1
|
Negrón-Piñeiro LJ, Wu Y, Popsuj S, José-Edwards DS, Stolfi A, Di Gregorio A. Cis-regulatory interfaces reveal the molecular mechanisms underlying the notochord gene regulatory network of Ciona. Nat Commun 2024; 15:3025. [PMID: 38589372 PMCID: PMC11001920 DOI: 10.1038/s41467-024-46850-3] [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: 11/03/2022] [Accepted: 03/12/2024] [Indexed: 04/10/2024] Open
Abstract
Tissue-specific gene expression is fundamental in development and evolution, and is mediated by transcription factors and by the cis-regulatory regions (enhancers) that they control. Transcription factors and their respective tissue-specific enhancers are essential components of gene regulatory networks responsible for the development of tissues and organs. Although numerous transcription factors have been characterized from different organisms, the knowledge of the enhancers responsible for their tissue-specific expression remains fragmentary. Here we use Ciona to study the enhancers associated with ten transcription factors expressed in the notochord, an evolutionary hallmark of the chordate phylum. Our results illustrate how two evolutionarily conserved transcription factors, Brachyury and Foxa2, coordinate the deployment of other notochord transcription factors. The results of these detailed cis-regulatory analyses delineate a high-resolution view of the essential notochord gene regulatory network of Ciona, and provide a reference for studies of transcription factors, enhancers, and their roles in development, disease, and evolution.
Collapse
Affiliation(s)
- Lenny J Negrón-Piñeiro
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Yushi Wu
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Sydney Popsuj
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Diana S José-Edwards
- Post-Baccalaureate Premedical Program, Washington University, St. Louis, MO, 63130, USA
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Anna Di Gregorio
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA.
| |
Collapse
|
2
|
Fritzsch B, Glover JC. Gene networks and the evolution of olfactory organs, eyes, hair cells and motoneurons: a view encompassing lancelets, tunicates and vertebrates. Front Cell Dev Biol 2024; 12:1340157. [PMID: 38533086 PMCID: PMC10963430 DOI: 10.3389/fcell.2024.1340157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
Key developmental pathways and gene networks underlie the formation of sensory cell types and structures involved in chemosensation, vision and mechanosensation, and of the efferents these sensory inputs can activate. We describe similarities and differences in these pathways and gene networks in selected species of the three main chordate groups, lancelets, tunicates, and vertebrates, leading to divergent development of olfactory receptors, eyes, hair cells and motoneurons. The lack of appropriately posited expression of certain transcription factors in lancelets and tunicates prevents them from developing vertebrate-like olfactory receptors and eyes, although they generate alternative structures for chemosensation and vision. Lancelets and tunicates lack mechanosensory cells associated with the sensation of acoustic stimuli, but have gravisensitive organs and ciliated epidermal sensory cells that may (and in some cases clearly do) provide mechanosensation and thus the capacity to respond to movement relative to surrounding water. Although functionally analogous to the vertebrate vestibular apparatus and lateral line, homology is questionable due to differences in the expression of the key transcription factors Neurog and Atoh1/7, on which development of vertebrate hair cells depends. The vertebrate hair cell-bearing inner ear and lateral line thus likely represent major evolutionary advances specific to vertebrates. Motoneurons develop in vertebrates under the control of the ventral signaling molecule hedgehog/sonic hedgehog (Hh,Shh), against an opposing inhibitory effect mediated by dorsal signaling molecules. Many elements of Shh-signaling and downstream genes involved in specifying and differentiating motoneurons are also exhibited by lancelets and tunicates, but the repertoire of MNs in vertebrates is broader, indicating greater diversity in motoneuron differentiation programs.
Collapse
Affiliation(s)
- Bernd Fritzsch
- Department of Biological Sciences, University of Nebraska Medical Center, Omaha, NE, United States
| | - Joel C. Glover
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
- Laboratory of Neural Development and Optical Recording (NDEVOR), Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| |
Collapse
|
3
|
Popsuj S, Di Gregorio A, Swalla BJ, Stolfi A. Loss of collagen gene expression in the notochord of the tailless tunicate Molgula occulta. Integr Comp Biol 2023; 63:990-998. [PMID: 37403333 PMCID: PMC10714901 DOI: 10.1093/icb/icad071] [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: 03/01/2023] [Revised: 05/22/2023] [Accepted: 06/11/2023] [Indexed: 07/06/2023] Open
Abstract
In tunicates, several species in the Molgulidae family have convergently lost the tailed, swimming larval body plan, including the morphogenesis of the notochord, a major chordate-defining trait. Through the comparison of tailless M. occulta and a close relative, the tailed species M. oculata, we show that notochord-specific expression of the Collagen Type I/II Alpha (Col1/2a) gene appears to have been lost specifically in the tailless species. Using CRISPR/Cas9-mediated mutagenesis in the tailed laboratory model tunicate Ciona robusta, we demonstrate that Col1/2a plays a crucial role in the convergent extension of notochord cells during tail elongation. Our results suggest that the expression of Col1/2a in the notochord, although necessary for its morphogenesis in tailed species, is dispensable for tailless species. This loss is likely a result of the accumulation of cis-regulatory mutations in the absence of purifying selective pressure. More importantly, the gene itself is not lost, likely due to its roles in other developmental processes, including during the adult stage. Our study further confirms the Molgulidae as an interesting family in which to study the evolutionary loss of tissue-specific expression of indispensable genes.
