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Gautam S, Fenner JL, Wang B, Range RC. Evolutionarily conserved Wnt/Sp5 signaling is critical for anterior-posterior axis patterning in sea urchin embryos. iScience 2024; 27:108616. [PMID: 38179064 PMCID: PMC10765061 DOI: 10.1016/j.isci.2023.108616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/30/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Studies across a diverse group of metazoan embryos indicate that Wnt signaling often activates the transcription factor Sp5, forming a signaling 'cassette' that plays critical roles in many developmental processes. This study explores the role of Wnt/Sp5 signaling during the specification and patterning of the primary germ layers during early anterior-posterior axis formation in the deuterostome sea urchin embryo. Our functional analyses show that Sp5 is critical for endomesoderm specification downstream of Wnt/β-catenin in posterior cells as well as anterior neuroectoderm patterning downstream of non-canonical Wnt/JNK signaling in anterior cells. Interestingly, expression and functional data comparisons show that Wnt/Sp5 signaling often plays similar roles in posterior endomesoderm as well as neuroectoderm patterning along the AP axis of several deuterostome embryos, including vertebrates. Thus, our findings provide strong support for the idea that Wnt-Sp5 signaling cassettes were critical for the establishment of early germ layers in the common deuterostome ancestor.
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Affiliation(s)
- Sujan Gautam
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Jennifer L. Fenner
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Boyuan Wang
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
| | - Ryan C. Range
- Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA
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2
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Shang Y, Zhang S, Cheng Y, Feng G, Dong Y, Li H, Fan S. Tetrabromobisphenol a exacerbates the overall radioactive hazard to zebrafish (Danio rerio). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 316:120424. [PMID: 36272602 DOI: 10.1016/j.envpol.2022.120424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/05/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
The major health risks of dual exposure to two hazardous factors of plastics and radioactive contamination are obscure. In the present study, we systematically evaluated the combinational toxic effects of tetrabromobisphenol A (TBBPA), one of the most influential plastic ingredients, mainly from electronic wastes, and γ-irradiation in zebrafish for the first time. TBBPA (0.25 μg/mL for embryos and larvae, 300 μg/L for adults) contamination aggravated the radiation (6 Gy for embryos and larvae, 20 Gy for adults)-induced early dysplasia and aberrant angiogenesis of embryos, further impaired the locomotor vitality of irradiated larvae, and worsened the radioactive multiorganic histologic injury, neurobehavioural disturbances and dysgenesis of zebrafish adults as well as the inter-generational neurotoxicity in offspring. TBBPA exaggerated the radiative toxic effects not only by enhancing the inflammatory and apoptotic response but also by further unbalancing the endocrine system and disrupting the underlying gene expression profiles. In conclusion, TBBPA exacerbates radiation-induced injury in zebrafish, including embryos, larvae, adults and even the next generation. Our findings provide new insights into the toxicology of TBBPA and γ-irradiation, shedding light on the severity of cocontamination of MP components and radioactive substances and thereby inspiring novel remediation and rehabilitation strategies for radiation-injured aqueous organisms and radiotherapy patients.
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Affiliation(s)
- Yue Shang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, 238 Baidi Road, 300192, Tianjin, China
| | - Shuqin Zhang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, 238 Baidi Road, 300192, Tianjin, China
| | - Yajia Cheng
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, 238 Baidi Road, 300192, Tianjin, China
| | - Guoxing Feng
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, 238 Baidi Road, 300192, Tianjin, China
| | - Yinping Dong
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, 238 Baidi Road, 300192, Tianjin, China
| | - Hang Li
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, 238 Baidi Road, 300192, Tianjin, China
| | - Saijun Fan
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, 238 Baidi Road, 300192, Tianjin, China.
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3
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Zhu B, He W, Hu S, Kong R, Yang L. The fate and oxidative stress of different sized SiO 2 nanoparticles in zebrafish (Danio rerio) larvae. CHEMOSPHERE 2019; 225:705-712. [PMID: 30904758 DOI: 10.1016/j.chemosphere.2019.03.091] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 06/09/2023]
Abstract
Nanoparticle such as silicon dioxide nanoparticles (nano-SiO2) are extensively produced and applied in society. Hence there is an increasing concern about their exposure and toxicity to human and wildlife. To understand the effects of sizes of NPs on their bioavailability and toxicity, zebrafish (Danio rerio) embryos (2 h post-fertilization, hpf) were exposed to 25, 50 and 100 mg/L of 15 or 30 nm nano-SiO2 for 5 days respectively. The results showed that SiO2 could be readily uptaken by zebrafish, and the accumulation of SiO2 was significantly higher in 15 nm treatments groups compared to 30 nm nano-SiO2 treated groups. Furthermore, exposure to 15 nm nano-SiO2 at the concentration of 100 mg/L resulted in more significant changes in reactive oxygen species (ROS) levels, perturbation of lipid peroxidative and antioxidant system than the same concentration of 30 nm nano-SiO2, indicating small sized nano-SiO2 evoked severer oxidative stress in zebrafish larvae. In addition, the more significant up-regulation of transcription of genes related to oxidative stress (e.g., nrf2 and sod1) in 15 nm nano-SiO2 at the 100 mg/L treatments groups provided more evidence for this speculation. Given the above, 15 nm nano-SiO2 were more likely to enter and accumulate in zebrafish larvae, thus causing more serious oxidative stress in vivo. These results may provide additional information on the fate and toxicities of different sizes of NPs.
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Affiliation(s)
- Biran Zhu
- School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan, 430065, China.
| | - Wei He
- School of Computer Science and Information Engineering, Hubei University, Wuhan, 430062, China
| | - Shengchao Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ren Kong
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lihua Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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Neitzel LR, Spencer ZT, Nayak A, Cselenyi CS, Benchabane H, Youngblood CQ, Zouaoui A, Ng V, Stephens L, Hann T, Patton JG, Robbins D, Ahmed Y, Lee E. Developmental regulation of Wnt signaling by Nagk and the UDP-GlcNAc salvage pathway. Mech Dev 2019; 156:20-31. [PMID: 30904594 DOI: 10.1016/j.mod.2019.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 11/19/2022]
Abstract
In a screen for human kinases that regulate Xenopus laevis embryogenesis, we identified Nagk and other components of the UDP-GlcNAc glycosylation salvage pathway as regulators of anteroposterior patterning and Wnt signaling. We find that the salvage pathway does not affect other major embryonic signaling pathways (Fgf, TGFβ, Notch, or Shh), thereby demonstrating specificity for Wnt signaling. We show that the role of the salvage pathway in Wnt signaling is evolutionarily conserved in zebrafish and Drosophila. Finally, we show that GlcNAc is essential for the growth of intestinal enteroids, which are highly dependent on Wnt signaling for growth and maintenance. We propose that the Wnt pathway is sensitive to alterations in the glycosylation state of a cell and acts as a nutritional sensor in order to couple growth/proliferation with its metabolic status. We also propose that the clinical manifestations observed in congenital disorders of glycosylation (CDG) in humans may be due, in part, to their effects on Wnt signaling during development.
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Affiliation(s)
- Leif R Neitzel
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA; Program in Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Zachary T Spencer
- Department of Molecular and Systems Biology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - Anmada Nayak
- Sylvester Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Christopher S Cselenyi
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA; Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hassina Benchabane
- Department of Molecular and Systems Biology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - CheyAnne Q Youngblood
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA; Department of Natural Science, Northeastern State University, Tahlequah, OK 74464, USA
| | - Alya Zouaoui
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Victoria Ng
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Leah Stephens
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Trevor Hann
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - David Robbins
- Sylvester Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Yashi Ahmed
- Department of Molecular and Systems Biology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - Ethan Lee
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA; Program in Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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5
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Peter IS. Methods for the experimental and computational analysis of gene regulatory networks in sea urchins. Methods Cell Biol 2018; 151:89-113. [PMID: 30948033 DOI: 10.1016/bs.mcb.2018.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The discovery of gene regulatory networks (GRNs) has opened a gate to access the genomic mechanisms controlling development. GRNs are systems of transcriptional regulatory circuits that control the differential specification of cell fates during development by regulating gene expression. The experimental analysis of GRNs involves a collection of methods, each revealing aspects of the overall control process. This review provides an overview of experimental and computational methods that have been successfully applied for solving developmental GRNs in the sea urchin embryo. The key in this approach is to obtain experimental evidence for functional interactions between transcription factors and regulatory DNA. In the second part of this review, a more generally applicable strategy is discussed that shows a path from experimental evidence to annotation of regulatory linkages to the generation of GRN models.
