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Li Y, Hui JHL. Small RNAs in Cnidaria: A review. Evol Appl 2023; 16:354-364. [PMID: 36793685 PMCID: PMC9923473 DOI: 10.1111/eva.13445] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 05/18/2022] [Accepted: 06/17/2022] [Indexed: 11/30/2022] Open
Abstract
As fundamental components of RNA silencing, small RNA (sRNA) molecules ranging from 20 to 32 nucleotides in length have been found as potent regulators of gene expression and genome stability in many biological processes of eukaryotes. Three major small RNAs are active in animals, including the microRNA (miRNA), short interfering RNA (siRNA), and PIWI-interacting RNA (piRNA). Cnidarians, the sister group to bilaterians, are at a critical phylogenetic node to better model eukaryotic small RNA pathway evolution. To date, most of our understanding of sRNA regulation and its potential contribution to evolution has been limited to a few triploblastic bilaterian and plant models. The diploblastic nonbilaterians, including the cnidarians, are understudied in this regard. Therefore, this review will present the current-known small RNA information in cnidarians to enhance our understanding of the development of the small RNA pathways in early branch animals.
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Affiliation(s)
- Yiqian Li
- Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, School of Life SciencesThe Chinese University of Hong KongHong Kong CityHong Kong
| | - Jerome H. L. Hui
- Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, School of Life SciencesThe Chinese University of Hong KongHong Kong CityHong Kong
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2
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Tursch A, Holstein TW. From injury to patterning—MAPKs and Wnt signaling in Hydra. Curr Top Dev Biol 2023; 153:381-417. [PMID: 36967201 DOI: 10.1016/bs.ctdb.2023.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Hydra has a regenerative capacity that is not limited to individual organs but encompasses the entire body. Various global and integrative genome, transcriptome and proteome approaches have shown that many of the signaling pathways and transcription factors present in vertebrates are already present in Cnidaria, the sister group of Bilateria, and are also activated in regeneration. It is now possible to investigate one of the central questions of regeneration biology, i.e., how does the patterning system become activated by the injury signals that initiate regeneration. This review will present the current data obtained in Hydra and draw parallels with regeneration in Bilateria. Important findings of this global analysis are that the Wnt signaling pathway has a dual function in the regeneration process. In the early phase Wnt is activated generically and in a second phase of pattern formation it is activated in a position specific manner. Thus, Wnt signaling is part of the generic injury response, in which mitogen-activated protein kinases (MAPKs) are initially activated via calcium and reactive oxygen species (ROS). The MAPKs, p38, c-Jun N-terminal kinases (JNKs) and extracellular signal-regulated kinases (ERK) are essential for Wnt activation in Hydra head and foot regenerates. Furthermore, the antagonism between the ERK signaling pathway and stress-induced MAPKs results in a balanced induction of apoptosis and mitosis. However, the early Wnt genes are activated by MAPK signaling rather than apoptosis. Early Wnt gene activity is differentially integrated with a stable, β-Catenin-based gradient along the primary body axis maintaining axial polarity and activating further Wnts in the regenerating head. Because MAPKs and Wnts are highly evolutionarily conserved, we hypothesize that this mechanism is also present in vertebrates but may be activated to different degrees at the level of early Wnt gene integration.
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siRNA-mediated gene knockdown via electroporation in hydrozoan jellyfish embryos. Sci Rep 2022; 12:16049. [PMID: 36180523 PMCID: PMC9525680 DOI: 10.1038/s41598-022-20476-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 09/13/2022] [Indexed: 11/09/2022] Open
Abstract
As the sister group to bilaterians, cnidarians stand in a unique phylogenetic position that provides insight into evolutionary aspects of animal development, physiology, and behavior. While cnidarians are classified into two types, sessile polyps and free-swimming medusae, most studies at the cellular and molecular levels have been conducted on representative polyp-type cnidarians and have focused on establishing techniques of genetic manipulation. Recently, gene knockdown by delivery of short hairpin RNAs into eggs via electroporation has been introduced in two polyp-type cnidarians, Nematostella vectensis and Hydractinia symbiolongicarpus, enabling systematic loss-of-function experiments. By contrast, current methods of genetic manipulation for most medusa-type cnidarians, or jellyfish, are quite limited, except for Clytia hemisphaerica, and reliable techniques are required to interrogate function of specific genes in different jellyfish species. Here, we present a method to knock down target genes by delivering small interfering RNA (siRNA) into fertilized eggs via electroporation, using the hydrozoan jellyfish, Clytia hemisphaerica and Cladonema paciificum. We show that siRNAs targeting endogenous GFP1 and Wnt3 in Clytia efficiently knock down gene expression and result in known planula phenotypes: loss of green fluorescence and defects in axial patterning, respectively. We also successfully knock down endogenous Wnt3 in Cladonema by siRNA electroporation, which circumvents the technical difficulty of microinjecting small eggs. Wnt3 knockdown in Cladonema causes gene expression changes in axial markers, suggesting a conserved Wnt/β-catenin-mediated pathway that controls axial polarity during embryogenesis. Our gene-targeting siRNA electroporation method is applicable to other animals, including and beyond jellyfish species, and will facilitate the investigation and understanding of myriad aspects of animal development.
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4
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Shum CW, Nong W, So WL, Li Y, Qu Z, Yip HY, Swale T, Ang PO, Chan KM, Chan TF, Chu KH, Chui AP, Lau KF, Ngai SM, Xu F, Hui JH. Genome of the sea anemone Exaiptasia pallida and transcriptome profiles during tentacle regeneration. Front Cell Dev Biol 2022; 10:900321. [PMID: 36072338 PMCID: PMC9444052 DOI: 10.3389/fcell.2022.900321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 07/08/2022] [Indexed: 12/19/2022] Open
Abstract
Cnidarians including sea anemones, corals, hydra, and jellyfishes are a group of animals well known for their regeneration capacity. However, how non-coding RNAs such as microRNAs (also known as miRNAs) contribute to cnidarian tissue regeneration is poorly understood. Here, we sequenced and assembled the genome of the sea anemone Exaiptasia pallida collected in Hong Kong waters. The assembled genome size of E. pallida is 229.21 Mb with a scaffold N50 of 10.58 Mb and BUSCO completeness of 91.1%, representing a significantly improved genome assembly of this species. The organization of ANTP-class homeobox genes in this anthozoan further supported the previous findings in jellyfishes, where most of these genes are mainly located on three scaffolds. Tentacles of E. pallida were excised, and both mRNA and miRNA were sequenced at 9 time points (0 h, 6 h, 12 h, 18 h, 1 day, 2, 3, 6, and 8 days) from regenerating tentacles. In addition to the Wnt signaling pathway and homeobox genes that are shown to be likely involved in tissue regeneration as in other cnidarians, we have shown that GLWamide neuropeptides, and for the first time sesquiterpenoid pathway genes could potentially be involved in the late phase of cnidarian tissue regeneration. The established sea anemone model will be useful for further investigation of biology and evolution in, and the effect of climate change on this important group of animals.
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Affiliation(s)
- Cheryl W.Y. Shum
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Wai Lok So
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yiqian Li
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Zhe Qu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ho Yin Yip
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Thomas Swale
- Dovetail Genomics, Scotts Valley, CA, United States
| | - Put O. Ang
- Institute of Space and Earth Information Science, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - King Ming Chan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ting Fung Chan
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Ka Hou Chu
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Apple P.Y. Chui
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kwok Fai Lau
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Sai Ming Ngai
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Fei Xu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Jerome H.L. Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- *Correspondence: Jerome H.L. Hui,
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Avalos PN, Forsthoefel DJ. An Emerging Frontier in Intercellular Communication: Extracellular Vesicles in Regeneration. Front Cell Dev Biol 2022; 10:849905. [PMID: 35646926 PMCID: PMC9130466 DOI: 10.3389/fcell.2022.849905] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/28/2022] [Indexed: 12/12/2022] Open
Abstract
Regeneration requires cellular proliferation, differentiation, and other processes that are regulated by secreted cues originating from cells in the local environment. Recent studies suggest that signaling by extracellular vesicles (EVs), another mode of paracrine communication, may also play a significant role in coordinating cellular behaviors during regeneration. EVs are nanoparticles composed of a lipid bilayer enclosing proteins, nucleic acids, lipids, and other metabolites, and are secreted by most cell types. Upon EV uptake by target cells, EV cargo can influence diverse cellular behaviors during regeneration, including cell survival, immune responses, extracellular matrix remodeling, proliferation, migration, and differentiation. In this review, we briefly introduce the history of EV research and EV biogenesis. Then, we review current understanding of how EVs regulate cellular behaviors during regeneration derived from numerous studies of stem cell-derived EVs in mammalian injury models. Finally, we discuss the potential of other established and emerging research organisms to expand our mechanistic knowledge of basic EV biology, how injury modulates EV biogenesis, cellular sources of EVs in vivo, and the roles of EVs in organisms with greater regenerative capacity.
