1
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Wilson K, Manner C, Miranda E, Berrio A, Wray GA, McClay DR. An RNA interference approach for functional studies in the sea urchin and its use in analysis of nodal signaling gradients. Dev Biol 2024; 516:59-70. [PMID: 39098630 PMCID: PMC11425896 DOI: 10.1016/j.ydbio.2024.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 07/31/2024] [Accepted: 08/02/2024] [Indexed: 08/06/2024]
Abstract
Dicer substrate interfering RNAs (DsiRNAs) destroy targeted transcripts using the RNA-Induced Silencing Complex (RISC) through a process called RNA interference (RNAi). This process is ubiquitous among eukaryotes. Here we report the utility of DsiRNA in embryos of the sea urchin Lytechinus variegatus (Lv). Specific knockdowns phenocopy known morpholino and inhibitor knockdowns, and DsiRNA offers a useful alternative to morpholinos. Methods are described for the design of specific DsiRNAs that lead to destruction of targeted mRNA. DsiRNAs directed against pks1, an enzyme necessary for pigment production, show how successful DsiRNA perturbations are monitored by RNA in situ analysis and by qPCR to determine relative destruction of targeted mRNA. DsiRNA-based knockdowns phenocopy morpholino- and drug-based inhibition of nodal and lefty. Other knockdowns demonstrate that the RISC operates early in development as well as on genes that are first transcribed hours after gastrulation is completed. Thus, DsiRNAs effectively mediate destruction of targeted mRNA in the sea urchin embryo. The approach offers significant advantages over other widely used methods in the urchin in terms of cost, and ease of procurement, and offers sizeable experimental advantages in terms of ease of handling, injection, and knockdown validation.
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Affiliation(s)
- Keen Wilson
- University of Cincinnati, Blue Ash College, Biology Dept. 9555 Plainfield Rd., Blue Ash, Ohio; Department of Biology, Duke University, Durham, NC, USA
| | - Carl Manner
- Department of Biology, Duke University, Durham, NC, USA
| | | | | | | | - David R McClay
- Department of Biology, Duke University, Durham, NC, USA.
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2
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Wilson K, Manner C, Miranda E, Berrio A, Wray GA, McClay DR. An RNA interference approach for functional studies in the sea urchin and its use in analysis of Nodal signaling gradients. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599930. [PMID: 38979202 PMCID: PMC11230266 DOI: 10.1101/2024.06.20.599930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Dicer substrate interfering RNAs (DsiRNAs) destroy targeted transcripts using the RNA-Induced Silencing Complex (RISC) through a process called RNA interference (RNAi). This process is ubiquitous among eukaryotes. Here we report the utility of DsiRNA in embryos of the sea urchin Lytechinus variagatus (Lv). Specific knockdowns phenocopy known morpholino and inhibitor knockdowns, and DsiRNA offers a useful alternative to morpholinos. Methods for designing and obtaining specific DsiRNAs that lead to destruction of targeted mRNA are described. DsiRNAs directed against pks1, an enzyme necessary for pigment production, show how successful DsiRNA perturbations are monitored by RNA in situ analysis and by qPCR to determine relative destruction of targeted mRNA. DsiRNA-based knockdowns phenocopy morpholino- and drug-based inhibition of nodal and lefty. Other knockdowns demonstrate that the RISC operates early in development as well as on genes that are first transcribed hours after gastrulation is completed. Thus, DsiRNAs effectively mediate destruction of targeted mRNA in the sea urchin embryo. The approach offers significant advantages over other widely used methods in the urchin in terms of cost, and ease of procurement, and offers sizeable experimental advantages in terms of ease of handling, injection, and knockdown validation.
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3
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Panyushev N, Selitskiy M, Melnichenko V, Lebedev E, Okorokova L, Adonin L. Dynamic Evolution of Repetitive Elements and Chromatin States in Apis mellifera Subspecies. Genes (Basel) 2024; 15:89. [PMID: 38254978 PMCID: PMC10815273 DOI: 10.3390/genes15010089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/07/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
In this study, we elucidate the contribution of repetitive DNA sequences to the establishment of social structures in honeybees (Apis mellifera). Despite recent advancements in understanding the molecular mechanisms underlying the formation of honeybee castes, primarily associated with Notch signaling, the comprehensive identification of specific genomic cis-regulatory sequences remains elusive. Our objective is to characterize the repetitive landscape within the genomes of two honeybee subspecies, namely A. m. mellifera and A. m. ligustica. An observed recent burst of repeats in A. m. mellifera highlights a notable distinction between the two subspecies. After that, we transitioned to identifying differentially expressed DNA elements that may function as cis-regulatory elements. Nevertheless, the expression of these sequences showed minimal disparity in the transcriptome during caste differentiation, a pivotal process in honeybee eusocial organization. Despite this, chromatin segmentation, facilitated by ATAC-seq, ChIP-seq, and RNA-seq data, revealed a distinct chromatin state associated with repeats. Lastly, an analysis of sequence divergence among elements indicates successive changes in repeat states, correlating with their respective time of origin. Collectively, these findings propose a potential role of repeats in acquiring novel regulatory functions.
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Affiliation(s)
- Nick Panyushev
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia; (N.P.); (M.S.)
- Bioinformatics Institute, 197342 St. Petersburg, Russia;
| | - Max Selitskiy
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia; (N.P.); (M.S.)
| | - Vasilina Melnichenko
- International Scientific and Research Institute of Bioengineering, ITMO University, 197101 St. Petersburg, Russia;
| | - Egor Lebedev
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia; (N.P.); (M.S.)
| | | | - Leonid Adonin
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia; (N.P.); (M.S.)
- Institute of Biomedical Chemistry, Group of Mechanisms for Nanosystems Targeted Delivery, 119121 Moscow, Russia
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4
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Drozdov A, Lebedev E, Adonin L. Comparative Analysis of Bivalve and Sea Urchin Genetics and Development: Investigating the Dichotomy in Bilateria. Int J Mol Sci 2023; 24:17163. [PMID: 38138992 PMCID: PMC10742642 DOI: 10.3390/ijms242417163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/19/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
This comprehensive review presents a comparative analysis of early embryogenesis in Protostomia and Deuterostomia, the first of which exhibit a mosaic pattern of development, where cells are fated deterministically, while Deuterostomia display a regulatory pattern of development, where the fate of cells is indeterminate. Despite these fundamental differences, there are common transcriptional mechanisms that underline their evolutionary linkages, particularly in the field of functional genomics. By elucidating both conserved and unique regulatory strategies, this review provides essential insights into the comparative embryology and developmental dynamics of these groups. The objective of this review is to clarify the shared and distinctive characteristics of transcriptional regulatory mechanisms. This will contribute to the extensive areas of functional genomics, evolutionary biology and developmental biology, and possibly lay the foundation for future research and discussion on this seminal topic.
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Affiliation(s)
- Anatoliy Drozdov
- Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, 690041 Vladivostok, Russia
| | - Egor Lebedev
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia;
| | - Leonid Adonin
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia;
- Institute of Biomedical Chemistry, 119121 Moscow, Russia
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5
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Konrad KD, Arnott M, Testa M, Suarez S, Song JL. microRNA-124 directly suppresses Nodal and Notch to regulate mesodermal development. Dev Biol 2023; 502:50-62. [PMID: 37419400 PMCID: PMC10719910 DOI: 10.1016/j.ydbio.2023.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/27/2023] [Accepted: 06/22/2023] [Indexed: 07/09/2023]
Abstract
MicroRNAs regulate gene expression post-transcriptionally by destabilizing and/or inhibiting translation of target mRNAs in animal cells. MicroRNA-124 (miR-124) has been examined mostly in the context of neurogenesis. This study discovers a novel role of miR-124 in regulating mesodermal cell differentiation in the sea urchin embryo. The expression of miR-124 is first detectable at 12hours post fertilization at the early blastula stage, during endomesodermal specification. Mesodermally-derived immune cells come from the same progenitor cells that give rise to blastocoelar cells (BCs) and pigment cells (PCs) that must make a binary fate decision. We determined that miR-124 directly represses Nodal and Notch to regulate BC and PC differentiation. miR-124 inhibition does not impact the dorsal-ventral axis formation, but result in a significant increase in number of cells expressing BC-specific transcription factors (TFs) and a concurrent reduction of differentiated PCs. In general, removing miR-124's suppression of Nodal phenocopies miR124 inhibition. Interestingly, removing miR-124's suppression of Notch leads to an increased number of both BCs and PCs, with a subset of hybrid cells that express both BC- and PC-specific TFs in the larvae. Removal of miR-124's suppression of Notch not only affects differentiation of both BCs and PCs, but also induces cell proliferation of these cells during the first wave of Notch signaling. This study demonstrates that post-transcriptional regulation by miR-124 impacts differentiation of BCs and PCs by regulating the Nodal and Notch signaling pathways.
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Affiliation(s)
- Kalin D Konrad
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Malcolm Arnott
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Michael Testa
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Santiago Suarez
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA; Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Jia L Song
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA.
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6
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Bronchain O, Ducos B, Putzer H, Delagrange M, Laalami S, Philippe-Caraty L, Saroul K, Ciapa B. Natural antisense transcription of presenilin in sea urchin reveals a possible role for natural antisense transcription in the general control of gene expression during development. J Cell Sci 2023; 136:jcs261284. [PMID: 37345489 DOI: 10.1242/jcs.261284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/07/2023] [Indexed: 06/23/2023] Open
Abstract
One presenilin gene (PSEN) is expressed in the sea urchin embryo, in the vegetal pole of the gastrula and then mainly in cilia cells located around the digestive system of the pluteus, as we recently have reported. PSEN expression must be accurately regulated for correct execution of these two steps of development. While investigating PSEN expression changes in embryos after expansion of endoderm with LiCl or of ectoderm with Zn2+ by whole-mount in situ hybridization (WISH) and quantitative PCR (qPCR), we detected natural antisense transcription of PSEN. We then found that Endo16 and Wnt5, markers of endo-mesoderm, and of Hnf6 and Gsc, markers of ectoderm, are also sense and antisense transcribed. We discuss that general gene expression could depend on both sense and antisense transcription. This mechanism, together with the PSEN gene, should be included in gene regulatory networks (GRNs) that theorize diverse processes in this species. We suggest that it would also be relevant to investigate natural antisense transcription of PSEN in the field of Alzheimer's disease (AD) where the role of human PSEN1 and PSEN2 is well known.