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Affiliation(s)
- Isabelle S Peter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States.
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6
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Liu Z, Woo S, Weiner OD. Nodal signaling has dual roles in fate specification and directed migration during germ layer segregation in zebrafish. Development 2018; 145:dev.163535. [PMID: 30111654 DOI: 10.1242/dev.163535] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 07/30/2018] [Indexed: 12/21/2022]
Abstract
During gastrulation, endodermal cells actively migrate to the interior of the embryo, but the signals that initiate and coordinate this migration are poorly understood. By transplanting ectopically induced endodermal cells far from the normal location of endoderm specification, we identified the inputs that drive internalization without the confounding influences of fate specification and global morphogenic movements. We find that Nodal signaling triggers an autocrine circuit for initiating endodermal internalization. Activation of the Nodal receptor directs endodermal specification through sox32 and also induces expression of more Nodal ligands. These ligands act in an autocrine fashion to initiate endodermal cell sorting. Our work defines an 'AND' gate consisting of sox32-dependent endodermal specification and Nodal ligand reception controlling endodermal cell sorting to the inner layer of the embryo at the onset of gastrulation.
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Affiliation(s)
- Zairan Liu
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Stephanie Woo
- Department of Molecular Cell Biology, School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Orion D Weiner
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA .,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
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7
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Ghosh P, Maurer JM, Sagerström CG. Analysis of novel caudal hindbrain genes reveals different regulatory logic for gene expression in rhombomere 4 versus 5/6 in embryonic zebrafish. Neural Dev 2018; 13:13. [PMID: 29945667 PMCID: PMC6020313 DOI: 10.1186/s13064-018-0112-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 06/19/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Previous work aimed at understanding the gene regulatory networks (GRNs) governing caudal hindbrain formation identified morphogens such as Retinoic Acid (RA) and Fibroblast growth factors (FGFs), as well as transcription factors like hoxb1b, hoxb1a, hnf1ba, and valentino as being required for rhombomere (r) r4-r6 formation in zebrafish. Considering that the caudal hindbrain is relatively complex - for instance, unique sets of neurons are formed in each rhombomere segment - it is likely that additional essential genes remain to be identified and integrated into the caudal hindbrain GRN. METHODS By taking advantage of gene expression data available in the Zebrafish Information Network (ZFIN), we identified 84 uncharacterized genes that are expressed in r4-r6. We selected a representative set of 22 genes and assayed their expression patterns in hoxb1b, hoxb1a, hnf1b, and valentino mutants with the goal of positioning them in the caudal hindbrain GRN. We also investigated the effects of RA and FGF on the expression of this gene set. To examine whether these genes are necessary for r4-r6 development, we analyzed germline mutants for six of the genes (gas6, gbx1, sall4, eglf6, celf2, and greb1l) for defects in hindbrain development. RESULTS Our results reveal that r4 gene expression is unaffected by the individual loss of hoxb1b, hoxb1a or RA, but is under the combinatorial regulation of RA together with hoxb1b. In contrast, r5/r6 gene expression is dependent on RA, FGF, hnf1ba and valentino - as individual loss of these factors abolishes r5/r6 gene expression. Our analysis of six mutant lines did not reveal rhombomere or neuronal defects, but transcriptome analysis of one line (gas6 mutant) identified expression changes for genes involved in several developmental processes - suggesting that these genes may have subtle roles in hindbrain development. CONCLUSION We conclude that r4-r6 formation is relatively robust, such that very few genes are absolutely required for this process. However, there are mechanistic differences in r4 versus r5/r6, such that no single factor is required for r4 development while several genes are individually required for r5/r6 formation.
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Affiliation(s)
- Priyanjali Ghosh
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St/LRB815, Worcester, MA, USA
| | - Jennifer M Maurer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St/LRB815, Worcester, MA, USA
| | - Charles G Sagerström
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St/LRB815, Worcester, MA, USA.
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8
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Zhu B, Zhao G, Yang L, Zhou B. Tetrabromobisphenol A caused neurodevelopmental toxicity via disrupting thyroid hormones in zebrafish larvae. CHEMOSPHERE 2018; 197:353-361. [PMID: 29407805 DOI: 10.1016/j.chemosphere.2018.01.080] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/14/2018] [Accepted: 01/16/2018] [Indexed: 05/27/2023]
Abstract
Tetrabromobisphenol A (TBBPA), one of the most widely used brominated flame retardants (BFRs), has resulted in worldwide environmental contamination. TBBPA has been reported as a thyroid endocrine disruptor and a potential neurotoxicant. However, the underlying mechanism is still not clear. In this study, zebrafish (Danio rerio) embryos (2 h post-fertilization, hpf) were exposed to different concentrations of TBBPA (50, 100, 200 and 400 μg/L) alone or in combination with 3,3',5-triiodo-l-thyronine (T3, 20 μg/L + TBBPA, 200 μg/L). The results confirmed that TBBPA could evoke thyroid disruption by observations of increased T4 contents and decreased T3 contents, accompanied by up-regulated tshβ, tg mRNA and down-regulated ttr and trβ mRNA levels in zebafish larvae. TBBPA-induced neurodevelopmental toxicity was also indicated by down-regulated transcription of genes related to central nervous system (CNS) development (e.g., α1-tubulin, mbp and shha), and decreased locomotor activity and average swimming speed. Our results further demonstrated that treatment with T3 could reverse or eliminate TBBPA-induced effects on thyroidal and neurodevelopmental parameters. Given the above, we hypothesize that the observed neurodevelopmental toxicity in the present study could be attributed to the thyroid hormone disruptions by TBBPA.
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Affiliation(s)
- Biran Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; Department of Basic Medicine, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Gang Zhao
- Department of Basic Medicine, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Lihua Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Bingsheng Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
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9
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Miccoli A, Dalla Valle L, Carnevali O. The maternal control in the embryonic development of zebrafish. Gen Comp Endocrinol 2017; 245:55-68. [PMID: 27013380 DOI: 10.1016/j.ygcen.2016.03.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/16/2016] [Accepted: 03/19/2016] [Indexed: 12/13/2022]
Abstract
The maternal control directing the very first hours of life is of pivotal importance for ensuring proper development to the growing embryo. Thanks to the finely regulated inheritance of maternal factors including mRNAs and proteins produced during oogenesis and stored into the mature oocyte, the embryo is sustained throughout the so-called maternal-to-zygotic transition, a period in development characterized by a species-specific length in time, during which critical biological changes regarding cell cycle and zygotic transcriptional activation occur. In order not to provoke any kind of persistent damage, the process must be delicately balanced. Surprisingly, our knowledge as to the possible effects of beneficial bacteria regarding the modulation of the quality and/or quantity of both maternally-supplied and zygotically-transcribed mRNAs, is very limited. To date, only one group has investigated the consequences of the parentally-supplied Lactobacillus rhamnosus on the storage of mRNAs into mature oocytes, leading to an altered maternal control process in the F1 generation. Particular attention was called on the monitoring of several biomarkers involved in autophagy, apoptosis and axis patterning, while data on miRNA generation and pluripotency maintenance are herein presented for the first time, and can assist in laying the ground for further investigations in this field. In this review, the reader is supplied with the current knowledge on the above-mentioned biological process, first by drawing the general background and then by emphasizing the most important findings that have highlighted their focal role in normal animal development.
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Affiliation(s)
- Andrea Miccoli
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| | | | - Oliana Carnevali
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy.
