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Guirandy N, Armant O, Frelon S, Pierron F, Geffroy B, Daffe G, Houdelet C, Gonzalez P, Simon O. Altered ovarian transcriptome is linked to early mortality and abnormalities in zebrafish embryos after maternal exposure to gamma irradiation. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 262:106660. [PMID: 37633173 DOI: 10.1016/j.aquatox.2023.106660] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 08/03/2023] [Accepted: 08/10/2023] [Indexed: 08/28/2023]
Abstract
Recent laboratory studies focusing on multigenerational approach demonstrated drastic phenotypic effects after chronic fish irradiation exposure. No irradiation effect at phenotypic scale was observed for F0 (reproductive performances) while early mortality and malformations were observed in F1 offspring whether they were irradiated or not. The objective was to study molecular mechanisms likely to be involved in these phenotypic effects induced by parental irradiation. Thus, F0 adult zebrafish were irradiated for ten days until reproduction and maternal involvement in offspring development was assessed. Levels of maternal provided cortisol and vitellogenin, needed for embryo development, were not impacted by irradiation. However, maternal transcriptome highlighted irradiation effect on processes involved in oocyte development, as well as on essential maternal factors needed for offspring development. Therefore, this study highlighted the importance of parental exposure on offspring fate and of the importance of multigenerational exposure in risk assessment.
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Affiliation(s)
- Noëmie Guirandy
- IRSN/PSE-ENV/SRTE/LECO, Centre de Cadarache-B.P. 3, Bat 183, St Paul Lez Durance 13115, France.
| | - Olivier Armant
- IRSN/PSE-ENV/SRTE/LECO, Centre de Cadarache-B.P. 3, Bat 183, St Paul Lez Durance 13115, France
| | - Sandrine Frelon
- IRSN/PSE-ENV/SRTE/LECO, Centre de Cadarache-B.P. 3, Bat 183, St Paul Lez Durance 13115, France
| | - Fabien Pierron
- University Bordeaux, CNRS, EPOC, EPHE, UMR 5805, Pessac F-33600, France
| | - Benjamin Geffroy
- MARBEC, University Montpellier, CNRS, Ifremer, IRD, Palavas-Les-Flots, France
| | - Guillemine Daffe
- University Bordeaux, CNRS, EPOC, EPHE, UMR 5805, Pessac F-33600, France
| | - Camille Houdelet
- MARBEC, University Montpellier, CNRS, Ifremer, IRD, Palavas-Les-Flots, France
| | - Patrice Gonzalez
- University Bordeaux, CNRS, EPOC, EPHE, UMR 5805, Pessac F-33600, France
| | - Olivier Simon
- IRSN/PSE-ENV/SRTE/LECO, Centre de Cadarache-B.P. 3, Bat 183, St Paul Lez Durance 13115, France
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2
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Liu Z, Wang W, Li X, Zhao X, Zhao H, Yang W, Zuo Y, Cai L, Xing Y. Temporal Dynamic Analysis of Alternative Splicing During Embryonic Development in Zebrafish. Front Cell Dev Biol 2022; 10:879795. [PMID: 35874832 PMCID: PMC9304896 DOI: 10.3389/fcell.2022.879795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing is pervasive in mammalian genomes and involved in embryo development, whereas research on crosstalk of alternative splicing and embryo development was largely restricted to mouse and human and the alternative splicing regulation during embryogenesis in zebrafish remained unclear. We constructed the alternative splicing atlas at 18 time-course stages covering maternal-to-zygotic transition, gastrulation, somitogenesis, pharyngula stages, and post-fertilization in zebrafish. The differential alternative splicing events between different developmental stages were detected. The results indicated that abundance alternative splicing and differential alternative splicing events are dynamically changed and remarkably abundant during the maternal-to-zygotic transition process. Based on gene expression profiles, we found splicing factors are expressed with specificity of developmental stage and largely expressed during the maternal-to-zygotic transition process. The better performance of cluster analysis was achieved based on the inclusion level of alternative splicing. The biological function analysis uncovered the important roles of alternative splicing during embryogenesis. The identification of isoform switches of alternative splicing provided a new insight into mining the regulated mechanism of transcript isoforms, which always is hidden by gene expression. In conclusion, we inferred that alternative splicing activation is synchronized with zygotic genome activation and discovered that alternative splicing is coupled with transcription during embryo development in zebrafish. We also unveiled that the temporal expression dynamics of splicing factors during embryo development, especially co-orthologous splicing factors. Furthermore, we proposed that the inclusion level of alternative splicing events can be employed for cluster analysis as a novel parameter. This work will provide a deeper insight into the regulation of alternative splicing during embryogenesis in zebrafish.
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Affiliation(s)
- Zhe Liu
- The Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Wei Wang
- The Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Xinru Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, China
- Digital College, Inner Mongolia Intelligent Union Big Data Academy, Inner Mongolia Wesure Date Technology Co., Ltd., Hohhot, China
| | - Xiujuan Zhao
- The Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Hongyu Zhao
- The Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Wuritu Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, China
- Hohhot Science and Technology Bureau, Hohhot, China
| | - Yongchun Zuo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, China
- Digital College, Inner Mongolia Intelligent Union Big Data Academy, Inner Mongolia Wesure Date Technology Co., Ltd., Hohhot, China
| | - Lu Cai
- The Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Yongqiang Xing
- The Inner Mongolia Key Laboratory of Functional Genome Bioinformatics, School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
- *Correspondence: Yongqiang Xing,
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Fu J, Zhu W, Wang L, Luo M, Jiang B, Dong Z. Dynamic Expression and Gene Regulation of MicroRNAs During Bighead Carp (Hypophthalmichthys nobilis) Early Development. Front Genet 2022; 12:821403. [PMID: 35126475 PMCID: PMC8809360 DOI: 10.3389/fgene.2021.821403] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/30/2021] [Indexed: 11/13/2022] Open
Abstract
The early development of fish is regulated through dynamic and complex mechanisms involving the regulation of various genes. Many genes are subjected to post-transcriptional regulation by microRNAs (miRNAs). In the Chinese aquaculture industry, the native species bighead carp (Hypophthalmichthys nobilis) is important. However, the genetic regulation related to the early development of bighead carp is unknown. Here, we generated developmental profiles by miRNA sequencing to study the dynamic regulation of miRNAs during bighead carp early development. This study identified 1 046 miRNAs, comprising 312 known miRNAs and 734 uncharacterized miRNAs. Changes in miRNA expression were identified in the six early development stages. An obviously increased expression trend was detected during the development process, with the main burst of activity occurring after the earliest stage (early blastula, DS1). Investigations revealed that several miRNAs were dominantly expressed during the development process, especially in the later stages (e.g., miR-10b-5p, miR-21, miR-92a-3p, miR-206-3p, and miR-430a-3p), suggesting that these miRNAs exerted important functions during embryonic development. The differentially expressed miRNAs (DEMs) and time-serial analysis (profiles) of DEMs were analyzed. A total of 372 miRNAs were identified as DEMs (fold-change >2, and false discovery rate <0.05), and three expression profiles of the DEMs were detected to have co-expression patterns (r > 0.7, and p < 0.05). The broad negative regulation of target genes by miRNAs was speculated, and many development-related biological processes and pathways were enriched for the targets of the DEMs, which might be associated with maternal genome degradation and embryogenesis processes. In conclusion, we revealed the repertoire of miRNAs that are active during early development of bighead carp. These findings will increase our understanding of the regulatory mechanisms of early development of fish.