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Affiliation(s)
- Odile Bronchain
- Paris-Saclay Institute of Neuroscience, CNRS, UMR CNRS 9197, Université Paris-Saclay, 75005 Paris, France
| | - Bertrand Ducos
- High Throughput qPCR Core Facility of the ENS, Université PSL, IBENS, Laboratoire de Physique de l'Ecole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005 Paris, France
| | - Harald Putzer
- CNRS, Université Paris Cité, Expression Génétique Microbienne, IBPC, 75005 Paris, France
| | - Marine Delagrange
- High Throughput qPCR Core Facility of the ENS, Université PSL, IBENS, Laboratoire de Physique de l'Ecole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005 Paris, France
| | - Soumaya Laalami
- CNRS, Université Paris Cité, Expression Génétique Microbienne, IBPC, 75005 Paris, France
| | - Laetitia Philippe-Caraty
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Krystel Saroul
- Institut CURIE, Université Paris-Saclay, INSERM U932, Immunité et Cancer, 91400 Orsay, France
| | - Brigitte Ciapa
- Paris-Saclay Institute of Neuroscience, CNRS, UMR CNRS 9197, Université Paris-Saclay, 75005 Paris, France
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7
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Yamakawa S, Yamazaki A, Morino Y, Wada H. Early expression onset of tissue-specific effector genes during the specification process in sea urchin embryos. EvoDevo 2023; 14:7. [PMID: 37101206 PMCID: PMC10131483 DOI: 10.1186/s13227-023-00210-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/01/2023] [Indexed: 04/28/2023] Open
Abstract
BACKGROUND In the course of animal developmental processes, various tissues are differentiated through complex interactions within the gene regulatory network. As a general concept, differentiation has been considered to be the endpoint of specification processes. Previous works followed this view and provided a genetic control scheme of differentiation in sea urchin embryos: early specification genes generate distinct regulatory territories in an embryo to express a small set of differentiation driver genes; these genes eventually stimulate the expression of tissue-specific effector genes, which provide biological identity to differentiated cells, in each region. However, some tissue-specific effector genes begin to be expressed in parallel with the expression onset of early specification genes, raising questions about the simplistic regulatory scheme of tissue-specific effector gene expression and the current concept of differentiation itself. RESULTS Here, we examined the dynamics of effector gene expression patterns during sea urchin embryogenesis. Our transcriptome-based analysis indicated that many tissue-specific effector genes begin to be expressed and accumulated along with the advancing specification GRN in the distinct cell lineages of embryos. Moreover, we found that the expression of some of the tissue-specific effector genes commences before cell lineage segregation occurs. CONCLUSIONS Based on this finding, we propose that the expression onset of tissue-specific effector genes is controlled more dynamically than suggested in the previously proposed simplistic regulation scheme. Thus, we suggest that differentiation should be conceptualized as a seamless process of accumulation of effector expression along with the advancing specification GRN. This pattern of effector gene expression may have interesting implications for the evolution of novel cell types.
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Affiliation(s)
- Shumpei Yamakawa
- Institute of Zoology and Evolutionary Research, Friedrich-Shiller University Jena, Erbertstraße 1, 07747, Jena, Germany.
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan.
| | - Atsuko Yamazaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yoshiaki Morino
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Hiroshi Wada
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
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8
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Remsburg CM, Konrad KD, Song JL. RNA localization to the mitotic spindle is essential for early development and is regulated by kinesin-1 and dynein. J Cell Sci 2023; 136:jcs260528. [PMID: 36751992 PMCID: PMC10038151 DOI: 10.1242/jcs.260528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/27/2023] [Indexed: 02/09/2023] Open
Abstract
Mitosis is a fundamental and highly regulated process that acts to faithfully segregate chromosomes into two identical daughter cells. Localization of gene transcripts involved in mitosis to the mitotic spindle might be an evolutionarily conserved mechanism to ensure that mitosis occurs in a timely manner. We identified many RNA transcripts that encode proteins involved in mitosis localized at the mitotic spindles in dividing sea urchin embryos and mammalian cells. Disruption of microtubule polymerization, kinesin-1 or dynein results in lack of spindle localization of these transcripts in the sea urchin embryo. Furthermore, results indicate that the cytoplasmic polyadenylation element (CPE) within the 3'UTR of the Aurora B transcript, a recognition sequence for CPEB, is essential for RNA localization to the mitotic spindle in the sea urchin embryo. Blocking this sequence results in arrested development during early cleavage stages, suggesting that RNA localization to the mitotic spindle might be a regulatory mechanism of cell division that is important for early development.
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Affiliation(s)
- Carolyn M. Remsburg
- University of Delaware, Department of Biological Sciences, Newark, DE 19716, USA
| | - Kalin D. Konrad
- University of Delaware, Department of Biological Sciences, Newark, DE 19716, USA
| | - Jia L. Song
- University of Delaware, Department of Biological Sciences, Newark, DE 19716, USA
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9
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Konrad KD, Song JL. microRNA-124 regulates Notch and NeuroD1 to mediate transition states of neuronal development. Dev Neurobiol 2023; 83:3-27. [PMID: 36336988 PMCID: PMC10440801 DOI: 10.1002/dneu.22902] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 09/12/2022] [Accepted: 10/12/2022] [Indexed: 11/09/2022]
Abstract
MicroRNAs regulate gene expression by destabilizing target mRNA and/or inhibiting translation in animal cells. The ability to mechanistically dissect miR-124's function during specification, differentiation, and maturation of neurons during development within a single system has not been accomplished. Using the sea urchin embryo, we take advantage of the manipulability of the embryo and its well-documented gene regulatory networks (GRNs). We incorporated NeuroD1 as part of the sea urchin neuronal GRN and determined that miR-124 inhibition resulted in aberrant gut contractions, swimming velocity, and neuronal development. Inhibition of miR-124 resulted in an increased number of cells expressing transcription factors (TFs) associated with progenitor neurons and a concurrent decrease of mature and functional neurons. Results revealed that in the early blastula/gastrula stages, miR-124 regulates undefined factors during neuronal specification and differentiation. In the late gastrula/larval stages, miR-124 regulates Notch and NeuroD1 during the transition between neuronal differentiation and maturation. Overall, we have improved the neuronal GRN and identified miR-124 to play a prolific role in regulating various transitions of neuronal development.
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Affiliation(s)
- Kalin D Konrad
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Jia L Song
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
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10
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Chang WL, Su YH. Zygotic hypoxia-inducible factor alpha regulates spicule elongation in the sea urchin embryo. Dev Biol 2022; 484:63-74. [DOI: 10.1016/j.ydbio.2022.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 01/28/2022] [Accepted: 02/09/2022] [Indexed: 12/15/2022]
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11
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Fromm B, Høye E, Domanska D, Zhong X, Aparicio-Puerta E, Ovchinnikov V, Umu SU, Chabot PJ, Kang W, Aslanzadeh M, Tarbier M, Mármol-Sánchez E, Urgese G, Johansen M, Hovig E, Hackenberg M, Friedländer MR, Peterson KJ. MirGeneDB 2.1: toward a complete sampling of all major animal phyla. Nucleic Acids Res 2021; 50:D204-D210. [PMID: 34850127 PMCID: PMC8728216 DOI: 10.1093/nar/gkab1101] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/20/2021] [Accepted: 11/23/2021] [Indexed: 12/03/2022] Open
Abstract
We describe an update of MirGeneDB, the manually curated microRNA gene database. Adhering to uniform and consistent criteria for microRNA annotation and nomenclature, we substantially expanded MirGeneDB with 30 additional species representing previously missing metazoan phyla such as sponges, jellyfish, rotifers and flatworms. MirGeneDB 2.1 now consists of 75 species spanning over ∼800 million years of animal evolution, and contains a total number of 16 670 microRNAs from 1549 families. Over 6000 microRNAs were added in this update using ∼550 datasets with ∼7.5 billion sequencing reads. By adding new phylogenetically important species, especially those relevant for the study of whole genome duplication events, and through updating evolutionary nodes of origin for many families and genes, we were able to substantially refine our nomenclature system. All changes are traceable in the specifically developed MirGeneDB version tracker. The performance of read-pages is improved and microRNA expression matrices for all tissues and species are now also downloadable. Altogether, this update represents a significant step toward a complete sampling of all major metazoan phyla, and a widely needed foundation for comparative microRNA genomics and transcriptomics studies. MirGeneDB 2.1 is part of RNAcentral and Elixir Norway, publicly and freely available at http://www.mirgenedb.org/.
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Affiliation(s)
- Bastian Fromm
- The Arctic University Museum of Norway, UiT- The Arctic University of Norway, Tromsø, Norway.,Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Eirik Høye
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Diana Domanska
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway.,Department of Pathology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Xiangfu Zhong
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Ernesto Aparicio-Puerta
- Department of Genetics, Faculty of Sciences, MNAT Excellence Unit, University of Granada, Granada, Spain.,Biotechnology Institute, CIBM, Granada, Spain.,Biohealth Research Institute (ibs.GRANADA), University Hospitals of Granada, University of Granada, Granada, Spain
| | - Vladimir Ovchinnikov
- Computational and Molecular Evolutionary Biology Research Group, School of life sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK
| | - Sinan U Umu
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Peter J Chabot
- Department of Biological Sciences, Dartmouth College, Hanover, USA
| | - Wenjing Kang
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Solna, Sweden
| | - Morteza Aslanzadeh
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Marcel Tarbier
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, Sweden
| | - Emilio Mármol-Sánchez
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | | | - Morten Johansen
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway.,Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Michael Hackenberg
- Department of Genetics, Faculty of Sciences, MNAT Excellence Unit, University of Granada, Granada, Spain.,Biotechnology Institute, CIBM, Granada, Spain.,Biohealth Research Institute (ibs.GRANADA), University Hospitals of Granada, University of Granada, Granada, Spain
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Kevin J Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, USA
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12
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Panyushev N, Okorokova L, Danilov L, Adonin L. Pattern of Repetitive Element Transcription Segregate Cell Lineages during the Embryogenesis of Sea Urchin Strongylocentrotus purpuratus. Biomedicines 2021; 9:1736. [PMID: 34829966 PMCID: PMC8615465 DOI: 10.3390/biomedicines9111736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 11/17/2022] Open
Abstract
Repetitive elements (REs) occupy a significant part of eukaryotic genomes and are shown to play diverse roles in genome regulation. During embryogenesis of the sea urchin, a large number of REs are expressed, but the role of these elements in the regulation of biological processes remains unknown. The aim of this study was to identify the RE expression at different stages of embryogenesis. REs occupied 44% of genomic DNA of Strongylocentrotus purpuratus. The most prevalent among these elements were the unknown elements-in total, they contributed 78.5% of REs (35% in total genome occupancy). It was revealed that the transcription pattern of genes and REs changes significantly during gastrulation. Using the de novo transcriptome assembly, we showed that the expression of RE is independent of its copy number in the genome. We also identified copies that are expressed. Only active RE copies were used for mapping and quantification of RE expression in the single-cell RNA sequencing data. REs expression was observed in all cell lineages and they were detected as population markers. Moreover, the primary mesenchyme cell (PMC) line had the greatest diversity of REs among the markers. Our data suggest a role for RE in the organization of developmental domains during the sea urchin embryogenesis at the single-cell resolution level.
