1
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Gigante ED, Piekarz KM, Gurgis A, Cohen L, Razy-Krajka F, Popsuj S, Johnson CJ, Ali HS, Mohana Sundaram S, Stolfi A. Specification and survival of post-metamorphic branchiomeric neurons in a non-vertebrate chordate. Development 2024; 151:dev202719. [PMID: 38895900 PMCID: PMC11273300 DOI: 10.1242/dev.202719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
Tunicates are the sister group to the vertebrates, yet most species have a life cycle split between swimming larva and sedentary adult phases. During metamorphosis, larval neurons are replaced by adult-specific ones. The regulatory mechanisms underlying this replacement remain largely unknown. Using tissue-specific CRISPR/Cas9-mediated mutagenesis in the tunicate Ciona, we show that orthologs of conserved hindbrain and branchiomeric neuron regulatory factors Pax2/5/8 and Phox2 are required to specify the 'neck', a cellular compartment set aside in the larva to give rise to cranial motor neuron-like neurons post-metamorphosis. Using bulk and single-cell RNA-sequencing analyses, we characterize the transcriptome of the neck downstream of Pax2/5/8. We present evidence that neck-derived adult ciliomotor neurons begin to differentiate in the larva and persist through metamorphosis, contrary to the assumption that the adult nervous system is formed after settlement and the death of larval neurons during metamorphosis. Finally, we show that FGF signaling during the larval phase alters the patterning of the neck and its derivatives. Suppression of FGF converts neck cells into larval neurons that fail to survive metamorphosis, whereas prolonged FGF signaling promotes an adult neural stem cell-like fate.
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Affiliation(s)
- Eduardo D. Gigante
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Katarzyna M. Piekarz
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alexandra Gurgis
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Leslie Cohen
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Florian Razy-Krajka
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sydney Popsuj
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Christopher J. Johnson
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Hussan S. Ali
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Shruthi Mohana Sundaram
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alberto Stolfi
- School of Biological Sciences, College of Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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2
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Ohta N, Christiaen L. Cellular remodeling and JAK inhibition promote zygotic gene expression in the Ciona germline. EMBO Rep 2024; 25:2188-2201. [PMID: 38649664 PMCID: PMC11094015 DOI: 10.1038/s44319-024-00139-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 04/25/2024] Open
Abstract
Transcription control is a major determinant of cell fate decisions in somatic tissues. By contrast, early germline fate specification in numerous vertebrate and invertebrate species relies extensively on RNA-level regulation, exerted on asymmetrically inherited maternal supplies, with little-to-no zygotic transcription. However delayed, a maternal-to-zygotic transition is nevertheless poised to complete the deployment of pre-gametic programs in the germline. Here, we focus on early germline specification in the tunicate Ciona to study zygotic genome activation. We first demonstrate that a peculiar cellular remodeling event excludes localized postplasmic Pem-1 mRNA, which encodes the general inhibitor of transcription. Subsequently, zygotic transcription begins in Pem-1-negative primordial germ cells (PGCs), as revealed by histochemical detection of elongating RNA Polymerase II, and nascent Mef2 transcripts. In addition, we uncover a provisional antagonism between JAK and MEK/BMPRI/GSK3 signaling, which controls the onset of zygotic gene expression, following cellular remodeling of PGCs. We propose a 2-step model for the onset of zygotic transcription in the Ciona germline and discuss the significance of germ plasm dislocation and remodeling in the context of developmental fate specification.
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Affiliation(s)
- Naoyuki Ohta
- Michael Sars Centre, University of Bergen, Bergen, Norway.
| | - Lionel Christiaen
- Michael Sars Centre, University of Bergen, Bergen, Norway.
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY, USA.
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3
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Frese AN, Mariossi A, Levine MS, Wühr M. Quantitative proteome dynamics across embryogenesis in a model chordate. iScience 2024; 27:109355. [PMID: 38510129 PMCID: PMC10951915 DOI: 10.1016/j.isci.2024.109355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/11/2023] [Accepted: 02/23/2024] [Indexed: 03/22/2024] Open
Abstract
The evolution of gene expression programs underlying the development of vertebrates remains poorly characterized. Here, we present a comprehensive proteome atlas of the model chordate Ciona, covering eight developmental stages and ∼7,000 translated genes, accompanied by a multi-omics analysis of co-evolution with the vertebrate Xenopus. Quantitative proteome comparisons argue against the widely held hourglass model, based solely on transcriptomic profiles, whereby peak conservation is observed during mid-developmental stages. Our analysis reveals maximal divergence at these stages, particularly gastrulation and neurulation. Together, our work provides a valuable resource for evaluating conservation and divergence of multi-omics profiles underlying the diversification of vertebrates.
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Affiliation(s)
- Alexander N. Frese
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Andrea Mariossi
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Michael S. Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Martin Wühr
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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4
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Hoyer J, Kolar K, Athira A, van den Burgh M, Dondorp D, Liang Z, Chatzigeorgiou M. Polymodal sensory perception drives settlement and metamorphosis of Ciona larvae. Curr Biol 2024; 34:1168-1182.e7. [PMID: 38335959 DOI: 10.1016/j.cub.2024.01.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 12/04/2023] [Accepted: 01/16/2024] [Indexed: 02/12/2024]
Abstract
The Earth's oceans brim with an incredible diversity of microscopic lifeforms, including motile planktonic larvae, whose survival critically depends on effective dispersal in the water column and subsequent exploration of the seafloor to identify a suitable settlement site. How their nervous systems mediate sensing of diverse multimodal cues remains enigmatic. Here, we uncover that the tunicate Ciona intestinalis larvae employ ectodermal sensory cells to sense various mechanical and chemical cues. Combining whole-brain imaging and chemogenetics, we demonstrate that stimuli encoded at the periphery are sufficient to drive global brain-state changes to promote or impede both larval attachment and metamorphosis behaviors. The ability of C. intestinalis larvae to leverage polymodal sensory perception to support information coding and chemotactile behaviors may explain how marine larvae make complex decisions despite streamlined nervous systems.
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Affiliation(s)
- Jorgen Hoyer
- Michael Sars Centre, Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen 5006, Norway
| | - Kushal Kolar
- Michael Sars Centre, Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen 5006, Norway
| | - Athira Athira
- Michael Sars Centre, Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen 5006, Norway
| | - Meike van den Burgh
- Michael Sars Centre, Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen 5006, Norway
| | - Daniel Dondorp
- Michael Sars Centre, Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen 5006, Norway
| | - Zonglai Liang
- Michael Sars Centre, Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen 5006, Norway
| | - Marios Chatzigeorgiou
- Michael Sars Centre, Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen 5006, Norway.
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5
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Wei J, Zhang W, Jiang A, Peng H, Zhang Q, Li Y, Bi J, Wang L, Liu P, Wang J, Ge Y, Zhang L, Yu H, Li L, Wang S, Leng L, Chen K, Dong B. Temporospatial hierarchy and allele-specific expression of zygotic genome activation revealed by distant interspecific urochordate hybrids. Nat Commun 2024; 15:2395. [PMID: 38493164 PMCID: PMC10944513 DOI: 10.1038/s41467-024-46780-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
Zygotic genome activation (ZGA) is a universal process in early embryogenesis of metazoan, when the quiescent zygotic nucleus initiates global transcription. However, the mechanisms related to massive genome activation and allele-specific expression (ASE) remain not well understood. Here, we develop hybrids from two deeply diverged (120 Mya) ascidian species to symmetrically document the dynamics of ZGA. We identify two coordinated ZGA waves represent early developmental and housekeeping gene reactivation, respectively. Single-cell RNA sequencing reveals that the major expression wave exhibits spatial heterogeneity and significantly correlates with cell fate. Moreover, allele-specific expression occurs in a species- rather than parent-related manner, demonstrating the divergence of cis-regulatory elements between the two species. These findings provide insights into ZGA in chordates.
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Affiliation(s)
- Jiankai Wei
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
- MoE Key Laboratory of Evolution and Marine Biodiversity, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Wei Zhang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - An Jiang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Hongzhe Peng
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Quanyong Zhang
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Yuting Li
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Jianqing Bi
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Linting Wang
- National Center of Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
| | - Penghui Liu
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Jing Wang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Yonghang Ge
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Liya Zhang
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Haiyan Yu
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Lei Li
- National Center of Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
| | - Shi Wang
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
| | - Liang Leng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Kai Chen
- State Key Laboratory of Primate Biomedical Research and Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), No. 1119 Haibin Rd, Nansha Dist., Guangzhou, 511458, China.
| | - Bo Dong
- Fang Zongxi Center for Marine EvoDevo, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266237, China.
- MoE Key Laboratory of Evolution and Marine Biodiversity, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
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6
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Johnson CJ, Zhang Z, Zhang H, Shang R, Piekarz KM, Bi P, Stolfi A. A change in cis-regulatory logic underlying obligate versus facultative muscle multinucleation in chordates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583753. [PMID: 38559144 PMCID: PMC10979880 DOI: 10.1101/2024.03.06.583753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Vertebrates and tunicates are sister groups that share a common fusogenic factor, Myomaker (Mymk), that drives myoblast fusion and muscle multinucleation. Yet they are divergent in when and where they express Mymk. In vertebrates, all developing skeletal muscles express Mymk and are obligately multinucleated. In tunicates, Mymk is only expressed in post-metamorphic multinucleated muscles, but is absent from mononucleated larval muscles. In this study, we demonstrate that cis-regulatory sequence differences in the promoter region of Mymk underlie the different spatiotemporal patterns of its transcriptional activation in tunicates and vertebrates. While in vertebrates Myogenic Regulatory Factors (MRFs) like MyoD1 alone are required and sufficient for Mymk transcription in all skeletal muscles, we show that transcription of Mymk in post-metamorphic muscles of the tunicate Ciona requires the combinatorial activity of MRF/MyoD and Early B-Cell Factor (Ebf). This macroevolutionary difference appears to be encoded in cis, likely due to the presence of a putative Ebf binding site adjacent to predicted MRF binding sites in the Ciona Mymk promoter. We further discuss how Mymk and myoblast fusion might have been regulated in the last common ancestor of tunicates and vertebrates, for which we propose two models.
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Affiliation(s)
| | - Zheng Zhang
- Department of Genetics, University of Georgia, Athens, GA, USA
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
| | - Haifeng Zhang
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
| | - Renjie Shang
- Department of Genetics, University of Georgia, Athens, GA, USA
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
| | - Katarzyna M Piekarz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Pengpeng Bi
- Department of Genetics, University of Georgia, Athens, GA, USA
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
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7
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Johnson CJ, Razy-Krajka F, Zeng F, Piekarz KM, Biliya S, Rothbächer U, Stolfi A. Specification of distinct cell types in a sensory-adhesive organ important for metamorphosis in tunicate larvae. PLoS Biol 2024; 22:e3002555. [PMID: 38478577 PMCID: PMC10962819 DOI: 10.1371/journal.pbio.3002555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 03/25/2024] [Accepted: 02/21/2024] [Indexed: 03/22/2024] Open
Abstract
The papillae of tunicate larvae contribute sensory, adhesive, and metamorphosis-regulating functions that are crucial for the biphasic lifestyle of these marine, non-vertebrate chordates. We have identified additional molecular markers for at least 5 distinct cell types in the papillae of the model tunicate Ciona, allowing us to further study the development of these organs. Using tissue-specific CRISPR/Cas9-mediated mutagenesis and other molecular perturbations, we reveal the roles of key transcription factors and signaling pathways that are important for patterning the papilla territory into a highly organized array of different cell types and shapes. We further test the contributions of different transcription factors and cell types to the production of the adhesive glue that allows for larval attachment during settlement, and to the processes of tail retraction and body rotation during metamorphosis. With this study, we continue working towards connecting gene regulation to cellular functions that control the developmental transition between the motile larva and sessile adult of Ciona.