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Affiliation(s)
- Priscilla N. Avalos
- Department of Cell Biology, College of Medicine, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - David J. Forsthoefel
- Department of Cell Biology, College of Medicine, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
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Vogg MC, Buzgariu W, Suknovic NS, Galliot B. Cellular, Metabolic, and Developmental Dimensions of Whole-Body Regeneration in Hydra. Cold Spring Harb Perspect Biol 2021; 13:a040725. [PMID: 34230037 PMCID: PMC8635000 DOI: 10.1101/cshperspect.a040725] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Here we discuss the developmental and homeostatic conditions necessary for Hydra regeneration. Hydra is characterized by populations of adult stem cells paused in the G2 phase of the cell cycle, ready to respond to injury signals. The body column can be compared to a blastema-like structure, populated with multifunctional epithelial stem cells that show low sensitivity to proapoptotic signals, and high inducibility of autophagy that promotes resistance to stress and starvation. Intact Hydra polyps also exhibit a dynamic patterning along the oral-aboral axis under the control of homeostatic organizers whose activity results from regulatory loops between activators and inhibitors. As in bilaterians, injury triggers the immediate production of reactive oxygen species (ROS) signals that promote wound healing and contribute to the reactivation of developmental programs via cell death and the de novo formation of new organizing centers from somatic tissues. In aging Hydra, regeneration is rapidly lost as homeostatic conditions are no longer pro-regenerative.
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Affiliation(s)
- Matthias Christian Vogg
- Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Sciences, University of Geneva, Geneva 4, Switzerland
| | - Wanda Buzgariu
- Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Sciences, University of Geneva, Geneva 4, Switzerland
| | - Nenad Slavko Suknovic
- Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Sciences, University of Geneva, Geneva 4, Switzerland
| | - Brigitte Galliot
- Department of Genetics and Evolution, Institute of Genetics and Genomics in Geneva (iGE3), Faculty of Sciences, University of Geneva, Geneva 4, Switzerland
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Murad R, Macias-Muñoz A, Wong A, Ma X, Mortazavi A. Coordinated Gene Expression and Chromatin Regulation during Hydra Head Regeneration. Genome Biol Evol 2021; 13:evab221. [PMID: 34877597 PMCID: PMC8651858 DOI: 10.1093/gbe/evab221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2021] [Indexed: 12/13/2022] Open
Abstract
The cnidarian model organism Hydra has long been studied for its remarkable ability to regenerate its head, which is controlled by a head organizer located near the hypostome. The canonical Wnt pathway plays a central role in head organizer function during regeneration and during bud formation, which is the asexual mode of reproduction in Hydra. However, it is unclear how shared the developmental programs of head organizer genesis are in budding and regeneration. Time-series analysis of gene expression changes during head regeneration and budding revealed a set of 298 differentially expressed genes during the 48-h head regeneration and 72-h budding time courses. In order to understand the regulatory elements controlling Hydra head regeneration, we first identified 27,137 open-chromatin elements that are open in one or more sections of the organism body or regenerating tissue. We used histone modification ChIP-seq to identify 9,998 candidate proximal promoter and 3,018 candidate enhancer-like regions respectively. We show that a subset of these regulatory elements is dynamically remodeled during head regeneration and identify a set of transcription factor motifs that are enriched in the enhancer regions activated during head regeneration. Our results show that Hydra displays complex gene regulatory structures of developmentally dynamic enhancers, which suggests that the evolution of complex developmental enhancers predates the split of cnidarians and bilaterians.
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Affiliation(s)
- Rabi Murad
- Department of Developmental and Cell Biology, University of California Irvine, USA
- Center for Complex Biological Systems, University of California Irvine, USA
| | - Aide Macias-Muñoz
- Department of Developmental and Cell Biology, University of California Irvine, USA
- Center for Complex Biological Systems, University of California Irvine, USA
| | - Ashley Wong
- Department of Developmental and Cell Biology, University of California Irvine, USA
- Center for Complex Biological Systems, University of California Irvine, USA
| | - Xinyi Ma
- Department of Developmental and Cell Biology, University of California Irvine, USA
- Center for Complex Biological Systems, University of California Irvine, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California Irvine, USA
- Center for Complex Biological Systems, University of California Irvine, USA
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Pillai A, Gungi A, Reddy PC, Galande S. Epigenetic Regulation in Hydra: Conserved and Divergent Roles. Front Cell Dev Biol 2021; 9:663208. [PMID: 34041242 PMCID: PMC8141815 DOI: 10.3389/fcell.2021.663208] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/13/2021] [Indexed: 12/12/2022] Open
Abstract
Transitions in gene regulatory processes responsible for the emergence of specialized cell types and spatiotemporal regulation of developmental signaling prior to the divergence of Cnidaria and Bilateria are poorly understood. As a sister group of Bilateria, the phylum Cnidaria can provide significant insights into these processes. Among the cnidarians, hydrae have been studied for >250 years to comprehend the mechanisms underlying their unique immortality and robust regenerative capacity. Studies on Hydra spp. and other pre-bilaterians alike have advanced our understanding of the evolutionary underpinnings governing eumetazoan tissue development, homeostasis, and regeneration. In addition to its regenerative potential, Hydra exhibits continuously active axial patterning due to its peculiar tissue dynamics. These distinctive physiological processes necessitate large scale gene expression changes that are governed by the multitude of epigenetic mechanisms operating in cells. This review highlights the contemporary knowledge of epigenetic regulation in Hydra with contemporary studies from other members of Cnidaria, as well as the interplay between regulatory mechanisms wherever demonstrated. The studies covered in the scope of this review reveal both ancestral and divergent roles played by conserved epigenetic mechanisms with emphasis on transcriptional regulation. Additionally, single-cell transcriptomics data was mined to predict the physiological relevance of putative gene regulatory components, which is in agreement with published findings and yielded insights into the possible functions of the gene regulatory mechanisms that are yet to be deciphered in Hydra, such as DNA methylation. Finally, we delineate potentially rewarding epigenetics research avenues that can further leverage the unique biology of Hydra.
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Affiliation(s)
| | | | - Puli Chandramouli Reddy
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Sanjeev Galande
- Centre of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research, Pune, India
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9
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Lakshmanan V, Sujith TN, Bansal D, Shivaprasad PV, Palakodeti D, Krishna S. Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs). RNA (NEW YORK, N.Y.) 2021; 27:477-495. [PMID: 33446492 PMCID: PMC7962491 DOI: 10.1261/rna.077701.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
tRNA-derived fragments (tRFs) have recently gained a lot of scientific interest due to their diverse regulatory roles in several cellular processes. However, their function in dynamic biological processes such as development and regeneration remains unexplored. Here, we show that tRFs are dynamically expressed during planarian regeneration, suggesting a possible role for these small RNAs in the regulation of regeneration. In order to characterize planarian tRFs, we first annotated 457 tRNAs in S. mediterranea combining two tRNA prediction algorithms. Annotation of tRNAs facilitated the identification of three main species of tRFs in planarians-the shorter tRF-5s and itRFs, and the abundantly expressed 5'-tsRNAs. Spatial profiling of tRFs in sequential transverse sections of planarians revealed diverse expression patterns of these small RNAs, including those that are enriched in the head and pharyngeal regions. Expression analysis of these tRF species revealed dynamic expression of these small RNAs over the course of regeneration suggesting an important role in planarian anterior and posterior regeneration. Finally, we show that 5'-tsRNA in planaria interact with all three SMEDWI proteins and an involvement of AGO1 in the processing of itRFs. In summary, our findings implicate a novel role for tRFs in planarian regeneration, highlighting their importance in regulating complex systemic processes. Our study adds to the catalog of posttranscriptional regulatory systems in planaria, providing valuable insights on the biogenesis and the function of tRFs in neoblasts and planarian regeneration.
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MESH Headings
- Algorithms
- Animals
- Argonaute Proteins/genetics
- Argonaute Proteins/metabolism
- Base Pairing
- Base Sequence
- Gene Expression Regulation
- Helminth Proteins/genetics
- Helminth Proteins/metabolism
- Molecular Sequence Annotation
- Nucleic Acid Conformation
- Planarians/genetics
- Planarians/metabolism
- RNA, Helminth/chemistry
- RNA, Helminth/classification
- RNA, Helminth/genetics
- RNA, Helminth/metabolism
- RNA, Small Untranslated/chemistry
- RNA, Small Untranslated/classification
- RNA, Small Untranslated/genetics
- RNA, Small Untranslated/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/classification
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Regeneration/genetics
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Affiliation(s)
- Vairavan Lakshmanan
- Institute for Stem Cell Science and Regenerative Medicine (inStem), 560065 Bangalore, India
- SASTRA University, 613401 Thanjavur, India
| | - T N Sujith
- National Centre for Biological Sciences (NCBS), 560065 Bangalore, India
| | - Dhiru Bansal
- Institute for Stem Cell Science and Regenerative Medicine (inStem), 560065 Bangalore, India
| | | | - Dasaradhi Palakodeti
- Institute for Stem Cell Science and Regenerative Medicine (inStem), 560065 Bangalore, India
| | - Srikar Krishna
- Institute for Stem Cell Science and Regenerative Medicine (inStem), 560065 Bangalore, India
- SASTRA University, 613401 Thanjavur, India
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Praher D, Zimmermann B, Dnyansagar R, Miller DJ, Moya A, Modepalli V, Fridrich A, Sher D, Friis-Møller L, Sundberg P, Fôret S, Ashby R, Moran Y, Technau U. Conservation and turnover of miRNAs and their highly complementary targets in early branching animals. Proc Biol Sci 2021; 288:20203169. [PMID: 33622129 PMCID: PMC7935066 DOI: 10.1098/rspb.2020.3169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 01/25/2021] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs (miRNAs) are crucial post-transcriptional regulators that have been extensively studied in Bilateria, a group comprising the majority of extant animals, where more than 30 conserved miRNA families have been identified. By contrast, bilaterian miRNA targets are largely not conserved. Cnidaria is the sister group to Bilateria and thus provides a unique opportunity for comparative studies. Strikingly, like their plant counterparts, cnidarian miRNAs have been shown to predominantly have highly complementary targets leading to transcript cleavage by Argonaute proteins. Here, we assess the conservation of miRNAs and their targets by small RNA sequencing followed by miRNA target prediction in eight species of Anthozoa (sea anemones and corals), the earliest-branching cnidarian class. We uncover dozens of novel miRNAs but only a few conserved ones. Further, given their high complementarity, we were able to computationally identify miRNA targets in each species. Besides evidence for conservation of specific miRNA target sites, which are maintained between sea anemones and stony corals across 500 Myr of evolution, we also find indications for convergent evolution of target regulation by different miRNAs. Our data indicate that cnidarians have only few conserved miRNAs and corresponding targets, despite their high complementarity, suggesting a high evolutionary turnover.