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10
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Cobbina SJ, Mao G, Zhao T, Xu H, Zhang Z, Liu H, Zou Y, Wu X, Yang L. Modulation of N-Methyl-D-Aspartate Receptors (NMDAR), Bcl-2 and C-Fos Gene Expressions on Exposure to Individual and Mixtures of Low Concentration Metals in Zebrafish (Danio rerio). ARCHIVES OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2017; 72:418-427. [PMID: 28255683 DOI: 10.1007/s00244-016-0352-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 12/21/2016] [Indexed: 06/06/2023]
Abstract
Currently, there is limited information on the toxicity of low concentration of metal mixtures in the environment. Of particular interest is the effect of low levels of metal mixtures on neurodevelopment of aquatic organisms. This study reports the neurological gene expressions after exposing zebrafish embryos to low concentration toxic heavy metals, 120 h post fertilization (hpf). Embryos were exposed to low concentration individual and mixtures of lead (Pb), mercury (Hg), arsenic (As), and cadmium (Cd). Quantitative real-time PCR was used to assess gene expressions. The findings of this study confirmed that exposure to low concentration heavy metals upregulated N-methyl-D-aspartate (NMDA) receptor subunits NMDAR2A (NR2A), NMDAR2B (NR2B), and NMDAR2D (NR2D) and B cell lymphoma (Bcl-2) genes. NR2A genes were significantly upregulated by 90 and 74%, respectively, on exposure to Pb + As and Pb + Cd. NR2B genes were upregulated by 85.3, 68.6, 62.7, and 62.7% on exposure to As, Pb + Hg, Pb + As, and Pb + Cd, respectively. Exposure to As, Pb + Cd, and Pb + Hg + As significantly upregulated Bcl-2 genes by 2.01-, 1.84-, and 1.80-fold, respectively. NR1A and C-fos gene expressions were not significantly different from control. Upregulation of NMDAR subunits and Bcl-2 genes in this study was largely a counter measure against insults from exposure to low concentration heavy metals. Principal component analysis confirmed the influence of low concentration individual and mixtures of Pb, Hg, As, and Cd on gene expression of NMDAR subunits and Bcl-2. These data suggest that altered expression of NMDA receptor subunits and Bcl-2 genes may explain toxicity of low concentration individual and mixtures of Pb, Hg, As, and Cd.
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Affiliation(s)
- Samuel Jerry Cobbina
- School of the Environment and Safety Engineering, Jiangsu University, Xuefu Rd. 301, Zhenjiang, 212013, Jiangsu, China
| | - Guanghua Mao
- School of the Environment and Safety Engineering, Jiangsu University, Xuefu Rd. 301, Zhenjiang, 212013, Jiangsu, China
| | - Ting Zhao
- School of Chemistry and Chemical Engineering, Jiangsu University, Xuefu Rd. 301, Zhenjiang, 212013, China
| | - Hai Xu
- School of the Environment and Safety Engineering, Jiangsu University, Xuefu Rd. 301, Zhenjiang, 212013, Jiangsu, China
| | - Zhen Zhang
- School of the Environment and Safety Engineering, Jiangsu University, Xuefu Rd. 301, Zhenjiang, 212013, Jiangsu, China
| | - Hongyang Liu
- School of the Environment and Safety Engineering, Jiangsu University, Xuefu Rd. 301, Zhenjiang, 212013, Jiangsu, China
| | - Yanmin Zou
- School of the Environment and Safety Engineering, Jiangsu University, Xuefu Rd. 301, Zhenjiang, 212013, Jiangsu, China
| | - Xiangyang Wu
- School of the Environment and Safety Engineering, Jiangsu University, Xuefu Rd. 301, Zhenjiang, 212013, Jiangsu, China.
| | - Liuqing Yang
- School of Chemistry and Chemical Engineering, Jiangsu University, Xuefu Rd. 301, Zhenjiang, 212013, China
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11
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Félix LM, Serafim C, Valentim AM, Antunes LM, Campos S, Matos M, Coimbra AM. Embryonic Stage-Dependent Teratogenicity of Ketamine in Zebrafish (Danio rerio). Chem Res Toxicol 2016; 29:1298-309. [DOI: 10.1021/acs.chemrestox.6b00122] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Luís M. Félix
- Centre
for the Research and Technology of Agro-Environmental and Biological
Sciences (CITAB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
- Laboratory
Animal Science (LAS), Institute for Molecular and Cell Biology (IBMC), University of Porto (UP), Porto, Portugal
- Institute
for Research and Innovation in Health (i3S), University of Porto (UP), Porto, Portugal
| | - Cindy Serafim
- Life
Sciences and Environment School (ECVA), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - Ana M. Valentim
- Centre
for the Research and Technology of Agro-Environmental and Biological
Sciences (CITAB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
- Laboratory
Animal Science (LAS), Institute for Molecular and Cell Biology (IBMC), University of Porto (UP), Porto, Portugal
- Institute
for Research and Innovation in Health (i3S), University of Porto (UP), Porto, Portugal
| | - Luís M. Antunes
- Centre
for the Research and Technology of Agro-Environmental and Biological
Sciences (CITAB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
- Laboratory
Animal Science (LAS), Institute for Molecular and Cell Biology (IBMC), University of Porto (UP), Porto, Portugal
- Institute
for Research and Innovation in Health (i3S), University of Porto (UP), Porto, Portugal
- School
of Agrarian and Veterinary Sciences (ECAV), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - Sónia Campos
- Centre
for the Research and Technology of Agro-Environmental and Biological
Sciences (CITAB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
- Laboratory
Animal Science (LAS), Institute for Molecular and Cell Biology (IBMC), University of Porto (UP), Porto, Portugal
- Institute
for Research and Innovation in Health (i3S), University of Porto (UP), Porto, Portugal
| | - Manuela Matos
- Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, Lisboa, Portugal
- Department
of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - Ana M. Coimbra
- Centre
for the Research and Technology of Agro-Environmental and Biological
Sciences (CITAB), University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
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12
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Perry KJ, Lyons DC, Truchado-Garcia M, Fischer AHL, Helfrich LW, Johansson KB, Diamond JC, Grande C, Henry JQ. Deployment of regulatory genes during gastrulation and germ layer specification in a model spiralian mollusc Crepidula. Dev Dyn 2016. [PMID: 26197970 DOI: 10.1002/dvdy.24308] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND During gastrulation, endoderm and mesoderm are specified from a bipotential precursor (endomesoderm) that is argued to be homologous across bilaterians. Spiralians also generate mesoderm from ectodermal precursors (ectomesoderm), which arises near the blastopore. While a conserved gene regulatory network controls specification of endomesoderm in deuterostomes and ecdysozoans, little is known about genes controlling specification or behavior of either source of spiralian mesoderm or the digestive tract. RESULTS Using the mollusc Crepidula, we examined conserved regulatory factors and compared their expression to fate maps to score expression in the germ layers, blastopore lip, and digestive tract. Many genes were expressed in both ecto- and endomesoderm, but only five were expressed in ectomesoderm exclusively. The latter may contribute to epithelial-to-mesenchymal transition seen in ectomesoderm. CONCLUSIONS We present the first comparison of genes expressed during spiralian gastrulation in the context of high-resolution fate maps. We found variation of genes expressed in the blastopore lip, mouth, and cells that will form the anus. Shared expression of many genes in both mesodermal sources suggests that components of the conserved endomesoderm program were either co-opted for ectomesoderm formation or that ecto- and endomesoderm are derived from a common mesodermal precursor that became subdivided into distinct domains during evolution.
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Affiliation(s)
- Kimberly J Perry
- University of Illinois, Department of Cell and Developmental Biology, Urbana, Illinois
| | | | - Marta Truchado-Garcia
- Departamento de Biología Molecular and Centro de Biología Molecular, "Severo Ochoa" (CSIC, Universidad Autónoma de Madrid), Madrid, Spain
| | - Antje H L Fischer
- Department of Metabolic Biochemistry, Ludwig-Maximilians-University, Munich, Germany.,Marine Biological Laboratory, Woods Hole, Massachusetts
| | | | - Kimberly B Johansson
- Marine Biological Laboratory, Woods Hole, Massachusetts.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts
| | | | - Cristina Grande
- Departamento de Biología Molecular and Centro de Biología Molecular, "Severo Ochoa" (CSIC, Universidad Autónoma de Madrid), Madrid, Spain
| | - Jonathan Q Henry
- University of Illinois, Department of Cell and Developmental Biology, Urbana, Illinois
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13
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He B, Tan K. Understanding transcriptional regulatory networks using computational models. Curr Opin Genet Dev 2016; 37:101-108. [PMID: 26950762 DOI: 10.1016/j.gde.2016.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 01/29/2016] [Accepted: 02/08/2016] [Indexed: 01/06/2023]
Abstract
Transcriptional regulatory networks (TRNs) encode instructions for animal development and physiological responses. Recent advances in genomic technologies and computational modeling have revolutionized our ability to construct models of TRNs. Here, we survey current computational methods for inferring TRN models using genome-scale data. We discuss their advantages and limitations. We summarize representative TRNs constructed using genome-scale data in both normal and disease development. We discuss lessons learned about the structure/function relationship of TRNs, based on examining various large-scale TRN models. Finally, we outline some open questions regarding TRNs, including how to improve model accuracy by integrating complementary data types, how to infer condition-specific TRNs, and how to compare TRNs across conditions and species in order to understand their structure/function relationship.