Collapse
Affiliation(s)
- Sydney Popsuj
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Anna Di Gregorio
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY 10010, USA
| | - Billie J Swalla
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| |
Collapse
|
4
|
Schifferl D, Scholze-Wittler M, Villaronga Luque A, Pustet M, Wittler L, Veenvliet JV, Koch F, Herrmann BG. Genome-wide identification of notochord enhancers comprising the regulatory landscape of the brachyury locus in mouse. Development 2023; 150:dev202111. [PMID: 37882764 PMCID: PMC10651091 DOI: 10.1242/dev.202111] [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: 06/22/2023] [Accepted: 10/17/2023] [Indexed: 10/27/2023]
Abstract
The node and notochord are important signaling centers organizing the dorso-ventral patterning of cells arising from neuro-mesodermal progenitors forming the embryonic body anlage. Owing to the scarcity of notochord progenitors and notochord cells, a comprehensive identification of regulatory elements driving notochord-specific gene expression has been lacking. Here, we have used ATAC-seq analysis of FACS-purified notochord cells from Theiler stage 12-13 mouse embryos to identify 8921 putative notochord enhancers. In addition, we established a new model for generating notochord-like cells in culture, and found 3728 of these enhancers occupied by the essential notochord control factors brachyury (T) and/or Foxa2. We describe the regulatory landscape of the T locus, comprising ten putative enhancers occupied by these factors, and confirmed the regulatory activity of three of these elements. Moreover, we characterized seven new elements by knockout analysis in embryos and identified one new notochord enhancer, termed TNE2. TNE2 cooperates with TNE in the trunk notochord, and is essential for notochord differentiation in the tail. Our data reveal an essential role of Foxa2 in directing T-expressing cells towards the notochord lineage.
Collapse
Affiliation(s)
- Dennis Schifferl
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Manuela Scholze-Wittler
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Alba Villaronga Luque
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Milena Pustet
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Lars Wittler
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Jesse V Veenvliet
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Frederic Koch
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Bernhard G Herrmann
- Max Planck Institute for Molecular Genetics, Department Developmental Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| |
Collapse
|
5
|
Di Gregorio A. Searching for marine embryos, finding my path. Genesis 2023; 61:e23576. [PMID: 37994390 PMCID: PMC10773608 DOI: 10.1002/dvg.23576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/03/2023] [Accepted: 11/04/2023] [Indexed: 11/24/2023]
Affiliation(s)
- Anna Di Gregorio
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, New York, USA
| |
Collapse
|
6
|
Raghavan R, Coppola U, Wu Y, Ihewulezi C, Negrón-Piñeiro LJ, Maguire JE, Hong J, Cunningham M, Kim HJ, Albert TJ, Ali AM, Saint-Jeannet JP, Ristoratore F, Dahia CL, Di Gregorio A. Gene expression in notochord and nuclei pulposi: a study of gene families across the chordate phylum. BMC Ecol Evol 2023; 23:63. [PMID: 37891482 PMCID: PMC10605842 DOI: 10.1186/s12862-023-02167-1] [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: 06/04/2023] [Accepted: 08/08/2023] [Indexed: 10/29/2023] Open
Abstract
The transition from notochord to vertebral column is a crucial milestone in chordate evolution and in prenatal development of all vertebrates. As ossification of the vertebral bodies proceeds, involutions of residual notochord cells into the intervertebral discs form the nuclei pulposi, shock-absorbing structures that confer flexibility to the spine. Numerous studies have outlined the developmental and evolutionary relationship between notochord and nuclei pulposi. However, the knowledge of the similarities and differences in the genetic repertoires of these two structures remains limited, also because comparative studies of notochord and nuclei pulposi across chordates are complicated by the gene/genome duplication events that led to extant vertebrates. Here we show the results of a pilot study aimed at bridging the information on these two structures. We have followed in different vertebrates the evolutionary trajectory of notochord genes identified in the invertebrate chordate Ciona, and we have evaluated the extent of conservation of their expression in notochord cells. Our results have uncovered evolutionarily conserved markers of both notochord development and aging/degeneration of the nuclei pulposi.
Collapse
Affiliation(s)
- Rahul Raghavan
- Hospital for Special Surgery, Orthopedic Soft Tissue Research Program, New York, NY, 10021, USA
| | - Ugo Coppola
- Stazione Zoologica 'A. Dohrn', Villa Comunale 1, 80121, Naples, Italy
- Present Address: Molecular Cardiovascular Biology Division and Heart Institute, Cincinnati Children's Research Foundation, Cincinnati, OH, 45229, USA
| | - Yushi Wu
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Chibuike Ihewulezi
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Lenny J Negrón-Piñeiro
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Julie E Maguire
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Justin Hong
- Hospital for Special Surgery, Orthopedic Soft Tissue Research Program, New York, NY, 10021, USA
| | - Matthew Cunningham
- Hospital for Special Surgery, New York, NY, 10021, USA
- Weill Cornell Medical College, New York, NY, 10065, USA
| | - Han Jo Kim
- Hospital for Special Surgery, New York, NY, 10021, USA
- Weill Cornell Medical College, New York, NY, 10065, USA
| | - Todd J Albert
- Hospital for Special Surgery, New York, NY, 10021, USA
- Weill Cornell Medical College, New York, NY, 10065, USA
| | - Abdullah M Ali
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Jean-Pierre Saint-Jeannet
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | | | - Chitra L Dahia
- Hospital for Special Surgery, Orthopedic Soft Tissue Research Program, New York, NY, 10021, USA.