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Affiliation(s)
- Daniela Praher
- Department of Neurosciences and Developmental Biology; Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Bob Zimmermann
- Department of Neurosciences and Developmental Biology; Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Rohit Dnyansagar
- Department of Neurosciences and Developmental Biology; Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - David J. Miller
- Department of Molecular and Cell Biology, Comparative Genomics Centre, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Aurelie Moya
- Department of Molecular and Cell Biology, Comparative Genomics Centre, James Cook University, Townsville, Queensland, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Vengamanaidu Modepalli
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Marine Biological Association of the United Kingdom, Citadel Hill, Plymouth, UK
| | - Arie Fridrich
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Daniel Sher
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
| | - Lene Friis-Møller
- Danish Shellfish Centre, DTU Aqua, Technical University of Denmark, Lyngby, Denmark
| | - Per Sundberg
- Department of Zoology, University of Gothenburg, Gothenburg, Sweden
| | - Sylvain Fôret
- Health Research Institute, Faculty of Education, Science, Technology and Mathematics, University of Canberra, Canberra, Australia
| | - Regan Ashby
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, Australia
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ulrich Technau
- Department of Neurosciences and Developmental Biology; Faculty of Life Sciences, University of Vienna, Vienna, Austria
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11
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Wu X, Pan Y, Fang Y, Zhang J, Xie M, Yang F, Yu T, Ma P, Li W, Shu Y. The Biogenesis and Functions of piRNAs in Human Diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:108-120. [PMID: 32516734 PMCID: PMC7283962 DOI: 10.1016/j.omtn.2020.05.023] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/17/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023]
Abstract
Piwi-interacting RNAs (piRNAs) are a novel type of small noncoding RNAs, which are 26-30 nt in length and bind to Piwi proteins. These short RNAs were originally discovered in germline cells and are considered as key regulators for germline maintenance. A growing body of evidence has now extended our views into piRNA biological significance showing that they can also regulate gene expression in somatic cells through transposon silencing, epigenetic programming, DNA rearrangements, mRNA turnover, and translational control. Mounting studies have revealed that the dysregulation of piRNAs may cause epigenetic changes and contribute to diverse diseases. This review illustrates piRNA biogenesis, mechanisms behind piRNA-mediated gene regulation, and changes of piRNAs in different diseases, especially in cancers.
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Affiliation(s)
- Xi Wu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China
| | - Yutian Pan
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China
| | - Yuan Fang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China
| | - Jingxin Zhang
- Department of General Surgery, The Affiliated People's Hospital of Jiangsu University, Zhenjiang 212002, People's Republic of China
| | - Mengyan Xie
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China
| | - Fengming Yang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China
| | - Tao Yu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China
| | - Pei Ma
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China.
| | - Wei Li
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China; Department of Oncology, Affiliated Sir Run Run Hospital of Nanjing Medical University, Nanjing 211166, People's Republic of China.
| | - Yongqian Shu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, People's Republic of China; Department of Oncology, Affiliated Sir Run Run Hospital of Nanjing Medical University, Nanjing 211166, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, People's Republic of China.
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12
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The novel microRNAs hsa-miR-nov7 and hsa-miR-nov3 are over-expressed in locally advanced breast cancer. PLoS One 2020; 15:e0225357. [PMID: 32298266 PMCID: PMC7162276 DOI: 10.1371/journal.pone.0225357] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 03/16/2020] [Indexed: 02/07/2023] Open
Abstract
miRNAs are an important class of small non-coding RNAs, which play a versatile role in gene regulation at the post-transcriptional level. Expression of miRNAs is often deregulated in human cancers. We analyzed small RNA massive parallel sequencing data from 50 locally advanced breast cancers aiming to identify novel breast cancer related miRNAs. We successfully predicted 10 novel miRNAs, out of which 2 (hsa-miR-nov3 and hsa-miR-nov7) were recurrent. Applying high sensitivity qPCR, we detected these two microRNAs in 206 and 214 out of 223 patients in the study from which the initial cohort of 50 samples were drawn. We found hsa-miR-nov3 and hsa-miR-nov7 both to be overexpressed in tumor versus normal breast tissue in a separate set of 13 patients (p = 0.009 and p = 0.016, respectively) from whom both tumor tissue and normal tissue were available. We observed hsa-miR-nov3 to be expressed at higher levels in ER-positive compared to ER-negative tumors (p = 0.037). Further stratifications revealed particularly low levels in the her2-like and basal-like cancers compared to other subtypes (p = 0.009 and 0.040, respectively). We predicted target genes for the 2 microRNAs and identified inversely correlated genes in mRNA expression array data available from 203 out of the 223 patients. Applying the KEGG and GO annotations to target genes revealed pathways essential to cell development, communication and homeostasis. Although a weak association between high expression levels of hsa-miR-nov7 and poor survival was observed, this did not reach statistical significance. hsa-miR-nov3 expression levels had no impact on patient survival.
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13
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Chemello F, Alessio E, Buson L, Pacchioni B, Millino C, Lanfranchi G, Cagnin S. Isolation and Transcriptomic Profiling of Single Myofibers from Mice. Bio Protoc 2019; 9:e3378. [PMID: 33654874 DOI: 10.21769/bioprotoc.3378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 11/02/2022] Open
Abstract
Skeletal muscle is composed of different cells and myofiber types, with distinct metabolic and structural features. Generally, transcriptomic analysis of skeletal muscle is performed using whole muscle, resulting in average information as all cells composing the organ contribute to the expression value detected for each gene with the loss of information about the distinctive features of each specific myofiber type. Since myofibers are the smallest complete contractile system of skeletal muscle influencing its contraction velocity and metabolism, it would be beneficial to have fiber-specific information about gene expression. Here, we describe a protocol for the isolation and the transcriptomic analysis of single individual myofibers. The protocol was set up using single myofibers isolated from soleus and Extensor Digitorum Longus (EDL) muscles, but it can be applied to all skeletal muscles. Briefly, muscles are enzymatically dissociated and individually collected. Long RNAs (> 200 nt) and short RNAs (< 200 nt) are separately purified from each myofiber and used to produce libraries for microarray or sequencing analysis. Through this approach, myofiber-specific transcriptional profiles can be produced, free from transcripts from other non-contractile cell types, in order to identify mRNA-miRNA-lncRNA regulatory networks specific for each myofiber type.
