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Beltran T, Barroso C, Birkle TY, Stevens L, Schwartz HT, Sternberg PW, Fradin H, Gunsalus K, Piano F, Sharma G, Cerrato C, Ahringer J, Martínez-Pérez E, Blaxter M, Sarkies P. Comparative Epigenomics Reveals that RNA Polymerase II Pausing and Chromatin Domain Organization Control Nematode piRNA Biogenesis. Dev Cell 2019; 48:793-810.e6. [PMID: 30713076 PMCID: PMC6436959 DOI: 10.1016/j.devcel.2018.12.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 12/06/2018] [Accepted: 12/27/2018] [Indexed: 12/30/2022]
Abstract
Piwi-interacting RNAs (piRNAs) are important for genome regulation across metazoans, but their biogenesis evolves rapidly. In Caenorhabditis elegans, piRNA loci are clustered within two 3-Mb regions on chromosome IV. Each piRNA locus possesses an upstream motif that recruits RNA polymerase II to produce an ∼28 nt primary transcript. We used comparative epigenomics across nematodes to gain insight into the origin, evolution, and mechanism of nematode piRNA biogenesis. We show that the piRNA upstream motif is derived from core promoter elements controlling snRNA transcription. We describe two alternative modes of piRNA organization in nematodes: in C. elegans and closely related nematodes, piRNAs are clustered within repressive H3K27me3 chromatin, while in other species, typified by Pristionchus pacificus, piRNAs are found within introns of active genes. Additionally, we discover that piRNA production depends on sequence signals associated with RNA polymerase II pausing. We show that pausing signals synergize with chromatin to control piRNA transcription. Nematode piRNA transcription evolved from small nuclear RNA biogenesis Clustered piRNAs are produced from regulated (H3K27me3) chromatin domains Dispersed piRNAs are produced from active (H3K36me3) chromatin domains RNA polymerase II pausing determines the short (∼28 nt) length of piRNA precursors
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Affiliation(s)
- Toni Beltran
- MRC London Institute of Medical Sciences, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, London W12 0NN, UK
| | - Consuelo Barroso
- MRC London Institute of Medical Sciences, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, London W12 0NN, UK
| | - Timothy Y Birkle
- MRC London Institute of Medical Sciences, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, London W12 0NN, UK
| | - Lewis Stevens
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3TF, UK
| | - Hillel T Schwartz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hélène Fradin
- Department of Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Kristin Gunsalus
- Department of Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Fabio Piano
- Department of Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA; Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Garima Sharma
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Chiara Cerrato
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Julie Ahringer
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, UK
| | - Enrique Martínez-Pérez
- MRC London Institute of Medical Sciences, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, London W12 0NN, UK
| | - Mark Blaxter
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3TF, UK.
| | - Peter Sarkies
- MRC London Institute of Medical Sciences, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, London W12 0NN, UK.
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Liposome-based transfection enhances RNAi and CRISPR-mediated mutagenesis in non-model nematode systems. Sci Rep 2019; 9:483. [PMID: 30679624 PMCID: PMC6345965 DOI: 10.1038/s41598-018-37036-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 11/28/2018] [Indexed: 11/09/2022] Open
Abstract
Nematodes belong to one of the most diverse animal phyla. However, functional genomic studies in nematodes, other than in a few species, have often been limited in their reliability and success. Here we report that by combining liposome-based technology with microinjection, we were able to establish a wide range of genomic techniques in the newly described nematode genus Auanema. The method also allowed heritable changes in dauer larvae of Auanema, despite the immaturity of the gonad at the time of the microinjection. As proof of concept for potential functional studies in other nematode species, we also induced RNAi in the free-living nematode Pristionchus pacificus and targeted the human parasite Strongyloides stercoralis.