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Affiliation(s)
- Bing He
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA
| | - Kai Tan
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA; Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA.
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14
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Paquette SM, Leinonen K, Longabaugh WJR. BioTapestry now provides a web application and improved drawing and layout tools. F1000Res 2016; 5:39. [PMID: 27134726 PMCID: PMC4841208 DOI: 10.12688/f1000research.7620.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/22/2015] [Indexed: 01/17/2023] Open
Abstract
Gene regulatory networks (GRNs) control embryonic development, and to understand this process in depth, researchers need to have a detailed understanding of both the network architecture and its dynamic evolution over time and space. Interactive visualization tools better enable researchers to conceptualize, understand, and share GRN models. BioTapestry is an established application designed to fill this role, and recent enhancements released in Versions 6 and 7 have targeted two major facets of the program. First, we introduced significant improvements for network drawing and automatic layout that have now made it much easier for the user to create larger, more organized network drawings. Second, we revised the program architecture so it could continue to support the current Java desktop Editor program, while introducing a new BioTapestry GRN Viewer that runs as a JavaScript web application in a browser. We have deployed a number of GRN models using this new web application. These improvements will ensure that BioTapestry remains viable as a research tool in the face of the continuing evolution of web technologies, and as our understanding of GRN models grows.
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15
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Shaped 3D singular spectrum analysis for quantifying gene expression, with application to the early zebrafish embryo. BIOMED RESEARCH INTERNATIONAL 2015; 2015:986436. [PMID: 26495320 PMCID: PMC4606214 DOI: 10.1155/2015/986436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Accepted: 05/01/2015] [Indexed: 02/08/2023]
Abstract
Recent progress in microscopy technologies, biological markers, and automated processing methods is making possible the development of gene expression atlases at cellular-level resolution over whole embryos. Raw data on gene expression is usually very noisy. This noise comes from both experimental (technical/methodological) and true biological sources (from stochastic biochemical processes). In addition, the cells or nuclei being imaged are irregularly arranged in 3D space. This makes the processing, extraction, and study of expression signals and intrinsic biological noise a serious challenge for 3D data, requiring new computational approaches. Here, we present a new approach for studying gene expression in nuclei located in a thick layer around a spherical surface. The method includes depth equalization on the sphere, flattening, interpolation to a regular grid, pattern extraction by Shaped 3D singular spectrum analysis (SSA), and interpolation back to original nuclear positions. The approach is demonstrated on several examples of gene expression in the zebrafish egg (a model system in vertebrate development). The method is tested on several different data geometries (e.g., nuclear positions) and different forms of gene expression patterns. Fully 3D datasets for developmental gene expression are becoming increasingly available; we discuss the prospects of applying 3D-SSA to data processing and analysis in this growing field.
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16
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Botman D, Jansson F, Röttinger E, Martindale MQ, de Jong J, Kaandorp JA. Analysis of a spatial gene expression database for sea anemone Nematostella vectensis during early development. BMC SYSTEMS BIOLOGY 2015; 9:63. [PMID: 26400098 PMCID: PMC4581490 DOI: 10.1186/s12918-015-0209-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 09/09/2015] [Indexed: 11/17/2022]
Abstract
Background The spatial distribution of many genes has been visualized during the embryonic development in the starlet sea anemone Nematostella vectensis in the last decade. In situ hybridization images are available in the Kahi Kai gene expression database, and a method has been developed to quantify spatial gene expression patterns of N. vectensis. In this paper, gene expression quantification is performed on a wide range of gene expression patterns from this database and descriptions of observed expression domains are stored in a separate database for further analysis. Methods Spatial gene expression from suitable in situ hybridization images has been quantified with the GenExp program. A correlation analysis has been performed on the resulting numerical gene expression profiles for each stage. Based on the correlated clusters of spatial gene expression and detailed descriptions of gene expression domains, various mechanisms for developmental gene expression are proposed. Results In the blastula and gastrula stages of development in N. vectensis, its continuous sheet of cells is partitioned into correlating gene expression domains. During progressing development, these regions likely correspond to different fates. A statistical analysis shows that genes generally remain expressed during the planula stages in those major regions that they occupy at the end of gastrulation. Discussion Observed shifts in gene expression domain boundaries suggest that elongation in the planula stage mainly occurs in the vegetal ring under the influence of the gene Rx. The secondary body axis in N. vectensis is proposed to be determined at the mid blastula transition. Conclusions Early gene expression domains in N. vectensis appear to maintain a positional order along the primary body axis. Early determination in N. vectensis occurs in two stages: expression in broad circles and rings in the blastula is consolidated during gastrulation, and more complex expression patterns appear in the planula within these broad regions. Quantification and comparison of gene expression patterns across a database can generate hypotheses about collective cell movements before these movements are measured directly. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0209-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel Botman
- Computational Science, University of Amsterdam, Science Park 904, Amsterdam, The Netherlands.
| | - Fredrik Jansson
- Computational Science, University of Amsterdam, Science Park 904, Amsterdam, The Netherlands.
| | - Eric Röttinger
- Université Nice Sophia Antipolis, Institute for Research on Cancer and Aging, Nice (IRCAN), UMR 7284, Nice, France. .,Centre National de la Recherche Scientifique (CNRS), Institute for Research on Cancer and Aging, Nice (IRCAN), UMR 7284, Nice, France. .,Institut National de la Santé et de la Recherche Médicale (INSERM), Institute for Research on Cancer and Aging, Nice (IRCAN), U1081, Nice, France.
| | - Mark Q Martindale
- Whitney Lab for Marine Bioscience, University of Florida, St. Augustine, FL, USA.
| | - Johann de Jong
- Computational Cancer Biology Group, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Jaap A Kaandorp
- Computational Science, University of Amsterdam, Science Park 904, Amsterdam, The Netherlands.
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17
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McCauley BS, Akyar E, Saad HR, Hinman VF. Dose-dependent nuclear β-catenin response segregates endomesoderm along the sea star primary axis. Development 2015; 142:207-17. [PMID: 25516976 DOI: 10.1242/dev.113043] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In many invertebrates, the nuclearization of β-catenin at one pole of the embryo initiates endomesoderm specification. An intriguing possibility is that a gradient of nuclear β-catenin (nβ-catenin), similar to that operating in vertebrate neural tube patterning, functions to distinguish cell fates in invertebrates. To test this hypothesis, we determined the function of nβ-catenin during the early development of the sea star, which undergoes a basal deuterostomal mode of embryogenesis. We show that low levels of nβ-catenin activity initiate bra, which is expressed in the future posterior endoderm-fated territory; intermediate levels are required for expression of foxa and gata4/5/6, which are later restricted to the endoderm; and activation of ets1 and erg in the mesoderm-fated territory requires the highest nβ-catenin activity. Transcription factors acting downstream of high nβ-catenin segregate the endoderm/mesoderm boundary, which is further reinforced by Delta/Notch signaling. Significantly, therefore, in sea stars, endomesoderm segregation arises through transcriptional responses to levels of nβ-catenin activity. Here, we describe the first empirical evidence of a dose-dependent response to a dynamic spatiotemporal nβ-catenin activity that patterns cell fates along the primary axis in an invertebrate.