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Affiliation(s)
| | - Enrico Alessio
- Department of Biology, University of Padova, Padova, Italy
| | - Lisa Buson
- Department of Biology, University of Padova, Padova, Italy
| | - Beniamina Pacchioni
- Department of Biology, University of Padova, Padova, Italy.,CRIBI Biotechnology Center, University of Padova, Padova, Italy
| | - Caterina Millino
- Department of Biology, University of Padova, Padova, Italy.,CRIBI Biotechnology Center, University of Padova, Padova, Italy
| | - Gerolamo Lanfranchi
- Department of Biology, University of Padova, Padova, Italy.,CRIBI Biotechnology Center, University of Padova, Padova, Italy.,CIR-Myo Myology Center, University of Padova, Padova, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padova, Padova, Italy.,CRIBI Biotechnology Center, University of Padova, Padova, Italy.,CIR-Myo Myology Center, University of Padova, Padova, Italy
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14
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Calcino AD, Fernandez-Valverde SL, Taft RJ, Degnan BM. Diverse RNA interference strategies in early-branching metazoans. BMC Evol Biol 2018; 18:160. [PMID: 30382896 PMCID: PMC6211395 DOI: 10.1186/s12862-018-1274-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 10/08/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Micro RNAs (miRNAs) and piwi interacting RNAs (piRNAs), along with the more ancient eukaryotic endogenous small interfering RNAs (endo-siRNAs) constitute the principal components of the RNA interference (RNAi) repertoire of most animals. RNAi in non-bilaterians - sponges, ctenophores, placozoans and cnidarians - appears to be more diverse than that of bilaterians, and includes structurally variable miRNAs in sponges, an enormous number of piRNAs in cnidarians and the absence of miRNAs in ctenophores and placozoans. RESULTS Here we identify thousands of endo-siRNAs and piRNAs from the sponge Amphimedon queenslandica, the ctenophore Mnemiopsis leidyi and the cnidarian Nematostella vectensis using a computational approach that clusters mapped small RNA sequences and annotates each cluster based on the read length and relative abundance of the constituent reads. This approach was validated on 11 small RNA libraries in Drosophila melanogaster, demonstrating the successful annotation of RNAi-associated loci with properties consistent with previous reports. In the non-bilaterians we uncover seven new miRNAs from Amphimedon and four from Nematostella as well as sub-populations of candidate cis-natural antisense transcript (cis-NAT) endo-siRNAs. We confirmed the absence of miRNAs in Mnemiopsis but detected an abundance of endo-siRNAs in this ctenophore. Analysis of putative piRNA structure suggests that conserved localised secondary structures in primary transcripts may be important for the production of mature piRNAs in Amphimedon and Nematostella, as is also the case for endo-siRNAs. CONCLUSION Together, these findings suggest that the last common ancestor of extant animals did not have the entrained RNAi system that typifies bilaterians. Instead it appears that bilaterians, cnidarians, ctenophores and sponges express unique repertoires and combinations of miRNAs, piRNAs and endo-siRNAs.
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Affiliation(s)
- Andrew D Calcino
- School of Biological Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.,Present address: Department of Integrative Zoology, University of Vienna, Althanstraße 1, 4A-1090, Vienna, Austria
| | - Selene L Fernandez-Valverde
- School of Biological Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.,Present address: CONACYT, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio). CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Ryan J Taft
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia.,Illumina Inc, San Diego, California, 92122, USA
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.
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15
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Urbarova I, Patel H, Forêt S, Karlsen BO, Jørgensen TE, Hall-Spencer JM, Johansen SD. Elucidating the Small Regulatory RNA Repertoire of the Sea Anemone Anemonia viridis Based on Whole Genome and Small RNA Sequencing. Genome Biol Evol 2018; 10:410-426. [PMID: 29385567 PMCID: PMC5793845 DOI: 10.1093/gbe/evy003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2018] [Indexed: 12/16/2022] Open
Abstract
Cnidarians harbor a variety of small regulatory RNAs that include microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs), but detailed information is limited. Here, we report the identification and expression of novel miRNAs and putative piRNAs, as well as their genomic loci, in the symbiotic sea anemone Anemonia viridis. We generated a draft assembly of the A. viridis genome with putative size of 313 Mb that appeared to be composed of about 36% repeats, including known transposable elements. We detected approximately equal fractions of DNA transposons and retrotransposons. Deep sequencing of small RNA libraries constructed from A. viridis adults sampled at a natural CO2 gradient off Vulcano Island, Italy, identified 70 distinct miRNAs. Eight were homologous to previously reported miRNAs in cnidarians, whereas 62 appeared novel. Nine miRNAs were recognized as differentially expressed along the natural seawater pH gradient. We found a highly abundant and diverse population of piRNAs, with a substantial fraction showing ping–pong signatures. We identified nearly 22% putative piRNAs potentially targeting transposable elements within the A. viridis genome. The A. viridis genome appeared similar in size to that of other hexacorals with a very high divergence of transposable elements resembling that of the sea anemone genus Exaiptasia. The genome encodes and expresses a high number of small regulatory RNAs, which include novel miRNAs and piRNAs. Differentially expressed small RNAs along the seawater pH gradient indicated regulatory gene responses to environmental stressors.
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Affiliation(s)
- Ilona Urbarova
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Hardip Patel
- Genomics and Predictive Medicine, Genome Biology Department, John Curtin School of Medical Research, ANU College of Medicine, Biology, and Environment, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Sylvain Forêt
- Evolution, Ecology, and Genetics, Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Bård Ove Karlsen
- Research Laboratory, Department of Laboratory Medicine, Nordland Hospital, Bodø, Norway
| | - Tor Erik Jørgensen
- Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Jason M Hall-Spencer
- Marine Biology and Ecology Research Centre, University of Plymouth, United Kingdom.,Shimoda Marine Research Centre, University of Tsukuba, Shimoda City, Shizuoka, Japan
| | - Steinar D Johansen
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway.,Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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16
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Rojas-Ríos P, Simonelig M. piRNAs and PIWI proteins: regulators of gene expression in development and stem cells. Development 2018; 145:145/17/dev161786. [PMID: 30194260 DOI: 10.1242/dev.161786] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PIWI proteins and Piwi-interacting RNAs (piRNAs) have established and conserved roles in repressing transposable elements (TEs) in the germline of animals. However, in several biological contexts, a large proportion of piRNAs are not related to TE sequences and, accordingly, functions for piRNAs and PIWI proteins that are independent of TE regulation have been identified. This aspect of piRNA biology is expanding rapidly. Indeed, recent reports have revealed the role of piRNAs in the regulation of endogenous gene expression programs in germ cells, as well as in somatic tissues, challenging dogma in the piRNA field. In this Review, we focus on recent data addressing the biological and developmental functions of piRNAs, highlighting their roles in embryonic patterning, germ cell specification, stem cell biology, neuronal activity and metabolism.
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Affiliation(s)
- Patricia Rojas-Ríos
- mRNA Regulation and Development, IGH, Univ. Montpellier, CNRS, Montpellier 34396, France
| | - Martine Simonelig
- mRNA Regulation and Development, IGH, Univ. Montpellier, CNRS, Montpellier 34396, France
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17
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Post-transcriptional regulation in planarian stem cells. Semin Cell Dev Biol 2018; 87:69-78. [PMID: 29870807 DOI: 10.1016/j.semcdb.2018.05.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 05/11/2018] [Accepted: 05/14/2018] [Indexed: 12/17/2022]
Abstract
Planarians are known for their immense regenerative abilities. A pluripotent stem cell population provides the cellular source for this process, as well as for the homeostatic cell turnover of the animals. These stem cells, known as neoblasts, present striking similarities at the morphological and molecular level to germ cells, but however, give rise to somatic tissue. Many RNA binding proteins known to be important for germ cell biology are also required for neoblast function, highlighting the importance of post-transcriptional regulation for stem cell control. Many of its aspects, including alternative splicing, alternative polyadenylation, translational control and mRNA deadenylation, as well as small RNAs such as microRNAs and piRNA are critical for stem cells. Their inhibition often abrogates both regeneration and cell turnover, resulting in lethality. Some of aspects of post-transcriptional regulation are conserved from planarian to mammalian stem cells.
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18
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Abstract
In bilaterian animals the 3′ ends of microRNAs (miRNAs) are frequently modified by tailing and trimming. These modifications affect miRNA-mediated gene regulation by modulating miRNA stability. Here, we analyzed data from three nonbilaterian animals: two cnidarians (Nematostella vectensis and Hydra magnipapillata) and one poriferan (Amphimedon queenslandica). Our analysis revealed that nonbilaterian miRNAs frequently undergo modifications like the bilaterian counterparts: the majority are expressed as different length isoforms and frequent modifications of the 3′ end by mono U or mono A tailing are observed. Moreover, as the factors regulating miRNA modifications are largely uncharacterized in nonbilaterian animal phyla, in present study, we investigated the evolution of 3′ terminal uridylyl transferases (TUTases) that are known to involved in miRNA 3′ nontemplated modifications in Bilateria. Phylogenetic analysis on TUTases showed that TUTase1 and TUTase6 are a result of duplication in bilaterians and that TUTase7 and TUTase4 are the result of a vertebrate-specific duplication. We also find an unexpected number of Drosophila-specific gene duplications and domain losses in most of the investigated gene families. Overall, our findings shed new light on the evolutionary history of TUTases in Metazoa, as they reveal that this core set of enzymes already existed in the last common ancestor of all animals and was probably involved in modifying small RNAs in a similar fashion to its present activity in bilaterians.