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Affiliation(s)
- Jianjun Fu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Wuxi, China
| | - Wenbin Zhu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Wuxi, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Lanmei Wang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Wuxi, China
| | - Mingkun Luo
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Wuxi, China
| | - Bingjie Jiang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Zaijie Dong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Wuxi, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
- *Correspondence: Zaijie Dong, ,
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Martín L, Kamstra JH, Hurem S, Lindeman LC, Brede DA, Aanes H, Babiak I, Arenal A, Oughton D, Salbu B, Lyche JL, Aleström P. Altered non-coding RNA expression profile in F 1 progeny 1 year after parental irradiation is linked to adverse effects in zebrafish. Sci Rep 2021; 11:4142. [PMID: 33602989 PMCID: PMC7893006 DOI: 10.1038/s41598-021-83345-3] [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: 10/10/2020] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
Gamma radiation produces DNA instability and impaired phenotype. Previously, we observed negative effects on phenotype, DNA methylation, and gene expression profiles, in offspring of zebrafish exposed to gamma radiation during gametogenesis. We hypothesize that previously observed effects are accompanied with changes in the expression profile of non-coding RNAs, inherited by next generations. Non-coding RNA expression profile was analysed in F1 offspring (5.5 h post-fertilization) by high-throughput sequencing 1 year after parental irradiation (8.7 mGy/h, 5.2 Gy total dose). Using our previous F1-γ genome-wide gene expression data (GSE98539), hundreds of mRNAs were predicted as targets of differentially expressed (DE) miRNAs, involved in pathways such as insulin receptor, NFkB and PTEN signalling, linking to apoptosis and cancer. snRNAs belonging to the five major spliceosomal snRNAs were down-regulated in the F1-γ group, Indicating transcriptional and post-transcriptional alterations. In addition, DEpiRNA clusters were associated to 9 transposable elements (TEs) (LTR, LINE, and TIR) (p = 0.0024), probable as a response to the activation of these TEs. Moreover, the expression of the lincRNAs malat-1, and several others was altered in the offspring F1, in concordance with previously observed phenotypical alterations. In conclusion, our results demonstrate diverse gamma radiation-induced alterations in the ncRNA profiles of F1 offspring observable 1 year after parental irradiation.
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Affiliation(s)
- Leonardo Martín
- grid.441252.40000 0000 9526 034XMorphophysiology Department, Faculty of Agricultural Sciences, University of Camagüey Ignacio Agramonte y Loynaz, 74 650 Camagüey, Cuba ,grid.19477.3c0000 0004 0607 975XCERAD CoE, Department of Paraclinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway
| | - Jorke H. Kamstra
- grid.19477.3c0000 0004 0607 975XCERAD CoE, Department of Paraclinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway ,grid.5477.10000000120346234Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Selma Hurem
- grid.19477.3c0000 0004 0607 975XCERAD CoE, Department of Paraclinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway ,grid.19477.3c0000 0004 0607 975XDepartment of Paraclinical Sciences, Norwegian University of Life Sciences, 0454 Oslo, Norway
| | - Leif C. Lindeman
- grid.19477.3c0000 0004 0607 975XCERAD CoE, Department of Paraclinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway ,grid.19477.3c0000 0004 0607 975XDepartment of Preclinical Sciences and Pathology, Norwegian University of Life Sciences, 0454 Oslo, Norway
| | - Dag A. Brede
- grid.19477.3c0000 0004 0607 975XCERAD CoE, Department of Paraclinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway ,grid.19477.3c0000 0004 0607 975XDepartment of Environmental Science, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Håvard Aanes
- grid.458778.1PatoGen AS, P.O.box 548, 6001 Ålesund, Norway
| | - Igor Babiak
- grid.465487.cFaculty of Biosciences and Aquaculture, Nord University, 8026 Bodø, Norway
| | - Amilcar Arenal
- grid.441252.40000 0000 9526 034XMorphophysiology Department, Faculty of Agricultural Sciences, University of Camagüey Ignacio Agramonte y Loynaz, 74 650 Camagüey, Cuba
| | - Deborah Oughton
- grid.19477.3c0000 0004 0607 975XCERAD CoE, Department of Paraclinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway ,grid.19477.3c0000 0004 0607 975XDepartment of Environmental Science, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Brit Salbu
- grid.19477.3c0000 0004 0607 975XCERAD CoE, Department of Paraclinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway ,grid.19477.3c0000 0004 0607 975XDepartment of Environmental Science, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Jan Ludvig Lyche
- grid.19477.3c0000 0004 0607 975XCERAD CoE, Department of Paraclinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway ,grid.19477.3c0000 0004 0607 975XDepartment of Paraclinical Sciences, Norwegian University of Life Sciences, 0454 Oslo, Norway
| | - Peter Aleström
- grid.19477.3c0000 0004 0607 975XCERAD CoE, Department of Paraclinical Sciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway ,grid.19477.3c0000 0004 0607 975XDepartment of Preclinical Sciences and Pathology, Norwegian University of Life Sciences, 0454 Oslo, Norway
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PlantMirP-Rice: An Efficient Program for Rice Pre-miRNA Prediction. Genes (Basel) 2020; 11:genes11060662. [PMID: 32570706 PMCID: PMC7349308 DOI: 10.3390/genes11060662] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/13/2020] [Accepted: 06/15/2020] [Indexed: 11/16/2022] Open
Abstract
Rice microRNAs (miRNAs) are important post-transcriptional regulation factors and play vital roles in many biological processes, such as growth, development, and stress resistance. Identification of these molecules is the basis of dissecting their regulatory functions. Various machine learning techniques have been developed to identify precursor miRNAs (pre-miRNAs). However, no tool is implemented specifically for rice pre-miRNAs. This study aims at improving prediction performance of rice pre-miRNAs by constructing novel features with high discriminatory power and developing a training model with species-specific data. PlantMirP-rice, a stand-alone random forest-based miRNA prediction tool, achieves a promising accuracy of 93.48% based on independent (unseen) rice data. Comparisons with other competitive pre-miRNA prediction methods demonstrate that plantMirP-rice performs better than existing tools for rice and other plant pre-miRNA classification.