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Rödelsperger C, Röseler W, Prabh N, Yoshida K, Weiler C, Herrmann M, Sommer RJ. Phylotranscriptomics of Pristionchus Nematodes Reveals Parallel Gene Loss in Six Hermaphroditic Lineages. Curr Biol 2018; 28:3123-3127.e5. [DOI: 10.1016/j.cub.2018.07.041] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 06/12/2018] [Accepted: 07/12/2018] [Indexed: 11/28/2022]
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Moreno E, Lenuzzi M, Rödelsperger C, Prabh N, Witte H, Roeseler W, Riebesell M, Sommer RJ. DAF‐19/RFX controls ciliogenesis and influences oxygen‐induced social behaviors in
Pristionchus pacificus. Evol Dev 2018; 20:233-243. [DOI: 10.1111/ede.12271] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Eduardo Moreno
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Maša Lenuzzi
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Christian Rödelsperger
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Neel Prabh
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Hanh Witte
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Waltraud Roeseler
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Metta Riebesell
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
| | - Ralf J. Sommer
- Max Planck Institute for Developmental BiologyDepartment of Evolutionary BiologyTübingenGermany
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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] [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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Prabh N, Roeseler W, Witte H, Eberhardt G, Sommer RJ, Rödelsperger C. Deep taxon sampling reveals the evolutionary dynamics of novel gene families in Pristionchus nematodes. Genome Res 2018; 28:1664-1674. [PMID: 30232197 PMCID: PMC6211646 DOI: 10.1101/gr.234971.118] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 09/05/2018] [Indexed: 01/20/2023]
Abstract
The widespread identification of genes without detectable homology in related taxa is a hallmark of genome sequencing projects in animals, together with the abundance of gene duplications. Such genes have been called novel, young, taxon-restricted, or orphans, but little is known about the mechanisms accounting for their origin, age, and mode of evolution. Phylogenomic studies relying on deep and systematic taxon sampling and using the comparative method can provide insight into the evolutionary dynamics acting on novel genes. We used a phylogenomic approach for the nematode model organism Pristionchus pacificus and sequenced six additional Pristionchus and two outgroup species. This resulted in 10 genomes with a ladder-like phylogeny, sequenced in one laboratory using the same platform and analyzed by the same bioinformatic procedures. Our analysis revealed that 68%-81% of genes are assignable to orthologous gene families, the majority of which defined nine age classes with presence/absence patterns that can be explained by single evolutionary events. Contrasting different age classes, we find that older age classes are concentrated at chromosome centers, whereas novel gene families preferentially arise at the periphery, are weakly expressed, evolve rapidly, and have a high propensity of being lost. Over time, they increase in expression and become more constrained. Thus, the detailed phylogenetic resolution allowed a comprehensive characterization of the evolutionary dynamics of Pristionchus genomes indicating that distribution of age classes and their associated differences shape chromosomal divergence. This study establishes the Pristionchus system for future research on the mechanisms that drive the formation of novel genes.
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Affiliation(s)
- Neel Prabh
- Department of Integrative Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | - Waltraud Roeseler
- Department of Integrative Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | - Hanh Witte
- Department of Integrative Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | - Gabi Eberhardt
- Department of Integrative Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | - Ralf J Sommer
- Department of Integrative Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Max-Planck-Ring 9, 72076 Tübingen, Germany
| | - Christian Rödelsperger
- Department of Integrative Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Max-Planck-Ring 9, 72076 Tübingen, Germany
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Namdeo S, Moreno E, Rödelsperger C, Baskaran P, Witte H, Sommer RJ. Two independent sulfation processes regulate mouth-form plasticity in the nematode Pristionchus pacificus. Development 2018; 145:145/13/dev166272. [PMID: 29967123 DOI: 10.1242/dev.166272] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/17/2018] [Indexed: 12/15/2022]
Abstract
Sulfation of biomolecules, like phosphorylation, is one of the most fundamental and ubiquitous biochemical modifications with important functions during detoxification. This process is reversible, involving two enzyme classes: a sulfotransferase, which adds a sulfo group to a substrate; and a sulfatase that removes the sulfo group. However, unlike phosphorylation, the role of sulfation in organismal development is poorly understood. In this study, we find that two independent sulfation events regulate the development of mouth morphology in the nematode Pristionchus pacificus. This nematode has the ability to form two alternative mouth morphologies depending on environmental cues, an example of phenotypic plasticity. We found that, in addition to a previously described sulfatase, a sulfotransferase is involved in regulating the mouth-form dimorphism in P. pacificus However, it is unlikely that both of these sulfation-associated enzymes act upon the same substrates, as they are expressed in different cell types. Furthermore, animals mutant in genes encoding both enzymes show condition-dependent epistatic interactions. Thus, our study highlights the role of sulfation-associated enzymes in phenotypic plasticity of mouth structures in Pristionchus.