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Affiliation(s)
- Vengamanaidu Modepalli
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel
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19
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Baumgarten S, Cziesielski MJ, Thomas L, Michell CT, Esherick LY, Pringle JR, Aranda M, Voolstra CR. Evidence for miRNA-mediated modulation of the host transcriptome in cnidarian-dinoflagellate symbiosis. Mol Ecol 2017; 27:403-418. [DOI: 10.1111/mec.14452] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/19/2017] [Accepted: 11/21/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Sebastian Baumgarten
- Division of Biological and Environmental Science and Engineering; Red Sea Research Center; King Abdullah University of Science and Technology; Thuwal Saudi Arabia
| | - Maha J. Cziesielski
- Division of Biological and Environmental Science and Engineering; Red Sea Research Center; King Abdullah University of Science and Technology; Thuwal Saudi Arabia
| | - Ludivine Thomas
- Bioscience Core Laboratory; King Abdullah University of Science and Technology; Thuwal Saudi Arabia
| | - Craig T. Michell
- Division of Biological and Environmental Science and Engineering; Red Sea Research Center; King Abdullah University of Science and Technology; Thuwal Saudi Arabia
| | - Lisl Y. Esherick
- Department of Genetics; Stanford University School of Medicine; Stanford CA USA
| | - John R. Pringle
- Department of Genetics; Stanford University School of Medicine; Stanford CA USA
| | - Manuel Aranda
- Division of Biological and Environmental Science and Engineering; Red Sea Research Center; King Abdullah University of Science and Technology; Thuwal Saudi Arabia
| | - Christian R. Voolstra
- Division of Biological and Environmental Science and Engineering; Red Sea Research Center; King Abdullah University of Science and Technology; Thuwal Saudi Arabia
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20
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Praher D, Zimmermann B, Genikhovich G, Columbus-Shenkar Y, Modepalli V, Aharoni R, Moran Y, Technau U. Characterization of the piRNA pathway during development of the sea anemone Nematostella vectensis. RNA Biol 2017; 14:1727-1741. [PMID: 28783426 PMCID: PMC5731801 DOI: 10.1080/15476286.2017.1349048] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/22/2017] [Accepted: 06/27/2017] [Indexed: 12/11/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs) and associated proteins comprise a conserved pathway for silencing transposons in metazoan germlines. piRNA pathway components are also expressed in multipotent somatic stem cells in various organisms. piRNA functions have been extensively explored in bilaterian model systems, however, comprehensive studies in non-bilaterian phyla remain limited. Here we investigate the piRNA pathway during the development of Nematostella vectensis, a well-established model system belonging to Cnidaria, the sister group to Bilateria. To date, no population of somatic stem cells has been identified in this organism, despite its long life-span and regenerative capacities that require a constant cell-renewal. We show that Nematostella piRNA pathway components are broadly expressed in early developmental stages, while piRNAs themselves show differential expression, suggesting specific developmental roles of distinct piRNA families. In adults, piRNA associated proteins are enriched in the germline but also expressed in somatic cells, indicating putative stem cell properties. Furthermore, we provide experimental evidence that Nematostella piRNAs cleave transposable elements as well as protein-coding genes. Our results demonstrate that somatic expression of piRNA associated proteins as well as the roles of piRNAs in transposon repression and gene regulation are likely ancestral features that evolved before the split between Cnidaria and Bilateria.
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Affiliation(s)
- Daniela Praher
- Department of Molecular Evolution and Development; Centre of Organismal Systems Biology, Faculty of Life Sciences, University of Vienna; Althanstrasse 14, Wien, Austria
| | - Bob Zimmermann
- Department of Molecular Evolution and Development; Centre of Organismal Systems Biology, Faculty of Life Sciences, University of Vienna; Althanstrasse 14, Wien, Austria
| | - Grigory Genikhovich
- Department of Molecular Evolution and Development; Centre of Organismal Systems Biology, Faculty of Life Sciences, University of Vienna; Althanstrasse 14, Wien, Austria
| | - Yaara Columbus-Shenkar
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem; Givat Ram, Jerusalem, Israel
| | - Vengamanaidu Modepalli
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem; Givat Ram, Jerusalem, Israel
| | - Reuven Aharoni
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem; Givat Ram, Jerusalem, Israel
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem; Givat Ram, Jerusalem, Israel
| | - Ulrich Technau
- Department of Molecular Evolution and Development; Centre of Organismal Systems Biology, Faculty of Life Sciences, University of Vienna; Althanstrasse 14, Wien, Austria
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21
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Girardi E, Miesen P, Pennings B, Frangeul L, Saleh MC, van Rij RP. Histone-derived piRNA biogenesis depends on the ping-pong partners Piwi5 and Ago3 in Aedes aegypti. Nucleic Acids Res 2017; 45:4881-4892. [PMID: 28115625 PMCID: PMC5416884 DOI: 10.1093/nar/gkw1368] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 01/04/2017] [Indexed: 12/13/2022] Open
Abstract
The piRNA pathway is of key importance in controlling transposable elements in most animal species. In the vector mosquito Aedes aegypti, the presence of eight PIWI proteins and the accumulation of viral piRNAs upon arbovirus infection suggest additional functions of the piRNA pathway beyond genome defense. To better understand the regulatory potential of this pathway, we analyzed in detail host-derived piRNAs in A. aegypti Aag2 cells. We show that a large repertoire of protein-coding genes and non-retroviral integrated RNA virus elements are processed into genic piRNAs by different combinations of PIWI proteins. Among these, we identify a class of genes that produces piRNAs from coding sequences in an Ago3- and Piwi5-dependent fashion. We demonstrate that the replication-dependent histone gene family is a genic source of ping-pong dependent piRNAs and that histone-derived piRNAs are dynamically expressed throughout the cell cycle, suggesting a role for the piRNA pathway in the regulation of histone gene expression. Moreover, our results establish the Aag2 cell line as an accessible experimental model to study gene-derived piRNAs.
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Affiliation(s)
- Erika Girardi
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Pascal Miesen
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Bas Pennings
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Lionel Frangeul
- Institut Pasteur, Viruses and RNA interference, CNRS URM 3569, 75724 Paris Cedex 15, France
| | - Maria-Carla Saleh
- Institut Pasteur, Viruses and RNA interference, CNRS URM 3569, 75724 Paris Cedex 15, France
| | - Ronald P van Rij
- Department of Medical Microbiology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
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22
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Courtial L, Picco V, Pagès G, Ferrier-Pagès C. Validation of commercial ERK antibodies against the ERK orthologue of the scleractinian coral Stylophora pistillata. F1000Res 2017; 6:577. [PMID: 28690832 PMCID: PMC5482343 DOI: 10.12688/f1000research.11365.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/30/2017] [Indexed: 12/15/2022] Open
Abstract
The extracellular signal-regulated protein kinase (ERK) signalling pathway controls key cellular processes, such as cell cycle regulation, cell fate determination and the response to external stressors. Although ERK functions are well studied in a variety of living organisms ranging from yeast to mammals, its functions in corals are still poorly known. The present work aims to give practical tools to study the expression level of ERK protein and the activity of the ERK signalling pathway in corals. The antibody characterisation experiment was performed five times and identical results were obtained. The present study validated the immune-reactivity of commercially available antibodies directed against ERK and its phosphorylated/activated forms on protein extracts of the reef-building coral
Stylophora pistillata.
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Affiliation(s)
- Lucile Courtial
- Marine Department, Centre Scientifique de Monaco, Monaco, MC-98000, Monaco.,Sorbonne Universités, Pierre and Marie Curie University, Paris, 75252, France.,Laboratoire d'Excellence, UMR ENTROPIE, Nouméa, 98848, New Caledonia
| | - Vincent Picco
- Biomedical Department, Centre Scientifique de Monaco, Monaco, MC-98000, Monaco
| | - Gilles Pagès
- Biomedical Department, Centre Scientifique de Monaco, Monaco, MC-98000, Monaco.,Institute for Research on Cancer and Aging of Nice (IRCAN), University Nice Sophia-Antipolis, CNRS UMR7284/INSERM U1081, Centre Antoine Lacassagne, Nice, 06189, France
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23
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Gajigan AP, Conaco C. A microRNA regulates the response of corals to thermal stress. Mol Ecol 2017; 26:3472-3483. [DOI: 10.1111/mec.14130] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 03/20/2017] [Accepted: 03/23/2017] [Indexed: 12/29/2022]
Affiliation(s)
- Andrian P. Gajigan
- Marine Science Institute; University of the Philippines Diliman; Quezon City Philippines
| | - Cecilia Conaco
- Marine Science Institute; University of the Philippines Diliman; Quezon City Philippines
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24
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The c-Jun N-terminal kinase prevents oxidative stress induced by UV and thermal stresses in corals and human cells. Sci Rep 2017; 7:45713. [PMID: 28374828 PMCID: PMC5379690 DOI: 10.1038/srep45713] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 03/03/2017] [Indexed: 12/26/2022] Open
Abstract
Coral reefs are of major ecological and socio-economic interest. They are threatened by global warming and natural pressures such as solar ultraviolet radiation. While great efforts have been made to understand the physiological response of corals to these stresses, the signalling pathways involved in the immediate cellular response exhibited by corals remain largely unknown. Here, we demonstrate that c-Jun N-terminal kinase (JNK) activation is involved in the early response of corals to thermal and UV stress. Furthermore, we found that JNK activity is required to repress stress-induced reactive oxygen species (ROS) accumulation in both the coral Stylophora pistillata and human skin cells. We also show that inhibiting JNK activation under stress conditions leads to ROS accumulation, subsequent coral bleaching and cell death. Taken together, our results suggest that an ancestral response, involving the JNK pathway, is remarkably conserved from corals to human, protecting cells from the adverse environmental effects.
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25
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Abstract
microRNAs (miRNAs) are a unique class of short endogenous RNAs that became known in the last few decades as major players in gene regulation at the post-transcriptional level. Their regulatory roles make miRNAs crucial for normal development and physiology in several distinct groups of eukaryotes including plants and animals. The common notion in the field is that miRNAs have evolved independently in those distinct lineages, but recent evidence from non-bilaterian metazoans, plants, as well as various algae raise the possibility that already the last common ancestor of these lineages might have employed a miRNA pathway for post-transcriptional regulation. In this review we present the commonalities and differences of the miRNA pathways in various eukaryotes and discuss the contrasting scenarios of their possible evolutionary origin and their proposed link to organismal complexity and multicellularity.