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Affiliation(s)
- Christopher J Johnson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Florian Razy-Krajka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Fan Zeng
- Department of Zoology, University of Innsbruck, Innsbruck, Austria
| | - Katarzyna M Piekarz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Shweta Biliya
- Molecular Evolution Core, Petit H. Parker Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Ute Rothbächer
- Department of Zoology, University of Innsbruck, Innsbruck, Austria
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
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8
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Peng H, Qiao J, Wang G, Shi W, Xia F, Qiao R, Dong B. A collagen-rich arch in the urochordate notochord coordinates cell shaping and multi-tissue elongation. Curr Biol 2023; 33:5390-5403.e3. [PMID: 37995694 DOI: 10.1016/j.cub.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 10/26/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023]
Abstract
Cell and tissue reshaping is crucial for coordinating three-dimensional pattern formation, in which the size and shape of the cells must be accurately regulated via signal transport and communication among tissues. However, the identity of signaling and transportation mechanisms in this process remains elusive. In our study, we identified an extracellular matrix (ECM) structure with a vertebra-like shape surrounding the central notochord tissue in the larval tail of the urochordate Ciona. Additionally, we verified that the ECM structure was formed de novo, mainly from collagens secreted by notochord cells. Fluorescence recovery after photobleaching and simulation results revealed that this structure was formed via diffusional collagen flow from a notochord that was restricted and molded in the spaces among tail tissues. We revealed that the collagen structure was essential for notochord cell arrangement and elongation. Furthermore, we observed that the central notochord connects with the epidermis through this ECM structure. The disruption of this structure by collagen knockdown and loss-of-collagen function caused the failure of notochord elongation. More importantly, the epidermis could not elongate proportionally with notochord, indicating that the collagen-rich structure serves as a scaffold to coordinate the concurrent elongation of the tail tissues. These findings provide insights into how the central tissue forms and molds its surrounding ECM structure, by not only regulating its own morphogenesis but also functioning as a scaffold for signal transmission to orchestrate the coordinated morphologic reshaping of the surrounding tissues.
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Affiliation(s)
- Hongzhe Peng
- Fang Zongxi Center, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Jinghan Qiao
- Fang Zongxi Center, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Guilin Wang
- Fang Zongxi Center, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Wenjie Shi
- Fang Zongxi Center, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Fan Xia
- Fang Zongxi Center, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Runyu Qiao
- Fang Zongxi Center, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Bo Dong
- Fang Zongxi Center, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laoshan Laboratory, Qingdao 266237, China; MoE Key Laboratory of Evolution & Marine Biodiversity, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China.
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9
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Long J, Mariossi A, Cao C, Mo Z, Thompson JW, Levine MS, Lemaire LA. Cereblon influences the timing of muscle differentiation in Ciona tadpoles. Proc Natl Acad Sci U S A 2023; 120:e2309989120. [PMID: 37856545 PMCID: PMC10614628 DOI: 10.1073/pnas.2309989120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/09/2023] [Indexed: 10/21/2023] Open
Abstract
Thalidomide has a dark history as a teratogen, but in recent years, its derivates have been shown to function as potent chemotherapeutic agents. These drugs bind cereblon (CRBN), the substrate receptor of an E3 ubiquitin ligase complex, and modify its degradation targets. Despite these insights, remarkably little is known about the normal function of cereblon in development. Here, we employ Ciona, a simple invertebrate chordate, to identify endogenous Crbn targets. In Ciona, Crbn is specifically expressed in developing muscles during tail elongation before they acquire contractile activity. Crbn expression is activated by Mrf, the ortholog of MYOD1, a transcription factor important for muscle differentiation. CRISPR/Cas9-mediated mutations of Crbn lead to precocious onset of muscle contractions. By contrast, overexpression of Crbn delays contractions and is associated with decreased expression of contractile protein genes such as troponin. This reduction is possibly due to reduced Mrf protein levels without altering Mrf mRNA levels. Our findings suggest that Mrf and Crbn form a negative feedback loop to control the precision of muscle differentiation during tail elongation.
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Affiliation(s)
- Juanjuan Long
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
| | - Andrea Mariossi
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
| | - Chen Cao
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
| | | | | | - Michael S. Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
- Department of Molecular Biology, Princeton University, Princeton, NJ08544
| | - Laurence A. Lemaire
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
- Department of Biology, Saint Louis University, St. Louis, MO63103
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10
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Johnson CJ, Kulkarni A, Buxton WJ, Hui TY, Kayastha A, Khoja AA, Leandre J, Mehta VV, Ostrowski L, Pareizs EG, Scotto RL, Vargas V, Vellingiri RM, Verzino G, Vohra R, Wakade SC, Winkeljohn VM, Winkeljohn VM, Rotterman TM, Stolfi A. Using CRISPR/Cas9 to identify genes required for mechanosensory neuron development and function. Biol Open 2023; 12:bio060002. [PMID: 37589291 PMCID: PMC10497037 DOI: 10.1242/bio.060002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023] Open
Abstract
Tunicates are marine, non-vertebrate chordates that comprise the sister group to the vertebrates. Most tunicates have a biphasic lifecycle that alternates between a swimming larva and a sessile adult. Recent advances have shed light on the neural basis for the tunicate larva's ability to sense a proper substrate for settlement and initiate metamorphosis. Work in the highly tractable laboratory model tunicate Ciona robusta suggests that sensory neurons embedded in the anterior papillae transduce mechanosensory stimuli to trigger larval tail retraction and initiate the process of metamorphosis. Here, we take advantage of the low-cost and simplicity of Ciona by using tissue-specific CRISPR/Cas9-mediated mutagenesis to screen for genes potentially involved in mechanosensation and metamorphosis, in the context of an undergraduate 'capstone' research course. This small screen revealed at least one gene, Vamp1/2/3, which appears crucial for the ability of the papillae to trigger metamorphosis. We also provide step-by-step protocols and tutorials associated with this course, in the hope that it might be replicated in similar CRISPR-based laboratory courses wherever Ciona are available.
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Affiliation(s)
| | - Akhil Kulkarni
- School of Biological Sciences, Georgia Institute of Technology, 30332 Atlanta, GO, USA
| | - William J. Buxton
- School of Biological Sciences, Georgia Institute of Technology, 30332 Atlanta, GO, USA
| | - Tsz Y. Hui
- School of Biological Sciences, Georgia Institute of Technology, 30332 Atlanta, GO, USA
| | - Anusha Kayastha
- School of Biological Sciences, Georgia Institute of Technology, 30332 Atlanta, GO, USA
| | - Alwin A. Khoja
- School of Biological Sciences, Georgia Institute of Technology, 30332 Atlanta, GO, USA
| | - Joviane Leandre
- School of Biological Sciences, Georgia Institute of Technology, 30332 Atlanta, GO, USA
| | - Vanshika V. Mehta
- School of Biological Sciences, Georgia Institute of Technology, 30332 Atlanta, GO, USA
| | - Logan Ostrowski
- School of Biological Sciences, Georgia Institute of Technology, 30332 Atlanta, GO, USA
| | - Erica G. Pareizs
- School of Biological Sciences, Georgia Institute of Technology, 30332 Atlanta, GO, USA
| | - Rebecca L. Scotto
- School of Biological Sciences, Georgia Institute of Technology, 30332 Atlanta, GO, USA
| | - Vanesa Vargas
- School of Biological Sciences, Georgia Institute of Technology, 30332 Atlanta, GO, USA
| | - Raveena M. Vellingiri
- School of Biological Sciences, Georgia Institute of Technology, 30332 Atlanta, GO, USA
| | - Giulia Verzino
- School of Biological Sciences, Georgia Institute of Technology, 30332 Atlanta, GO, USA
| | - Rhea Vohra
- School of Biological Sciences, Georgia Institute of Technology, 30332 Atlanta, GO, USA
| | - Saurabh C. Wakade
- School of Biological Sciences, Georgia Institute of Technology, 30332 Atlanta, GO, USA
| | | | | | - Travis M. Rotterman
- School of Biological Sciences, Georgia Institute of Technology, 30332 Atlanta, GO, USA
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, 30332 Atlanta, GO, USA
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11
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Gigante ED, Piekarz KM, Gurgis A, Cohen L, Razy-Krajka F, Popsuj S, Ali HS, Sundaram SM, Stolfi A. Specification and survival of post-metamorphic branchiomeric neurons in the hindbrain of a non-vertebrate chordate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.16.545305. [PMID: 37645866 PMCID: PMC10461979 DOI: 10.1101/2023.06.16.545305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Tunicates are the sister group to the vertebrates, yet most species have a life cycle split between swimming larva and sedentary adult phases. During metamorphosis, larval neurons are largely replaced by adult-specific ones. Yet the regulatory mechanisms underlying this neural replacement remain largely unknown. Using tissue-specific CRISPR/Cas9-mediated mutagenesis in the tunicate Ciona, we show that orthologs of conserved hindbrain and branchiomeric neuron regulatory factors Pax2/5/8 and Phox2 are required to specify the "Neck", a compartment of cells set aside in the larva to give rise to cranial motor neuron-like neurons in the adult. Using bulk and single-cell RNAseq analyses, we also characterize the transcriptome of the Neck downstream of Pax2/5/8. Surprisingly, we find that Neck-derived adult ciliomotor neurons begin to differentiate in the larva, contrary to the long-held assumption that the adult nervous system is formed only after settlement and the death of larval neurons during metamorphosis. Finally, we show that manipulating FGF signaling during the larval phase alters the patterning of the Neck and its derivatives. Suppression of FGF converts Neck cells into larval neurons that fail to survive metamorphosis, while prolonged FGF signaling promotes an adult neural stem cell-like fate instead.
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Affiliation(s)
- Eduardo D Gigante
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
| | - Katarzyna M Piekarz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
| | - Alexandra Gurgis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
- Department of Biology, Case Western Reserve University, Cleveland, OH, 44106; USA
| | - Leslie Cohen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
| | - Florian Razy-Krajka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
| | - Sydney Popsuj
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
| | - Hussan S Ali
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
| | | | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332; USA
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12
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Vitrinel B, Vogel C, Christiaen L. Ring Finger 149-Related Is an FGF/MAPK-Independent Regulator of Pharyngeal Muscle Fate Specification. Int J Mol Sci 2023; 24:8865. [PMID: 37240211 PMCID: PMC10219245 DOI: 10.3390/ijms24108865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/26/2023] [Accepted: 04/29/2023] [Indexed: 05/28/2023] Open
Abstract
During embryonic development, cell-fate specification gives rise to dedicated lineages that underlie tissue formation. In olfactores, which comprise tunicates and vertebrates, the cardiopharyngeal field is formed by multipotent progenitors of both cardiac and branchiomeric muscles. The ascidian Ciona is a powerful model to study cardiopharyngeal fate specification with cellular resolution, as only two bilateral pairs of multipotent cardiopharyngeal progenitors give rise to the heart and to the pharyngeal muscles (also known as atrial siphon muscles, ASM). These progenitors are multilineage primed, in as much as they express a combination of early ASM- and heart-specific transcripts that become restricted to their corresponding precursors, following oriented and asymmetric divisions. Here, we identify the primed gene ring finger 149 related (Rnf149-r), which later becomes restricted to the heart progenitors, but appears to regulate pharyngeal muscle fate specification in the cardiopharyngeal lineage. CRISPR/Cas9-mediated loss of Rnf149-r function impairs atrial siphon muscle morphogenesis, and downregulates Tbx1/10 and Ebf, two key determinants of pharyngeal muscle fate, while upregulating heart-specific gene expression. These phenotypes are reminiscent of the loss of FGF/MAPK signaling in the cardiopharyngeal lineage, and an integrated analysis of lineage-specific bulk RNA-seq profiling of loss-of-function perturbations has identified a significant overlap between candidate FGF/MAPK and Rnf149-r target genes. However, functional interaction assays suggest that Rnf149-r does not directly modulate the activity of the FGF/MAPK/Ets1/2 pathway. Instead, we propose that Rnf149-r acts both in parallel to the FGF/MAPK signaling on shared targets, as well as on FGF/MAPK-independent targets through (a) separate pathway(s).