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Sarropoulou E, Kaitetzidou E, Papandroulakis N, Tsalafouta A, Pavlidis M. Inventory of European Sea Bass ( Dicentrarchus labrax) sncRNAs Vital During Early Teleost Development. Front Genet 2019; 10:657. [PMID: 31404269 PMCID: PMC6670005 DOI: 10.3389/fgene.2019.00657] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/21/2019] [Indexed: 01/25/2023] Open
Abstract
During early animal ontogenesis, a plethora of small non-coding RNAs (sncRNAs) are greatly expressed and have been shown to be involved in several regulatory pathways vital to proper development. The rapid advancements in sequencing and computing methodologies in the last decade have paved the way for the production of sequencing data in a broad range of organisms, including teleost species. Consequently, this has led to the discovery of sncRNAs as well as the potentially novel roles of sncRNA in gene regulation. Among the several classes of sncRNAs, microRNAs (miRNAs) have, in particular, been shown to play a key role in development. The present work aims to identify the miRNAs that play important roles during early European sea bass (Dicentrarchus labrax) development. The European sea bass is a species of high commercial impact in European and especially Mediterranean aquaculture. This study reports, for the first time, the identification and characterization of small RNAs that play a part in the 10 developmental stages (from morula to all fins) of the European sea bass. From 10 developmental stages, more than 135 million reads, generated by next-generation sequencing, were retrieved from publicly available databases as well as newly generated. The analysis resulted in about 2,000 sample grouped reads, and their subsequently annotation revealed that the majority of transcripts belonged to the class of miRNAs followed by small nuclear RNAs and small nucleolar RNAs. The analysis of small RNA expression among the developmental stages under study revealed that miRNAs are active throughout development, with the main activity occurring after the earlier stages (morula and 50% epiboly) and at the later stages (first feeding, flexion, and all fins). Furthermore, investigating miRNAs exclusively expressed in one of the stages unraveled five miRNAs with a higher abundance only in the morula stage (miR-155, miR-430a, d1, d2, and miR-458), indicating possible important key roles of those miRNAs in further embryonic development. An additional target search showed putative miRNA-mRNA interactions with possible direct and indirect regulatory functions of the identified miRNAs.
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Affiliation(s)
- Elena Sarropoulou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Center for Marine Research, Heraklion, Greece
| | - Elizabet Kaitetzidou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Center for Marine Research, Heraklion, Greece
| | - Nikos Papandroulakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Center for Marine Research, Heraklion, Greece
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Facchin F, Alviano F, Canaider S, Bianconi E, Rossi M, Bonsi L, Casadei R, Biava PM, Ventura C. Early Developmental Zebrafish Embryo Extract to Modulate Senescence in Multisource Human Mesenchymal Stem Cells. Int J Mol Sci 2019; 20:ijms20112646. [PMID: 31146388 PMCID: PMC6600478 DOI: 10.3390/ijms20112646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/24/2019] [Accepted: 05/25/2019] [Indexed: 12/14/2022] Open
Abstract
Stem cells undergo senescence both in vivo, contributing to the progressive decline in self-healing mechanisms, and in vitro during prolonged expansion. Here, we show that an early developmental zebrafish embryo extract (ZF1) could act as a modulator of senescence in human mesenchymal stem cells (hMSCs) isolated from both adult tissues, including adipose tissue (hASCs), bone marrow (hBM-MSCs), dental pulp (hDP-MSCs), and a perinatal tissue such as the Wharton’s Jelly (hWJ-MSCs). In all the investigated hMSCs, ZF1 decreased senescence-associated β-galactosidase (SA β-gal) activity and enhanced the transcription of TERT, encoding the catalytic telomerase core. In addition, it was associated, only in hASCs, with a transcriptional induction of BMI1, a pleiotropic repressor of senescence. In hBM-MSCs, hDP-MSCs, and hWJ-MSCs, TERT over-expression was concomitant with a down-regulation of two repressors of TERT, TP53 (p53), and CDKN1A (p21). Furthermore, ZF1 increased the natural ability of hASCs to perform adipogenesis. These results indicate the chance of using ZF1 to modulate stem cell senescence in a source-related manner, to be potentially used as a tool to affect stem cell senescence in vitro. In addition, its anti-senescence action could also set the basis for future in vivo approaches promoting tissue rejuvenation bypassing stem cell transplantation.
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Affiliation(s)
- Federica Facchin
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy.
- National Laboratory of Molecular Biology and Stem Cell Bioengineering of the National Institute of Biostructures and Biosystems (NIBB)-Eldor Lab, at the Innovation Accelerator, CNR, Via Piero Gobetti 101, 40129 Bologna, Italy.
| | - Francesco Alviano
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy.
| | - Silvia Canaider
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy.