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Affiliation(s)
- Suryesh Namdeo
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076 Tuebingen, Germany
| | - Eduardo Moreno
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076 Tuebingen, Germany
| | - Christian Rödelsperger
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076 Tuebingen, Germany
| | - Praveen Baskaran
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076 Tuebingen, Germany
| | - Hanh Witte
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076 Tuebingen, Germany
| | - Ralf J Sommer
- Max Planck Institute for Developmental Biology, Department for Integrative Evolutionary Biology, Max-Planck-Ring 9, 72076 Tuebingen, Germany
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Akduman N, Rödelsperger C, Sommer RJ. Culture-based analysis of Pristionchus-associated microbiota from beetles and figs for studying nematode-bacterial interactions. PLoS One 2018; 13:e0198018. [PMID: 29864131 PMCID: PMC5986141 DOI: 10.1371/journal.pone.0198018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 05/12/2018] [Indexed: 12/20/2022] Open
Abstract
The interplay with bacteria is of crucial importance for the interaction of multicellular organisms with their environments. Studying the associations between the nematode model organisms Caenorhabditis elegans and Pristionchus pacificus with bacteria constitutes a powerful system to investigate these interactions at a mechanistic level. P. pacificus is found in association with scarab beetles in nature and recent studies revealed the succession and dynamics of this nematode and its microbiome during the decomposition of one particular host species, the rhinoceros beetle Oryctes borbonicus on La Réunion Island. However, these studies were performed using culture-free methods, with no attempt made to establish bacterial cultures from the beetle-nematode ecosystem and to investigate the effects of these microbes on life history traits in P. pacificus. Here, we establish and characterize a collection of 136 bacterial strains that have been isolated from scarab beetles and figs, another Pristionchus-associated environment, as a resource for studying their effect on various nematode traits. Classification based on 16S sequencing identified members of four bacterial phyla with the class of Gammaproteobacteria representing the majority with 81 strains. Assessing the survival of P. pacificus on individual bacteria allowed us to propose candidate groups of pathogens such as Bacillaceae, Actinobacteria, and Serratia. In combination with chemoattraction data, it was revealed that P. pacificus is able to recognize and avoid certain groups of pathogens, but not others. Our collection of bacterial strains forms a natural resource to study the effects of bacterial diet on development and other traits. Furthermore, these results will form the basis of future studies to elucidate the molecular mechanisms of recognition and pathogenicity.
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Affiliation(s)
- Nermin Akduman
- Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Max-Planck-Ring 5, Tübingen, Germany
| | - Christian Rödelsperger
- Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Max-Planck-Ring 5, Tübingen, Germany
| | - Ralf J. Sommer
- Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Max-Planck-Ring 5, Tübingen, Germany
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Yoshida K, Herrmann M, Kanzaki N, Weiler C, Rödelsperger C, Sommer RJ. Two New Species of Pristionchus (Nematoda: Diplogastridae) from Taiwan and the Definition of the pacificus Species-Complex Sensu Stricto. J Nematol 2018; 50:355-368. [PMID: 30451420 PMCID: PMC6909367 DOI: 10.21307/jofnem-2018-019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Indexed: 11/11/2022] Open
Abstract
Pristionchus pacificus Sommer, Carta, Kim, and Sternberg, 1996 is an important model organism in evolutionary biology that aims to integrate developmental biology and evo-devo with population genetics and ecology. Functional studies in P. pacificus are supported by a well-established phylogenetic framework of around 30 species of the genus Pristionchus that have been described in the last decade based on their entomophilic and necromenic association with scarab beetles. Biogeographically, East Asia has emerged as a hotspot of Pristionchus speciation and recent samplings have therefore focused on Islands and mainland settings in East Asia. Here, we describe in a series of three publications the results of our sampling efforts in Taiwan, Japan, and Hongkong in 2016 and 2017. We describe a total of nine new species that cover different phylogenetic species-complexes of the Pristionchus genus. In this first publication, we describe two new species, Pristionchus sikae sp. n. and Pristionchus kurosawai sp. n. that are closely related to P. pacificus . Together with five previously described species they form the " pacificus species-complex sensu stricto" that is characterized by all species forming viable, but sterile F1 hybrids indicating reproductive isolation. P. sikae sp. n. and P. kurosawai sp. n. have a gonochorist mode of reproduction and they are described using morphology, morphometrics, mating experiments, and genome-wide sequence analysis. We discuss the extreme diversification in the pacificus species-complex sensu stricto in East Asia and its potential power to study speciation processes.
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Affiliation(s)
- Kohta Yoshida
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstraße 37, Tübingen, Germany
| | - Matthias Herrmann
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstraße 37, Tübingen, Germany
| | - Natsumi Kanzaki
- Kansai Research Center, Forestry and Forest Products Research Institute, Kyoto 612-0855, Japan
| | - Christian Weiler
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstraße 37, Tübingen, Germany
| | - Christian Rödelsperger
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstraße 37, Tübingen, Germany
| | - Ralf J. Sommer
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstraße 37, Tübingen, Germany
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