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Affiliation(s)
- Burcu Vitrinel
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA
| | - Christine Vogel
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Lionel Christiaen
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA
- Michael Sars Centre, University of Bergen, P.O. Box 7800, 5020 Bergen, Norway
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13
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Johnson CJ, Kulkarni A, Buxton WJ, Hui TY, Kayastha A, Khoja AA, Leandre J, Mehta VV, Ostrowski L, Pareizs EG, Scotto RL, Vargas V, Vellingiri RM, Verzino G, Vohra R, Wakade SC, Winkeljohn VM, Winkeljohn VM, Rotterman TM, Stolfi A. Using CRISPR/Cas9 to identify genes required for mechanosensory neuron development and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539861. [PMID: 37214826 PMCID: PMC10197531 DOI: 10.1101/2023.05.08.539861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Tunicates are marine, non-vertebrate chordates that comprise the sister group to the vertebrates. Most tunicates have a biphasic lifecycle that alternates between a swimming larva and a sessile adult. Recent advances have shed light on the neural basis for the tunicate larva's ability to sense a proper substrate for settlement and initiate metamorphosis. Work in the highly tractable laboratory model tunicate Ciona robusta suggests that sensory neurons embedded in the anterior papillae of transduce mechanosensory stimuli to trigger larval tail retraction and initiate the process of metamorphosis. Here, we take advantage of the low-cost and simplicity of Ciona by using tissue-specific CRISPR/Cas9-mediated mutagenesis to screen for genes potentially involved in mechanosensation and metamorphosis, in the context of an undergraduate "capstone" research course. This small screen revealed at least one gene, Vamp1/2/3 , that appears crucial for the ability of the papillae to trigger metamorphosis. We also provide step-by-step protocols and tutorials associated with this course, in the hope that it might be replicated in similar CRISPR-based laboratory courses wherever Ciona are available.
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14
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Quantitative Phosphoproteomics Reveals the Requirement of DYRK1-Mediated Phosphorylation of Ion Transport- and Cell Junction-Related Proteins for Notochord Lumenogenesis in Ascidian. Cells 2023; 12:cells12060921. [PMID: 36980262 PMCID: PMC10047359 DOI: 10.3390/cells12060921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023] Open
Abstract
The dual-specificity tyrosine phosphorylation-regulated kinase (DYRK1) phosphorylates diverse substrates involved in various cellular processes. Here, we found that blocking the kinase activity of DYRK1 inhibited notochord development and lumenogenesis in ascidian Ciona savignyi. By performing phosphoproteomics in conjunction with notochord-specific proteomics, we identified 1065 notochord-specific phosphoproteins that were present during lumen inflation, of which 428 differentially phosphorylated proteins (DPPs) were identified after inhibition of DYRK1 kinase activity. These DPPs were significantly enriched in metal ion transmembrane transporter activity, protein transport and localization, and tight junction. We next analyzed the downregulated phosphoproteins and focused on those belonging to the solute carrier (SLC), Ras-related protein (RAB), and tight junction protein (TJP) families. In vivo phospho-deficient study showed that alanine mutations on the phosphosites of these proteins resulted in defects of lumenogenesis during Ciona notochord development, demonstrating the crucial roles of phosphorylation of transmembrane transport-, vesicle trafficking-, and tight junction-related proteins in lumen formation. Overall, our study provides a valuable data resource for investigating notochord lumenogenesis and uncovers the molecular mechanisms of DYRK1-mediated notochord development and lumen inflation.
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15
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Kim K, Orvis J, Stolfi A. Pax3/7 regulates neural tube closure and patterning in a non-vertebrate chordate. Front Cell Dev Biol 2022; 10:999511. [PMID: 36172287 PMCID: PMC9511217 DOI: 10.3389/fcell.2022.999511] [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: 07/21/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022] Open
Abstract
Pax3/7 factors play numerous roles in the development of the dorsal nervous system of vertebrates. From specifying neural crest at the neural plate borders, to regulating neural tube closure and patterning of the resulting neural tube. However, it is unclear which of these roles are conserved in non-vertebrate chordates. Here we investigate the expression and function of Pax3/7 in the model tunicate Ciona. Pax3/7 is expressed in neural plate border cells during neurulation, and in central nervous system progenitors shortly after neural tube closure. We find that separate cis-regulatory elements control the expression in these two distinct lineages. Using CRISPR/Cas9-mediated mutagenesis, we knocked out Pax3/7 in F0 embryos specifically in these two separate territories. Pax3/7 knockout in the neural plate borders resulted in neural tube closure defects, suggesting an ancient role for Pax3/7 in this chordate-specific process. Furthermore, knocking out Pax3/7 in the neural impaired Motor Ganglion neuron specification, confirming a conserved role for this gene in patterning the neural tube as well. Taken together, these results suggests that key functions of Pax3/7 in neural tube development are evolutionarily ancient, dating back at least to the last common ancestor of vertebrates and tunicates.
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16
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Zhang H, Shang R, Kim K, Zheng W, Johnson CJ, Sun L, Niu X, Liu L, Zhou J, Liu L, Zhang Z, Uyeno TA, Pei J, Fissette SD, Green SA, Samudra SP, Wen J, Zhang J, Eggenschwiler JT, Menke DB, Bronner ME, Grishin NV, Li W, Ye K, Zhang Y, Stolfi A, Bi P. Evolution of a chordate-specific mechanism for myoblast fusion. SCIENCE ADVANCES 2022; 8:eadd2696. [PMID: 36054355 PMCID: PMC10848958 DOI: 10.1126/sciadv.add2696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Vertebrate myoblast fusion allows for multinucleated muscle fibers to compound the size and strength of mononucleated cells, but the evolution of this important process is unknown. We investigated the evolutionary origins and function of membrane-coalescing agents Myomaker and Myomixer in various groups of chordates. Here, we report that Myomaker likely arose through gene duplication in the last common ancestor of tunicates and vertebrates, while Myomixer appears to have evolved de novo in early vertebrates. Functional tests revealed a complex evolutionary history of myoblast fusion. A prevertebrate phase of muscle multinucleation driven by Myomaker was followed by the later emergence of Myomixer that enables the highly efficient fusion system of vertebrates. Evolutionary comparisons between vertebrate and nonvertebrate Myomaker revealed key structural and mechanistic insights into myoblast fusion. Thus, our findings suggest an evolutionary model of chordate fusogens and illustrate how new genes shape the emergence of novel morphogenetic traits and mechanisms.
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Affiliation(s)
- Haifeng Zhang
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
| | - Renjie Shang
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Kwantae Kim
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Wei Zheng
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | | | - Lei Sun
- The Fifth People’s Hospital of Shanghai, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xiang Niu
- Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, USA
| | - Liang Liu
- Department of Statistics, University of Georgia, Athens, GA, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Jingqi Zhou
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Lingshu Liu
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Zheng Zhang
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
| | | | - Jimin Pei
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Skye D. Fissette
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Stephen A. Green
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - Junfei Wen
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
| | - Jianli Zhang
- College of Engineering, University of Georgia, Athens, GA, USA
| | | | | | - Marianne E. Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Nick V. Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Weiming Li
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Kaixiong Ye
- Department of Genetics, University of Georgia, Athens, GA, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Pengpeng Bi
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
- Department of Genetics, University of Georgia, Athens, GA, USA
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17
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Athira A, Dondorp D, Rudolf J, Peytral O, Chatzigeorgiou M. Comprehensive analysis of locomotion dynamics in the protochordate Ciona intestinalis reveals how neuromodulators flexibly shape its behavioral repertoire. PLoS Biol 2022; 20:e3001744. [PMID: 35925898 PMCID: PMC9352054 DOI: 10.1371/journal.pbio.3001744] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 07/06/2022] [Indexed: 11/19/2022] Open
Abstract
Vertebrate nervous systems can generate a remarkable diversity of behaviors. However, our understanding of how behaviors may have evolved in the chordate lineage is limited by the lack of neuroethological studies leveraging our closest invertebrate relatives. Here, we combine high-throughput video acquisition with pharmacological perturbations of bioamine signaling to systematically reveal the global structure of the motor behavioral repertoire in the Ciona intestinalis larvae. Most of Ciona’s postural variance can be captured by 6 basic shapes, which we term “eigencionas.” Motif analysis of postural time series revealed numerous stereotyped behavioral maneuvers including “startle-like” and “beat-and-glide.” Employing computational modeling of swimming dynamics and spatiotemporal embedding of postural features revealed that behavioral differences are generated at the levels of motor modules and the transitions between, which may in part be modulated by bioamines. Finally, we show that flexible motor module usage gives rise to diverse behaviors in response to different light stimuli. Vertebrate nervous systems can generate a remarkable diversity of behaviors, but how did these evolve in the chordate lineage? A study of the protochordate Ciona intestinalis reveals novel insights into how a simple chordate brain uses neuromodulators to control its behavioral repertoire.
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Affiliation(s)
- Athira Athira
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Daniel Dondorp
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Jerneja Rudolf
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Olivia Peytral
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Marios Chatzigeorgiou
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
- * E-mail:
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18
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Song M, Yuan X, Racioppi C, Leslie M, Stutt N, Aleksandrova A, Christiaen L, Wilson MD, Scott IC. GATA4/5/6 family transcription factors are conserved determinants of cardiac versus pharyngeal mesoderm fate. SCIENCE ADVANCES 2022; 8:eabg0834. [PMID: 35275720 PMCID: PMC8916722 DOI: 10.1126/sciadv.abg0834] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
GATA4/5/6 transcription factors play essential, conserved roles in heart development. To understand how GATA4/5/6 modulates the mesoderm-to-cardiac fate transition, we labeled, isolated, and performed single-cell gene expression analysis on cells that express gata5 at precardiac time points spanning zebrafish gastrulation to somitogenesis. We found that most mesendoderm-derived lineages had dynamic gata5/6 expression. In the absence of Gata5/6, the population structure of mesendoderm-derived cells was substantially altered. In addition to the expected absence of cardiac mesoderm, we confirmed a concomitant expansion of cranial-pharyngeal mesoderm. Moreover, Gata5/6 loss led to extensive changes in chromatin accessibility near cardiac and pharyngeal genes. Functional analyses in zebrafish and the tunicate Ciona, which has a single GATA4/5/6 homolog, revealed that GATA4/5/6 acts upstream of tbx1 to exert essential and cell-autonomous roles in promoting cardiac and inhibiting pharyngeal mesoderm identity. Overall, cardiac and pharyngeal mesoderm fate choices are achieved through an evolutionarily conserved GATA4/5/6 regulatory network.
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Affiliation(s)
- Mengyi Song
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Xuefei Yuan
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Claudia Racioppi
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY, USA
| | - Meaghan Leslie
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Nathan Stutt
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Anastasiia Aleksandrova
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Canada
| | - Lionel Christiaen
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY, USA
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
- Department of Heart Disease, Haukeland University Hospital, Bergen, Norway
| | - Michael D. Wilson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Corresponding author. (M.D.W.); (I.C.S.)
| | - Ian C. Scott
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Corresponding author. (M.D.W.); (I.C.S.)