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Affiliation(s)
- Brenna S McCauley
- Department of Biological Sciences, Carnegie Mellon University, 4400 5th Ave, Pittsburgh, PA 15213, USA
| | - Eda Akyar
- Department of Biological Sciences, Carnegie Mellon University, 4400 5th Ave, Pittsburgh, PA 15213, USA
| | - H Rosa Saad
- Department of Biological Sciences, Carnegie Mellon University, 4400 5th Ave, Pittsburgh, PA 15213, USA
| | - Veronica F Hinman
- Department of Biological Sciences, Carnegie Mellon University, 4400 5th Ave, Pittsburgh, PA 15213, USA
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18
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Tarrant AM, Gilmore TD, Reitzel AM, Levy O, Technau U, Martindale MQ. Current directions and future perspectives from the third Nematostella research conference. ZOOLOGY 2014; 118:135-40. [PMID: 25450665 DOI: 10.1016/j.zool.2014.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Revised: 06/16/2014] [Accepted: 06/17/2014] [Indexed: 12/16/2022]
Abstract
The third Nematostella vectensis Research Conference took place in December 2013 in Eilat, Israel, as a satellite to the 8th International Conference on Coelenterate Biology. The starlet sea anemone, N. vectensis, has emerged as a powerful cnidarian model, in large part due to the extensive genomic and transcriptomic resources and molecular approaches that are becoming available for Nematostella, which were the focus of several presentations. In addition, research was presented highlighting the broader utility of this species for studies of development, circadian rhythms, signal transduction, and gene-environment interactions.
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Affiliation(s)
- Ann M Tarrant
- Biology Department, Woods Hole Oceanographic Institution, 45 Water Street, Woods Hole, MA 02543, USA.
| | - Thomas D Gilmore
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA
| | - Adam M Reitzel
- Department of Biological Sciences, The University of North Carolina at Charlotte, Woodward Hall 245, Charlotte, NC 28223, USA
| | - Oren Levy
- The Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Ramat Gan 52900, Israel
| | - Ulrich Technau
- Department of Molecular Evolution and Development, University of Vienna, Althanstr. 14, A-1090 Vienna, Austria
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Boulevard, St. Augustine, FL 32136, USA
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19
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Castro-González C, Luengo-Oroz MA, Duloquin L, Savy T, Rizzi B, Desnoulez S, Doursat R, Kergosien YL, Ledesma-Carbayo MJ, Bourgine P, Peyriéras N, Santos A. A digital framework to build, visualize and analyze a gene expression atlas with cellular resolution in zebrafish early embryogenesis. PLoS Comput Biol 2014; 10:e1003670. [PMID: 24945246 PMCID: PMC4063669 DOI: 10.1371/journal.pcbi.1003670] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 04/28/2014] [Indexed: 01/30/2023] Open
Abstract
A gene expression atlas is an essential resource to quantify and understand the multiscale processes of embryogenesis in time and space. The automated reconstruction of a prototypic 4D atlas for vertebrate early embryos, using multicolor fluorescence in situ hybridization with nuclear counterstain, requires dedicated computational strategies. To this goal, we designed an original methodological framework implemented in a software tool called Match-IT. With only minimal human supervision, our system is able to gather gene expression patterns observed in different analyzed embryos with phenotypic variability and map them onto a series of common 3D templates over time, creating a 4D atlas. This framework was used to construct an atlas composed of 6 gene expression templates from a cohort of zebrafish early embryos spanning 6 developmental stages from 4 to 6.3 hpf (hours post fertilization). They included 53 specimens, 181,415 detected cell nuclei and the segmentation of 98 gene expression patterns observed in 3D for 9 different genes. In addition, an interactive visualization software, Atlas-IT, was developed to inspect, supervise and analyze the atlas. Match-IT and Atlas-IT, including user manuals, representative datasets and video tutorials, are publicly and freely available online. We also propose computational methods and tools for the quantitative assessment of the gene expression templates at the cellular scale, with the identification, visualization and analysis of coexpression patterns, synexpression groups and their dynamics through developmental stages. We propose a workflow to map the expression domains of multiple genes onto a series of 3D templates, or “atlas”, during early embryogenesis. It was applied to the zebrafish at different stages between 4 and 6.3 hpf, generating 6 templates. Our system overcomes the lack of significant morphological landmarks in early development by relying on the expression of a reference gene (goosecoid, gsc) and nuclear staining to guide the registration of the analyzed genes. The proposed method also successfully maps gene domains from partially imaged embryos, thus allowing greater microscope magnification and cellular resolution. By using the workflow to construct a spatiotemporal database of zebrafish, we opened the way to a systematic analysis of vertebrate embryogenesis. The atlas database, together with the mapping software (Match-IT), a custom-made visualization platform (Atlas-IT), and step-by-step user guides are available from the Supplementary Material. We expect that this will encourage other laboratories to generate, map, visualize and analyze new gene expression datasets.
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Affiliation(s)
- Carlos Castro-González
- Biomedical Image Technologies, ETSIT, Universidad Politécnica de Madrid, CEIMoncloa, Madrid, Spain
- Research Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
- Madrid-MIT M+Visión Consortium, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Miguel A. Luengo-Oroz
- Biomedical Image Technologies, ETSIT, Universidad Politécnica de Madrid, CEIMoncloa, Madrid, Spain
- Research Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Louise Duloquin
- MDAM UPR3294, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
- Institut des Systèmes Complexes, Paris, France
- BioEmergences-IBiSA, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
| | - Thierry Savy
- MDAM UPR3294, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
- Institut des Systèmes Complexes, Paris, France
- BioEmergences-IBiSA, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
| | - Barbara Rizzi
- MDAM UPR3294, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
- Institut des Systèmes Complexes, Paris, France
- BioEmergences-IBiSA, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
| | - Sophie Desnoulez
- MDAM UPR3294, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
- BioEmergences-IBiSA, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
| | - René Doursat
- Institut des Systèmes Complexes, Paris, France
- BioEmergences-IBiSA, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
- School of Biomedical Engineering, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Yannick L. Kergosien
- MDAM UPR3294, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
- BioEmergences-IBiSA, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
- LIMICS-INSERM UMR 1142, UFR SMBH, Université Paris 13, Bobigny, France
| | - María J. Ledesma-Carbayo
- Biomedical Image Technologies, ETSIT, Universidad Politécnica de Madrid, CEIMoncloa, Madrid, Spain
- Research Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Paul Bourgine
- MDAM UPR3294, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
- Institut des Systèmes Complexes, Paris, France
- BioEmergences-IBiSA, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
| | - Nadine Peyriéras
- MDAM UPR3294, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
- Institut des Systèmes Complexes, Paris, France
- BioEmergences-IBiSA, Institut de Neurobiologie Alfred Fessard, CNRS, Gif-sur-Yvette, France
- * E-mail: (NP); (AS)
| | - Andrés Santos
- Biomedical Image Technologies, ETSIT, Universidad Politécnica de Madrid, CEIMoncloa, Madrid, Spain
- Research Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
- * E-mail: (NP); (AS)
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20
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Hinman VF, Cheatle Jarvela AM. Developmental gene regulatory network evolution: insights from comparative studies in echinoderms. Genesis 2014; 52:193-207. [PMID: 24549884 DOI: 10.1002/dvg.22757] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/10/2014] [Accepted: 02/12/2014] [Indexed: 12/17/2022]
Abstract
One of the central concerns of Evolutionary Developmental biology is to understand how the specification of cell types can change during evolution. In the last decade, developmental biology has progressed toward a systems level understanding of cell specification processes. In particular, the focus has been on determining the regulatory interactions of the repertoire of genes that make up gene regulatory networks (GRNs). Echinoderms provide an extraordinary model system for determining how GRNs evolve. This review highlights the comparative GRN analyses arising from the echinoderm system. This work shows that certain types of GRN subcircuits or motifs, i.e., those involving positive feedback, tend to be conserved and may provide a constraint on development. This conservation may be due to a required arrangement of transcription factor binding sites in cis regulatory modules. The review will also discuss ways in which novelty may arise, in particular through the co-option of regulatory genes and subcircuits. The development of the sea urchin larval skeleton, a novel feature that arose in echinoderms, has provided a model for study of co-option mechanisms. Finally, the types of GRNs that can permit the great diversity in the patterns of ciliary bands and their associated neurons found among these taxa are discussed. The availability of genomic resources is rapidly expanding for echinoderms, including genome sequences not only for multiple species of sea urchins but also a species of sea star, sea cucumber, and brittle star. This will enable echinoderms to become a particularly powerful system for understanding how developmental GRNs evolve.