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Affiliation(s)
- Nick Panyushev
- Bioinformatics Institute, 197342 St. Petersburg, Russia; (N.P.); (L.O.)
| | - Larisa Okorokova
- Bioinformatics Institute, 197342 St. Petersburg, Russia; (N.P.); (L.O.)
| | - Lavrentii Danilov
- St. Petersburg State University, Department of Genetics and Biotechnology, 199034 St. Petersburg, Russia;
| | - Leonid Adonin
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
- Institute of Biomedical Chemistry, Group of Mechanisms for Nanosystems Targeted Delivery, 119121 Moscow, Russia
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia
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13
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Huang JH, Jiao YH, Li L, Li DW, Li HY, Yang WD. Small RNA analysis of Perna viridis after exposure to Prorocentrum lima, a DSP toxins-producing dinoflagellate. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 239:105950. [PMID: 34474269 DOI: 10.1016/j.aquatox.2021.105950] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
Diarrheic shellfish poisoning toxins (DSP toxins) are a set of the most important phycotoxins produced by some dinoflagellates. Studies have shown that DSP toxins have various toxicities such as genotoxicity, cytotoxicity, and immunotoxicity to bivalve mollusks. However, these toxicities appear decreasing with exposure time and concentration of DSP toxins. The underlying mechanism involved remains unclear. In this study, small RNA sequencing was performed in the digestive gland of the mussel Perna viridis after exposure to DSP toxins-producing dinoflagellate Prorocentrum lima for different time periods. The potential roles of miRNAs in response and detoxification to DSP toxins in the mussel were analyzed. Small RNA sequencing of 12 samples from 72 individuals was conducted by BGISEQ-500. A total of 123 mature miRNAs were identified, including 90 conserved miRNAs and 33 potential novel miRNAs. After exposure to P. lima, multiple important miRNAs displayed some alterations. Further miRNA target prediction revealed some important genes involved in cytoskeleton, apoptosis, complement system and immune stress. qPCR demonstrated that miR-71_5, miR-750_1 and novel_mir4 were significantly up-regulated at 6 h after exposure to P. lima, while miR-100_2 was significantly down-regulated after 96 h of exposure. Accordingly, putative target genes of these differentially expressed miRNAs experienced some changes. After 6 h of DSP toxins exposure, NHLRC2 and C1q-like were significantly down-regulated. After 96 h of DSP toxins exposure, NHLRC2 was significantly up-regulated. It is reasonable to speculate that the mussel P. viridis might respond to DSP toxins through miR-750_1, novel_mir4 and miR-71_5 regulating the expression of relevant target genes involved in apoptosis, cytoskeleton, and immune response, etc. This study might provide new clues to uncover the toxic response of bivalve to DSP toxins and lay a foundation for revealing the roles of miRNAs in the environmental adaptation in shellfish.
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Affiliation(s)
- Jia-Hui Huang
- College of Life Science and Technology, Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, Jinan University, Guangzhou 510632, China
| | - Yu-Hu Jiao
- College of Life Science and Technology, Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, Jinan University, Guangzhou 510632, China
| | - Li Li
- College of Life Science and Technology, Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, Jinan University, Guangzhou 510632, China
| | - Da-Wei Li
- College of Life Science and Technology, Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, Jinan University, Guangzhou 510632, China
| | - Hong-Ye Li
- College of Life Science and Technology, Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, Jinan University, Guangzhou 510632, China
| | - Wei-Dong Yang
- College of Life Science and Technology, Key Laboratory of Aquatic Eutrophication and Control of Harmful Algal Blooms of Guangdong Higher Education Institute, Jinan University, Guangzhou 510632, China.
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14
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La Rocca G, King B, Shui B, Li X, Zhang M, Akat KM, Ogrodowski P, Mastroleo C, Chen K, Cavalieri V, Ma Y, Anelli V, Betel D, Vidigal J, Tuschl T, Meister G, Thompson CB, Lindsten T, Haigis K, Ventura A. Inducible and reversible inhibition of miRNA-mediated gene repression in vivo. eLife 2021; 10:e70948. [PMID: 34463618 PMCID: PMC8476124 DOI: 10.7554/elife.70948] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/24/2021] [Indexed: 12/23/2022] Open
Abstract
Although virtually all gene networks are predicted to be controlled by miRNAs, the contribution of this important layer of gene regulation to tissue homeostasis in adult animals remains unclear. Gain and loss-of-function experiments have provided key insights into the specific function of individual miRNAs, but effective genetic tools to study the functional consequences of global inhibition of miRNA activity in vivo are lacking. Here we report the generation and characterization of a genetically engineered mouse strain in which miRNA-mediated gene repression can be reversibly inhibited without affecting miRNA biogenesis or abundance. We demonstrate the usefulness of this strategy by investigating the consequences of acute inhibition of miRNA function in adult animals. We find that different tissues and organs respond differently to global loss of miRNA function. While miRNA-mediated gene repression is essential for the homeostasis of the heart and the skeletal muscle, it is largely dispensable in the majority of other organs. Even in tissues where it is not required for homeostasis, such as the intestine and hematopoietic system, miRNA activity can become essential during regeneration following acute injury. These data support a model where many metazoan tissues primarily rely on miRNA function to respond to potentially pathogenic events.
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Affiliation(s)
- Gaspare La Rocca
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Bryan King
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Bing Shui
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, United States
| | - Xiaoyi Li
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Minsi Zhang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Kemal M Akat
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, United States
| | - Paul Ogrodowski
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Chiara Mastroleo
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Kevin Chen
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy
| | - Yilun Ma
- Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program, New York, United States
| | - Viviana Anelli
- Center of Integrative Biology, University of Trento, Trento, Italy
| | - Doron Betel
- Hem/Oncology, Medicine and Institution for Computational Biomedicine, Weill Cornell Medical College, New York, United States
| | - Joana Vidigal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, Bethesda, United States
| | - Thomas Tuschl
- Laboratory of RNA Molecular Biology, The Rockefeller University, New York, United States
| | - Gunter Meister
- Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Craig B Thompson
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Tullia Lindsten
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, United States
| | - Kevin Haigis
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, United States
| | - Andrea Ventura
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, United States
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15
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Adonin L, Drozdov A, Barlev NA. Sea Urchin as a Universal Model for Studies of Gene Networks. Front Genet 2021; 11:627259. [PMID: 33552139 PMCID: PMC7854572 DOI: 10.3389/fgene.2020.627259] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 12/10/2020] [Indexed: 01/06/2023] Open
Abstract
The purple sea urchin Strongylocentrotus purpuratus has been used for over 150 years as a model organism in developmental biology. Using this model species, scientists have been able to describe, in detail, the mechanisms of cell cycle control and cell adhesion, fertilization, calcium signaling, cell differentiation, and death. Massive parallel sequencing of the sea urchin genome enabled the deciphering of the main components of gene regulatory networks during the activation of embryonic signaling pathways. This knowledge helped to extrapolate aberrations in somatic cells that may lead to diseases, including cancer in humans. Furthermore, since many, if not all, developmental signaling pathways were shown to be controlled by non-coding RNAs (ncRNAs), the sea urchin organism represents an attractive experimental model. In this review, we discuss the main discoveries in the genetics, genomics, and transcriptomics of sea urchins during embryogenesis with the main focus on the role of ncRNAs. This information may be useful for comparative studies between different organisms, and may help identify new regulatory networks controlled by ncRNAs.
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Affiliation(s)
- Leonid Adonin
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, Tyumen, Russia.,Orekhovich Institute of Biomedical Chemistry, Moscow, Russia
| | - Anatoliy Drozdov
- Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Nickolai A Barlev
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Orekhovich Institute of Biomedical Chemistry, Moscow, Russia.,Institute of Cytology, Russian Academy of Sciences, Saint-Petersburg, Russia
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16
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Dexheimer PJ, Wang J, Cochella L. Two MicroRNAs Are Sufficient for Embryonic Patterning in C. elegans. Curr Biol 2020; 30:5058-5065.e5. [PMID: 33125867 PMCID: PMC7758728 DOI: 10.1016/j.cub.2020.09.066] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/25/2020] [Accepted: 09/21/2020] [Indexed: 11/17/2022]
Abstract
MicroRNAs (miRNAs) are a class of post-transcriptional repressors with diverse roles in animal development and physiology [1]. The Microprocessor complex, composed of Drosha and Pasha/DGCR8, is necessary for the biogenesis of all canonical miRNAs and essential for the early stages of animal embryogenesis [2, 3, 4, 5, 6, 7, 8]. However, the cause for this requirement is largely unknown. Animals often express hundreds of miRNAs, and it remains unclear whether the Microprocessor is required to produce one or few essential miRNAs or many individually non-essential miRNAs. Additionally, both Drosha and Pasha/DGCR8 bind and cleave a variety of non-miRNA substrates [9, 10, 11, 12, 13, 14, 15], and it is unknown whether these activities account for the Microprocessor’s essential requirement. To distinguish between these possibilities, we developed a system in C. elegans to stringently deplete embryos of Microprocessor activity. Using a combination of auxin-inducible degradation (AID) and RNA interference (RNAi), we achieved Drosha and Pasha/DGCR8 depletion starting in the maternal germline, resulting in Microprocessor and miRNA-depleted embryos, which fail to undergo morphogenesis or form organs. Using a Microprocessor-bypass strategy, we show that this early embryonic arrest is rescued by the addition of just two miRNAs, one miR-35 and one miR-51 family member, resulting in morphologically normal larvae. Thus, just two out of ∼150 canonical miRNAs are sufficient for morphogenesis and organogenesis, and the processing of these miRNAs accounts for the essential requirement for Drosha and Pasha/DGCR8 during the early stages of C. elegans embryonic development. Video Abstract
Depletion of Drosha and Pasha results in embryos that fail to undergo morphogenesis The mirtron pathway enables expression of miRNAs in the absence of Drosha and Pasha Two miRNAs are sufficient to rescue embryogenesis in the absence of Drosha and Pasha miR-35 and miR-51 play an unexplored, likely conserved role in animal development
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Affiliation(s)
- Philipp J Dexheimer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Jingkui Wang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria.