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19
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Popsuj S, Stolfi A. Ebf Activates Expression of a Cholinergic Locus in a Multipolar Motor Ganglion Interneuron Subtype in Ciona. Front Neurosci 2022; 15:784649. [PMID: 34975385 PMCID: PMC8719597 DOI: 10.3389/fnins.2021.784649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
Conserved transcription factors termed “terminal selectors” regulate neuronal sub-type specification and differentiation through combinatorial transcriptional regulation of terminal differentiation genes. The unique combinations of terminal differentiation gene products in turn contribute to the functional identities of each neuron. One well-characterized terminal selector is COE (Collier/Olf/Ebf), which has been shown to activate cholinergic gene batteries in C. elegans motor neurons. However, its functions in other metazoans, particularly chordates, is less clear. Here we show that the sole COE ortholog in the non-vertebrate chordate Ciona robusta, Ebf, controls the expression of the cholinergic locus VAChT/ChAT in a single dorsal interneuron of the larval Motor Ganglion, which is presumed to be homologous to the vertebrate spinal cord. We propose that, while the function of Ebf as a regulator of cholinergic neuron identity conserved across bilaterians, its exact role may have diverged in different cholinergic neuron subtypes (e.g., interneurons vs. motor neurons) in chordate-specific motor circuits.
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Affiliation(s)
- Sydney Popsuj
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
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20
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Bernadskaya YY, Yue H, Copos C, Christiaen L, Mogilner A. Supracellular organization confers directionality and mechanical potency to migrating pairs of cardiopharyngeal progenitor cells. eLife 2021; 10:e70977. [PMID: 34842140 PMCID: PMC8700272 DOI: 10.7554/elife.70977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 11/26/2021] [Indexed: 12/26/2022] Open
Abstract
Physiological and pathological morphogenetic events involve a wide array of collective movements, suggesting that multicellular arrangements confer biochemical and biomechanical properties contributing to tissue-scale organization. The Ciona cardiopharyngeal progenitors provide the simplest model of collective cell migration, with cohesive bilateral cell pairs polarized along the leader-trailer migration path while moving between the ventral epidermis and trunk endoderm. We use the Cellular Potts Model to computationally probe the distributions of forces consistent with shapes and collective polarity of migrating cell pairs. Combining computational modeling, confocal microscopy, and molecular perturbations, we identify cardiopharyngeal progenitors as the simplest cell collective maintaining supracellular polarity with differential distributions of protrusive forces, cell-matrix adhesion, and myosin-based retraction forces along the leader-trailer axis. 4D simulations and experimental observations suggest that cell-cell communication helps establish a hierarchy to align collective polarity with the direction of migration, as observed with three or more cells in silico and in vivo. Our approach reveals emerging properties of the migrating collective: cell pairs are more persistent, migrating longer distances, and presumably with higher accuracy. Simulations suggest that cell pairs can overcome mechanical resistance of the trunk endoderm more effectively when they are polarized collectively. We propose that polarized supracellular organization of cardiopharyngeal progenitors confers emergent physical properties that determine mechanical interactions with their environment during morphogenesis.
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Affiliation(s)
- Yelena Y Bernadskaya
- Center for Developmental Genetics, Department of Biology, New York UniversityNew YorkUnited States
| | - Haicen Yue
- Courant Institute of Mathematical Sciences and Department of Biology, New York UniversityNew YorkUnited States
| | - Calina Copos
- Mathematics and Computational Medicine, University of North Carolina at Chapel HillChapel HillUnited States
| | - Lionel Christiaen
- Center for Developmental Genetics, Department of Biology, New York UniversityNew YorkUnited States
- Sars International Centre for Marine Molecular BiologyBergenNorway
- Department of Heart Disease, Haukeland University HospitalBergenNorway
| | - Alex Mogilner
- Courant Institute of Mathematical Sciences and Department of Biology, New York UniversityNew YorkUnited States
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21
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Kolar K, Dondorp D, Zwiggelaar JC, Høyer J, Chatzigeorgiou M. Mesmerize is a dynamically adaptable user-friendly analysis platform for 2D and 3D calcium imaging data. Nat Commun 2021; 12:6569. [PMID: 34772921 PMCID: PMC8589933 DOI: 10.1038/s41467-021-26550-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 10/13/2021] [Indexed: 01/09/2023] Open
Abstract
Calcium imaging is an increasingly valuable technique for understanding neural circuits, neuroethology, and cellular mechanisms. The analysis of calcium imaging data presents challenges in image processing, data organization, analysis, and accessibility. Tools have been created to address these problems independently, however a comprehensive user-friendly package does not exist. Here we present Mesmerize, an efficient, expandable and user-friendly analysis platform, which uses a Findable, Accessible, Interoperable and Reproducible (FAIR) system to encapsulate the entire analysis process, from raw data to interactive visualizations for publication. Mesmerize provides a user-friendly graphical interface to state-of-the-art analysis methods for signal extraction & downstream analysis. We demonstrate the broad scientific scope of Mesmerize's applications by analyzing neuronal datasets from mouse and a volumetric zebrafish dataset. We also applied contemporary time-series analysis techniques to analyze a novel dataset comprising neuronal, epidermal, and migratory mesenchymal cells of the protochordate Ciona intestinalis.
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Affiliation(s)
- Kushal Kolar
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5006, Bergen, Norway.
| | - Daniel Dondorp
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5006, Bergen, Norway
| | | | - Jørgen Høyer
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5006, Bergen, Norway
| | - Marios Chatzigeorgiou
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5006, Bergen, Norway.
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22
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Kourakis MJ, Bostwick M, Zabriskie A, Smith WC. Disruption of left-right axis specification in Ciona induces molecular, cellular, and functional defects in asymmetric brain structures. BMC Biol 2021; 19:141. [PMID: 34256748 PMCID: PMC8276506 DOI: 10.1186/s12915-021-01075-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/17/2021] [Indexed: 11/28/2022] Open
Abstract
Background Left-right asymmetries are a common feature of metazoans and can be found in a number of organs including the nervous system. These asymmetries are particularly pronounced in the simple central nervous system (CNS) of the swimming tadpole larva of the tunicate Ciona, which displays a chordate ground plan. While common pathway elements for specifying the left/right axis are found among chordates, particularly a requirement for Nodal signaling, Ciona differs temporally from its vertebrate cousins by specifying its axis at the neurula stage, rather than at gastrula. Additionally, Ciona and other ascidians require an intact chorionic membrane for proper left-right specification. Whether such differences underlie distinct specification mechanisms between tunicates and vertebrates will require broad understanding of their influence on CNS formation. Here, we explore the consequences of disrupting left-right axis specification on Ciona larval CNS cellular anatomy, gene expression, synaptic connectivity, and behavior. Results We show that left-right asymmetry disruptions caused by removal of the chorion (dechorionation) are highly variable and present throughout the Ciona larval nervous system. While previous studies have documented disruptions to the conspicuously asymmetric sensory systems in the anterior brain vesicle, we document asymmetries in seemingly symmetric structures such as the posterior brain vesicle and motor ganglion. Moreover, defects caused by dechorionation include misplaced or absent neuron classes, loss of asymmetric gene expression, aberrant synaptic projections, and abnormal behaviors. In the motor ganglion, a brain structure that has been equated with the vertebrate hindbrain, we find that despite the apparent left-right symmetric distribution of interneurons and motor neurons, AMPA receptors are expressed exclusively on the left side, which equates with asymmetric swimming behaviors. We also find that within a population of dechorionated larvae, there is a small percentage with apparently normal left-right specification and approximately equal population with inverted (mirror-image) asymmetry. We present a method based on a behavioral assay for isolating these larvae. When these two classes of larvae (normal and inverted) are assessed in a light dimming assay, they display mirror-image behaviors, with normal larvae responding with counterclockwise swims, while inverted larvae respond with clockwise swims. Conclusions Our findings highlight the importance of left-right specification pathways not only for proper CNS anatomy, but also for correct synaptic connectivity and behavior. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01075-4.
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Affiliation(s)
- Matthew J Kourakis
- Neuroscience Research Institute, University of California, Santa Barbara, CA, 93106, USA
| | - Michaela Bostwick
- College of Creative Studies, University of California, Santa Barbara, CA, 93106, USA
| | - Amanda Zabriskie
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - William C Smith
- Neuroscience Research Institute, University of California, Santa Barbara, CA, 93106, USA. .,Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA.
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23
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Wang Z, Sun X, Zhang X, Dong B, Yu H. Development of a miRNA Sensor by an Inducible CRISPR-Cas9 Construct in Ciona Embryogenesis. Mol Biotechnol 2021; 63:613-620. [PMID: 33880702 DOI: 10.1007/s12033-021-00324-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/29/2021] [Indexed: 11/28/2022]
Abstract
MicroRNAs (miRNAs) regulate multicellular processes and diverse signaling pathways in organisms. The detection of the spatiotemporal expression of miRNA in vivo is crucial for uncovering the function of miRNA. However, most of the current detecting techniques cannot reflect the dynamics of miRNA sensitively in vivo. Here, we constructed a miRNA-induced CRISPR-Cas9 platform (MICR) used in marine chordate Ciona. The key component of MICR is a pre-single guide RNA (sgRNA) flanked by miRNA-binding sites that can be released by RNA-induced silencing complex (RISC) cleavage to form functional sgRNA in the presence of complementary miRNA. By using the miRNA-inducible CRISPR-on system (MICR-ON), we successfully detected the dynamic expression of a miRNA csa-miR-4018a during development of Ciona embryo. The detected patterns were validated to be consistent with the results by in situ hybridization. It is worth noting that the expression of csa-miR-4018a was examined by MICR-ON to be present in additional tissues, where no obvious signaling was detected by in situ hybridization, suggesting that the MICR-ON might be a more sensitive approach to detect miRNA signal in living animal. Thus, MICR-ON was demonstrated to be a sensitive and highly efficient approach for monitoring the dynamics of expression of miRNA in vivo and will facilitate the exploration of miRNA functions in biological systems.
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Affiliation(s)
- Zhuqing Wang
- Sars-Fang Centre, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xueping Sun
- Sars-Fang Centre, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoming Zhang
- Sars-Fang Centre, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Bo Dong
- Sars-Fang Centre, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
| | - Haiyan Yu
- Sars-Fang Centre, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, China.
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24
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Lemaire LA, Cao C, Yoon PH, Long J, Levine M. The hypothalamus predates the origin of vertebrates. SCIENCE ADVANCES 2021; 7:7/18/eabf7452. [PMID: 33910896 PMCID: PMC8081355 DOI: 10.1126/sciadv.abf7452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/09/2021] [Indexed: 05/02/2023]
Abstract
The hypothalamus coordinates neuroendocrine functions in vertebrates. To explore its evolutionary origin, we describe integrated transcriptome/connectome brain maps for swimming tadpoles of Ciona, which serves as an approximation of the ancestral proto-vertebrate. This map features several cell types related to different regions of the vertebrate hypothalamus, including the mammillary nucleus, the arcuate nucleus, and magnocellular neurons. Coronet cells express melanopsin and share additional properties with the saccus vasculosus, a specialized region of the hypothalamus that mediates photoperiodism in nontropical fishes. Comparative transcriptome analyses identified orthologous cell types for mechanosensory switch neurons, and VP+ and VPR+ relay neurons in different regions of the mouse hypothalamus. These observations provide evidence that the hypothalamus predates the evolution of the vertebrate brain. We discuss the possibility that switch neurons, coronet cells, and FoxP+ /VPR+ relay neurons comprise a behavioral circuit that helps trigger metamorphosis of Ciona larvae in response to twilight.