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Affiliation(s)
- Veronica F Hinman
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania
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21
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Robertson JK, Danzmann K, Charles S, Blake K, Olivares A, Bamikole S, Olson M, Raay TJV. Targeting the Wnt pathway in zebrafish as a screening method to identify novel therapeutic compounds. Exp Biol Med (Maywood) 2014; 239:169-76. [DOI: 10.1177/1535370213514322] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Activating mutations in the Wnt signaling pathway account for the initiation of greater than 90% of all colorectal cancers and this pathway has been implicated in numerous other diseases. Therefore, identifying small molecule inhibitors of this pathway is of critical importance towards identifying clinically relevant drugs. Numerous screens have been employed to identify therapeutic reagents, but none have made it to advanced clinical trials, suggesting that traditional screening methods are ineffective at identifying clinically relevant targets. Here, we describe a novel in vivo screen to identify small molecule inhibitors of the Wnt pathway. Specifically, treatment of zebrafish embryos with LiCl inhibits GSK3 kinase function, resulting in hyperactivation of the signaling pathway and an eyeless phenotype at 1 day post fertilization. Using the small molecule XAV939, a known inhibitor of Wnt signaling, we rescued the LiCl induced eyeless phenotype, confirming efficacy of the screen. We next tested our assay with 400 known small molecule kinase inhibitors, none of which should inhibit Wnt signaling below the level of GSK3 based on their known targets. Accordingly, none of these small molecules rescued the eyeless phenotype, which demonstrates the stringency of the assay. However, several of these small molecule kinase inhibitors did generate a non-Wnt phenotype in accordance with the kinase they targeted. Therefore, combining the efficacy, sensitivity, and stringency of this preliminary screen, this model will provide an alternative to the traditional in vitro screen, generating potentially clinical relevant drugs in a rapid and cost-effective way.
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Affiliation(s)
- Joshua K Robertson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON Canada N1L 1A3
| | - Kestral Danzmann
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON Canada N1L 1A3
| | - Sherise Charles
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON Canada N1L 1A3
| | - Katherine Blake
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON Canada N1L 1A3
| | - Annia Olivares
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON Canada N1L 1A3
| | - Solape Bamikole
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON Canada N1L 1A3
| | - Meghan Olson
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON Canada N1L 1A3
| | - Terence J Van Raay
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON Canada N1L 1A3
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22
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Aanes H, Collas P, Aleström P. Transcriptome dynamics and diversity in the early zebrafish embryo. Brief Funct Genomics 2013; 13:95-105. [PMID: 24335756 DOI: 10.1093/bfgp/elt049] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Recent years advances in high-throughput sequencing have improved our understanding of how transcripts regulate early vertebrate development. Here, we review the transcriptome dynamics and diversity during early stages of zebrafish embryogenesis. Transcriptome dynamics is characterized by different patterns of mRNA degradation, activation of dormant transcripts and onset of transcription. Several studies have shown a striking diversity of both coding and non-coding transcripts. However, in the aftermath of this immense increase in data, functional studies of both protein-coding and non-coding transcripts are lagging behind. We anticipate that the forthcoming years will see studies relying on different high-throughput sequencing technologies and genomic tools developed for zebrafish embryos to further pin down yet un-annotated transcript-function relationships.
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Affiliation(s)
- Håvard Aanes
- BasAM, Norwegian School of Veterinary Science, Dep., 0033 Oslo, Norway.
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23
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Hemphill J, Chou C, Chin JW, Deiters A. Genetically encoded light-activated transcription for spatiotemporal control of gene expression and gene silencing in mammalian cells. J Am Chem Soc 2013; 135:13433-9. [PMID: 23931657 DOI: 10.1021/ja4051026] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Photocaging provides a method to spatially and temporally control biological function and gene expression with high resolution. Proteins can be photochemically controlled through the site-specific installation of caging groups on amino acid side chains that are essential for protein function. The photocaging of a synthetic gene network using unnatural amino acid mutagenesis in mammalian cells was demonstrated with an engineered bacteriophage RNA polymerase. A caged T7 RNA polymerase was expressed in cells with an expanded genetic code and used in the photochemical activation of genes under control of an orthogonal T7 promoter, demonstrating tight spatial and temporal control. The synthetic gene expression system was validated with two reporter genes (luciferase and EGFP) and applied to the light-triggered transcription of short hairpin RNA constructs for the induction of RNA interference.
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Affiliation(s)
- James Hemphill
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
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24
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Full transcriptome analysis of early dorsoventral patterning in zebrafish. PLoS One 2013; 8:e70053. [PMID: 23922899 PMCID: PMC3726443 DOI: 10.1371/journal.pone.0070053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Accepted: 06/14/2013] [Indexed: 11/20/2022] Open
Abstract
Understanding the molecular interactions that lead to the establishment of the major body axes during embryogenesis is one of the main goals of developmental biology. Although the past two decades have revolutionized our knowledge about the genetic basis of these patterning processes, the list of genes involved in axis formation is unlikely to be complete. In order to identify new genes involved in the establishment of the dorsoventral (DV) axis during early stages of zebrafish embryonic development, we employed next generation sequencing for full transcriptome analysis of normal embryos and embryos lacking overt DV pattern. A combination of different statistical approaches yielded 41 differentially expressed candidate genes and we confirmed by in situ hybridization the early dorsal expression of 32 genes that are transcribed shortly after the onset of zygotic transcription. Although promoter analysis of the validated genes suggests no general enrichment for the binding sites of early acting transcription factors, most of these genes carry “bivalent” epigenetic histone modifications at the time when zygotic transcription is initiated, suggesting a “poised” transcriptional status. Our results reveal some new candidates of the dorsal gene regulatory network and suggest that a plurality of the earliest upregulated genes on the dorsal side have a role in the modulation of the canonical Wnt pathway.
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Aanes H, Østrup O, Andersen IS, Moen LF, Mathavan S, Collas P, Alestrom P. Differential transcript isoform usage pre- and post-zygotic genome activation in zebrafish. BMC Genomics 2013; 14:331. [PMID: 23676078 PMCID: PMC3747860 DOI: 10.1186/1471-2164-14-331] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 04/25/2013] [Indexed: 11/27/2022] Open
Abstract
Background Zebrafish embryos are transcriptionally silent until activation of the zygotic
genome during the 10th cell cycle. Onset of transcription is followed
by cellular and morphological changes involving cell speciation and gastrulation.
Previous genome-wide surveys of transcriptional changes only assessed gene
expression levels; however, recent studies have shown the necessity to map
isoform-specific transcriptional changes. Here, we perform isoform discovery and
quantification on transcriptome sequences from before and after zebrafish zygotic
genome activation (ZGA). Results We identify novel isoforms and isoform switches during ZGA for genes related to
cell adhesion, pluripotency and DNA methylation. Isoform switching events include
alternative splicing and changes in transcriptional start sites and in 3’
untranslated regions. New isoforms are identified even for well-characterized
genes such as pou5f1, sall4 and dnmt1. Genes involved
in cell-cell interactions such as f11r and magi1 display isoform
switches with alterations of coding sequences. We also detect over 1000
transcripts that acquire a longer 3’ terminal exon when transcribed by the
zygote compared to their maternal transcript counterparts. ChIP-sequencing data
mapped onto skipped exon events reveal a correlation between histone H3K36
trimethylation peaks and skipped exons, suggesting epigenetic marks being part of
alternative splicing regulation. Conclusions The novel isoforms and isoform switches reported here include regulators of
transcriptional, cellular and morphological changes taking place around ZGA. Our
data display an array of isoform-related functional changes and represent a
valuable resource complementary to existing early embryo transcriptomes.