- National Laboratory of Molecular Biology and Stem Cell Bioengineering of the National Institute of Biostructures and Biosystems (NIBB)-Eldor Lab, at the Innovation Accelerator, CNR, Via Piero Gobetti 101, 40129 Bologna, Italy.
| | - Eva Bianconi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy.
- National Laboratory of Molecular Biology and Stem Cell Bioengineering of the National Institute of Biostructures and Biosystems (NIBB)-Eldor Lab, at the Innovation Accelerator, CNR, Via Piero Gobetti 101, 40129 Bologna, Italy.
| | - Martina Rossi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy.
| | - Laura Bonsi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy.
| | - Raffaella Casadei
- Department for Life Quality Studies (QuVi), University of Bologna, Corso D'Augusto 237, 47921 Rimini, Italy.
| | - Pier Mario Biava
- Scientific Institute of Research and Care Multimedica, Via Milanese 300, 20099 Sesto San Giovanni (Milano), Italy.
| | - Carlo Ventura
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Via Massarenti 9, 40138 Bologna, Italy.
- National Laboratory of Molecular Biology and Stem Cell Bioengineering of the National Institute of Biostructures and Biosystems (NIBB)-Eldor Lab, at the Innovation Accelerator, CNR, Via Piero Gobetti 101, 40129 Bologna, Italy.
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8
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Calcino AD, Fernandez-Valverde SL, Taft RJ, Degnan BM. Diverse RNA interference strategies in early-branching metazoans. BMC Evol Biol 2018; 18:160. [PMID: 30382896 PMCID: PMC6211395 DOI: 10.1186/s12862-018-1274-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 10/08/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Micro RNAs (miRNAs) and piwi interacting RNAs (piRNAs), along with the more ancient eukaryotic endogenous small interfering RNAs (endo-siRNAs) constitute the principal components of the RNA interference (RNAi) repertoire of most animals. RNAi in non-bilaterians - sponges, ctenophores, placozoans and cnidarians - appears to be more diverse than that of bilaterians, and includes structurally variable miRNAs in sponges, an enormous number of piRNAs in cnidarians and the absence of miRNAs in ctenophores and placozoans. RESULTS Here we identify thousands of endo-siRNAs and piRNAs from the sponge Amphimedon queenslandica, the ctenophore Mnemiopsis leidyi and the cnidarian Nematostella vectensis using a computational approach that clusters mapped small RNA sequences and annotates each cluster based on the read length and relative abundance of the constituent reads. This approach was validated on 11 small RNA libraries in Drosophila melanogaster, demonstrating the successful annotation of RNAi-associated loci with properties consistent with previous reports. In the non-bilaterians we uncover seven new miRNAs from Amphimedon and four from Nematostella as well as sub-populations of candidate cis-natural antisense transcript (cis-NAT) endo-siRNAs. We confirmed the absence of miRNAs in Mnemiopsis but detected an abundance of endo-siRNAs in this ctenophore. Analysis of putative piRNA structure suggests that conserved localised secondary structures in primary transcripts may be important for the production of mature piRNAs in Amphimedon and Nematostella, as is also the case for endo-siRNAs. CONCLUSION Together, these findings suggest that the last common ancestor of extant animals did not have the entrained RNAi system that typifies bilaterians. Instead it appears that bilaterians, cnidarians, ctenophores and sponges express unique repertoires and combinations of miRNAs, piRNAs and endo-siRNAs.
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Affiliation(s)
- Andrew D Calcino
- School of Biological Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.,Present address: Department of Integrative Zoology, University of Vienna, Althanstraße 1, 4A-1090, Vienna, Austria
| | - Selene L Fernandez-Valverde
- School of Biological Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.,Present address: CONACYT, Laboratorio Nacional de Genómica para la Biodiversidad (Langebio). CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Ryan J Taft
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4072, Australia.,Illumina Inc, San Diego, California, 92122, USA
| | - Bernard M Degnan
- School of Biological Sciences, University of Queensland, Brisbane, QLD, 4072, Australia.
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9
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Liu L, Zhu W, Liu J, Wang S, Jiang J. Identification and differential regulation of microRNAs during thyroid hormone-dependent metamorphosis in Microhyla fissipes. BMC Genomics 2018; 19:507. [PMID: 29954327 PMCID: PMC6025837 DOI: 10.1186/s12864-018-4848-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 05/31/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Anuran metamorphosis, which is obligatorily initiated and sustained by thyroid hormone (TH), is a dramatic example of extensive morphological, biochemical and cellular changes occurring during post-embryonic development. Thus, it provides an ideal model to understand the actions of the hormone and molecular mechanisms underlying these developmental and apoptotic processes. In addition to transcriptional factors, microRNAs (miRNAs) play key roles in diverse biological processes via post-transcriptional repression of mRNAs. However, the possible role of miRNAs in anuran metamorphosis is not well understood. Screening and identification of TH-responding miRNAs are required to reveal the integrated regulatory mechanisms of TH during metamorphosis. Given the specific role of TRs during M. fissipes metamorphosis and the characteristics of M. fissipes as an ideal model, Illumina sequencing technology was employed to get a full scope of miRNA in M. fissipes metamorphosis treated by T3. RESULTS Morphological and histological analysis revealed that 24 h T3 treatment M. fissipes tadpoles resembled that at the climax of natural metamorphosis. Thus, small RNA libraries were constructed from control and 24 h T3 treatment groups. A total of 164 conserved miRNAs and 36 predicted novel miRNAs were characterized. Furthermore, 5' first and ninth nucleotides of miRNAs were significantly enriched in U in our study. In all, 21 miRNAs were differentially expressed between the T3 and control groups (p < 0.01). A total of 10,206 unigenes were identified as target genes of these differentially expressed miRNAs. KEGG pathway analysis indicated that the most overrepresented miRNA target genes were enriched in the "PI3k-Akt signaling pathway". In addition, a network associated with the TH signaling pathway provides an opportunity to further understand the complex biological processes that occur in metamorphosis. CONCLUSIONS We identified a large number of miRNAs during M. fissipes metamorphosis, and 21 of them were differentially expressed in the two groups that represented two different metamorphic stages. These miRNAs may play important roles during metamorphosis. The study gives us clues for further studies of the mechanisms of anuran metamorphosis and provides a model to study the mechanism of TH-affected biological processes in humans.