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Affiliation(s)
- Laurence A Lemaire
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Chen Cao
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Peter H Yoon
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Juanjuan Long
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Michael Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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25
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Lowe EK, Racioppi C, Peyriéras N, Ristoratore F, Christiaen L, Swalla BJ, Stolfi A. A cis-regulatory change underlying the motor neuron-specific loss of Ebf expression in immotile tunicate larvae. Evol Dev 2021; 23:72-85. [PMID: 33355999 PMCID: PMC7920938 DOI: 10.1111/ede.12364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 10/23/2020] [Accepted: 12/06/2020] [Indexed: 11/26/2022]
Abstract
Many species in the tunicate family Molgulidae have independently lost their swimming larval form and instead develop as tailless, immotile larvae. These larvae do not develop structures that are essential for swimming such as the notochord, otolith, and tail muscles. However, little is known about neural development in these nonswimming larvae. Here, we studied the patterning of the Motor Ganglion (MG) of Molgula occulta, a nonswimming species. We found that spatial patterns of MG neuron regulators in this species are conserved, compared with species with swimming larvae, suggesting that the gene networks regulating their expression are intact despite the loss of swimming. However, expression of the key motor neuron regulatory gene Ebf (Collier/Olf/EBF) was reduced in the developing MG of M. occulta when compared with molgulid species with swimming larvae. This was corroborated by measuring allele-specific expression of Ebf in hybrid embryos from crosses of M. occulta with the swimming species M. oculata. Heterologous reporter construct assays in the model tunicate species Ciona robusta revealed a specific cis-regulatory sequence change that reduces expression of Ebf in the MG, but not in other cells. Taken together, these data suggest that MG neurons are still specified in M. occulta larvae, but their differentiation might be impaired due to reduction of Ebf expression levels.
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Affiliation(s)
- Elijah K. Lowe
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Station Biologique de Roscoff, Roscoff, France
| | - Claudia Racioppi
- Station Biologique de Roscoff, Roscoff, France
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY, USA
| | - Nadine Peyriéras
- Station Biologique de Roscoff, Roscoff, France
- UPS3611 Complex Systems Institute Paris Ile-de-France (ISC-PIF), CNRS, Paris, France
- USR3695 BioEmergences, CNRS, Paris-Saclay University, Gif-sur-Yvette, France
| | - Filomena Ristoratore
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Lionel Christiaen
- Station Biologique de Roscoff, Roscoff, France
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY, USA
| | - Billie J. Swalla
- Station Biologique de Roscoff, Roscoff, France
- Department of Biology, University of Washington, Seattle, WA, USA
- Friday Harbor Laboratories, University of Washington, Friday Harbor, WA, USA
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Station Biologique de Roscoff, Roscoff, France
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26
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Zhang T, Xu Y, Imai K, Fei T, Wang G, Dong B, Yu T, Satou Y, Shi W, Bao Z. A single-cell analysis of the molecular lineage of chordate embryogenesis. SCIENCE ADVANCES 2020; 6:eabc4773. [PMID: 33148647 PMCID: PMC7673699 DOI: 10.1126/sciadv.abc4773] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/16/2020] [Indexed: 05/05/2023]
Abstract
Progressive unfolding of gene expression cascades underlies diverse embryonic lineage development. Here, we report a single-cell RNA sequencing analysis of the complete and invariant embryonic cell lineage of the tunicate Ciona savignyi from fertilization to the onset of gastrulation. We reconstructed a developmental landscape of 47 cell types over eight cell cycles in the wild-type embryo and identified eight fate transformations upon fibroblast growth factor (FGF) inhibition. For most FGF-dependent asymmetric cell divisions, the bipotent mother cell displays the gene signature of the default daughter fate. In convergent differentiation of the two notochord lineages, we identified additional gene pathways parallel to the master regulator T/Brachyury Last, we showed that the defined Ciona cell types can be matched to E6.5-E8.5 stage mouse cell types and display conserved expression of limited number of transcription factors. This study provides a high-resolution single-cell dataset to understand chordate early embryogenesis and cell lineage differentiation.
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Affiliation(s)
- Tengjiao Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200123, China
| | - Yichi Xu
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Kaoru Imai
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan
| | - Teng Fei
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Guilin Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Bo Dong
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Tianwei Yu
- School of Data Science, The Chinese University of Hong Kong-Shenzhen, Shenzhen, Guangdong 518172, China
| | - Yutaka Satou
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Weiyang Shi
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.
| | - Zhirong Bao
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA.
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27
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Coppola U, Kamal AK, Stolfi A, Ristoratore F. The Cis-Regulatory Code for Kelch-like 21/30 Specific Expression in Ciona robusta Sensory Organs. Front Cell Dev Biol 2020; 8:569601. [PMID: 33043001 PMCID: PMC7517041 DOI: 10.3389/fcell.2020.569601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/17/2020] [Indexed: 12/18/2022] Open
Abstract
The tunicate Ciona robusta is an emerging model system to study the evolution of the nervous system. Due to their small embryos and compact genomes, tunicates, like Ciona robusta, have great potential to comprehend genetic circuitry underlying cell specific gene repertoire, among different neuronal cells. Their simple larvae possess a sensory vesicle comprising two pigmented sensory organs, the ocellus and the otolith. We focused here on Klhl21/30, a gene belonging to Kelch family, that, in Ciona robusta, starts to be expressed in pigmented cell precursors, becoming specifically maintained in the otolith precursor during embryogenesis. Evolutionary analyses demonstrated the conservation of Klhl21/30 in all the chordates. Cis-regulatory analyses and CRISPR/Cas9 mutagenesis of potential upstream factors, revealed that Klhl21/30 expression is controlled by the combined action of three transcription factors, Mitf, Dmrt, and Msx, which are downstream of FGF signaling. The central role of Mitf is consistent with its function as a fundamental regulator of vertebrate pigment cell development. Moreover, our results unraveled a new function for Dmrt and Msx as transcriptional co-activators in the context of the Ciona otolith.
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Affiliation(s)
- Ugo Coppola
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Naples, Italy.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Ashwani Kumar Kamal
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Naples, Italy
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Filomena Ristoratore
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn Napoli, Naples, Italy
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28
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Coppola U, Olivo P, D’Aniello E, Johnson CJ, Stolfi A, Ristoratore F. Rimbp, a New Marker for the Nervous System of the Tunicate Ciona robusta. Genes (Basel) 2020; 11:genes11091006. [PMID: 32867148 PMCID: PMC7565545 DOI: 10.3390/genes11091006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/16/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022] Open
Abstract
Establishment of presynaptic mechanisms by proteins that regulate neurotransmitter release in the presynaptic active zone is considered a fundamental step in animal evolution. Rab3 interacting molecule-binding proteins (Rimbps) are crucial components of the presynaptic active zone and key players in calcium homeostasis. Although Rimbp involvement in these dynamics has been described in distantly related models such as fly and human, the role of this family in most invertebrates remains obscure. To fill this gap, we defined the evolutionary history of Rimbp family in animals, from sponges to mammals. We report, for the first time, the expression of the two isoforms of the unique Rimbp family member in Ciona robusta in distinct domains of the larval nervous system. We identify intronic enhancers that are able to drive expression in different nervous system territories partially corresponding to Rimbp endogenous expression. The analysis of gene expression patterns and the identification of regulatory elements of Rimbp will positively impact our understanding of this family of genes in the context of Ciona embryogenesis.
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Affiliation(s)
- Ugo Coppola
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy; (U.C.); (P.O.); (E.D.)
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Paola Olivo
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy; (U.C.); (P.O.); (E.D.)
| | - Enrico D’Aniello
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy; (U.C.); (P.O.); (E.D.)
| | | | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA;
- Correspondence: (A.S.); (F.R.)
| | - Filomena Ristoratore
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy; (U.C.); (P.O.); (E.D.)
- Correspondence: (A.S.); (F.R.)
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29
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Asymmetric Fitness of Second-Generation Interspecific Hybrids Between Ciona robusta and Ciona intestinalis. G3-GENES GENOMES GENETICS 2020; 10:2697-2711. [PMID: 32518083 PMCID: PMC7407461 DOI: 10.1534/g3.120.401427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Reproductive isolation is central to speciation, but interspecific crosses between two closely related species can produce viable and fertile hybrids. Two different species of tunicates in the same ascidian genus, Ciona robusta and Ciona intestinalis, can produce hybrids. However, wild sympatric populations display limited gene flow, suggesting the existence of obstacles to interspecific reproduction that remain unknown. Here, we took advantage of a closed culture system to cross C. robusta with C. intestinalis and established F1 and F2 hybrids. We monitored post-embryonic development, survival, and sexual maturation to characterize the genetic basis of simple traits, and further probe the physiological mechanisms underlying reproductive isolation. Partial viability of first and second generation hybrids suggested that both pre- and postzygotic mechanisms contributed to genomic incompatibilities in hybrids. We observed asymmetric fitness, whereby the C. intestinalis maternal lines fared more poorly in our system, pointing to maternal origins of species-specific sensitivity. We discuss the possibility that asymmetrical second generation inviability and infertility emerge from interspecific incompatibilities between the nuclear and mitochondrial genomes, or other maternal effect genes. This work paves the way to quantitative genetic approaches to study the mechanisms underlying genomic incompatibilities and other complex traits in the genome-enabled Ciona model.
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30
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Johnson CJ, Razy-Krajka F, Stolfi A. Expression of smooth muscle-like effectors and core cardiomyocyte regulators in the contractile papillae of Ciona. EvoDevo 2020; 11:15. [PMID: 32774829 PMCID: PMC7397655 DOI: 10.1186/s13227-020-00162-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/22/2020] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The evolution of vertebrate smooth muscles is obscured by lack of identifiable smooth muscle-like cells in tunicates, the invertebrates most closely related to vertebrates. A recent evolutionary model was proposed in which smooth muscles arose before the last bilaterian common ancestor, and were later diversified, secondarily lost or modified in the branches leading to extant animal taxa. However, there is currently no data from tunicates to support this scenario. METHODS AND RESULTS Here, we show that the axial columnar cells, a unique cell type in the adhesive larval papillae of the tunicate Ciona, are enriched for orthologs of vertebrate smooth/non-muscle-specific effectors of contractility, in addition to developing from progenitors that express conserved cardiomyocyte regulatory factors. We show that these cells contract during the retraction of the Ciona papillae during larval settlement and metamorphosis. CONCLUSIONS We propose that the axial columnar cells of Ciona are a myoepithelial cell type required for transducing external stimuli into mechanical forces that aid in the attachment of the motile larva to its final substrate. Furthermore, they share developmental and functional features with vertebrate myoepithelial cells, vascular smooth muscle cells, and cardiomyocytes. We discuss these findings in the context of the proposed models of vertebrate smooth muscle and cardiomyocyte evolution.
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31
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Vitrinel B, Iannitelli DE, Mazzoni EO, Christiaen L, Vogel C. Simple Method to Quantify Protein Abundances from 1000 Cells. ACS OMEGA 2020; 5:15537-15546. [PMID: 32637829 PMCID: PMC7331059 DOI: 10.1021/acsomega.0c01191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/09/2020] [Indexed: 05/29/2023]
Abstract
The rise of single-cell transcriptomics has created an urgent need for similar approaches that use a minimal number of cells to quantify expression levels of proteins. We integrated and optimized multiple recent developments to establish a proteomics workflow to quantify proteins from as few as 1000 mammalian stem cells. The method uses chemical peptide labeling, does not require specific equipment other than cell lysis tools, and quantifies >2500 proteins with high reproducibility. We validated the method by comparing mouse embryonic stem cells and in vitro differentiated motor neurons. We identify differentially expressed proteins with small fold changes and a dynamic range in abundance similar to that of standard methods. Protein abundance measurements obtained with our protocol compared well to corresponding transcript abundance and to measurements using standard inputs. The protocol is also applicable to other systems, such as fluorescence-activated cell sorting (FACS)-purified cells from the tunicate Ciona. Therefore, we offer a straightforward and accurate method to acquire proteomics data from minimal input samples.