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17
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Chiu HS, Martínez MR, Komissarova EV, Llobet-Navas D, Bansal M, Paull EO, Silva J, Yang X, Sumazin P, Califano A. The number of titrated microRNA species dictates ceRNA regulation. Nucleic Acids Res 2019; 46:4354-4369. [PMID: 29684207 PMCID: PMC5961349 DOI: 10.1093/nar/gky286] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/04/2018] [Indexed: 12/14/2022] Open
Abstract
microRNAs (miRNAs) play key roles in cancer, but their propensity to couple their targets as competing endogenous RNAs (ceRNAs) has only recently emerged. Multiple models have studied ceRNA regulation, but these models did not account for the effects of co-regulation by miRNAs with many targets. We modeled ceRNA and simulated its effects using established parameters for miRNA/mRNA interaction kinetics while accounting for co-regulation by multiple miRNAs with many targets. Our simulations suggested that co-regulation by many miRNA species is more likely to produce physiologically relevant context-independent couplings. To test this, we studied the overlap of inferred ceRNA networks from four tumor contexts-our proposed pan-cancer ceRNA interactome (PCI). PCI was composed of interactions between genes that were co-regulated by nearly three-times as many miRNAs as other inferred ceRNA interactions. Evidence from expression-profiling datasets suggested that PCI interactions are predictive of gene expression in 12 independent tumor- and non-tumor contexts. Biochemical assays confirmed ceRNA couplings for two PCI subnetworks, including oncogenes CCND1, HIF1A and HMGA2, and tumor suppressors PTEN, RB1 and TP53. Our results suggest that PCI is enriched for context-independent interactions that are coupled by many miRNA species and are more likely to be context independent.
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Affiliation(s)
- Hua-Sheng Chiu
- Texas Children's Cancer Center and Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | | | - Elena V Komissarova
- Department of Systems Biology, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA.,Department of Pathology and Cell Biology, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - David Llobet-Navas
- Bellvitge Biomedical Research Institute (IDIBELL), Gran via de l'Hospitalet, 199, L'Hospitalet de Llobregat 08908, Spain
| | - Mukesh Bansal
- Department of Systems Biology, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - Evan O Paull
- Department of Systems Biology, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
| | - José Silva
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xuerui Yang
- MOE Key Laboratory of Bioinformatics, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Pavel Sumazin
- Texas Children's Cancer Center and Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Andrea Califano
- Department of Systems Biology, Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA.,Department of Biomedical Informatics, and Department of Biochemistry and Molecular Biophysics, and Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Center for Computational Biology and Bioinformatics, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
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18
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Wang Z, Cui J, Song J, Gou M, Wang H, Gao K, Qiu X, Wang X, Chang Y. Integration of small RNAs and mRNAs by high-throughput sequencing reveals a complex regulatory network in Chinese sea cucumber, Russian sea cucumber and their hybrids. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 29:1-13. [DOI: 10.1016/j.cbd.2018.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 10/13/2018] [Indexed: 11/30/2022]
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19
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Pinzón N, Bertrand S, Subirana L, Busseau I, Escrivá H, Seitz H. Functional lability of RNA-dependent RNA polymerases in animals. PLoS Genet 2019; 15:e1007915. [PMID: 30779744 PMCID: PMC6396948 DOI: 10.1371/journal.pgen.1007915] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 03/01/2019] [Accepted: 12/24/2018] [Indexed: 11/18/2022] Open
Abstract
RNA interference (RNAi) requires RNA-dependent RNA polymerases (RdRPs) in many eukaryotes, and RNAi amplification constitutes the only known function for eukaryotic RdRPs. Yet in animals, classical model organisms can elicit RNAi without possessing RdRPs, and only nematode RNAi was shown to require RdRPs. Here we show that RdRP genes are much more common in animals than previously thought, even in insects, where they had been assumed not to exist. RdRP genes were present in the ancestors of numerous clades, and they were subsequently lost at a high frequency. In order to probe the function of RdRPs in a deuterostome (the cephalochordate Branchiostoma lanceolatum), we performed high-throughput analyses of small RNAs from various Branchiostoma developmental stages. Our results show that Branchiostoma RdRPs do not appear to participate in RNAi: we did not detect any candidate small RNA population exhibiting classical siRNA length or sequence features. Our results show that RdRPs have been independently lost in dozens of animal clades, and even in a clade where they have been conserved (cephalochordates) their function in RNAi amplification is not preserved. Such a dramatic functional variability reveals an unexpected plasticity in RNA silencing pathways. RNA interference (RNAi) is a conserved gene regulation system in eukaryotes. In non-animal eukaryotes, it necessitates RNA-dependent RNA polymerases (“RdRPs”). Among animals, only nematodes appear to require RdRPs for RNAi. Yet additional animal clades have RdRPs and it is assumed that they participate in RNAi. Here, we find that RdRPs are much more common in animals than previously thought, but their genes were independently lost in many lineages. Focusing on a species with RdRP genes (a cephalochordate), we found that it does not use them for RNAi. While RNAi is the only known function for eukaryotic RdRPs, our results suggest additional roles. Eukaryotic RdRPs thus have a complex evolutionary history in animals, with frequent independent losses and apparent functional diversification.
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Affiliation(s)
- Natalia Pinzón
- Institut de Génétique Humaine, UMR 9002 CNRS and université de Montpellier, 141, rue de la Cardonille, 34396 Montpellier CEDEX 5, France
| | - Stéphanie Bertrand
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Lucie Subirana
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Isabelle Busseau
- Institut de Génétique Humaine, UMR 9002 CNRS and université de Montpellier, 141, rue de la Cardonille, 34396 Montpellier CEDEX 5, France
| | - Hector Escrivá
- Sorbonne Université, CNRS, Biologie Intégrative des Organismes Marins, BIOM, F-66650 Banyuls-sur-Mer, France
| | - Hervé Seitz
- Institut de Génétique Humaine, UMR 9002 CNRS and université de Montpellier, 141, rue de la Cardonille, 34396 Montpellier CEDEX 5, France
- * E-mail:
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20
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Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that repress the translation and reduce the stability of target mRNAs in animal cells. Post-transcriptional regulation mediated by miRNAs is a highly conserved mechanism utilized by organisms throughout phylogeny to fine tune gene expression. We document the approaches used to study the function of a single miRNA and miRNA regulation of biological pathways in the sea urchin embryo. The protocols that are described include selection of miRNA inhibitors, test of miRNA direct targets, and the use of target protector morpholinos to evaluate the impact of miRNA inhibition on its targets. Using the described techniques and strategies, the sea urchin researcher will be able to validate a miRNA's direct targets and evaluate how inhibition of the miRNA affects developmental processes. These results will contribute to our understanding of the regulatory roles of miRNAs in development.
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Affiliation(s)
- Carolyn Remsburg
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Kalin Konrad
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Nina Faye Sampilo
- Department of Biological Sciences, University of Delaware, Newark, DE, United States
| | - Jia L Song
- Department of Biological Sciences, University of Delaware, Newark, DE, United States.
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21
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Sampilo NF, Stepicheva NA, Zaidi SAM, Wang L, Wu W, Wikramanayake A, Song JL. Inhibition of microRNA suppression of Dishevelled results in Wnt pathway-associated developmental defects in sea urchin. Development 2018; 145:dev167130. [PMID: 30389855 PMCID: PMC6288383 DOI: 10.1242/dev.167130] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/29/2018] [Indexed: 11/20/2022]
Abstract
MicroRNAs (miRNAs) are highly conserved, small non-coding RNAs that regulate gene expressions by binding to the 3' untranslated region of target mRNAs thereby silencing translation. Some miRNAs are key regulators of the Wnt signaling pathways, which impact developmental processes. This study investigates miRNA regulation of different isoforms of Dishevelled (Dvl/Dsh), which encode a key component in the Wnt signaling pathway. The sea urchin Dvl mRNA isoforms have similar spatial distribution in early development, but one isoform is distinctively expressed in the larval ciliary band. We demonstrated that Dvl isoforms are directly suppressed by miRNAs. By blocking miRNA suppression of Dvl isoforms, we observed dose-dependent defects in spicule length, patterning of the primary mesenchyme cells, gut morphology, and cilia. These defects likely result from increased Dvl protein levels, leading to perturbation of Wnt-dependent signaling pathways and additional Dvl-mediated processes. We further demonstrated that overexpression of Dvl isoforms recapitulated some of the Dvl miRNATP-induced phenotypes. Overall, our results indicate that miRNA suppression of Dvl isoforms plays an important role in ensuring proper development and function of primary mesenchyme cells and cilia.
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Affiliation(s)
- Nina Faye Sampilo
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Nadezda A Stepicheva
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | | | - Lingyu Wang
- Department of Biology, University of Miami, Coral Gables, FL 33124, USA
| | - Wei Wu
- Department of Biology, University of Miami, Coral Gables, FL 33124, USA
| | | | - Jia L Song
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
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22
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Abstract
The control processes that underlie the progression of development can be summarized in maps of gene regulatory networks (GRNs). A critical step in their assembly is the systematic perturbation of network candidates. In sea urchins the most important method for interfering with expression in a gene-specific way is application of morpholino antisense oligonucleotides (MOs). MOs act by binding to their sequence complement in transcripts resulting in a block in translation or a change in splicing and thus result in a loss of function. Despite the tremendous success of this technology, recent comparisons to mutants generated by genome editing have led to renewed criticism and challenged its reliability. As with all methods based on sequence recognition, MOs are prone to off-target binding that may result in phenotypes that are erroneously ascribed to the loss of the intended target. However, the slow progression of development in sea urchins has enabled extremely detailed studies of gene activity in the embryo. This wealth of knowledge paired with the simplicity of the sea urchin embryo enables careful analysis of MO phenotypes through a variety of methods that do not rely on terminal phenotypes. This article summarizes the use of MOs in probing GRNs and the steps that should be taken to assure their specificity.
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23
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Gaitán-Espitia JD, Sánchez R, Bruning P, Cárdenas L. Functional insights into the testis transcriptome of the edible sea urchin Loxechinus albus. Sci Rep 2016; 6:36516. [PMID: 27805042 PMCID: PMC5090362 DOI: 10.1038/srep36516] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 10/13/2016] [Indexed: 11/21/2022] Open
Abstract
The edible sea urchin Loxechinus albus (Molina, 1782) is a keystone species in the littoral benthic systems of the Pacific coast of South America. The international demand for high-quality gonads of this echinoderm has led to an extensive exploitation and decline of its natural populations. Consequently, a more thorough understanding of L. albus gonad development and gametogenesis could provide valuable resources for aquaculture applications, management, conservation and studies about the evolution of functional and structural pathways that underlie the reproductive toolkit of marine invertebrates. Using a high-throughput sequencing technology, we explored the male gonad transcriptome of this highly fecund sea urchin. Through a de novo assembly approach we obtained 42,530 transcripts of which 15,544 (36.6%) had significant alignments to known proteins in public databases. From these transcripts, approximately 73% were functionally annotated allowing the identification of several candidate genes that are likely to play a central role in developmental processes, nutrient reservoir activity, sexual reproduction, gamete generation, meiosis, sex differentiation, sperm motility, male courtship behavior and fertilization. Additionally, comparisons with the male gonad transcriptomes of other echinoderms revealed several conserved orthologous genes, suggesting that similar functional and structural pathways underlie the reproductive development in this group and other marine invertebrates.