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26
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Marine genomics: News and views. Mar Genomics 2017; 31:1-8. [DOI: 10.1016/j.margen.2016.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 11/23/2022]
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27
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Gao F, Nan F, Feng J, Lv J, Liu Q, Xie S. Identification of conserved and novel microRNAs in Porphyridium purpureum via deep sequencing and bioinformatics. BMC Genomics 2016; 17:612. [PMID: 27516065 PMCID: PMC4981961 DOI: 10.1186/s12864-016-2985-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/01/2016] [Indexed: 11/22/2022] Open
Abstract
Background Porphyridium purpureum has been utilized in important industrial and pharmaceutical fields. The identification of microRNAs (miRNAs) in this unique species is of great importance: such identification can help fill gaps in the small RNA (sRNA) studies of this organism and help to elucidate essential biological processes and their regulation mechanisms in this special micro alga. Results In this study, 254 high-confidence miRNAs (203 conserved miRNAs and 51 novel miRNAs) were identified by sRNA deep sequencing (sRNA-seq) combined with bioinformatics. A total of 235 putative miRNA families were predicted, including 192 conserved families and 43 species-specific families. The conservation and diversity of predicted miRNA families were analysed in different plant species. Both the 100 % northern blot validation rate (VR) of four randomly selected miRNAs and the results of stem-loop quantitative real time RT-PCR (qRT-PCR) assays of 25 randomly selected miRNAs demonstrated that the majority of the miRNAs identified in this study are credible. A total of 14,958 and 2184 genes were predicted to be targeted by the 186 conserved and 41 novel miRNAs. Gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that some target genes likely provide valuable references for further understanding of vital functions in P. purpureum. In addition, a cytoscape network will provide some clues for research into the complex biological processes that occur in this unique alga. Conclusions We first identified a large set of conserved and novel miRNAs in P. purpureum. The characteristic and validation analysis on miRNAs demonstrated authenticity of identification data. Functional annotation of target genes and metabolic pathways they involved in illuminated the direction for further utilization and development this micro alga based on its unique properties. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2985-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fan Gao
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Fangru Nan
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Jia Feng
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Junping Lv
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Qi Liu
- School of Life Science, Shanxi University, Taiyuan, 030006, China
| | - Shulian Xie
- School of Life Science, Shanxi University, Taiyuan, 030006, China.
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Rentzsch F, Technau U. Genomics and development of Nematostella vectensis and other anthozoans. Curr Opin Genet Dev 2016; 39:63-70. [PMID: 27318695 DOI: 10.1016/j.gde.2016.05.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/14/2016] [Accepted: 05/30/2016] [Indexed: 01/10/2023]
Abstract
Due to their rather simple body plan with only few organs and a low number of cell types, cnidarians have long been recognized as an important animal group for evolutionary comparisons of animal body plans. Recent studies have shown, however, that the genomes of cnidarians and their epigenetic and posttranscriptional regulation are more complex than their morphology might suggest. How these complex genomes are deployed during embryonic development is an open question. With a focus on the sea anemone Nematostella vectensis we describe new findings about the development of the nervous system from neural progenitor cells and how Wnt and BMP signalling control axial patterning. These studies show that beyond evolutionary comparisons, cnidarian model organisms can provide new insights into generic questions in developmental biology.
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Affiliation(s)
- Fabian Rentzsch
- Sars International Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt 55, 5008 Bergen, Norway.
| | - Ulrich Technau
- Department of Molecular Evolution and Development, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
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Lim RSM, Kai T. A piece of the pi(e): The diverse roles of animal piRNAs and their PIWI partners. Semin Cell Dev Biol 2015; 47-48:17-31. [PMID: 26582251 DOI: 10.1016/j.semcdb.2015.10.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Small non-coding RNAs are indispensable to many biological processes. A class of endogenous small RNAs, termed PIWI-interacting RNAs (piRNAs) because of their association with PIWI proteins, has known roles in safeguarding the genome against inordinate transposon mobilization, embryonic development, and stem cell regulation, among others. This review discusses the biogenesis of animal piRNAs and their diverse functions together with their PIWI protein partners, both in the germline and in somatic cells, and highlights the evolutionarily conserved aspects of these molecular players in animal biology.
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Affiliation(s)
- Robyn S M Lim
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
| | - Toshie Kai
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
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30
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SINKOVICS JOSEPHG. The cnidarian origin of the proto-oncogenes NF-κB/STAT and WNT-like oncogenic pathway drives the ctenophores (Review). Int J Oncol 2015; 47:1211-29. [PMID: 26239915 PMCID: PMC4583530 DOI: 10.3892/ijo.2015.3102] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 06/26/2015] [Indexed: 01/09/2023] Open
Abstract
The cell survival pathways of the diploblastic early multicellular eukaryotic hosts contain and operate the molecular machinery resembling those of malignantly transformed individual cells of highly advanced multicellular hosts (including Homo). In the present review, the STAT/NF-κB pathway of the cnidarian Nematostella vectensis is compared with that of human tumors (malignant lymphomas, including Reed-Sternberg cells) pointing out similarities, including possible viral initiation in both cases. In the ctenophore genome and proteome, β-catenin gains intranuclear advantages due to a physiologically weak destructive complex in the cytoplasm, and lack of natural inhibitors (the dickkopfs). Thus, a scenario similar to what tumor cells initiate and achieve is presented through several constitutive loss-of-function type mutations in the destructive complex and in the elimination of inhibitors. Vice versa, malignantly transformed individual cells of advanced multicellular hosts assume pheno-genotypic resemblance to cells of unicellular or early multicellular hosts, and presumably to their ancient predecessors, by returning to the semblance of immortality and to the resumption of the state of high degree of resistance to physicochemical insults. Human leukemogenic and oncogenic pathways are presented for comparisons. The supreme bioengineers RNA/DNA complex encoded both the malignantly transformed immortal cell and the human cerebral cortex. The former generates molecules for the immortality of cellular life in the Universe. The latter invents the inhibitors of the process in order to gain control over it.
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Affiliation(s)
- JOSEPH G. SINKOVICS
- St. Joseph Hospital's Cancer Institute Affiliated with the H.L. Moffitt Comprehensive Cancer Center; Department of Molecular Medicine, The University of South Florida Morsani College of Medicine, Tampa, FL, USA
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31
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Petersen HO, Höger SK, Looso M, Lengfeld T, Kuhn A, Warnken U, Nishimiya-Fujisawa C, Schnölzer M, Krüger M, Özbek S, Simakov O, Holstein TW. A Comprehensive Transcriptomic and Proteomic Analysis of Hydra Head Regeneration. Mol Biol Evol 2015; 32:1928-47. [PMID: 25841488 PMCID: PMC4833066 DOI: 10.1093/molbev/msv079] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The cnidarian freshwater polyp Hydra sp. exhibits an unparalleled regeneration capacity in the animal kingdom. Using an integrative transcriptomic and stable isotope labeling by amino acids in cell culture proteomic/phosphoproteomic approach, we studied stem cell-based regeneration in Hydra polyps. As major contributors to head regeneration, we identified diverse signaling pathways adopted for the regeneration response as well as enriched novel genes. Our global analysis reveals two distinct molecular cascades: an early injury response and a subsequent, signaling driven patterning of the regenerating tissue. A key factor of the initial injury response is a general stabilization of proteins and a net upregulation of transcripts, which is followed by a subsequent activation cascade of signaling molecules including Wnts and transforming growth factor (TGF) beta-related factors. We observed moderate overlap between the factors contributing to proteomic and transcriptomic responses suggesting a decoupled regulation between the transcriptional and translational levels. Our data also indicate that interstitial stem cells and their derivatives (e.g., neurons) have no major role in Hydra head regeneration. Remarkably, we found an enrichment of evolutionarily more recent genes in the early regeneration response, whereas conserved genes are more enriched in the late phase. In addition, genes specific to the early injury response were enriched in transposon insertions. Genetic dynamicity and taxon-specific factors might therefore play a hitherto underestimated role in Hydra regeneration.
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Affiliation(s)
- Hendrik O Petersen
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Stefanie K Höger
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Mario Looso
- Max Planck Institute (MPI) for Heart and Lung Research, Bad Nauheim, Germany
| | - Tobias Lengfeld
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Anne Kuhn
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Uwe Warnken
- Functional Proteome Analysis Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Chiemi Nishimiya-Fujisawa
- Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, Myodaiji, Okazaki, Japan
| | - Martina Schnölzer
- Functional Proteome Analysis Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcus Krüger
- Max Planck Institute (MPI) for Heart and Lung Research, Bad Nauheim, Germany CECAD, University of Cologne, Germany
| | - Suat Özbek
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Oleg Simakov
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany Molecular Genetics Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Thomas W Holstein
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
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Bellantuono AJ, Bridge D, Martínez DE. Hydra as a tractable, long-lived model system for senescence. INVERTEBR REPROD DEV 2014; 59:39-44. [PMID: 26136619 PMCID: PMC4464093 DOI: 10.1080/07924259.2014.938196] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 06/02/2014] [Indexed: 12/14/2022]
Abstract
Hydra represents a unique model system for the study of senescence, with the opportunity for the comparison of non-aging and induced senescence. Hydra maintains three stem cell lineages, used for continuous tissue morphogenesis and replacement. Recent work has elucidated the roles of the insulin/IGF-1 signaling target FoxO, of Myc proteins, and of PIWI proteins in Hydra stem cells. Under laboratory culture conditions, Hydra vulgaris show no signs of aging even under long-term study. In contrast, Hydra oligactis can be experimentally induced to undergo reproduction-associated senescence. This provides a powerful comparative system for future studies.