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Affiliation(s)
- Burcu Vitrinel
- Center
for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, United States
- Center
for Developmental Genetics, Department of Biology, New York University, New York, New York 10003, United States
| | - Dylan E. Iannitelli
- Center
for Developmental Genetics, Department of Biology, New York University, New York, New York 10003, United States
| | - Esteban O. Mazzoni
- Center
for Developmental Genetics, Department of Biology, New York University, New York, New York 10003, United States
- NYU
Neuroscience Institute, NYU Langone Medical
Center, New York, New York 10016, United
States
| | - Lionel Christiaen
- Center
for Developmental Genetics, Department of Biology, New York University, New York, New York 10003, United States
| | - Christine Vogel
- Center
for Genomics and Systems Biology, Department of Biology, New York University, New York, New York 10003, United States
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32
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Kim K, Gibboney S, Razy-Krajka F, Lowe EK, Wang W, Stolfi A. Regulation of Neurogenesis by FGF Signaling and Neurogenin in the Invertebrate Chordate Ciona. Front Cell Dev Biol 2020; 8:477. [PMID: 32656209 PMCID: PMC7324659 DOI: 10.3389/fcell.2020.00477] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/21/2020] [Indexed: 12/22/2022] Open
Abstract
Neurogenesis is a complex sequence of cellular processes and behaviors driven by the coordinated expression of conserved effectors. The bipolar tail neurons (BTNs) of Ciona develop according to a highly dynamic, yet highly stereotyped developmental program and thus could serve as an accessible model system for neurogenesis, including underlying cell behaviors like neuronal delamination, migration, and polarized axon outgrowth. Here we investigate both the upstream events that shape BTN neurogenesis through spatiotemporal regulation of the conserved proneural factor Neurog, spatiotemporal, and the gene expression profile of differentiating BTNs downstream of Neurog activity. We show that, although early FGF signaling is required for Neurog expression and BTN specification, Fgf8/17/18 is expressed in tail tip cells at later stages and suppresses sustained Neurog expression in the anterior BTN (aBTN) lineage, such that only one cell (the one furthest from the source of Fgf8/17/18) maintains Neurog expression and becomes a neuron. Curiously, Fgf8/17/18 might not affect neurogenesis of the posterior BTNs (pBTNs), which are in direct contact with the Fgf8/17/18-expressing cells. Finally, to profile gene expression associated with BTN neurogenesis we performed RNAseq of isolated BTN lineage cells in which BTN neurogenesis was enhanced or suppressed by perturbing Neurog function. This allowed us to identify several candidate genes that might play conserved roles in neurogenesis and neuronal migration in other animals, including mammals.
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Affiliation(s)
- Kwantae Kim
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Susanne Gibboney
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Florian Razy-Krajka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Elijah K. Lowe
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Wei Wang
- Department of Biology, New York University, New York, NY, United States
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
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33
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Gibboney S, Orvis J, Kim K, Johnson CJ, Martinez-Feduchi P, Lowe EK, Sharma S, Stolfi A. Effector gene expression underlying neuron subtype-specific traits in the Motor Ganglion of Ciona. Dev Biol 2020; 458:52-63. [PMID: 31639337 PMCID: PMC6987015 DOI: 10.1016/j.ydbio.2019.10.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/11/2019] [Accepted: 10/16/2019] [Indexed: 12/31/2022]
Abstract
The central nervous system of the Ciona larva contains only 177 neurons. The precise regulation of neuron subtype-specific morphogenesis and differentiation observed during the formation of this minimal connectome offers a unique opportunity to dissect gene regulatory networks underlying chordate neurodevelopment. Here we compare the transcriptomes of two very distinct neuron types in the hindbrain/spinal cord homolog of Ciona, the Motor Ganglion (MG): the Descending decussating neuron (ddN, proposed homolog of Mauthner Cells in vertebrates) and the MG Interneuron 2 (MGIN2). Both types are invariantly represented by a single bilaterally symmetric left/right pair of cells in every larva. Supernumerary ddNs and MGIN2s were generated in synchronized embryos and isolated by fluorescence-activated cell sorting for transcriptome profiling. Differential gene expression analysis revealed ddN- and MGIN2-specific enrichment of a wide range of genes, including many encoding potential "effectors" of subtype-specific morphological and functional traits. More specifically, we identified the upregulation of centrosome-associated, microtubule-stabilizing/bundling proteins and extracellular guidance cues part of a single intrinsic regulatory program that might underlie the unique polarization of the ddNs, the only descending MG neurons that cross the midline. Consistent with our predictions, CRISPR/Cas9-mediated, tissue-specific elimination of two such candidate effectors, Efcab6-related and Netrin1, impaired ddN polarized axon outgrowth across the midline.
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Affiliation(s)
- Susanne Gibboney
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Jameson Orvis
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Kwantae Kim
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Christopher J Johnson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | | | - Elijah K Lowe
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Sarthak Sharma
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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Magri MS, Jiménez-Gancedo S, Bertrand S, Madgwick A, Escrivà H, Lemaire P, Gómez-Skarmeta JL. Assaying Chromatin Accessibility Using ATAC-Seq in Invertebrate Chordate Embryos. Front Cell Dev Biol 2020; 7:372. [PMID: 32039199 PMCID: PMC6992535 DOI: 10.3389/fcell.2019.00372] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/16/2019] [Indexed: 01/30/2023] Open
Abstract
Cis-regulatory elements (CREs) are non-coding DNA regions involved in the spatio-temporal regulation of gene expression. Gene regulatory changes drive animal development and play major roles during evolution of animal body plans. Therefore, we believe that determining CREs at different developmental stages and across animal lineages is critical to understand how evolution operates through development. The Assay for Transposase-Accessible Chromatin followed by high-throughput sequencing (ATAC-seq) is a powerful technique for the study of CREs that takes advantage of Tn5 transposase activity. Starting from fewer than 105 cells, in a 1-day procedure, it is possible to detect, at a genome-wide level, CREs located in open chromatin regions with high resolution. Here, we describe a detailed step-by-step ATAC-seq protocol for invertebrate chordate marine embryos. We have successfully applied this technique to amphioxus and two species of tunicate embryos. We also show an easy workflow to analyze data generated with this technique. Moreover, we point out that this method and our bioinformatic pipeline are efficient to detect CREs associated with Wnt signaling pathway by simply using embryos treated with a drug that perturbs this pathway. This approach can be extended to other signaling pathways and also to embryo mutants for critical genes. Our results therefore demonstrate the power of ATAC-seq for the identification of CREs that play essential functions during animal development in a wide range of invertebrate or vertebrate animals.
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Affiliation(s)
- Marta Silvia Magri
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Sandra Jiménez-Gancedo
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Stephanie Bertrand
- Sorbonne Université, CNRS, UMR 7232, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Alicia Madgwick
- Centre de Recherche en Biologie Cellulaire de Montpellier, CNRS, UMR 5237, Université de Montpellier, Montpellier, France
| | - Hector Escrivà
- Sorbonne Université, CNRS, UMR 7232, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Patrick Lemaire
- Centre de Recherche en Biologie Cellulaire de Montpellier, CNRS, UMR 5237, Université de Montpellier, Montpellier, France
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
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Racioppi C, Wiechecki KA, Christiaen L. Combinatorial chromatin dynamics foster accurate cardiopharyngeal fate choices. eLife 2019; 8:49921. [PMID: 31746740 PMCID: PMC6952182 DOI: 10.7554/elife.49921] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/18/2019] [Indexed: 12/22/2022] Open
Abstract
During embryogenesis, chromatin accessibility profiles control lineage-specific gene expression by modulating transcription, thus impacting multipotent progenitor states and subsequent fate choices. Subsets of cardiac and pharyngeal/head muscles share a common origin in the cardiopharyngeal mesoderm, but the chromatin landscapes that govern multipotent progenitors competence and early fate choices remain largely elusive. Here, we leveraged the simplicity of the chordate model Ciona to profile chromatin accessibility through stereotyped transitions from naive Mesp+ mesoderm to distinct fate-restricted heart and pharyngeal muscle precursors. An FGF-Foxf pathway acts in multipotent progenitors to establish cardiopharyngeal-specific patterns of accessibility, which govern later heart vs. pharyngeal muscle-specific expression profiles, demonstrating extensive spatiotemporal decoupling between early cardiopharyngeal enhancer accessibility and late cell-type-specific activity. We found that multiple cis-regulatory elements, with distinct chromatin accessibility profiles and motif compositions, are required to activate Ebf and Tbx1/10, two key determinants of cardiopharyngeal fate choices. We propose that these 'combined enhancers' foster spatially and temporally accurate fate choices, by increasing the repertoire of regulatory inputs that control gene expression, through either accessibility and/or activity.
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Affiliation(s)
- Claudia Racioppi
- Center for Developmental Genetics, Department of Biology, New York University, New York, United States
| | - Keira A Wiechecki
- Center for Developmental Genetics, Department of Biology, New York University, New York, United States
| | - Lionel Christiaen
- Center for Developmental Genetics, Department of Biology, New York University, New York, United States
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36
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Cao C, Lemaire LA, Wang W, Yoon PH, Choi YA, Parsons LR, Matese JC, Wang W, Levine M, Chen K. Comprehensive single-cell transcriptome lineages of a proto-vertebrate. Nature 2019; 571:349-354. [PMID: 31292549 PMCID: PMC6978789 DOI: 10.1038/s41586-019-1385-y] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 06/10/2019] [Indexed: 11/17/2022]
Abstract
Ascidian embryos highlight the importance of cell lineages in animal development. As simple proto-vertebrates they also provide insights into the evolutionary origins of novel cell types, such as cranial placodes and neural crest. To build upon these efforts we have determined single cell transcriptomes for more than 90,000 cells spanning the entirety of Ciona intestinalis development, from the onset of gastrulation to swimming tadpoles. This represents an average of over 12-fold coverage for every cell at every stage of development, owing to the small cell numbers of ascidian embryos. Single cell transcriptome trajectories were used to construct “virtual” cell lineage maps and provisional gene networks for nearly 40 different neuronal subtypes comprising the larval nervous system. We summarize several applications of these datasets, including annotating the synaptome of swimming tadpoles and tracing the evolutionary origin of novel cell types such as the vertebrate telencephalon.
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Affiliation(s)
- Chen Cao
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Laurence A Lemaire
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Wei Wang
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Peter H Yoon
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Yoolim A Choi
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Lance R Parsons
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - John C Matese
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Wei Wang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Michael Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA. .,Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
| | - Kai Chen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA. .,The Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China.
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37
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Sharma S, Wang W, Stolfi A. Single-cell transcriptome profiling of the Ciona larval brain. Dev Biol 2019; 448:226-236. [PMID: 30392840 PMCID: PMC6487232 DOI: 10.1016/j.ydbio.2018.09.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/10/2018] [Accepted: 09/10/2018] [Indexed: 11/27/2022]
Abstract
The tadpole-type larva of Ciona has emerged as an intriguing model system for the study of neurodevelopment. The Ciona intestinalis connectome has been recently mapped, revealing the smallest central nervous system (CNS) known in any chordate, with only 177 neurons. This minimal CNS is highly reminiscent of larger CNS of vertebrates, sharing many conserved developmental processes, anatomical compartments, neuron subtypes, and even specific neural circuits. Thus, the Ciona tadpole offers a unique opportunity to understand the development and wiring of a chordate CNS at single-cell resolution. Here we report the use of single-cell RNAseq to profile the transcriptomes of single cells isolated by fluorescence-activated cell sorting (FACS) from the whole brain of Ciona robusta (formerly intestinalis Type A) larvae. We have also compared these profiles to bulk RNAseq data from specific subsets of brain cells isolated by FACS using cell type-specific reporter plasmid expression. Taken together, these datasets have begun to reveal the compartment- and cell-specific gene expression patterns that define the organization of the Ciona larval brain.