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Affiliation(s)
- Juan Diego Gaitán-Espitia
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567 Valdivia, Chile
- CSIRO Oceans & Atmosphere, GPO Box 1538, Hobart 7001, TAS, Australia
| | - Roland Sánchez
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567 Valdivia, Chile
| | - Paulina Bruning
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567 Valdivia, Chile
| | - Leyla Cárdenas
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567 Valdivia, Chile
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24
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STEPICHEVA NADEZDAA, SONG JIAL. Function and regulation of microRNA-31 in development and disease. Mol Reprod Dev 2016; 83:654-74. [PMID: 27405090 PMCID: PMC6040227 DOI: 10.1002/mrd.22678] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 06/29/2016] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that orchestrate numerous cellular processes both under normal physiological conditions as well as in diseases. This review summarizes the functional roles and transcriptional regulation of the highly evolutionarily conserved miRNA, microRNA-31 (miR-31). miR-31 is an important regulator of embryonic implantation, development, bone and muscle homeostasis, and immune system function. Its own regulation is disrupted during the onset and progression of cancer and autoimmune disorders such as psoriasis and systemic lupus erythematosus. Limited studies suggest that miR-31 is transcriptionally regulated by epigenetics, such as methylation and acetylation, as well as by a number of transcription factors. Overall, miR-31 regulates diverse cellular and developmental processes by targeting genes involved in cell proliferation, apoptosis, cell differentiation, and cell motility. Mol. Reprod. Dev. 83: 654-674, 2016 © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
| | - JIA L. SONG
- Department of Biological Sciences, University of Delaware, Newark, Delaware
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25
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Dallaire A, Simard MJ. The implication of microRNAs and endo-siRNAs in animal germline and early development. Dev Biol 2016; 416:18-25. [PMID: 27287880 DOI: 10.1016/j.ydbio.2016.06.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 05/31/2016] [Accepted: 06/06/2016] [Indexed: 01/13/2023]
Abstract
Germ cells provide maternal mRNAs that are stored in the oocyte, and later translated at a specific time of development. In this context, gene regulation depends mainly on post-transcriptional mechanisms that contribute to keep maternal transcripts in a stable and translationally silent state. In recent years, small non-coding RNAs, such as microRNAs have emerged as key post-transcriptional regulators of gene expression. microRNAs control the translation efficiency and/or stability of targeted mRNAs. microRNAs are present in animal germ cells and maternally inherited microRNAs are abundant in early embryos. However, it is not known how microRNAs control the stability and translation of maternal transcripts. In this review, we will discuss the implication of germline microRNAs in regulating animal oogenesis and early embryogenesis as well as compare their roles with endo-siRNAs, small RNA species that share key molecular components with the microRNA pathway.
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Affiliation(s)
- Alexandra Dallaire
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Centre (Hôtel-Dieu de Québec), Quebec City, Québec, Canada G1R 2J6; Laval University Cancer Research Centre, Quebec City, Québec, Canada G1R 2J6
| | - Martin J Simard
- St-Patrick Research Group in Basic Oncology, Centre Hospitalier Universitaire de Québec-Université Laval Research Centre (Hôtel-Dieu de Québec), Quebec City, Québec, Canada G1R 2J6; Laval University Cancer Research Centre, Quebec City, Québec, Canada G1R 2J6.
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Mature maternal mRNAs are longer than zygotic ones and have complex degradation kinetics in sea urchin. Dev Biol 2016; 414:121-31. [PMID: 27085752 DOI: 10.1016/j.ydbio.2016.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 03/16/2016] [Accepted: 04/10/2016] [Indexed: 11/22/2022]
Abstract
Early in embryogenesis, maternally deposited transcripts are degraded and new zygotic transcripts are generated during the maternal to zygotic transition. Recent works have shown that early zygotic transcripts are short compared to maternal transcripts, in zebrafish and Drosophila species. The reduced zygotic transcript length was attributed to the short cell cycle in these organisms that prevents the transcription of long primary transcripts (intron delay). Here we study the length of maternal mRNAs and their degradation kinetics in two sea urchin species to further the understanding of maternal gene usage and processing. Early zygotic primary transcripts and mRNAs are shorter than maternal ones in the sea urchin, Strongylocentrotus purpuratus. Yet, while primary transcripts length increases when cell cycle lengthens, typical for intron delay, the relatively short length of zygotic mRNAs is consistent. The enhanced mRNA length is due to significantly longer maternal open reading frames and 3'UTRs compared to the zygotic lengths, a ratio that does not change with developmental time. This implies unique usage of both coding sequences and regulatory information in the maternal stage compared to the zygotic stages. We extracted the half-lifetimes due to maternal and zygotic degradation mechanisms from high-density time course of a set of maternal mRNAs in Paracentrotus lividus. The degradation rates due to maternal and zygotic degradation mechanisms are not correlated, indicating that these mechanisms are independent and relay on different regulatory information. Our studies illuminate specific structural and kinetic properties of sea urchin maternal mRNAs that might be broadly shared by other organisms.
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Stepicheva NA, Song JL. microRNA-31 modulates skeletal patterning in the sea urchin embryo. Development 2015; 142:3769-80. [PMID: 26400092 DOI: 10.1242/dev.127969] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/03/2015] [Indexed: 01/25/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that repress the translation and reduce the stability of target mRNAs in animal cells. microRNA-31 (miR-31) is known to play a role in cancer, bone formation and lymphatic development. However, studies to understand the function of miR-31 in embryogenesis have been limited. We examined the regulatory role of miR-31 in early development using the sea urchin as a model. miR-31 is expressed at all stages of development and its knockdown (KD) disrupts the patterning and function of primary mesenchyme cells (PMCs), which form the embryonic skeleton spicules. We identified that miR-31 directly represses Pmar1, Alx1, Snail and VegfR7 within the PMC gene regulatory network using reporter constructs. Further, blocking the miR-31-mediated repression of Alx1 and/or VegfR7 in the developing embryo resulted in defects in PMC patterning and skeletogenesis. The majority of the mislocalized PMCs in miR-31 KD embryos did not express VegfR10, indicating that miR-31 regulates VegfR gene expression within PMCs. In addition, miR-31 indirectly suppresses Vegf3 expression in the ectoderm. These results indicate that miR-31 coordinately suppresses genes within the PMCs and in the ectoderm to impact PMC patterning and skeletogenesis. This study identifies the novel function and molecular mechanism of miR-31-mediated regulation in the developing embryo.
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Affiliation(s)
- Nadezda A Stepicheva
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Jia L Song
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
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Abstract
With few exceptions, all animals acquire the ability to produce eggs or sperm at some point in their life cycle. Despite this near-universal requirement for sexual reproduction, there exists an incredible diversity in germ line development. For example, animals exhibit a vast range of differences in the timing at which the germ line, which retains reproductive potential, separates from the soma, or terminally differentiated, nonreproductive cells. This separation may occur during embryonic development, after gastrulation, or even in adults, depending on the organism. The molecular mechanisms of germ line segregation are also highly diverse, and intimately intertwined with the overall transition from a fertilized egg to an embryo. The earliest embryonic stages of many species are largely controlled by maternally supplied factors. Later in development, patterning control shifts to the embryonic genome and, concomitantly with this transition, the maternally supplied factors are broadly degraded. This chapter attempts to integrate these processes--germ line segregation, and how the divergence of germ line and soma may utilize the egg to embryo transitions differently. In some embryos, this difference is subtle or maybe lacking altogether, whereas in other embryos, this difference in utilization may be a key step in the divergence of the two lineages. Here, we will focus our discussion on the echinoderms, and in particular the sea urchins, in which recent studies have provided mechanistic understanding in germ line determination. We propose that the germ line in sea urchins requires an acquisition of maternal factors from the egg and, when compared to other members of the taxon, this appears to be a derived mechanism. The acquisition is early--at the 32-cell stage--and involves active protection of maternal mRNAs, which are instead degraded in somatic cells with the maternal-to-embryonic transition. We collectively refer to this model as the Time Capsule method for germ line determination.
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Affiliation(s)
- S Zachary Swartz
- Department of Molecular and Cellular Biology, Brown University, Providence, Rhode Island, USA
| | - Gary M Wessel
- Department of Molecular and Cellular Biology, Brown University, Providence, Rhode Island, USA.
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Wang H, Liu S, Cui J, Li C, Hu Y, Zhou W, Chang Y, Qiu X, Liu Z, Wang X. Identification and Characterization of MicroRNAs from Longitudinal Muscle and Respiratory Tree in Sea Cucumber (Apostichopus japonicus) Using High-Throughput Sequencing. PLoS One 2015; 10:e0134899. [PMID: 26244987 PMCID: PMC4526669 DOI: 10.1371/journal.pone.0134899] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 07/15/2015] [Indexed: 01/01/2023] Open
Abstract
MicroRNAs (miRNAs), as a family of non-coding small RNAs, play important roles in the post-transcriptional regulation of gene expression. Sea cucumber (Apostichopus japonicus) is an important economic species which is widely cultured in East Asia. The longitudinal muscle (LTM) and respiratory tree (RPT) are two important tissues in sea cucumber, playing important roles such as respiration and movement. In this study, we identified and characterized miRNAs in the LTM and RPT of sea cucumber (Apostichopus japonicus) using Illumina HiSeq 2000 platform. A total of 314 and 221 conserved miRNAs were identified in LTM and RPT, respectively. In addition, 27 and 34 novel miRNAs were identified in the LTM and RPT, respectively. A set of 58 miRNAs were identified to be differentially expressed between LTM and RPT. Among them, 9 miRNAs (miR-31a-3p, miR-738, miR-1692, let-7a, miR-72a, miR-100b-5p, miR-31b-5p, miR-429-3p, and miR-2008) in RPT and 7 miRNAs (miR-127, miR-340, miR-381, miR-3543, miR-434-5p, miR-136-3p, and miR-300-3p) in LTM were differentially expressed with foldchange value being greater than 10. A total of 14,207 and 12,174 target genes of these miRNAs were predicted, respectively. Functional analysis of these target genes of miRNAs were performed by GO analysis and pathway analysis. This result provided in this work will be useful for understanding biological characteristics of the LTM and RPT of sea cucumber and assisting molecular breeding of sea cucumber for aquaculture.