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Affiliation(s)
| | - Diane Bridge
- Department of Biology, Elizabethtown College , Elizabethtown , PA , USA
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Abstract
Adult stem cells face the challenge of maintaining tissue homeostasis by self-renewal while maintaining their proliferation potential over the lifetime of an organism. Continuous proliferation can cause genotoxic/metabolic stress that can compromise the genomic integrity of stem cells. To prevent stem cell exhaustion, highly proliferative adult tissues maintain a pool of quiescent stem cells that divide only in response to injury and thus remain protected from genotoxic stress. Hydra is a remarkable organism with highly proliferative stem cells and ability to regenerate at whole animal level. Intriguingly, hydra does not display consequences of high proliferation, such as senescence or tumour formation. In this study, we investigate if hydra harbours a pool of slow-cycling stem cells that could help prevent undesirable consequences of continuous proliferation. Hydra were pulsed with the thymidine analogue 5-ethynyl-2′-deoxyuridine (EdU) and then chased in the absence of EdU to monitor the presence of EdU-retaining cells. A significant number of undifferentiated cells of all three lineages in hydra retained EdU for about 8–10 cell cycles, indicating that these cells did not enter cell cycle. These label-retaining cells were resistant to hydroxyurea treatment and were predominantly in the G2 phase of cell cycle. Most significantly, similar to mammalian quiescent stem cells, these cells rapidly entered cell division during head regeneration. This study shows for the first time that, contrary to current beliefs, cells in hydra display heterogeneity in their cell cycle potential and the slow-cycling cells in this population enter cell cycle during head regeneration. These results suggest an early evolution of slow-cycling stem cells in multicellular animals.
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Affiliation(s)
- Niraimathi Govindasamy
- Institute for Stem Cell Biology and Regenerative Medicine (inStem), National Centre for Biological Sciences, GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Supriya Murthy
- Institute for Stem Cell Biology and Regenerative Medicine (inStem), National Centre for Biological Sciences, GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Yashoda Ghanekar
- Institute for Stem Cell Biology and Regenerative Medicine (inStem), National Centre for Biological Sciences, GKVK Campus, Bellary Road, Bangalore 560065, India
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34
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Tomczyk S, Fischer K, Austad S, Galliot B. Hydra, a powerful model for aging studies. INVERTEBR REPROD DEV 2014; 59:11-16. [PMID: 26120246 PMCID: PMC4463768 DOI: 10.1080/07924259.2014.927805] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 04/22/2014] [Indexed: 01/25/2023]
Abstract
Cnidarian Hydra polyps escape senescence, most likely due to the robust activity of their three stem cell populations. These stem cells continuously self-renew in the body column and differentiate at the extremities following a tightly coordinated spatial pattern. Paul Brien showed in 1953 that in one particular species, Hydra oligactis, cold-dependent sexual differentiation leads to rapid aging and death. Here, we review the features of this inducible aging phenotype. These cellular alterations, detected several weeks after aging was induced, are characterized by a decreasing density of somatic interstitial cell derivatives, a disorganization of the apical nervous system, and a disorganization of myofibers of the epithelial cells. Consequently, tissue replacement required to maintain homeostasis, feeding behavior, and contractility of the animal are dramatically affected. Interestingly, this aging phenotype is not observed in all H. oligactis strains, thus providing a powerful experimental model for investigations of the genetic control of aging. Given the presence in the cnidarian genome of a large number of human orthologs that have been lost in ecdysozoans, such approaches might help uncover novel regulators of aging in vertebrates.
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Affiliation(s)
- Szymon Tomczyk
- Faculty of Sciences, Department of Genetics and Evolution, University of Geneva , Geneva , Switzerland
| | - Kathleen Fischer
- Department of Biology, University of Alabama at Birmingham UAB , Birmingham , AL , USA
| | - Steven Austad
- Department of Biology, University of Alabama at Birmingham UAB , Birmingham , AL , USA
| | - Brigitte Galliot
- Faculty of Sciences, Department of Genetics and Evolution, University of Geneva , Geneva , Switzerland
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Rouhana L, Weiss JA, King RS, Newmark PA. PIWI homologs mediate histone H4 mRNA localization to planarian chromatoid bodies. Development 2014; 141:2592-601. [PMID: 24903754 DOI: 10.1242/dev.101618] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The well-known regenerative abilities of planarian flatworms are attributed to a population of adult stem cells called neoblasts that proliferate and differentiate to produce all cell types. A characteristic feature of neoblasts is the presence of large cytoplasmic ribonucleoprotein granules named chromatoid bodies, the function of which has remained largely elusive. This study shows that histone mRNAs are a common component of chromatoid bodies. Our experiments also demonstrate that accumulation of histone mRNAs, which is typically restricted to the S phase of eukaryotic cells, is extended during the cell cycle of neoblasts. The planarian PIWI homologs SMEDWI-1 and SMEDWI-3 are required for proper localization of germinal histone H4 (gH4) mRNA to chromatoid bodies. The association between histone mRNA and chromatoid body components extends beyond gH4 mRNA, since transcripts of other core histone genes were also found in these structures. Additionally, piRNAs corresponding to loci of every core histone type have been identified. Altogether, this work provides evidence that links PIWI proteins and chromatoid bodies to histone mRNA regulation in planarian stem cells. The molecular similarities between neoblasts and undifferentiated cells of other organisms raise the possibility that PIWI proteins might also regulate histone mRNAs in stem cells and germ cells of other metazoans.
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Affiliation(s)
- Labib Rouhana
- Department of Biological Sciences, Wright State University, 3640 Colonel Glenn Highway, Dayton, OH 45435, USA Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave., Urbana, IL 61801, USA
| | - Jennifer A Weiss
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave., Urbana, IL 61801, USA
| | - Ryan S King
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave., Urbana, IL 61801, USA
| | - Phillip A Newmark
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S. Goodwin Ave., Urbana, IL 61801, USA
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36
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Gao Z, Wang M, Blair D, Zheng Y, Dou Y. Phylogenetic analysis of the endoribonuclease Dicer family. PLoS One 2014; 9:e95350. [PMID: 24748168 PMCID: PMC3991619 DOI: 10.1371/journal.pone.0095350] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 03/25/2014] [Indexed: 01/08/2023] Open
Abstract
Dicers are proteins of the ribonuclease III family with the ability to process dsRNA, involved in regulation of gene expression at the post-transcriptional level. Dicers are conserved from basal metazoans to higher metazoans and contain a number of functional domains that interact with dsRNA. The completed genome sequences of over 34 invertebrate species allowed us to systematically investigate Dicer genes over a diverse range of phyla. The majority of invertebrate Dicers clearly fell into the Dicer1 or Dicer2 subfamilies. Most nematodes possessed only one Dicer gene, a member of the Dicer1 subfamily, whereas two Dicer genes (Dicer1 and Dicer2) were present in all platyhelminths surveyed. Analysis of the key domains showed that a 5′ pocket was conserved across members of the Dicer1 subfamily, with the exception of the nematode Bursaphelenchus xylophilus. Interestingly, Nematostella vectensis DicerB grouped into Dicer2 subfamily harbored a 5′ pocket, which is commonly present in Dicer1. Similarly, the 3′ pocket was also found to be conserved in all Dicer proteins with the exceptions of Schmidtea mediterranea Dicer2 and Trichoplax adherens Dicer A. The loss of catalytic residues in the RNase III domain was noted in platyhelminths and cnidarians, and the ‘ball’ and ‘socket’ junction between two RNase III domains in platyhelminth Dicers was different from the canonical junction, suggesting the possibility of different conformations. The present data suggest that Dicers might have duplicated and diversified independently, and have evolved for various functions in invertebrates.