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Affiliation(s)
- Sarthak Sharma
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, United States
| | - Wei Wang
- New York University, Department of Biology, New York, NY, United States
| | - Alberto Stolfi
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, United States.
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38
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Racioppi C, Coppola U, Christiaen L, Ristoratore F. Transcriptional regulation of Rab32/38, a specific marker of pigment cell formation in Ciona robusta. Dev Biol 2019; 448:111-118. [DOI: 10.1016/j.ydbio.2018.11.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 01/22/2023]
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39
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Automated behavioural analysis reveals the basic behavioural repertoire of the urochordate Ciona intestinalis. Sci Rep 2019; 9:2416. [PMID: 30787329 PMCID: PMC6382837 DOI: 10.1038/s41598-019-38791-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/09/2019] [Indexed: 12/17/2022] Open
Abstract
Quantitative analysis of animal behaviour in model organisms is becoming an increasingly essential approach for tackling the great challenge of understanding how activity in the brain gives rise to behaviour. Here we used automated image-based tracking to extract behavioural features from an organism of great importance in understanding the evolution of chordates, the free-swimming larval form of the tunicate Ciona intestinalis, which has a compact and fully mapped nervous system composed of only 231 neurons. We analysed hundreds of videos of larvae and we extracted basic geometric and physical descriptors of larval behaviour. Importantly, we used machine learning methods to create an objective ontology of behaviours for C. intestinalis larvae. We identified eleven behavioural modes using agglomerative clustering. Using our pipeline for quantitative behavioural analysis, we demonstrate that C. intestinalis larvae exhibit sensory arousal and thigmotaxis. Notably, the anxiotropic drug modafinil modulates thigmotactic behaviour. Furthermore, we tested the robustness of the larval behavioural repertoire by comparing different rearing conditions, ages and group sizes. This study shows that C. intestinalis larval behaviour can be broken down to a set of stereotyped behaviours that are used to different extents in a context-dependent manner.
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40
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Madgwick A, Magri MS, Dantec C, Gailly D, Fiuza UM, Guignard L, Hettinger S, Gomez-Skarmeta JL, Lemaire P. Evolution of embryonic cis-regulatory landscapes between divergent Phallusia and Ciona ascidians. Dev Biol 2019; 448:71-87. [PMID: 30661644 DOI: 10.1016/j.ydbio.2019.01.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 12/31/2018] [Accepted: 01/01/2019] [Indexed: 01/21/2023]
Abstract
Ascidian species of the Phallusia and Ciona genera are distantly related, their last common ancestor dating several hundred million years ago. Although their genome sequences have extensively diverged since this radiation, Phallusia and Ciona species share almost identical early morphogenesis and stereotyped cell lineages. Here, we explored the evolution of transcriptional control between P. mammillata and C. robusta. We combined genome-wide mapping of open chromatin regions in both species with a comparative analysis of the regulatory sequences of a test set of 10 pairs of orthologous early regulatory genes with conserved expression patterns. We find that ascidian chromatin accessibility landscapes obey similar rules as in other metazoa. Open-chromatin regions are short, highly conserved within each genus and cluster around regulatory genes. The dynamics of chromatin accessibility and closest-gene expression are strongly correlated during early embryogenesis. Open-chromatin regions are highly enriched in cis-regulatory elements: 73% of 49 open chromatin regions around our test genes behaved as either distal enhancers or proximal enhancer/promoters following electroporation in Phallusia eggs. Analysis of this datasets suggests a pervasive use in ascidians of "shadow" enhancers with partially overlapping activities. Cross-species electroporations point to a deep conservation of both the trans-regulatory logic between these distantly-related ascidians and the cis-regulatory activities of individual enhancers. Finally, we found that the relative order and approximate distance to the transcription start site of open chromatin regions can be conserved between Ciona and Phallusia species despite extensive sequence divergence, a property that can be used to identify orthologous enhancers, whose regulatory activity can partially diverge.
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Affiliation(s)
- Alicia Madgwick
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France
| | - Marta Silvia Magri
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Sevilla, Spain
| | - Christelle Dantec
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France
| | - Damien Gailly
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France
| | - Ulla-Maj Fiuza
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France
| | - Léo Guignard
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix drive, Ashburn, VA, USA
| | - Sabrina Hettinger
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France
| | - Jose Luis Gomez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Sevilla, Spain
| | - Patrick Lemaire
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), Université de Montpellier, CNRS, Montpellier, France.
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Lowe EK, Stolfi A. Developmental system drift in motor ganglion patterning between distantly related tunicates. EvoDevo 2018; 9:18. [PMID: 30062003 PMCID: PMC6057086 DOI: 10.1186/s13227-018-0107-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/18/2018] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The larval nervous system of the solitary tunicate Ciona is a simple model for the study of chordate neurodevelopment. The development and connectivity of the Ciona motor ganglion have been studied in fine detail, but how this important structure develops in other tunicates is not well known. METHODS AND RESULTS By comparing gene expression patterns in the developing MG of the distantly related tunicate Molgula occidentalis, we found that its patterning is highly conserved compared to the Ciona MG. MG neuronal subtypes in Molgula were specified in the exact same positions as in Ciona, though the timing of subtype-specific gene expression onset was slightly shifted to begin earlier, relative to mitotic exit and differentiation. In transgenic Molgula embryos electroporated with Dmbx reporter plasmids, we were also able to characterize the morphology of the lone pair of descending decussating neurons (ddNs) in Molgula, revealing the same unique contralateral projection seen in Ciona ddNs and their putative vertebrate homologs the Mauthner cells. Although Dmbx expression labels the ddNs in both species, cross-species transgenic assays revealed significant changes to the regulatory logic underlying Dmbx transcription. We found that Dmbx cis-regulatory DNAs from Ciona can drive highly specific reporter gene expression in Molgula ddNs, but Molgula sequences are not active in Ciona ddNs. CONCLUSIONS This acute divergence in the molecular mechanisms that underlie otherwise functionally conserved cis-regulatory DNAs supports the recently proposed idea that the extreme genetic plasticity observed in tunicates may be attributed to the extreme rigidity of the spatial organization of their embryonic cell lineages.
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Affiliation(s)
- Elijah K. Lowe
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA USA
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA USA
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42
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Razy-Krajka F, Gravez B, Kaplan N, Racioppi C, Wang W, Christiaen L. An FGF-driven feed-forward circuit patterns the cardiopharyngeal mesoderm in space and time. eLife 2018; 7:e29656. [PMID: 29431097 PMCID: PMC5809146 DOI: 10.7554/elife.29656] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 01/26/2018] [Indexed: 12/16/2022] Open
Abstract
In embryos, multipotent progenitors divide to produce distinct progeny and express their full potential. In vertebrates, multipotent cardiopharyngeal progenitors produce second-heart-field-derived cardiomyocytes, and branchiomeric skeletal head muscles. However, the mechanisms underlying these early fate choices remain largely elusive. The tunicate Ciona emerged as an attractive model to study early cardiopharyngeal development at high resolution: through two asymmetric and oriented divisions, defined cardiopharyngeal progenitors produce distinct first and second heart precursors, and pharyngeal muscle (aka atrial siphon muscle, ASM) precursors. Here, we demonstrate that differential FGF-MAPK signaling distinguishes between heart and ASM precursors. We characterize a feed-forward circuit that promotes the successive activations of essential ASM determinants, Hand-related, Tbx1/10 and Ebf. Finally, we show that coupling FGF-MAPK restriction and cardiopharyngeal network deployment with cell divisions defines the timing of gene expression and permits the emergence of diverse cell types from multipotent progenitors.
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Affiliation(s)
- Florian Razy-Krajka
- Center for Developmental Genetics, Department of BiologyCollege of Arts and Science, New York UniversityNew YorkUnited States
| | - Basile Gravez
- Center for Developmental Genetics, Department of BiologyCollege of Arts and Science, New York UniversityNew YorkUnited States
| | - Nicole Kaplan
- Center for Developmental Genetics, Department of BiologyCollege of Arts and Science, New York UniversityNew YorkUnited States
| | - Claudia Racioppi
- Center for Developmental Genetics, Department of BiologyCollege of Arts and Science, New York UniversityNew YorkUnited States
| | - Wei Wang
- Center for Developmental Genetics, Department of BiologyCollege of Arts and Science, New York UniversityNew YorkUnited States
| | - Lionel Christiaen
- Center for Developmental Genetics, Department of BiologyCollege of Arts and Science, New York UniversityNew YorkUnited States
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43
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Navarrete IA, Levine M. Nodal and FGF coordinate ascidian neural tube morphogenesis. Development 2016; 143:4665-4675. [PMID: 27827820 DOI: 10.1242/dev.144733] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 10/21/2016] [Indexed: 01/06/2023]
Abstract
Formation of the vertebrate neural tube represents one of the premier examples of morphogenesis in animal development. Here, we investigate this process in the simple chordate Ciona intestinalis Previous studies have implicated Nodal and FGF signals in the specification of lateral and ventral neural progenitors. We show that these signals also control the detailed cellular behaviors underlying morphogenesis of the neural tube. Live-imaging experiments show that FGF controls the intercalary movements of ventral neural progenitors, whereas Nodal is essential for the characteristic stacking behavior of lateral cells. Ectopic activation of FGF signaling is sufficient to induce intercalary behaviors in cells that have not received Nodal. In the absence of FGF and Nodal, neural progenitors exhibit a default behavior of sequential cell divisions, and fail to undergo the intercalary and stacking behaviors essential for normal morphogenesis. Thus, cell specification events occurring prior to completion of gastrulation coordinate the morphogenetic movements underlying the organization of the neural tube.
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Affiliation(s)
- Ignacio A Navarrete
- Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, University of California, Berkeley, CA 94720, USA
| | - Michael Levine
- Department of Molecular and Cell Biology, Division of Genetics, Genomics and Development, University of California, Berkeley, CA 94720, USA
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Karakostis K, Ponnuswamy A, Fusée LTS, Bailly X, Laguerre L, Worall E, Vojtesek B, Nylander K, Fåhraeus R. p53 mRNA and p53 Protein Structures Have Evolved Independently to Interact with MDM2. Mol Biol Evol 2016; 33:1280-92. [PMID: 26823446 DOI: 10.1093/molbev/msw012] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The p53 tumor suppressor and its key regulator MDM2 play essential roles in development, ageing, cancer, and cellular stress responses in mammals. Following DNA damage, MDM2 interacts with p53 mRNA in an ATM kinase-dependent fashion and stimulates p53 synthesis, whereas under normal conditions, MDM2 targets the p53 protein for degradation. The peptide- and RNA motifs that interact with MDM2 are encoded by the same conserved BOX-I sequence, but how these interactions have evolved is unknown. Here, we show that a temperature-sensitive structure in the invertebrate Ciona intestinalis (Ci) p53 mRNA controls its interaction with MDM2. We also show that a nonconserved flanking region of Ci-BOX-I domain prevents the p53-MDM2 protein-protein interaction. These results indicate that the temperature-regulated p53 mRNA-MDM2 interaction evolved to become kinase regulated in the mammalian DNA damage response. The data also suggest that the negative regulation of p53 by MDM2 via protein-protein interaction evolved in vertebrates following changes in the BOX-I flanking sequence.