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Affiliation(s)
- Hongdi Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, United States of America
| | - Jun Cui
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China
| | - Chengze Li
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China
| | - Yucai Hu
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China
- School of Science, Dalian Ocean University, Dalian 116023, China
| | - Wei Zhou
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China
| | - Xuemei Qiu
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China
| | - Zhanjiang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, United States of America
| | - Xiuli Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture, Dalian Ocean University, Dalian 116023, China
- * E-mail:
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Song JL, Nigam P, Tektas SS, Selva E. microRNA regulation of Wnt signaling pathways in development and disease. Cell Signal 2015; 27:1380-91. [PMID: 25843779 PMCID: PMC4437805 DOI: 10.1016/j.cellsig.2015.03.018] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 03/24/2015] [Accepted: 03/24/2015] [Indexed: 12/19/2022]
Abstract
Wnt signaling pathways and microRNAs (miRNAs) are critical regulators of development. Aberrant Wnt signaling pathways and miRNA levels lead to developmental defects and diverse human pathologies including but not limited to cancer. Wnt signaling pathways regulate a plethora of cellular processes during embryonic development and maintain homeostasis of adult tissues. A majority of Wnt signaling components are regulated by miRNAs which are small noncoding RNAs that are expressed in both animals and plants. In animal cells, miRNAs fine tune gene expression by pairing primarily to the 3'untranslated region of protein coding mRNAs to repress target mRNA translation and/or induce target degradation. miRNA-mediated regulation of signaling transduction pathways is important in modulating dose-sensitive response of cells to signaling molecules. This review discusses components of the Wnt signaling pathways that are regulated by miRNAs in the context of development and diseases. A fundamental understanding of miRNA functions in Wnt signaling transduction pathways may yield new insight into crosstalks of regulatory mechanisms essential for development and disease pathophysiology leading to novel therapeutics.
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Affiliation(s)
- Jia L Song
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA.
| | - Priya Nigam
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Senel S Tektas
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Erica Selva
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
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Yajima M, Wessel GM. Essential elements for translation: the germline factor Vasa functions broadly in somatic cells. Development 2015; 142:1960-70. [PMID: 25977366 PMCID: PMC4460737 DOI: 10.1242/dev.118448] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 03/30/2015] [Indexed: 01/23/2023]
Abstract
Vasa is a conserved RNA-helicase found in the germ lines of all metazoans tested. Whereas Vasa presence is often indicated as a metric for germline determination in animals, it is also expressed in stem cells of diverse origin. Recent research suggests, however, that Vasa has a much broader function, including a significant role in cell cycle regulation. Results herein indicate that Vasa is utilized widely, and often induced transiently, during development in diverse somatic cells and adult precursor tissues. We identified that Vasa in the sea urchin is essential for: (1) general mRNA translation during embryogenesis, (2) developmental re-programming upon manipulations to the embryo and (3) larval wound healing. We also learned that Vasa interacted with mRNAs in the perinuclear area and at the spindle in an Importin-dependent manner during cell cycle progression. These results suggest that, when present, Vasa functions are essential to contributing to developmental regulation.
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Affiliation(s)
- Mamiko Yajima
- MCB Department, Brown University, 185 Meeting Street, BOX-GL173, Providence, RI 02912, USA
| | - Gary M Wessel
- MCB Department, Brown University, 185 Meeting Street, BOX-GL173, Providence, RI 02912, USA
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32
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Stepicheva N, Nigam PA, Siddam AD, Peng CF, Song JL. microRNAs regulate β-catenin of the Wnt signaling pathway in early sea urchin development. Dev Biol 2015; 402:127-41. [PMID: 25614238 DOI: 10.1016/j.ydbio.2015.01.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 12/18/2014] [Accepted: 01/09/2015] [Indexed: 12/19/2022]
Abstract
Development of complex multicellular organisms requires careful regulation at both transcriptional and post-transcriptional levels. Post-transcriptional gene regulation is in part mediated by a class of non-coding RNAs of 21-25 nucleotides in length known as microRNAs (miRNAs). β-catenin, regulated by the canonical Wnt signaling pathway, has a highly evolutionarily conserved function in patterning early metazoan embryos, in forming the Anterior-Posterior axis, and in establishing the endomesoderm. Using reporter constructs and site-directed mutagenesis, we identified at least three miRNA binding sites within the 3' untranslated region (3'UTR) of the sea urchin β-catenin. Further, blocking these three miRNA binding sites within the β-catenin 3'UTR to prevent regulation of endogenous β-catenin by miRNAs resulted in a minor increase in β-catenin protein accumulation that is sufficient to induce aberrant gut morphology and circumesophageal musculature. These phenotypes are likely the result of increased transcript levels of Wnt responsive endomesodermal regulatory genes. This study demonstrates the importance of miRNA regulation of β-catenin in early development.
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Affiliation(s)
- Nadezda Stepicheva
- Department of Biological Sciences, University of Delaware, 323 Wolf Hall, Newark, DE 19716, USA
| | - Priya A Nigam
- Department of Biological Sciences, University of Delaware, 323 Wolf Hall, Newark, DE 19716, USA
| | - Archana D Siddam
- Department of Biological Sciences, University of Delaware, 323 Wolf Hall, Newark, DE 19716, USA
| | - Chieh Fu Peng
- Department of Biology, University of Miami, Coral Gables, FL 33124, USA
| | - Jia L Song
- Department of Biological Sciences, University of Delaware, 323 Wolf Hall, Newark, DE 19716, USA.
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33
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Lee M, Choi Y, Kim K, Jin H, Lim J, Nguyen TA, Yang J, Jeong M, Giraldez AJ, Yang H, Patel DJ, Kim VN. Adenylation of maternally inherited microRNAs by Wispy. Mol Cell 2014; 56:696-707. [PMID: 25454948 DOI: 10.1016/j.molcel.2014.10.011] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 09/03/2014] [Accepted: 10/10/2014] [Indexed: 12/31/2022]
Abstract
Early development depends heavily on accurate control of maternally inherited mRNAs, and yet it remains unknown how maternal microRNAs are regulated during maternal-to-zygotic transition (MZT). We here find that maternal microRNAs are highly adenylated at their 3' ends in mature oocytes and early embryos. Maternal microRNA adenylation is widely conserved in fly, sea urchin, and mouse. We identify Wispy, a noncanonical poly(A) polymerase, as the enzyme responsible for microRNA adenylation in flies. Knockout of wispy abrogates adenylation and results in microRNA accumulation in eggs, whereas overexpression of Wispy increases adenylation and reduces microRNA levels in S2 cells. Wispy interacts with Ago1 through protein-protein interaction, which may allow the effective and selective adenylation of microRNAs. Thus, adenylation may contribute to the clearance of maternally deposited microRNAs during MZT. Our work provides mechanistic insights into the regulation of maternal microRNAs and illustrates the importance of RNA tailing in development.
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Affiliation(s)
- Mihye Lee
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Yeon Choi
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Kijun Kim
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Hua Jin
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Jaechul Lim
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Tuan Anh Nguyen
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Jihye Yang
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
| | - Minsun Jeong
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Antonio J Giraldez
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Yale Stem Cell Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Hui Yang
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 151-742, Korea; School of Biological Sciences, Seoul National University, Seoul 151-742, Korea.
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Wang H, Liu S, Cui J, Li C, Qiu X, Chang Y, Liu Z, Wang X. Characterization and expression analysis of microRNAs in the tube foot of sea cucumber Apostichopus japonicus. PLoS One 2014; 9:e111820. [PMID: 25372871 PMCID: PMC4221132 DOI: 10.1371/journal.pone.0111820] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 09/30/2014] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs (miRNAs) are a class of endogenous non-coding small RNA with average length of 22 nucleotides, participating in the post-transcriptional regulation of gene expression. In this study, we report the identification and characterization of miRNAs in the tube foot of sea cucumber (Apostichopus japonicus) by next generation sequencing with Illumina HiSeq 2000 platform. Through the bioinformatic analysis, we identified 260 conserved miRNAs and six novel miRNAs from the tube foot small RNA transcriptome. Quantitative realtime PCR (qRT-PCR) was performed to characterize the specific expression in the tube foot. The results indicated that four miRNAs, including miR-29a, miR-29b, miR-2005 and miR-278-3p, were significantly up-regulated in the tube foot. The target genes of the four specifically expressed miRNAs were predicted in silico and validated by performing qRT-PCR. Gene ontology (GO) and KEGG pathway analyses with the target genes of these four miRNAs were conducted to further understand the regulatory function in the tube foot. This is the first study to profile the miRNA transcriptome of the tube foot in sea cucumber. This work will provide valuable genomic resources to understand the mechanisms of gene regulation in the tube foot, and will be useful to assist the molecular breeding in sea cucumber.
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Affiliation(s)
- Hongdi Wang
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, Alabama, United States of America
| | - Jun Cui
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | - Chengze Li
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | - Xuemei Qiu
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | - Yaqing Chang
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
| | - Zhanjiang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, Alabama, United States of America
| | - Xiuli Wang
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China
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35
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Wessel GM, Brayboy L, Fresques T, Gustafson EA, Oulhen N, Ramos I, Reich A, Swartz SZ, Yajima M, Zazueta V. The biology of the germ line in echinoderms. Mol Reprod Dev 2014; 81:679-711. [PMID: 23900765 PMCID: PMC4102677 DOI: 10.1002/mrd.22223] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 07/23/2013] [Indexed: 12/16/2022]
Abstract
The formation of the germ line in an embryo marks a fresh round of reproductive potential. The developmental stage and location within the embryo where the primordial germ cells (PGCs) form, however, differs markedly among species. In many animals, the germ line is formed by an inherited mechanism, in which molecules made and selectively partitioned within the oocyte drive the early development of cells that acquire this material to a germ-line fate. In contrast, the germ line of other animals is fated by an inductive mechanism that involves signaling between cells that directs this specialized fate. In this review, we explore the mechanisms of germ-line determination in echinoderms, an early-branching sister group to the chordates. One member of the phylum, sea urchins, appears to use an inherited mechanism of germ-line formation, whereas their relatives, the sea stars, appear to use an inductive mechanism. We first integrate the experimental results currently available for germ-line determination in the sea urchin, for which considerable new information is available, and then broaden the investigation to the lesser-known mechanisms in sea stars and other echinoderms. Even with this limited insight, it appears that sea stars, and perhaps the majority of the echinoderm taxon, rely on inductive mechanisms for germ-line fate determination. This enables a strongly contrasted picture for germ-line determination in this phylum, but one for which transitions between different modes of germ-line determination might now be experimentally addressed.