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Affiliation(s)
- Lusha Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
| | - Wei Zhu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
| | - Jiongyu Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
| | - Shouhong Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jianping Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041 China
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10
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Zhang H, Ali A, Gao J, Ban R, Jiang X, Zhang Y, Shi Q. IsopiRBank: a research resource for tracking piRNA isoforms. Database (Oxford) 2018; 2018:5046757. [PMID: 29961820 PMCID: PMC6025188 DOI: 10.1093/database/bay059] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 05/16/2018] [Accepted: 05/28/2018] [Indexed: 11/24/2022]
Abstract
PIWI-interacting RNAs (piRNAs) are essential for transcriptional and post-transcriptional regulation of transposons and coding genes in germline. With the development of sequencing technologies, length variations of piRNAs have been identified in several species. However, the extent to which, piRNA isoforms exist, and whether these isoforms are functionally distinct from canonical piRNAs remain uncharacterized. Through data mining from 2154 datasets of small RNA sequencing data from four species (Homo sapiens, Mus musculus, Danio rerio and Drosophila melanogaster), we have identified 8 749 139 piRNA isoforms from 175 454 canonical piRNAs, and classified them on the basis of variations on 5' or 3' end via the alignment of isoforms with canonical sequence. We thus established a database named IsopiRBank. Each isoforms has detailed annotation as follows: normalized expression data, classification, spatiotemporal expression data and genome origin. Users can also select interested isoforms for further analysis, including target prediction and Enrichment analysis. Taken together, IsopiRBank is an interactive database that aims to present the first integrated resource of piRNA isoforms, and broaden the research of piRNA biology. IsopiRBank can be accessed at http://mcg.ustc.edu.cn/bsc/isopir/index.html without any registration or log in requirement. Database URL: http://mcg.ustc.edu.cn/bsc/isopir/index.html.
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Affiliation(s)
- Huan Zhang
- Hefei National Laboratory for Physical Sciences at Microscale, The First Affiliated Hospital of USTC, USTC-SJH Joint Center of Human Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Asim Ali
- Hefei National Laboratory for Physical Sciences at Microscale, The First Affiliated Hospital of USTC, USTC-SJH Joint Center of Human Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Jianing Gao
- Hefei National Laboratory for Physical Sciences at Microscale, The First Affiliated Hospital of USTC, USTC-SJH Joint Center of Human Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Rongjun Ban
- Hefei National Laboratory for Physical Sciences at Microscale, The First Affiliated Hospital of USTC, USTC-SJH Joint Center of Human Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Xiaohua Jiang
- Hefei National Laboratory for Physical Sciences at Microscale, The First Affiliated Hospital of USTC, USTC-SJH Joint Center of Human Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Yuanwei Zhang
- Hefei National Laboratory for Physical Sciences at Microscale, The First Affiliated Hospital of USTC, USTC-SJH Joint Center of Human Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
| | - Qinghua Shi
- Hefei National Laboratory for Physical Sciences at Microscale, The First Affiliated Hospital of USTC, USTC-SJH Joint Center of Human Reproduction and Genetics, The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, CAS Center for Excellence in Molecular Cell Science, University of Science and Technology of China, Collaborative Innovation Center of Genetics and Development, Collaborative Innovation Center for Cancer Medicine, Hefei, Anhui 230027, China
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11
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Alberti C, Cochella L. A framework for understanding the roles of miRNAs in animal development. Development 2017; 144:2548-2559. [PMID: 28720652 DOI: 10.1242/dev.146613] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
MicroRNAs (miRNAs) contribute to the progressive changes in gene expression that occur during development. The combined loss of all miRNAs results in embryonic lethality in all animals analyzed, illustrating the crucial role that miRNAs play collectively. However, although the loss of some individual miRNAs also results in severe developmental defects, the roles of many other miRNAs have been challenging to uncover. This has been mostly attributed to their proposed function as tuners of gene expression or providers of robustness. Here, we present a view of miRNAs in the context of development as a hierarchical and canalized series of gene regulatory networks. In this scheme, only a fraction of embryonic miRNAs act at the top of this hierarchy, with their loss resulting in broad developmental defects, whereas most other miRNAs are expressed with high cellular specificity and play roles at the periphery of development, affecting the terminal features of specialized cells. This view could help to shed new light on our understanding of miRNA function in development, disease and evolution.