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Affiliation(s)
- Konstantinos Karakostis
- Équipe Labellisée Ligue Contre le Cancer, Université Paris 7, INSERM UMR 1162, Paris, France
| | - Anand Ponnuswamy
- Équipe Labellisée Ligue Contre le Cancer, Université Paris 7, INSERM UMR 1162, Paris, France
| | - Leïla T S Fusée
- Équipe Labellisée Ligue Contre le Cancer, Université Paris 7, INSERM UMR 1162, Paris, France
| | - Xavier Bailly
- UPMC-CNRS, FR2424, Station Biologique de Roscoff, Roscoff, France
| | - Laurent Laguerre
- UPMC-CNRS, FR2424, Station Biologique de Roscoff, Roscoff, France
| | - Erin Worall
- Edinburgh Cancer Research UK Centre, the University of Edinburgh, Edinburgh, United Kingdom
| | - Borek Vojtesek
- Regional Centre for Applied Molecular Oncology, RECAMO and Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Karin Nylander
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Robin Fåhraeus
- Équipe Labellisée Ligue Contre le Cancer, Université Paris 7, INSERM UMR 1162, Paris, France Regional Centre for Applied Molecular Oncology, RECAMO and Masaryk Memorial Cancer Institute, Brno, Czech Republic Department of Medical Biosciences, Umeå University, Umeå, Sweden
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45
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Stach T, Anselmi C. High-precision morphology: bifocal 4D-microscopy enables the comparison of detailed cell lineages of two chordate species separated for more than 525 million years. BMC Biol 2015; 13:113. [PMID: 26700477 PMCID: PMC4690324 DOI: 10.1186/s12915-015-0218-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 12/08/2015] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Understanding the evolution of divergent developmental trajectories requires detailed comparisons of embryologies at appropriate levels. Cell lineages, the accurate visualization of cleavage patterns, tissue fate restrictions, and morphogenetic movements that occur during the development of individual embryos are currently available for few disparate animal taxa, encumbering evolutionarily meaningful comparisons. Tunicates, considered to be close relatives of vertebrates, are marine invertebrates whose fossil record dates back to 525 million years ago. Life-history strategies across this subphylum are radically different, and include biphasic ascidians with free swimming larvae and a sessile adult stage, and the holoplanktonic larvaceans. Despite considerable progress, notably on the molecular level, the exact extent of evolutionary conservation and innovation during embryology remain obscure. RESULTS Here, using the innovative technique of bifocal 4D-microscopy, we demonstrate exactly which characteristics in the cell lineages of the ascidian Phallusia mammillata and the larvacean Oikopleura dioica were conserved and which were altered during evolution. Our accurate cell lineage trees in combination with detailed three-dimensional representations clearly identify conserved correspondence in relative cell position, cell identity, and fate restriction in several lines from all prospective larval tissues. At the same time, we precisely pinpoint differences observable at all levels of development. These differences comprise fate restrictions, tissue types, complex morphogenetic movement patterns, numerous cases of heterochronous acceleration in the larvacean embryo, and differences in bilateral symmetry. CONCLUSIONS Our results demonstrate in extraordinary detail the multitude of developmental levels amenable to evolutionary innovation, including subtle changes in the timing of fate restrictions as well as dramatic alterations in complex morphogenetic movements. We anticipate that the precise spatial and temporal cell lineage data will moreover serve as a high-precision guide to devise experimental investigations of other levels, such as molecular interactions between cells or changes in gene expression underlying the documented structural evolutionary changes. Finally, the quantitative amount of digital high-precision morphological data will enable and necessitate software-based similarity assessments as the basis of homology hypotheses.
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Affiliation(s)
- Thomas Stach
- Institut für Biologie, Kompetenzzentrum Elektronenmikroskopie, Humboldt-Universität zu Berlin, Philippstrasse 13, Haus 14, 10115, Berlin, Germany.
| | - Chiara Anselmi
- Dipartimento di Biologia, Università degli Studi di Padova, Via Ugo Bassi 58/B, 35131, Padova, Italy.
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46
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Detection of mRNA and microRNA Expression in Basal Chordates, Amphioxus and Ascidians. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/978-1-4939-2303-8_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
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47
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Diverse ETS transcription factors mediate FGF signaling in the Ciona anterior neural plate. Dev Biol 2015; 399:218-25. [PMID: 25576927 DOI: 10.1016/j.ydbio.2014.12.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 12/23/2014] [Accepted: 12/24/2014] [Indexed: 11/24/2022]
Abstract
The ascidian Ciona intestinalis is a marine invertebrate belonging to the sister group of the vertebrates, the tunicates. Its compact genome and simple, experimentally tractable embryos make Ciona well-suited for the study of cell-fate specification in chordates. Tunicate larvae possess a characteristic chordate body plan, and many developmental pathways are conserved between tunicates and vertebrates. Previous studies have shown that FGF signals are essential for neural induction and patterning at sequential steps of Ciona embryogenesis. Here we show that two different ETS family transcription factors, Ets1/2 and Elk1/3/4, have partially redundant activities in the anterior neural plate of gastrulating embryos. Whereas Ets1/2 promotes pigment cell formation in lateral lineages, both Ets1/2 and Elk1/3/4 are involved in the activation of Myt1L in medial lineages and the restriction of Six3/6 expression to the anterior-most regions of the neural tube. We also provide evidence that photoreceptor cells arise from posterior regions of the presumptive sensory vesicle, and do not depend on FGF signaling. Cells previously identified as photoreceptor progenitors instead form ependymal cells and neurons of the larval brain. Our results extend recent findings on FGF-dependent patterning of anterior-posterior compartments in the Ciona central nervous system.
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Gline S, Kaplan N, Bernadskaya Y, Abdu Y, Christiaen L. Surrounding tissues canalize motile cardiopharyngeal progenitors towards collective polarity and directed migration. Development 2015; 142:544-54. [PMID: 25564651 DOI: 10.1242/dev.115444] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Collectively migrating cells maintain group polarity and interpret external cues to reach their destination. The cardiogenic progenitors (also known as trunk ventral cells, TVCs) of the ascidian Ciona intestinalis provide a simple chordate model with which to study collective migration. Bilateral pairs of associated TVCs undergo a stereotyped polarized migration away from the tail towards the ventral trunk, arguably constituting the simplest possible example of directed collective migration. To identify tissues contributing to TVC polarity and migration, we quantified the contact between TVCs and surrounding tissues, and blocked the secretory pathway in a tissue-specific manner. Even though TVCs normally migrate as an invariably determined leader-trailer polarized pair of adherent cells, they are capable of migrating individually, albeit a shorter distance and with altered morphology. The mesenchyme contacts newborn TVCs and contributes to robust specification of the trailer but appears to have only minor effects on directed migration. The notochord does not contact the TVCs but contributes to the onset of migration. The trunk endoderm first contacts the leader TVC, then 'encases' both migrating cells and provides the inputs maintaining leader-trailer polarity. Migrating TVCs adhere to the epidermis and need this contact for their cohesion. These phenomenological studies reveal that inherently motile cardiopharyngeal progenitors are channeled into stereotyped behaviors by interactions with surrounding tissues.
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Affiliation(s)
- Stephanie Gline
- Center for Developmental Genetics, Department of Biology, New York University, NY 10003, USA
| | - Nicole Kaplan
- Center for Developmental Genetics, Department of Biology, New York University, NY 10003, USA
| | - Yelena Bernadskaya
- Center for Developmental Genetics, Department of Biology, New York University, NY 10003, USA
| | - Yusuff Abdu
- Center for Developmental Genetics, Department of Biology, New York University, NY 10003, USA
| | - Lionel Christiaen
- Center for Developmental Genetics, Department of Biology, New York University, NY 10003, USA
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Stolfi A, Gandhi S, Salek F, Christiaen L. Tissue-specific genome editing in Ciona embryos by CRISPR/Cas9. Development 2014; 141:4115-20. [PMID: 25336740 DOI: 10.1242/dev.114488] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The CRISPR/Cas9 system has ushered in a new era of targeted genetic manipulations. Here, we report the use of CRISPR/Cas9 to induce double-stranded breaks in the genome of the sea squirt Ciona intestinalis. We use electroporation to deliver CRISPR/Cas9 components for tissue-specific disruption of the Ebf (Collier/Olf/EBF) gene in hundreds of synchronized Ciona embryos. Phenotyping of transfected embryos in the 'F0' generation revealed that endogenous Ebf function is required for specification of Islet-expressing motor ganglion neurons and atrial siphon muscles. We demonstrate that CRISPR/Cas9 is sufficiently effective and specific to generate large numbers of embryos carrying mutations in a targeted gene of interest, which should allow for rapid screening of gene function in Ciona.
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Affiliation(s)
- Alberto Stolfi
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA
| | - Shashank Gandhi
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA
| | - Farhana Salek
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA
| | - Lionel Christiaen
- Center for Developmental Genetics, Department of Biology, New York University, New York, NY 10003, USA
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Belyaeva OV, Chang C, Berlett MC, Kedishvili NY. Evolutionary origins of retinoid active short-chain dehydrogenases/reductases of SDR16C family. Chem Biol Interact 2014; 234:135-43. [PMID: 25451586 DOI: 10.1016/j.cbi.2014.10.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 10/09/2014] [Accepted: 10/17/2014] [Indexed: 12/11/2022]
Abstract
Vertebrate enzymes that belong to the 16C family of short-chain dehydrogenases/reductases (SDR16C) were shown to play an essential role in the control of retinoic acid (RA) levels during development. To trace the evolution of enzymatic function of SDR16C family, and to examine the origins of the pathway for RA biosynthesis from vitamin A, we identified putative SDR16C enzymes through the extensive search of available genome sequencing data in a subset of species representing major metazoan phyla. The phylogenetic analysis revealed that enzymes from protostome, non-chordate deuterostome and invertebrate chordate species are found in three clades of SDR16C family containing retinoid active enzymes, which are retinol dehydrogenase 10 (RDH10), retinol dehydrogenases E2 (RDHE2) and RDHE2-similar, and dehydrogenase reductase (SDR family) member 3 (DHRS3). For the initial functional analysis, we cloned RDH10- and RDHE2-related enzymes from the early developmental stages of a non-chordate deuterostome, green sea urchin Lytechinus variegatus, and an invertebrate chordate, sea squirt Ciona intestinalis. In situ hybridization revealed that these proteins are expressed in a pattern relevant to development, while assays performed on proteins expressed in mammalian cell culture showed that they possess retinol-oxidizing activity as their vertebrate homologs. The existence of invertebrate homologs of DHRS3 was inferred from the analysis of phylogeny and cofactor-binding residues characteristic of preference for NADP(H). The presence of invertebrate homologs in the DHRS3 group of SDR16C is interesting in light of the complex mutually activating interaction, which we have recently described for human RDH10 and DHRS3 enzymes. Further functional analysis of these homologs will establish whether this interaction evolved to control retinoid homeostasis only in vertebrates, or is also conserved in pre-vertebrates.
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Affiliation(s)
- Olga V Belyaeva
- Department of Biochemistry and Molecular Genetics, University of Alabama - Birmingham, Birmingham, AL 35294, USA.
| | - Chenbei Chang
- Department of Cell, Developmental and Integrative Biology, University of Alabama - Birmingham, Birmingham, AL 35294, USA
| | - Michael C Berlett
- Department of Biochemistry and Molecular Genetics, University of Alabama - Birmingham, Birmingham, AL 35294, USA
| | - Natalia Y Kedishvili
- Department of Biochemistry and Molecular Genetics, University of Alabama - Birmingham, Birmingham, AL 35294, USA
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