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Affiliation(s)
- Håvard Aanes
- BasAM, Norwegian School of Veterinary Science, 0033 Dep, Oslo, Norway
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Botman D, Kaandorp JA. Spatial gene expression quantification: a tool for analysis of in situ hybridizations in sea anemone Nematostella vectensis. BMC Res Notes 2012; 5:555. [PMID: 23039089 PMCID: PMC3532226 DOI: 10.1186/1756-0500-5-555] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 09/26/2012] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Spatial gene expression quantification is required for modeling gene regulation in developing organisms. The fruit fly Drosophila melanogaster is the model system most widely applied for spatial gene expression analysis due to its unique embryonic properties: the shape does not change significantly during its early cleavage cycles and most genes are differentially expressed along a straight axis. This system of development is quite exceptional in the animal kingdom.In the sea anemone Nematostella vectensis the embryo changes its shape during early development; there are cell divisions and cell movement, like in most other metazoans. Nematostella is an attractive case study for spatial gene expression since its transparent body wall makes it accessible to various imaging techniques. FINDINGS Our new quantification method produces standardized gene expression profiles from raw or annotated Nematostella in situ hybridizations by measuring the expression intensity along its cell layer. The procedure is based on digital morphologies derived from high-resolution fluorescence pictures. Additionally, complete descriptions of nonsymmetric expression patterns have been constructed by transforming the gene expression images into a three-dimensional representation. CONCLUSIONS We created a standard format for gene expression data, which enables quantitative analysis of in situ hybridizations from embryos with various shapes in different developmental stages. The obtained expression profiles are suitable as input for optimization of gene regulatory network models, and for correlation analysis of genes from dissimilar Nematostella morphologies. This approach is potentially applicable to many other metazoan model organisms and may also be suitable for processing data from three-dimensional imaging techniques.
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Affiliation(s)
- Daniel Botman
- Section Computational Science, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Jaap A Kaandorp
- Section Computational Science, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
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Longabaugh WJR. BioTapestry: a tool to visualize the dynamic properties of gene regulatory networks. Methods Mol Biol 2012; 786:359-394. [PMID: 21938637 DOI: 10.1007/978-1-61779-292-2_21] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
BioTapestry is an open source, freely available software tool that has been developed to handle the -challenges of modeling genetic regulatory networks (GRNs). Using BioTapestry, a researcher can -construct a network model and use it to visualize and understand the dynamic behavior of a complex, spatially and temporally distributed GRN. Here we provide a step-by-step example of a way to use BioTapestry to build a GRN model and discuss some common issues that can arise during this process.
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Lindeman L, Andersen I, Reiner A, Li N, Aanes H, Østrup O, Winata C, Mathavan S, Müller F, Aleström P, Collas P. Prepatterning of Developmental Gene Expression by Modified Histones before Zygotic Genome Activation. Dev Cell 2011; 21:993-1004. [DOI: 10.1016/j.devcel.2011.10.008] [Citation(s) in RCA: 162] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 08/12/2011] [Accepted: 10/11/2011] [Indexed: 12/29/2022]
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Flynn C, Sharma T, Ruffins S, Guerra S, Crowley J, Ettensohn C. High-resolution, three-dimensional mapping of gene expression using GeneExpressMap (GEM). Dev Biol 2011; 357:532-40. [DOI: 10.1016/j.ydbio.2011.06.033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 06/20/2011] [Accepted: 06/22/2011] [Indexed: 10/18/2022]
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Tseng WF, Jang TH, Huang CB, Yuh CH. An evolutionarily conserved kernel of gata5, gata6, otx2 and prdm1a operates in the formation of endoderm in zebrafish. Dev Biol 2011; 357:541-57. [PMID: 21756893 DOI: 10.1016/j.ydbio.2011.06.040] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 06/09/2011] [Accepted: 06/23/2011] [Indexed: 10/18/2022]
Abstract
An evolutionarily conserved subcircuit (kernel) dedicated to a specific developmental function is found at the top of the gene regulatory networks (GRNs) hierarchy. Here we comprehensively demonstrate that a pan-deuterostome endoderm specification kernel exists in zebrafish. We analyzed interactions among gata5, gata6, otx2 and prdm1a using specific morpholino knockdowns and measured the gene expression profiles by quantitative real-time RT-PCR and in situ hybridization. The mRNA rescue experiment validated the specificity of the morpholino knockdown. We found that the interactions among gata5, gata6, otx2 and prdm1a determine the initial specification of the zebrafish endoderm. Although otx2 can activate both gata5 and gata6, and the prdm1a/krox homologue also activates some endoderm transcription factors, a feedback loop from Gata to otx2 and prdm1a is missing. Furthermore, we found the positive regulation between gata5 and gata6 to further lock-on the mesendoderm specification by the Gata family. Chromatin immunoprecipitation was used to further validate the recruitment of Otx2 to the gata5 and gata6 loci. Functional assays revealed that module B of gata6 and the basal promoter of gata5 drive the gene at the mesendoderm, and mutational analysis demonstrated that Otx2 and Gata5/6 contribute to reporter gene activation. This is the first direct evidence for evolutionarily conserved endoderm specification across echinoderms and vertebrates.
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Affiliation(s)
- Wen-Fang Tseng
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan Town, Miaoli County 350, Taiwan, ROC
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Lu JW, Hsia Y, Tu HC, Hsiao YC, Yang WY, Wang HD, Yuh CH. Liver development and cancer formation in zebrafish. ACTA ACUST UNITED AC 2011; 93:157-72. [DOI: 10.1002/bdrc.20205] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Abstract
Gene regulatory networks (GRNs) provide system level explanations of developmental and physiological functions in the terms of the genomic regulatory code. Depending on their developmental functions, GRNs differ in their degree of hierarchy, and also in the types of modular sub-circuit of which they are composed, although there is a commonly employed sub-circuit repertoire. Mathematical modelling of some types of GRN sub-circuit has deepened biological understanding of the functions they mediate. The structural organization of various kinds of GRN reflects their roles in the life process, and causally illuminates both developmental and evolutionary process.
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Affiliation(s)
- Eric H Davidson
- Division of Biology 156-29, California Institute of Technology, Pasadena, California 91125, USA.
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Amore G, Casares F. Size matters: the contribution of cell proliferation to the progression of the specification Drosophila eye gene regulatory network. Dev Biol 2010; 344:569-77. [PMID: 20599903 DOI: 10.1016/j.ydbio.2010.06.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 06/03/2010] [Accepted: 06/08/2010] [Indexed: 01/02/2023]
Abstract
Organ development is a complex process in which the activity of scores of interacting transcription factors and signaling pathways need to be integrated with proliferative growth. Developmental gene regulatory networks (GRNs) allow capturing essential regulatory pathways at a systems-level and provide an effective way of approaching such complexity. However typical GRNs studies focus on very early embryonic stages (usually pre-gastrulation) or late stages, when there is little or no cell proliferation, and therefore do not consider how organ growth is integrated in the developmental process. This can be conveniently investigated in the Drosophila melanogaster eye primordium. Here we present a working model meant to illustrate how during a critical period, the second larval stage, changes in cells' proliferative pattern are coordinated with the initiation of the Retinal Determination (RD) gene program. Such changes are regulated in response to two different sources of signal (Wnt1/wg and BMP2/4/dpp) produced by the anterior and posterior ends of the primordium, respectively. The dpp signaling is necessary to trigger the RD program. However in order for it to be effective, cells receiving Dpp have to be out of the wg signaling range. This is obtained thanks to the proliferative growth that precedes the onset of RD expression. With this network model many of the gene regulatory steps previously known to participate in growth and patterning are linked. Analysis of the model highlights a few essential regulatory principles, as well as poses new questions. In addition, these principles might operate during the growth and patterning of other organs.
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Affiliation(s)
- Gabriele Amore
- Animal Physiology and Evolutionary Laboratory-Stazione Zoologica Anton Dohrn, Napoli, Italy.