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Affiliation(s)
- Chiara Alberti
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Luisa Cochella
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030 Vienna, Austria
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12
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Rauwerda H, Pagano JFB, de Leeuw WC, Ensink W, Nehrdich U, de Jong M, Jonker M, Spaink HP, Breit TM. Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos. BMC Genomics 2017; 18:287. [PMID: 28399811 PMCID: PMC5387192 DOI: 10.1186/s12864-017-3672-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 03/29/2017] [Indexed: 02/08/2023] Open
Abstract
Background Recently, much progress has been made in the field of gene-expression in early embryogenesis. However, the dynamic behaviour of transcriptomes in individual embryos has hardly been studied yet and the time points at which pools of embryos are collected are usually still quite far apart. Here, we present a high-resolution gene-expression time series with 180 individual zebrafish embryos, obtained from nine different spawns, developmentally ordered and profiled from late blastula to mid-gastrula stage. On average one embryo per minute was analysed. The focus was on identification and description of the transcriptome dynamics of the expressed genes in this embryonic stage, rather than to biologically interpret profiles in cellular processes and pathways. Results In the late blastula to mid-gastrula stage, we found 6,734 genes being expressed with low variability and rather gradual changes. Ten types of dynamic behaviour were defined, such as genes with continuously increasing or decreasing expression, and all expressed genes were grouped into these types. Also, the exact expression starting and stopping points of several hundred genes during this developmental period could be pinpointed. Although the resolution of the experiment was so high, that we were able to clearly identify four known oscillating genes, no genes were observed with a peaking expression. Additionally, several genes showed expression at two or three distinct levels that strongly related to the spawn an embryo originated from. Conclusion Our unique experimental set-up of whole-transcriptome analysis of 180 individual embryos, provided an unparalleled in-depth insight into the dynamics of early zebrafish embryogenesis. The existence of a tightly regulated embryonic transcriptome program, even between individuals from different spawns is shown. We have made the expression profile of all genes available for domain experts. The fact that we were able to separate the different spawns by their gene-expression variance over all expressed genes, underlines the importance of spawn specificity, as well as the unexpectedly tight gene-expression regulation in early zebrafish embryogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3672-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Han Rauwerda
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Johanna F B Pagano
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Wim C de Leeuw
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Wim Ensink
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Ulrike Nehrdich
- Institute Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Mark de Jong
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands.,Present address: GenomeScan B.V., Plesmanlaan, Leiden, The Netherlands
| | - Martijs Jonker
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Herman P Spaink
- Institute Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Timo M Breit
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands. .,Institute Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands. .,MAD/AB&RB, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
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13
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Svoboda P, Fulka H, Malik R. Clearance of Parental Products. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 953:489-535. [DOI: 10.1007/978-3-319-46095-6_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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14
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Yao Y, Ma C, Deng H, Liu Q, Zhang J, Yi M. plantMirP: an efficient computational program for the prediction of plant pre-miRNA by incorporating knowledge-based energy features. MOLECULAR BIOSYSTEMS 2016; 12:3124-31. [PMID: 27472470 DOI: 10.1039/c6mb00295a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
MicroRNAs are a predominant type of small non-coding RNAs approximately 21 nucleotides in length that play an essential role at the post-transcriptional level by either RNA degradation, translational repression or both through an RNA-induced silencing complex. Identification of these molecules can aid the dissecting of their regulatory functions. The secondary structures of plant pre-miRNAs are much more complex than those of animal pre-miRNAs. In contrast to prediction tools for animal pre-miRNAs, much less effort has been contributed to plant pre-miRNAs. In this study, a set of novel knowledge-based energy features that has very high discriminatory power is proposed and incorporated with the existing features for specifically distinguishing the hairpins of real/pseudo plant pre-miRNAs. A promising performance area under a receiver operating characteristic curve of 0.9444 indicates that 5 knowledge-based energy features have very high discriminatory power. The 10-fold cross-validation result demonstrates that plantMirP with full features has a promising sensitivity of 92.61% and a specificity of 98.88%. Based on various different datasets, it was found that plantMirP has a higher prediction performance by comparison with miPlantPreMat, PlantMiRNAPred, triplet-SVM, and microPred. Meanwhile, plantMirP can greatly balance sensitivity and specificity for real/pseudo plant pre-miRNAs. Taken together, we developed a promising SVM-based program, plantMirP, for predicting plant pre-miRNAs by incorporating knowledge-based energy features. This study shows it to be a valuable tool for miRNA-related studies.
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Affiliation(s)
- Yuangen Yao
- Department of Physics, College of Science, Huazhong Agricultural University, Wuhan, Hubei, China.
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15
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Deng H, Liu Q, Cao W, Gui R, Ma C, Yi M, Yao Y. qiRNApredictor: A Novel Computational Program for the Prediction of qiRNAs in Neurospora crassa. PLoS One 2016; 11:e0159487. [PMID: 27428111 PMCID: PMC4948831 DOI: 10.1371/journal.pone.0159487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 07/05/2016] [Indexed: 11/18/2022] Open
Abstract
Recently, a new type of small interfering RNAs (qiRNAs) of typically 20~21 nucleotides was found in Neurospora crassa and rice and has been shown to regulate gene silencing in the DNA damage response. Identification of qiRNAs is fundamental for dissecting regulatory functions and molecular mechanisms. In contrast to other expensive and time-consuming experimental methods, the computational prediction of qiRNAs is a conveniently rapid method for gaining valuable information for a subsequent experimental verification. However, no tool existed to date for the prediction of qiRNAs. To this purpose, we developed the novel qiRNA prediction software package qiRNApredictor. This software demonstrates a promising sensitivity of 93.55% and a specificity of 71.61% from the leave-one-out validation. These studies might be beneficial for further experimental investigation. Furthermore, the local package of qiRNApredictor was implemented and made freely available to the academic community at Supplementary material.
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Affiliation(s)
- Haiyou Deng
- Department of Physics, College of Science, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Quan Liu
- Department of Physics, College of Science, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Wei Cao
- Department of Physics, College of Science, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Rong Gui
- Department of Physics, College of Science, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chengzhang Ma
- Department of Physics, College of Science, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ming Yi
- Department of Physics, College of Science, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yuangen Yao
- Department of Physics, College of Science, Huazhong Agricultural University, Wuhan, Hubei, China
- * E-mail:
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16
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D'Aurizio R, Russo F, Chiavacci E, Baumgart M, Groth M, D'Onofrio M, Arisi I, Rainaldi G, Pitto L, Pellegrini M. Discovering miRNA Regulatory Networks in Holt-Oram Syndrome Using a Zebrafish Model. Front Bioeng Biotechnol 2016; 4:60. [PMID: 27471727 PMCID: PMC4943955 DOI: 10.3389/fbioe.2016.00060] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 06/24/2016] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that play an important role in the post-transcriptional regulation of gene expression. miRNAs are involved in the regulation of many biological processes such as differentiation, apoptosis, and cell proliferation. miRNAs are expressed in embryonic, postnatal, and adult hearts, and they have a key role in the regulation of gene expression during cardiovascular development and disease. Aberrant expression of miRNAs is associated with abnormal cardiac cell differentiation and dysfunction. Tbx5 is a member of the T-box gene family, which acts as transcription factor involved in the vertebrate heart development. Alteration of Tbx5 level affects the expression of hundreds of genes. Haploinsufficiency and gene duplication of Tbx5 are at the basis of the cardiac abnormalities associated with Holt–Oram syndrome (HOS). Recent data indicate that miRNAs might be an important part of the regulatory circuit through which Tbx5 controls heart development. Using high-throughput technologies, we characterized genome-widely the miRNA and mRNA expression profiles in WT- and Tbx5-depleted zebrafish embryos at two crucial developmental time points, 24 and 48 h post fertilization (hpf). We found that several miRNAs, which are potential effectors of Tbx5, are differentially expressed; some of them are already known to be involved in cardiac development and functions, such as miR-30, miR-34, miR-190, and miR-21. We performed an integrated analysis of miRNA expression data with gene expression profiles to refine computational target prediction approaches by means of the inversely correlation of miRNA–mRNA expressions, and we highlighted targets, which have roles in cardiac contractility, cardiomyocyte proliferation/apoptosis, and morphogenesis, crucial functions regulated by Tbx5. This approach allowed to discover complex regulatory circuits involving novel miRNAs and protein coding genes not considered before in the HOS such as miR-34a and miR-30 and their targets.