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Affiliation(s)
- Gary M. Wessel
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island
| | - Lynae Brayboy
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island
| | - Tara Fresques
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island
| | - Eric A. Gustafson
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island
| | - Nathalie Oulhen
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island
| | - Isabela Ramos
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island
| | - Adrian Reich
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island
| | - S. Zachary Swartz
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island
| | - Mamiko Yajima
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island
| | - Vanessa Zazueta
- Department of Molecular Biology, Cellular Biology, and Biochemistry, Brown University, Providence, Rhode Island
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Swartz SZ, Reich AM, Oulhen N, Raz T, Milos PM, Campanale JP, Hamdoun A, Wessel GM. Deadenylase depletion protects inherited mRNAs in primordial germ cells. Development 2014; 141:3134-42. [PMID: 25100654 PMCID: PMC4197533 DOI: 10.1242/dev.110395] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 06/22/2014] [Indexed: 12/12/2022]
Abstract
A crucial event in animal development is the specification of primordial germ cells (PGCs), which become the stem cells that create sperm and eggs. How PGCs are created provides a valuable paradigm for understanding stem cells in general. We find that the PGCs of the sea urchin Strongylocentrotus purpuratus exhibit broad transcriptional repression, yet enrichment for a set of inherited mRNAs. Enrichment of several germline determinants in the PGCs requires the RNA-binding protein Nanos to target the transcript that encodes CNOT6, a deadenylase, for degradation in the PGCs, thereby creating a stable environment for RNA. Misexpression of CNOT6 in the PGCs results in their failure to retain Seawi transcripts and Vasa protein. Conversely, broad knockdown of CNOT6 expands the domain of Seawi RNA as well as exogenous reporters. Thus, Nanos-dependent spatially restricted CNOT6 differential expression is used to selectively localize germline RNAs to the PGCs. Our findings support a 'time capsule' model of germline determination, whereby the PGCs are insulated from differentiation by retaining the molecular characteristics of the totipotent egg and early embryo.
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Affiliation(s)
- S Zachary Swartz
- Department of Molecular, Cellular Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Adrian M Reich
- Department of Molecular, Cellular Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Nathalie Oulhen
- Department of Molecular, Cellular Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Tal Raz
- Helicos BioSciences Corporation, One Kendall Square, Building 700, Cambridge, MA 02139, USA
| | - Patrice M Milos
- Helicos BioSciences Corporation, One Kendall Square, Building 700, Cambridge, MA 02139, USA
| | - Joseph P Campanale
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, 8750 Biological Grade Road, La Jolla, CA 92037, USA
| | - Amro Hamdoun
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, 8750 Biological Grade Road, La Jolla, CA 92037, USA
| | - Gary M Wessel
- Department of Molecular, Cellular Biology and Biochemistry, Brown University, Providence, RI 02912, USA
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Hausser J, Zavolan M. Identification and consequences of miRNA-target interactions--beyond repression of gene expression. Nat Rev Genet 2014; 15:599-612. [PMID: 25022902 DOI: 10.1038/nrg3765] [Citation(s) in RCA: 458] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Comparative genomics analyses and high-throughput experimental studies indicate that a microRNA (miRNA) binds to hundreds of sites across the transcriptome. Although the knockout of components of the miRNA biogenesis pathway has profound phenotypic consequences, most predicted miRNA targets undergo small changes at the mRNA and protein levels when the expression of the miRNA is perturbed. Alternatively, miRNAs can establish thresholds in and increase the coherence of the expression of their target genes, as well as reduce the cell-to-cell variability in target gene expression. Here, we review the recent progress in identifying miRNA targets and the emerging paradigms of how miRNAs shape the dynamics of target gene expression.
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Affiliation(s)
- Jean Hausser
- Department of Molecular Cell Biology, Weizmann Institute of Science, Herzl Street 234, 76100 Rehovot, Israel
| | - Mihaela Zavolan
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4156 Basel, Switzerland
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Brümmer A, Hausser J. MicroRNA binding sites in the coding region of mRNAs: extending the repertoire of post-transcriptional gene regulation. Bioessays 2014; 36:617-26. [PMID: 24737341 DOI: 10.1002/bies.201300104] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
It is well established that microRNAs (miRNAs) induce mRNA degradation by binding to 3' untranslated regions (UTRs). The functionality of sites in the coding domain sequence (CDS), on the other hand, remains under discussion. Such sites have limited impact on target mRNA abundance and recent work suggests that miRNAs bind in the CDS to inhibit translation. What then could be the regulatory benefits of translation inhibition through CDS targeting compared to mRNA degradation following 3' UTR binding? We propose that these domain-dependent effects serve to diversify the functional repertoire of post-transcriptional gene expression control. Possible regulatory benefits may include tuning the time-scale and magnitude of post-transcriptional regulation, regulating protein abundance depending on or independently of the cellular state, and regulation of the protein abundance of alternative splice variants. Finally, we review emerging evidence that these ideas may generalize to RNA-binding proteins beyond miRNAs and Argonaute proteins.
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Fresques T, Zazueta-Novoa V, Reich A, Wessel GM. Selective accumulation of germ-line associated gene products in early development of the sea star and distinct differences from germ-line development in the sea urchin. Dev Dyn 2014; 243:568-87. [PMID: 24038550 PMCID: PMC3996927 DOI: 10.1002/dvdy.24038] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 08/12/2013] [Accepted: 08/16/2013] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Echinodermata is a diverse phylum, a sister group to chordates, and contains diverse organisms that may be useful to understand varied mechanisms of germ-line specification. RESULTS We tested 23 genes in development of the sea star Patiria miniata that fall into five categories: (1) Conserved germ-line factors; (2) Genes involved in the inductive mechanism of germ-line specification; (3) Germ-line associated genes; (4) Molecules involved in left-right asymmetry; and (5) Genes involved in regulation and maintenance of the genome during early embryogenesis. Overall, our results support the contention that the posterior enterocoel is a source of the germ line in the sea star P. miniata. CONCLUSIONS The germ line in this organism appears to be specified late in embryogenesis, and in a pattern more consistent with inductive interactions amongst cells. This is distinct from the mechanism seen in sea urchins, a close relative of the sea star clad. We propose that P. miniata may serve as a valuable model to study inductive mechanisms of germ-cell specification and when compared with germ-line formation in the sea urchin S. purpuratus may reveal developmental transitions that occur in the evolution of inherited and inductive mechanisms of germ-line specification.
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Affiliation(s)
| | | | - Adrian Reich
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence RI 02912 USA
| | - Gary M. Wessel
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence RI 02912 USA
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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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Chen G, Zhang C, Jiang F, Wang Y, Xu Z, Wang C. Bioinformatics analysis of hemocyte miRNAs of scallop Chlamys farreri against acute viral necrobiotic virus (AVNV). FISH & SHELLFISH IMMUNOLOGY 2014; 37:75-86. [PMID: 24457045 DOI: 10.1016/j.fsi.2014.01.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 12/01/2013] [Accepted: 01/02/2014] [Indexed: 06/03/2023]
Abstract
The sustainable development of the scallop Chlamys farreri industry in China is hindered by mass mortality mainly caused by a novel pathogen known as acute viral necrosis virus (AVNV). A better understanding of host-virus interactions, especially those at the molecular level, may facilitate the prevention and cure of AVNV infections. MicroRNAs (miRNAs) represent a class of small RNA molecules involved in several biological processes, including mediating host-pathogen responses. In this study, two hemocyte small RNA libraries were constructed from control (control library, CL) and AVNV-infected (infection library, IL) C. farreri for high throughput sequencing using Solexa technology. Acquired data were further used to identify conserved and novel miRNAs, screen differentially expressed miRNAs, and predict their target genes through bioinformatics analysis. Solexa sequencing produced 19,485,719 and 20,594,513 clean reads representing 2,248,814 and 1,510,256 unique small RNAs from CL and IL, respectively. A total of 57 conserved miRNAs were identified in both libraries, among which only two were unique to IL. Novel miRNA prediction using the Crassostrea gigas genome as a reference revealed 11 candidate miRNAs, 10 of which were validated by RT-PCR. Differential expression (p < 0.001) between libraries was observed in 37 miRNAs, among which 30 and 7 miRNAs were up- and downregulated, respectively. Expression differences were further confirmed by qRT-PCR. A sequence homology search against available C. farreri ESTs showed that these differentially expressed miRNAs may target 177 genes involved in a broad range of biological processes including immune defense and stress response. This study is the first to characterize C. farreri miRNAs and miRNA expression profiles in response to AVNV infection by deep sequencing. The results presented here will deepen our understanding of the pathogenesis of AVNV at the molecular level and provide new insights into the molecular basis of host-pathogen interactions in C. farreri.
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Affiliation(s)
- Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai 264209, PR China.
| | - Chunyun Zhang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai 264209, PR China.
| | - Fengjuan Jiang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai 264209, PR China
| | - Yuanyuan Wang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai 264209, PR China
| | - Zhong Xu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai 264209, PR China
| | - Chongming Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, PR China
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Yajima M, Gustafson EA, Song JL, Wessel GM. Piwi regulates Vasa accumulation during embryogenesis in the sea urchin. Dev Dyn 2014; 243:451-8. [PMID: 24218044 PMCID: PMC4018429 DOI: 10.1002/dvdy.24096] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 10/29/2013] [Accepted: 11/07/2013] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Piwi proteins are essential for germ line development, stem cell maintenance, and more recently found to function in epigenetic and somatic gene regulation. In the sea urchin Strongylocentrotus purpuratus, two Piwi proteins, Seawi and Piwi-like1, have been identified, yet their functional contributions have not been reported. RESULTS Here we found that Seawi protein was localized uniformly in the early embryo and then became enriched in the primordial germ cells (PGCs) (the small micromere lineage) from blastula stage and thereafter. Morpholino knockdown of Sp-seawi diminished PGC-specific localization of Seawi proteins, and altered expression of other germ line markers such as Vasa and Gustavus, but had no effect on Nanos. Furthermore, Seawi knockdown transiently resulted in Vasa positive cell proliferation in the right coelomic pouch that appear to be derived from the small micromere lineage, yet they quickly disappeared with an indication of apoptosis by larval stage. Severe Seawi knockdown resulted in an increased number of apoptotic cells in the entire gut area. CONCLUSION Piwi proteins appear to regulate PGC proliferation perhaps through control of Vasa accumulation. In this organism, Piwi is likely regulating mRNAs, not just transposons, and is potentially functioning both inside and outside of the germ line during embryogenesis.
