative diabetic retinopathy (PDR) (35.2%), trauma (18.3%), retinal vein occlusion (7.4%), retinal tear without a detachment (7.0%), posterior vitreous detachment (6.5%), proliferative sickle retinopathy (5.7%), retinal tear with a detachment (4.8%), subretinal neovascularization from macular degeneration (2.2%), hypertensive retinopathy (1.7%), unknown (2.5%), and other causes (8.7%). Among black patients with spontaneous vitreous hemorrhage, sickle cell retinopathy and retinal vein occlusion were major causes, each accounting for more than 15% of the cases. Systemic hypertension was associated with vitreous hemorrhage from retinal vein occlusion. CONCLUSION The authors propose that despite the wide array of causative factors of vitreous hemorrhage, the evaluation of demographic, ocular, and medical variables can significantly aid clinicians in identifying its etiologic patterns.
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Affiliation(s)
- M R Dana
- Department of Ophthalmology and Visual Sciences, Eye and Ear Infirmary, UIC Eye Center, University of Illinois, Chicago College of Medicine
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Abstract
Viable composite grafting is a technique used in eyelid reconstruction in which the graft is obtained from the contralateral eyelid. We reviewed the charts of 51 patients who underwent composite grafting of the eyelid since 1983. The average horizontal length of the defect repaired with this technique was 17.3 mm, and the most common indication for its use was basal cell carcinoma. Postoperatively, 39 (91%) of the 43 patients with available measurements had within 2.0 mm of palpebral fissure symmetry. Furthermore, this method of reconstruction allows survival of the eyelid margin and eyelid margin cilia. Composite grafting of the eyelid is a valuable method for eyelid reconstruction that provides acceptable cosmetic results.
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Affiliation(s)
- M S Werner
- Department of Ophthalmology and Visual Sciences, University of Illinois, Chicago Eye Center 60612
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Dana MR, Werner MS. "Sterile" endophthalmitis after sutureless cataract extraction. Ophthalmology 1993; 100:441-2. [PMID: 8479695 DOI: 10.1016/s0161-6420(13)32373-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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Abstract
To evaluate the hemodynamic effects of external cardiac pacing, ten subjects with normal left ventricular function were paced at rates approximating their resting heart rates using an external pacemaker while continuous-wave Doppler measurements from the aortic outflow were recorded. The Doppler flow velocity integral was used as an index of stroke volume and the product of heart rate and flow velocity integral was used as an index of cardiac output. At a pacing rate 13% faster (range -5% to 32%) than the rate during sinus rhythm, the mean index of stroke volume was reduced 24% from 17.7 cm to 13.5 cm (P less than 0.0002). However, the faster rate during external pacing partially compensated for the reduced stroke volume resulting in an index of cardiac output that was 14% lower compared to the prepaced index (1,297 vs 1,121 cm [P less than 0.02]). Thus, in subjects with normal LV function, external pacing results in a small drop in cardiac output that may be partially overcome by increasing the pacing rate.
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Affiliation(s)
- U Talit
- New Britain General Hospital, Connecticut
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Leodori M, Hart TJ, Werner MS. Surgical management of the deep plantar abscess in the diabetic patient. J Foot Surg 1988; 27:139-44. [PMID: 3372947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The authors report the case of a deep plantar abscess in a diabetic patient. The pathophysiology of diabetic foot lesions as well as classification is discussed. The philosophy of local radical debridement involving ray resection, as well as postdebridement management is discussed in detail.
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Affiliation(s)
- M Leodori
- Department of Podiatric Surgery, Kennedy Memorial Hospitals, SaddleBrook, New Jersey 07662
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Sollitto RJ, Werner MS, Hart T. A modification of the Hibbs tenosuspension for flexible cavus deformity. J Foot Surg 1987; 26:72-4. [PMID: 3559045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The authors present a modification of the Hibbs tenosuspension for the correction of clawtoes associated with flexible cavus deformity. A release of the plantar fascia is performed along with the procedure. The major advantages offered by this procedure are the ease in which it can be performed, the vector of the extensor digitorum longus tendon at the ankle is not disrupted, and the only osseous work necessary is digital arthroplasty.
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Sollitto RJ, Werner MS. A preliminary report on the status of implants for the lesser toes. J Foot Surg 1985; 24:453-5. [PMID: 4078241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The authors present a retrospective study of 47 digits, with an average follow-up of 15 months, using the Silastic Hammertoe Implant H.P. The complications inherent with all implants are reviewed and the specific problems noted with this implant, including dislocation, bony regrowth, and lack of a superior cosmetic result, are discussed.
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Werner MS. Friends of Nepal's hearing handicapped--an outreach by the private sector. ASHA 1981; 23:210-4. [PMID: 7236339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Werner MS. Synchronous stabilization of visual perception by voice vibration. J Opt Soc Am 1974; 64:890. [PMID: 4837670 DOI: 10.1364/josa.64.000890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Werner MS. Alterations in the duration, pitch, and intensity of spoken passages successively heard and repeated several times. J Acoust Soc Am 1969; 46:1051-1052. [PMID: 5824029 DOI: 10.1121/1.1911802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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