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Affiliation(s)
- Romina D'Aurizio
- Laboratory of Integrative Systems Medicine (LISM), Institute of Informatics and Telematics (IIT), Institute of Clinical Physiology (IFC), National Research Council (CNR) , Pisa , Italy
| | - Francesco Russo
- Laboratory of Integrative Systems Medicine (LISM), Institute of Informatics and Telematics (IIT), Institute of Clinical Physiology (IFC), National Research Council (CNR), Pisa, Italy; Department of Computer Science, University of Pisa, Pisa, Italy
| | - Elena Chiavacci
- Institute of Clinical Physiology (IFC), National Research Council (CNR) , Pisa , Italy
| | - Mario Baumgart
- Leibniz Institute on Ageing, Fritz Lipmann Institute (FLI) , Jena , Germany
| | - Marco Groth
- Leibniz Institute on Ageing, Fritz Lipmann Institute (FLI) , Jena , Germany
| | - Mara D'Onofrio
- Genomics Facility, Fondazione EBRI Rita Levi-Montalcini , Roma , Italy
| | - Ivan Arisi
- Genomics Facility, Fondazione EBRI Rita Levi-Montalcini , Roma , Italy
| | - Giuseppe Rainaldi
- Laboratory of Integrative Systems Medicine (LISM), Institute of Informatics and Telematics (IIT), Institute of Clinical Physiology (IFC), National Research Council (CNR) , Pisa , Italy
| | - Letizia Pitto
- Institute of Clinical Physiology (IFC), National Research Council (CNR) , Pisa , Italy
| | - Marco Pellegrini
- Laboratory of Integrative Systems Medicine (LISM), Institute of Informatics and Telematics (IIT), Institute of Clinical Physiology (IFC), National Research Council (CNR) , Pisa , Italy
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17
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Rauwerda H, Wackers P, Pagano JFB, de Jong M, Ensink W, Dekker R, Nehrdich U, Spaink HP, Jonker M, Breit TM. Mother-Specific Signature in the Maternal Transcriptome Composition of Mature, Unfertilized Zebrafish Eggs. PLoS One 2016; 11:e0147151. [PMID: 26799215 PMCID: PMC4723340 DOI: 10.1371/journal.pone.0147151] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 12/28/2015] [Indexed: 12/19/2022] Open
Abstract
Maternal mRNA present in mature oocytes plays an important role in the proper development of the early embryo. As the composition of the maternal transcriptome in general has been studied with pooled mature eggs, potential differences between individual eggs are unknown. Here we present a transcriptome study on individual zebrafish eggs from clutches of five mothers in which we focus on the differences in maternal mRNA abundance per gene between and within clutches. To minimize technical interference, we used mature, unfertilized eggs from siblings. About half of the number of analyzed genes was found to be expressed as maternal RNA. The expressed and non-expressed genes showed that maternal mRNA accumulation is a non-random process, as it is related to specific biological pathways and processes relevant in early embryogenesis. Moreover, it turned out that overall the composition of the maternal transcriptome is tightly regulated as about half of the expressed genes display a less than twofold expression range between the observed minimum and maximum expression values of a gene in the experiment. Even more, the maximum gene-expression difference within clutches is for 88% of the expressed genes lower than twofold. This means that expression differences observed in maternally expressed genes are primarily caused by differences between mothers, with only limited variability between eggs from the same mother. This was underlined by the fact that 99% of the expressed genes were found to be differentially expressed between any of the mothers in an ANOVA test. Furthermore, linking chromosome location, transcription factor binding sites, and miRNA target sites of the genes in clusters of distinct and unique mother-specific gene-expression, suggest biological relevance of the mother-specific signatures in the maternal transcriptome composition. Altogether, the maternal transcriptome composition of mature zebrafish oocytes seems to be tightly regulated with a distinct mother-specific signature.
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Affiliation(s)
- Han Rauwerda
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Paul Wackers
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Johanna F. B. Pagano
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Mark de Jong
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Wim Ensink
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Rob Dekker
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Ulrike Nehrdich
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, the Netherlands
| | - Herman P. Spaink
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, the Netherlands
| | - Martijs Jonker
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
| | - Timo M. Breit
- RNA Biology & Applied Bioinformatics research group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, the Netherlands
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18
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Jia KT, Zhang J, Jia P, Zeng L, Jin Y, Yuan Y, Chen J, Hong Y, Yi M. Identification of MicroRNAs in Zebrafish Spermatozoa. Zebrafish 2015; 12:387-97. [PMID: 26418264 DOI: 10.1089/zeb.2015.1115] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) participate in almost all biological processes. Plenty of evidences show that some testis- or spermatozoa-specific miRNAs play crucial roles in the process of gonad and germ cell development. In this study, the spermatozoa miRNA profiles were investigated through a combination of illumina deep sequencing and bioinformatics analysis in zebrafish. Deep sequencing of small RNAs yielded 11,820,680 clean reads. By mapping to the zebrafish genome, we identified 400 novel and 204 known miRNAs that could be grouped into 104 families. Furthermore, we selected the six highest expressions of known miRNAs to detect their expression patterns in different tissues by stem-loop quantitative real-time polymerase chain reaction. We found that among the six miRNAs, dre-miR-202-5p displayed specific and high expression in zebrafish spermatozoa and testis. Fluorescence in situ hybridization analysis indicated that dre-miR-202-5p was predominantly expressed in all kind of germ cells at different spermatogenetic stages, including spermatogonia and spermatozoa, but barely expressed in the germ cells in the ovary. This sex-biased expression pattern suggests that dre-miR-202-5p might be related to spermatogenesis and the functioning of spermatozoa. The identification of miRNAs in zebrafish spermatozoa and germ cells offers new insights into the spermatogenesis and spermatozoa in the teleost and other vertebrates.