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Affiliation(s)
- Mamiko Yajima
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 185 Meeting Street, BOX-GL173, Providence, RI 02912, USA
| | - Eric A. Gustafson
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 185 Meeting Street, BOX-GL173, Providence, RI 02912, USA
| | | | - Gary M. Wessel
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 185 Meeting Street, BOX-GL173, Providence, RI 02912, USA
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Yao Y, Ma L, Jia Q, Deng W, Liu Z, Zhang Y, Ren J, Xue Y, Jia H, Yang Q. Systematic characterization of small RNAome during zebrafish early developmental stages. BMC Genomics 2014; 15:117. [PMID: 24507755 PMCID: PMC3932949 DOI: 10.1186/1471-2164-15-117] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 02/07/2014] [Indexed: 11/16/2022] Open
Abstract
Background During early vertebrate development, various small non-coding RNAs (sRNAs) such as MicroRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs) are dynamically expressed for orchestrating the maternal-to-zygotic transition (MZT). Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development. Results We first determined the expression profiles of sRNAs during eight distinct stages of early zebrafish development by sRNA-seq technology. Integrative analyses with a new computational platform of CSZ (characterization of small RNAome for zebrafish) demonstrated an sRNA class transition from piRNAs to miRNAs as development proceeds. We observed that both the abundance and diversity of miRNAs are gradually increased, while the abundance is enhanced more dramatically than the diversity during development. However, although both the abundance and diversity of piRNAs are gradually decreased, the diversity was firstly increased then rapidly decreased. To evaluate the computational accuracy, the expression levels of four known miRNAs were experimentally validated. We also predicted 25 potentially novel miRNAs, whereas two candidates were verified by Northern blots. Conclusions Taken together, our analyses revealed the piRNA to miRNA transition as a conserved mechanism in zebrafish, although two different types of sRNAs exhibit distinct expression dynamics in abundance and diversity, respectively. Our study not only generated a better understanding for sRNA regulations in early zebrafish development, but also provided a useful platform for analyzing sRNA-seq data. The CSZ was implemented in Perl and freely downloadable at: http://csz.biocuckoo.org.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Haibo Jia
- Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
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Identification and profiling of sex-biased microRNAs from sea urchin Strongylocentrotus nudus gonad by Solexa deep sequencing. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2014; 10:1-8. [PMID: 24486540 DOI: 10.1016/j.cbd.2014.01.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 12/23/2013] [Accepted: 01/02/2014] [Indexed: 02/03/2023]
Abstract
MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs that regulate gene expression by post-transcriptional repression of messenger RNA. The echinoderm, Strongylocentrotus nudus, is an excellent model organism for studying development and commercially important as a food source. However, to date no miRNAs have been reported to modulate sex gonad differentiation in S. nudus. In this study, we constructed two small RNA libraries from male and female S. nudus gonad respectively for Solexa sequencing. A total of 184 miRNAs including 60 known and 124 novel miRNAs were identified from the two libraries. Furthermore, the nucleotide bias and end variation of the known miRNAs were also analyzed. In addition, 67 differently expressed of the 86 co-expressed and 98 gender-specific (47 male-specific and 51 female-specific) miRNAs that may be involved in sexual differentiation were found by comparing the miRNA expression profiles in the two libraries. This study reveals the first miRNA profile related to the gonad differentiation of the S. nudus. This study gives a first insight into sex differences in miRNA expression of sea urchin which could facilitate studies of the reproductive organ-specific roles of miRNAs.
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Timescales and bottlenecks in miRNA-dependent gene regulation. Mol Syst Biol 2013; 9:711. [PMID: 24301800 PMCID: PMC3882800 DOI: 10.1038/msb.2013.68] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 10/30/2013] [Indexed: 11/08/2022] Open
Abstract
Application of a kinetic model of miRNA-mediated gene regulation to experimental data sets shows that the timescale of regulation is slower than previously assumed, due to bottlenecks imposed by miRNA turnover in the RNA-induced silencing complex and by slow protein decay. ![]()
A mathematical model links the dynamics of miRNA expression and loading into the Argonaute protein to the dynamics of miRNA targets. Loading of miRNAs into Argonaute and the slow decay of proteins impose two bottlenecks on the speed of miRNA-mediated regulation. Accelerated miRNA turnover is necessary for regulating target expression on the timescale of a day.
MiRNAs are post-transcriptional regulators that contribute to the establishment and maintenance of gene expression patterns. Although their biogenesis and decay appear to be under complex control, the implications of miRNA expression dynamics for the processes that they regulate are not well understood. We derived a mathematical model of miRNA-mediated gene regulation, inferred its parameters from experimental data sets, and found that the model describes well time-dependent changes in mRNA, protein and ribosome density levels measured upon miRNA transfection and induction. The inferred parameters indicate that the timescale of miRNA-dependent regulation is slower than initially thought. Delays in miRNA loading into Argonaute proteins and the slow decay of proteins relative to mRNAs can explain the typically small changes in protein levels observed upon miRNA transfection. For miRNAs to regulate protein expression on the timescale of a day, as miRNAs involved in cell-cycle regulation do, accelerated miRNA turnover is necessary.
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OULHEN NATHALIE, WESSEL GARYM. Retention of exogenous mRNAs selectively in the germ cells of the sea urchin requires only a 5'-cap and a 3'-UTR. Mol Reprod Dev 2013; 80:561-9. [PMID: 23686945 PMCID: PMC4379035 DOI: 10.1002/mrd.22193] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 04/30/2013] [Indexed: 12/26/2022]
Abstract
The abundance of an mRNA in a cell depends on its overall rates of synthesis and decay. RNA stability is an important element in the regulation of gene expression, and is achieved by a variety of processes including specific recruitment of nucleases and RNAi-associated mechanisms. These mechanisms are particularly important in stem cells, which, in many cases, have attenuated transcription. Here we report that exogenous mRNA injected into fertilized eggs of the sea urchin is selectively retained in the small micromeres, which contribute to the germ line in this organism, beginning in blastulae, when compared to adjacent somatic cells. We show that modification of this exogenous RNA using cap analogs and poly-adenosine tail deletions do not affect its selective retention in the small micromeres, but removal of the cap or of the 3'-untranslated region eliminates any selective mRNA retention in the presumptive germ line. Our results illuminate a likely ancient mechanism used by stem cells to prolong the lifespan of RNAs-either through RNA protection or by the absence of basic RNA degradation mechanisms, which are employed by most other cells of an organism.
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Affiliation(s)
- NATHALIE OULHEN
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - GARY M. WESSEL
- Department of Molecular and Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
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Oulhen N, Yoshida T, Yajima M, Song JL, Sakuma T, Sakamoto N, Yamamoto T, Wessel GM. The 3'UTR of nanos2 directs enrichment in the germ cell lineage of the sea urchin. Dev Biol 2013; 377:275-83. [PMID: 23357540 DOI: 10.1016/j.ydbio.2013.01.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Revised: 01/15/2013] [Accepted: 01/18/2013] [Indexed: 12/30/2022]
Abstract
Nanos is a translational regulator required for the survival and maintenance of primordial germ cells during embryogenesis. Three nanos homologs are present in the genome of the sea urchin Strongylocentrotus purpuratus (Sp), and each nanos mRNA accumulates specifically in the small micromere (sMic) lineage. We found that a highly conserved element in the 3' UTR of nanos2 is sufficient for reporter expression selectively in the sMic lineage: microinjection into a Sp fertilized egg of an RNA that contains the GFP open reading frame followed by Sp nanos2 3'UTR leads to selective reporter enrichment in the small micromeres in blastulae. The same result was seen with nanos2 from the sea urchin Hemicentrotus pulcherrimus (Hp). In both species, the 5'UTR alone is not sufficient for the sMic localization but it always increased the sMic reporter enrichment when present with the 3'UTR. We defined an element conserved between Hp and Sp in the nanos2 3'UTR which is necessary and sufficient for protein enrichment in the sMic, and refer to it as GNARLE (Global Nanos Associated RNA Lability Element). We also found that the nanos2 3'UTR is essential for the selective RNA retention in the small micromeres; GNARLE is required but not sufficient for this process. These results show that a combination of selective RNA retention and translational control mechanisms instills nanos accumulation uniquely in the sMic lineage.
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Affiliation(s)
- Nathalie Oulhen
- Department of Molecular and Cell Biology and Biochemistry, Brown University, 185 Meeting Street, Providence, RI 02912, USA
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Bobbs AS, Saarela AV, Yatskievych TA, Antin PB. Fibroblast growth factor (FGF) signaling during gastrulation negatively modulates the abundance of microRNAs that regulate proteins required for cell migration and embryo patterning. J Biol Chem 2012; 287:38505-14. [PMID: 22995917 PMCID: PMC3493895 DOI: 10.1074/jbc.m112.400598] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 09/19/2012] [Indexed: 01/08/2023] Open
Abstract
FGF signaling plays a pivotal role in regulating cell movements and lineage induction during gastrulation. Here we identify 44 microRNAs that are expressed in the primitive streak region of gastrula stage chicken embryos. We show that the primary effect of FGF signaling on microRNA abundance is to negatively regulate the levels of miR-let-7b, -9, -19b, -107, -130b, and -218. LIN28B inhibits microRNA processing and is positively regulated by FGF signaling. Gain- and loss-of-function experiments show that LIN28B negatively regulates the expression of miR-19b, -130b, and let-7b, whereas negative modulation of miR-9, -107, and -218 appears to be independent of LIN28B function. Predicted mRNA targets of the FGF-regulated microRNAs are over-represented in serine/threonine and tyrosine kinase receptors, including ACVR1, ACVR2B, PDGFRA, TGFBR1, and TGFBR3. Luciferase assays show that these and other candidates are targeted by FGF-regulated microRNAs. PDGFRA, a receptor whose activity is required for cell migration through the primitive streak, is a target of miR-130b and -218 in vivo. These results identify a novel mechanism by which FGF signaling regulates gene expression by negatively modulating microRNA abundance through both LIN28B-dependent and LIN28B-independent pathways.
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Affiliation(s)
| | | | | | - Parker B. Antin
- From the Departments of Molecular and Cellular Biology and
- Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona 85724
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Li C, Feng W, Qiu L, Xia C, Su X, Jin C, Zhou T, Zeng Y, Li T. Characterization of skin ulceration syndrome associated microRNAs in sea cucumber Apostichopus japonicus by deep sequencing. FISH & SHELLFISH IMMUNOLOGY 2012; 33:436-441. [PMID: 22626809 DOI: 10.1016/j.fsi.2012.04.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 04/24/2012] [Accepted: 04/24/2012] [Indexed: 06/01/2023]
Abstract
MicroRNAs (miRNAs) constitute a family of small RNA species which have been demonstrated to be one of key effectors in mediating host-pathogen interaction. In this study, two haemocytes miRNA libraries were constructed with deep sequenced by illumina Hiseq2000 from healthy (L1) and skin ulceration syndrome Apostichopus japonicus (L2). The high throughput solexa sequencing resulted in 9,579,038 and 7,742,558 clean data from L1 and L2, respectively. Sequences analysis revealed that 40 conserved miRNAs were found in both libraries, in which let-7 and mir-125 were speculated to be clustered together and expressed accordingly. Eighty-six miRNA candidates were also identified by reference genome search and stem-loop structure prediction. Importantly, mir-31 and mir-2008 displayed significant differential expression between the two libraries according to FPKM model, which might be considered as promising targets for elucidating the intrinsic mechanism of skin ulceration syndrome outbreak in the species.
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Affiliation(s)
- Chenghua Li
- School of Marine Science, Ningbo University, Ningbo, Zhejiang Province, PR China.
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