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Affiliation(s)
- Zeqian Gao
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, Gansu, China
| | - Miao Wang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, Gansu, China
| | - David Blair
- School of Marine and Tropical Biology, James Cook University, Townsville, Qld, Australia
| | - Yadong Zheng
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, Gansu, China
- * E-mail: (YD); (YZ)
| | - Yongxi Dou
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, Lanzhou, Gansu, China
- * E-mail: (YD); (YZ)
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Moran Y, Fredman D, Praher D, Li XZ, Wee LM, Rentzsch F, Zamore PD, Technau U, Seitz H. Cnidarian microRNAs frequently regulate targets by cleavage. Genome Res 2014; 24:651-63. [PMID: 24642861 PMCID: PMC3975064 DOI: 10.1101/gr.162503.113] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In bilaterians, which comprise most of extant animals, microRNAs (miRNAs) regulate the majority of messenger RNAs (mRNAs) via base-pairing of a short sequence (the miRNA “seed”) to the target, subsequently promoting translational inhibition and transcript instability. In plants, many miRNAs guide endonucleolytic cleavage of highly complementary targets. Because little is known about miRNA function in nonbilaterian animals, we investigated the repertoire and biological activity of miRNAs in the sea anemone Nematostella vectensis, a representative of Cnidaria, the sister phylum of Bilateria. Our work uncovers scores of novel miRNAs in Nematostella, increasing the total miRNA gene count to 87. Yet only a handful are conserved in corals and hydras, suggesting that microRNA gene turnover in Cnidaria greatly exceeds that of other metazoan groups. We further show that Nematostella miRNAs frequently direct the cleavage of their mRNA targets via nearly perfect complementarity. This mode of action resembles that of small interfering RNAs (siRNAs) and plant miRNAs. It appears to be common in Cnidaria, as several of the miRNA target sites are conserved among distantly related anemone species, and we also detected miRNA-directed cleavage in Hydra. Unlike in bilaterians, Nematostella miRNAs are commonly coexpressed with their target transcripts. In light of these findings, we propose that post-transcriptional regulation by miRNAs functions differently in Cnidaria and Bilateria. The similar, siRNA-like mode of action of miRNAs in Cnidaria and plants suggests that this may be an ancestral state.
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Affiliation(s)
- Yehu Moran
- Department for Molecular Evolution and Development, Center for Organismal Systems Biology, Faculty of Life Sciences, University of Vienna, 1090 Vienna, Austria
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Stefanik DJ, Lubinski TJ, Granger BR, Byrd AL, Reitzel AM, DeFilippo L, Lorenc A, Finnerty JR. Production of a reference transcriptome and transcriptomic database (EdwardsiellaBase) for the lined sea anemone, Edwardsiella lineata, a parasitic cnidarian. BMC Genomics 2014; 15:71. [PMID: 24467778 PMCID: PMC3909931 DOI: 10.1186/1471-2164-15-71] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 12/11/2013] [Indexed: 12/20/2022] Open
Abstract
Background The lined sea anemone Edwardsiella lineata is an informative model system for evolutionary-developmental studies of parasitism. In this species, it is possible to compare alternate developmental pathways leading from a larva to either a free-living polyp or a vermiform parasite that inhabits the mesoglea of a ctenophore host. Additionally, E. lineata is confamilial with the model cnidarian Nematostella vectensis, providing an opportunity for comparative genomic, molecular and organismal studies. Description We generated a reference transcriptome for E. lineata via high-throughput sequencing of RNA isolated from five developmental stages (parasite; parasite-to-larva transition; larva; larva-to-adult transition; adult). The transcriptome comprises 90,440 contigs assembled from >15 billion nucleotides of DNA sequence. Using a molecular clock approach, we estimated the divergence between E. lineata and N. vectensis at 215–364 million years ago. Based on gene ontology and metabolic pathway analyses and gene family surveys (bHLH-PAS, deiodinases, Fox genes, LIM homeodomains, minicollagens, nuclear receptors, Sox genes, and Wnts), the transcriptome of E. lineata is comparable in depth and completeness to N. vectensis. Analyses of protein motifs and revealed extensive conservation between the proteins of these two edwardsiid anemones, although we show the NF-κB protein of E. lineata reflects the ancestral structure, while the NF-κB protein of N. vectensis has undergone a split that separates the DNA-binding domain from the inhibitory domain. All contigs have been deposited in a public database (EdwardsiellaBase), where they may be searched according to contig ID, gene ontology, protein family motif (Pfam), enzyme commission number, and BLAST. The alignment of the raw reads to the contigs can also be visualized via JBrowse. Conclusions The transcriptomic data and database described here provide a platform for studying the evolutionary developmental genomics of a derived parasitic life cycle. In addition, these data from E. lineata will aid in the interpretation of evolutionary novelties in gene sequence or structure that have been reported for the model cnidarian N. vectensis (e.g., the split NF-κB locus). Finally, we include custom computational tools to facilitate the annotation of a transcriptome based on high-throughput sequencing data obtained from a “non-model system.”
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Affiliation(s)
| | | | | | | | | | | | | | - John R Finnerty
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA.
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PIWI proteins and PIWI-interacting RNAs function in Hydra somatic stem cells. Proc Natl Acad Sci U S A 2013; 111:337-42. [PMID: 24367095 DOI: 10.1073/pnas.1320965111] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PIWI proteins and their bound PIWI-interacting RNAs (piRNAs) are found in animal germlines and are essential for fertility, but their functions outside of the gonad are not well understood. The cnidarian Hydra is a simple metazoan with well-characterized stem/progenitor cells that provides a unique model for analysis of PIWI function. Here we report that Hydra has two PIWI proteins, Hydra PIWI (Hywi) and Hydra PIWI-like (Hyli), both of which are expressed in all Hydra stem/progenitor cells, but not in terminally differentiated cells. We identified ∼15 million piRNAs associated with Hywi and/or Hyli and found that they exhibit the ping-pong signature of piRNA biogenesis. Hydra PIWI proteins are strictly cytoplasmic and thus likely act as posttranscriptional regulators. To explore this function, we generated a Hydra transcriptome for piRNA mapping. piRNAs map to transposons with a 25- to 35-fold enrichment compared with the abundance of transposon transcripts. By sequencing the small RNAs specific to the interstitial, ectodermal, and endodermal lineages, we found that the targeting of transposons appears to be largely restricted to the interstitial lineage. We also identified putative nontransposon targets of the pathway unique to each lineage. Finally we demonstrate that hywi function is essential in the somatic epithelial lineages. This comprehensive analysis of the PIWI-piRNA pathway in the somatic stem/progenitor cells of a nonbilaterian animal suggests that this pathway originated with broader stem cell functionality.
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40
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Analysis of Hydra PIWI proteins and piRNAs uncover early evolutionary origins of the piRNA pathway. Dev Biol 2013; 386:237-51. [PMID: 24355748 DOI: 10.1016/j.ydbio.2013.12.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 12/03/2013] [Accepted: 12/05/2013] [Indexed: 11/24/2022]
Abstract
To preserve genome integrity, an evolutionarily conserved small RNA-based silencing mechanism involving PIWI proteins and PIWI-interacting RNAs (piRNAs) represses potentially deleterious transposons in animals. Although there has been extensive research into PIWI proteins in bilaterians, these proteins remain to be examined in ancient phyla. Here, we investigated the PIWI proteins Hywi and Hyli in the cnidarian Hydra, and found that both PIWI proteins are enriched in multipotent stem cells, germline stem cells, and in the female germline. Hywi and Hyli localize to the nuage, a perinuclear organelle that has been implicated in piRNA-mediated transposon silencing, together with other conserved nuage and piRNA pathway components. Our findings provide the first report of nuage protein localization patterns in a non-bilaterian. Hydra PIWI proteins possess symmetrical dimethylarginines: modified residues that are known to aid in PIWI protein localization to the nuage and proper piRNA loading. piRNA profiling suggests that transposons are the major targets of the piRNA pathway in Hydra. Our data suggest that piRNA biogenesis through the ping-pong amplification cycle occurs in Hydra and that Hywi and Hyli are likely to preferentially bind primary and secondary piRNAs, respectively. Presumptive piRNA clusters are unidirectionally transcribed and primarily give rise to piRNAs that are antisense to transposons. These results indicate that various conserved features of PIWI proteins, the piRNA pathway, and their associations with the nuage were likely established before the evolution of bilaterians.
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Moran Y, Praher D, Fredman D, Technau U. The evolution of microRNA pathway protein components in Cnidaria. Mol Biol Evol 2013; 30:2541-52. [PMID: 24030553 PMCID: PMC3840309 DOI: 10.1093/molbev/mst159] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In the last decade, it became evident that posttranscriptional regulation of gene expression by microRNAs is a central biological process in both plants and animals. Yet, our knowledge about microRNA biogenesis and utilization in animals stems mostly from the study of Bilateria. In this study, we identified genes encoding the protein components of different parts of the microRNA pathway in Cnidaria, the likely sister phylum of Bilateria. These genes originated from three cnidarian lineages (sea anemones, stony corals, and hydras) that are separated by at least 500 My from one another. We studied the expression and phylogeny of the cnidarian homologs of Drosha and Pasha (DGCR8) that compose the microprocessor, the RNAse III enzyme Dicer and its partners, the HEN1 methyltransferase, the Argonaute protein effectors, as well as members of the GW182 protein family. We further reveal that whereas the bilaterian dicer partners Loquacious/TRBP and PACT are absent from Cnidaria, this phylum contains homologs of the double-stranded RNA-binding protein HYL1, the Dicer partner found in plants. We also identified HYL1 homologs in a sponge and a ctenophore. This finding raises questions regarding the independent evolution of the microRNA pathway in plants and animals, and together with the other results shed new light on the evolution of an important regulatory pathway.
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Affiliation(s)
- Yehu Moran
- Department for Molecular Evolution and Development, Center for Organismal Systems Biology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
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