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Affiliation(s)
- Kun-Tong Jia
- 1 School of Marine Sciences, Sun Yat-sen University , Guangzhou, China .,2 Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University , Guangzhou, China .,3 South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Sun Yat-sen University , Guangzhou, China
| | - Jing Zhang
- 1 School of Marine Sciences, Sun Yat-sen University , Guangzhou, China .,2 Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University , Guangzhou, China .,3 South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Sun Yat-sen University , Guangzhou, China
| | - Peng Jia
- 1 School of Marine Sciences, Sun Yat-sen University , Guangzhou, China .,2 Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University , Guangzhou, China .,3 South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Sun Yat-sen University , Guangzhou, China
| | - Lin Zeng
- 1 School of Marine Sciences, Sun Yat-sen University , Guangzhou, China .,2 Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University , Guangzhou, China .,3 South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Sun Yat-sen University , Guangzhou, China
| | - Yilin Jin
- 1 School of Marine Sciences, Sun Yat-sen University , Guangzhou, China .,2 Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University , Guangzhou, China .,3 South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Sun Yat-sen University , Guangzhou, China
| | - Yongming Yuan
- 4 Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Jieying Chen
- 1 School of Marine Sciences, Sun Yat-sen University , Guangzhou, China .,2 Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University , Guangzhou, China
| | - Yunhan Hong
- 4 Department of Biological Sciences, National University of Singapore , Singapore, Singapore
| | - Meisheng Yi
- 1 School of Marine Sciences, Sun Yat-sen University , Guangzhou, China .,2 Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Sun Yat-sen University , Guangzhou, China .,3 South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, Sun Yat-sen University , Guangzhou, China
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Svoboda P, Franke V, Schultz RM. Sculpting the Transcriptome During the Oocyte-to-Embryo Transition in Mouse. Curr Top Dev Biol 2015; 113:305-49. [PMID: 26358877 DOI: 10.1016/bs.ctdb.2015.06.004] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In mouse, the oocyte-to-embryo transition entails converting a highly differentiated oocyte to totipotent blastomeres. This transition is driven by degradation of maternal mRNAs, which results in loss of oocyte identity, and reprogramming of gene expression during the course of zygotic gene activation, which occurs primarily during the two-cell stage and confers blastomere totipotency. Full-grown oocytes are transcriptionally quiescent and mRNAs are remarkably stable in oocytes due to the RNA-binding protein MSY2, which stabilizes mRNAs, and low activity of the 5' and 3' RNA degradation machinery. Oocyte maturation initiates a transition from mRNA stability to instability due to phosphorylation of MSY2, which makes mRNAs more susceptible to the RNA degradation machinery, and recruitment of dormant maternal mRNAs that encode for critical components of the 5' and 3' RNA degradation machinery. Small RNAs (miRNA, siRNA, and piRNA) play little, if any, role in mRNA degradation that occurs during maturation. Many mRNAs are totally degraded but a substantial fraction is only partially degraded, their degradation completed by the end of the two-cell stage. Genome activation initiates during the one-cell stage, is promiscuous, low level, and genome wide (and includes both inter- and intragenic regions) and produces transcripts that are inefficiently spliced and polyadenylated. The major wave of genome activation in two-cell embryos involves expression of thousands of new genes. This unique pattern of gene expression is the product of maternal mRNAs recruited during maturation that encode for transcription factors and chromatin remodelers, as well as dramatic changes in chromatin structure due to incorporation of histone variants and modified histones.
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Affiliation(s)
- Petr Svoboda
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
| | - Vedran Franke
- Bioinformatics Group, Division of Biology, Faculty of Science, Zagreb University, Zagreb, Croatia
| | - Richard M Schultz
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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Biggar KK, Storey KB. New Approaches to Comparative and Animal Stress Biology Research in the Post-genomic Era: A Contextual Overview. Comput Struct Biotechnol J 2014; 11:138-46. [PMID: 25408848 PMCID: PMC4232569 DOI: 10.1016/j.csbj.2014.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/07/2014] [Accepted: 09/11/2014] [Indexed: 02/06/2023] Open
Abstract
Although much is known about the physiological responses of many environmental stresses in tolerant animals, studies evaluating the regulation of stress-induced mechanisms that regulate the transitions to and from this state are beginning to explore new and fascinating areas of molecular research. Current findings have developed a general, but refined, view of the important molecular pathways contributing to stress-survival. However, studies utilizing newly developed technologies that broadly focus on genomic and proteomic screening are beginning to identify many new targets for future study. This minireview will provide a contextual overview on the use of DNA/RNA sequencing, microRNA annotation and prediction software, protein structure and function prediction tools, as well as methods of high-throughput protein expression analysis. We will also use select examples to highlight the existing use of these technologies in stress biology research. Such tools can be used in comparative stress biology in the characterization of animal responses to environmental challenges. Although there are many areas of study left to be explored, research in comparative stress biology will always be continuing as new technologies allow the further analysis of cell function, and new paradigms in gene regulation and regulatory molecules (such as microRNAs) are continuing to be discovered. Building upon the findings of past research, while utilizing new technologies in the appropriate manner, future studies can be carried out in new and exciting areas still unexplored. Proper use of rapidly developing technologies will help to create a complete understanding of the animal stress response and survival mechanisms utilized by many diverse organisms.
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Affiliation(s)
| | - Kenneth B. Storey
- Institute of Biochemistry, Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON K1S 5B6, Canada
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