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Chao CH, Wang HD, Yuh CH. Complexity of cis-regulatory organization of six3a during forebrain and eye development in zebrafish. BMC DEVELOPMENTAL BIOLOGY 2010; 10:35. [PMID: 20346166 PMCID: PMC2858731 DOI: 10.1186/1471-213x-10-35] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Accepted: 03/26/2010] [Indexed: 11/10/2022]
Abstract
BACKGROUND Six3a belongs to the SIX family of homeodomain proteins and is expressed in the most anterior neural plate at the beginning of neurogenesis in various species. Though the function of Six3a as a crucial regulator of eye and forebrain development has been thoroughly investigated, the transcriptional regulation of six3a is not well understood. RESULTS To elucidate the transcriptional regulation of six3a, we performed an in vivo reporter assay. Alignment of the 21-kb region surrounding the zebrafish six3a gene with the analogous region from different species identified several conserved non-coding modules. Transgenesis in zebrafish identified two enhancer elements and one suppressor. The D module drives the GFP reporter in the forebrain and eyes at an early stage, while the A module is responsible for the later expression. The A module also works as a repressor suppressing ectopic expression from the D module. Mutational analysis further minimized the A module to four highly conserved elements and the D module to three elements. Using electrophoresis mobility shift assays, we also provided evidence for the presence of DNA-binding proteins in embryonic nuclear extracts. The transcription factors that may occupy those highly conserved elements were also predicted. CONCLUSION This study provides a comprehensive view of six3a transcription regulation during brain and eye development and offers an opportunity to establish the gene regulatory networks underlying neurogenesis in zebrafish.
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Affiliation(s)
- Chung-Hao Chao
- Division of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan
- College of Life Science and Institute of Biotechnology, National Tsing-Hua University, HsinChu, Taiwan
| | - Horng-Dar Wang
- College of Life Science and Institute of Biotechnology, National Tsing-Hua University, HsinChu, Taiwan
| | - Chiou-Hwa Yuh
- Division of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan Town, Miaoli County, Taiwan
- College of Life Science and Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, HsinChu, Taiwan
- Department of Biological Science & Technology, National Chiao Tung University, HsinChu, Taiwan
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Herpin A, Braasch I, Kraeussling M, Schmidt C, Thoma EC, Nakamura S, Tanaka M, Schartl M. Transcriptional rewiring of the sex determining dmrt1 gene duplicate by transposable elements. PLoS Genet 2010; 6:e1000844. [PMID: 20169179 PMCID: PMC2820524 DOI: 10.1371/journal.pgen.1000844] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Accepted: 01/12/2010] [Indexed: 02/01/2023] Open
Abstract
Control and coordination of eukaryotic gene expression rely on transcriptional and posttranscriptional regulatory networks. Evolutionary innovations and adaptations often require rapid changes of such networks. It has long been hypothesized that transposable elements (TE) might contribute to the rewiring of regulatory interactions. More recently it emerged that TEs might bring in ready-to-use transcription factor binding sites to create alterations to the promoters by which they were captured. A process where the gene regulatory architecture is of remarkable plasticity is sex determination. While the more downstream components of the sex determination cascades are evolutionary conserved, the master regulators can switch between groups of organisms even on the interspecies level or between populations. In the medaka fish (Oryzias latipes) a duplicated copy of dmrt1, designated dmrt1bY or DMY, on the Y chromosome was shown to be the master regulator of male development, similar to Sry in mammals. We found that the dmrt1bY gene has acquired a new feedback downregulation of its expression. Additionally, the autosomal dmrt1a gene is also able to regulate transcription of its duplicated paralog by binding to a unique target Dmrt1 site nested within the dmrt1bY proximal promoter region. We could trace back this novel regulatory element to a highly conserved sequence within a new type of TE that inserted into the upstream region of dmrt1bY shortly after the duplication event. Our data provide functional evidence for a role of TEs in transcriptional network rewiring for sub- and/or neo-functionalization of duplicated genes. In the particular case of dmrt1bY, this contributed to create new hierarchies of sex-determining genes. Evolutionary innovations and adaptations often require rapid changes in gene regulation. Transposable elements constitute the most dynamic part of eukaryotic genomes. Insertions of transposable elements can influence the expression of surrounding genes by donating new regulatory elements. A longstanding hypothesis postulates that the dispersal of transposable elements may rewire regulatory links between genes, thereby changing regulatory networks and shuffling regulatory cascades. A regulatory hierarchy of remarkable plasticity is the sex determination cascade. In the course of animal evolution, new master regulators frequently replace the sex determination gene on top of the hierarchy. In the medaka fish, a duplicate of the dmrt1 transcription factor gene, dmrt1bY, has become the sex master regulator. Its ancestor dmrt1a, in contrast, has a downstream position in the sex determination cascade. We show that after the duplication of the dmrt1 gene, the new hierarchy has been established by the insertion of a transposable element into the regulatory region of the dmrt1bY gene on the sex chromosome. This transposable element, harboring a Dmrt1 binding site, enables the self- and cross-regulation of dmrt1bY expression by Dmrt1 proteins. Our study therefore provides strong evidence for the important role of transposable elements in the rewiring of gene regulatory networks.
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Affiliation(s)
- Amaury Herpin
- University of Würzburg, Physiological Chemistry I, Biozentrum, Würzburg, Germany.
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Abstract
The endoderm germ layer contributes to the respiratory and gastrointestinal tracts and to all of their associated organs. Over the past decade, studies in vertebrate model organisms, including frog, fish, chick, and mouse, have greatly enhanced our understanding of the molecular basis of endoderm organ development. We review this progress with a focus on early stages of endoderm organogenesis including endoderm formation, gut tube morphogenesis and patterning, and organ specification. Lastly, we discuss how developmental mechanisms that regulate endoderm organogenesis are used to direct differentiation of embryonic stem cells into specific adult cell types, which function to alleviate disease symptoms in animal models.
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Affiliation(s)
- Aaron M Zorn
- Division of Developmental Biology, Cincinnati Children's Research Foundation and Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, Ohio 45229, USA.
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Bacha J, Brodie JS, Loose MW. myGRN: a database and visualisation system for the storage and analysis of developmental genetic regulatory networks. BMC DEVELOPMENTAL BIOLOGY 2009; 9:33. [PMID: 19500400 PMCID: PMC2702357 DOI: 10.1186/1471-213x-9-33] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2009] [Accepted: 06/06/2009] [Indexed: 11/23/2022]
Abstract
Background Biological processes are regulated by complex interactions between transcription factors and signalling molecules, collectively described as Genetic Regulatory Networks (GRNs). The characterisation of these networks to reveal regulatory mechanisms is a long-term goal of many laboratories. However compiling, visualising and interacting with such networks is non-trivial. Current tools and databases typically focus on GRNs within simple, single celled organisms. However, data is available within the literature describing regulatory interactions in multi-cellular organisms, although not in any systematic form. This is particularly true within the field of developmental biology, where regulatory interactions should also be tagged with information about the time and anatomical location of development in which they occur. Description We have developed myGRN (), a web application for storing and interrogating interaction data, with an emphasis on developmental processes. Users can submit interaction and gene expression data, either curated from published sources or derived from their own unpublished data. All interactions associated with publications are publicly visible, and unpublished interactions can only be shared between collaborating labs prior to publication. Users can group interactions into discrete networks based on specific biological processes. Various filters allow dynamic production of network diagrams based on a range of information including tissue location, developmental stage or basic topology. Individual networks can be viewed using myGRV, a tool focused on displaying developmental networks, or exported in a range of formats compatible with third party tools. Networks can also be analysed for the presence of common network motifs. We demonstrate the capabilities of myGRN using a network of zebrafish interactions integrated with expression data from the zebrafish database, ZFIN. Conclusion Here we are launching myGRN as a community-based repository for interaction networks, with a specific focus on developmental networks. We plan to extend its functionality, as well as use it to study networks involved in embryonic development in the future.
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Affiliation(s)
- Jamil Bacha
- Institute of Genetics, University of Nottingham, Nottingham, UK.
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Longabaugh WJR, Davidson EH, Bolouri H. Visualization, documentation, analysis, and communication of large-scale gene regulatory networks. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2008; 1789:363-74. [PMID: 18757046 DOI: 10.1016/j.bbagrm.2008.07.014] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2008] [Accepted: 07/30/2008] [Indexed: 10/21/2022]
Abstract
Genetic regulatory networks (GRNs) are complex, large-scale, and spatially and temporally distributed. These characteristics impose challenging demands on software tools for building GRN models, and so there is a need for custom tools. In this paper, we report on our ongoing development of BioTapestry, an open source, freely available computational tool designed specifically for building GRN models. We also outline our future development plans, and give some examples of current applications of BioTapestry.
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