- Department of Cell and Developmental Biology, Weill Cornell Medicine, Graduate School of Medical Science, New York, NY, 10065, USA.
| | - Anna Di Gregorio
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA.
| |
Collapse
|
7
|
Wang Y, Liu Y, Peng J, Wang H. Regulation mechanisms underlying tail resorption in Bufo gargarizans metamorphosis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 47:101113. [PMID: 37517282 DOI: 10.1016/j.cbd.2023.101113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/01/2023]
Abstract
Anurans have been excellent organisms for studying amphibian metamorphosis. Tail resorption is a remarkable event that occurs during amphibian metamorphosis. Although tail resorption has been previously studied in other anurans like Xenopus laevis and Rana chensinensis, there is no report on Bufo gargarizans. This paper thus explored the mechanism of tail resorption during metamorphosis in Bufo gargarizans tadpoles through some biological research methods. Histological results showed that the tail tissues of tadpoles gradually degraded as metamorphosis progressed. RNA sequencing analysis was performed to examine the expression level and functional enrichment of differentially expressed genes in the tail. In addition, we analyzed the mRNA expression levels of genes related to tail resorption by quantitative real-time polymerase chain reaction. We also speculated on three pathways that participate in the regulation of tail resorption based on the above results. The present study might provide a theoretical basis and novel insights for further research of complex molecular mechanisms of tail resorption in amphibians.
Collapse
Affiliation(s)
- Yaxi Wang
- College of Life Science, Shaanxi Normal University, Xi'an 710119, People's Republic of China
| | - Ying Liu
- College of Life Science, Shaanxi Normal University, Xi'an 710119, People's Republic of China
| | - Jufang Peng
- Basic Experimental Teaching Center, Shaanxi Normal University, Xi'an 710119, People's Republic of China
| | - Hongyuan Wang
- College of Life Science, Shaanxi Normal University, Xi'an 710119, People's Republic of China.
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Song BP, Ragsac MF, Tellez K, Jindal GA, Grudzien JL, Le SH, Farley EK. Diverse logics and grammar encode notochord enhancers. Cell Rep 2023; 42:112052. [PMID: 36729834 PMCID: PMC10387507 DOI: 10.1016/j.celrep.2023.112052] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/07/2022] [Accepted: 01/17/2023] [Indexed: 02/03/2023] Open
Abstract
The notochord is a defining feature of all chordates. The transcription factors Zic and ETS regulate enhancer activity within the notochord. We conduct high-throughput screens of genomic elements within developing Ciona embryos to understand how Zic and ETS sites encode notochord activity. Our screen discovers an enhancer located near Lama, a gene critical for notochord development. Reversing the orientation of an ETS site within this enhancer abolishes expression, indicating that enhancer grammar is critical for notochord activity. Similarly organized clusters of Zic and ETS sites occur within mouse and human Lama1 introns. Within a Brachyury (Bra) enhancer, FoxA and Bra, in combination with Zic and ETS binding sites, are necessary and sufficient for notochord expression. This binding site logic also occurs within other Ciona and vertebrate Bra enhancers. Collectively, this study uncovers the importance of grammar within notochord enhancers and discovers signatures of enhancer logic and grammar conserved across chordates.
Collapse
Affiliation(s)
- Benjamin P Song
- Department of Medicine, Health Sciences, University of California San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA; Biological Sciences Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Michelle F Ragsac
- Department of Medicine, Health Sciences, University of California San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Krissie Tellez
- Department of Medicine, Health Sciences, University of California San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Granton A Jindal
- Department of Medicine, Health Sciences, University of California San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jessica L Grudzien
- Department of Medicine, Health Sciences, University of California San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Sophia H Le
- Department of Medicine, Health Sciences, University of California San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Emma K Farley
- Department of Medicine, Health Sciences, University of California San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
10
|
Lu Z, Chen P, Xu Q, Li B, Jiang S, Jiang L, Zheng X. Constitutive and conditional gene knockout mice for the study of intervertebral disc degeneration: Current status, decision considerations, and future possibilities. JOR Spine 2023; 6:e1242. [PMID: 36994464 PMCID: PMC10041386 DOI: 10.1002/jsp2.1242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 12/13/2022] [Accepted: 12/22/2022] [Indexed: 01/09/2023] Open
Abstract
There have been an increasing number of patients with degenerative disc diseases due to the aging population. In light of this, studies on the pathogenesis of intervertebral disc degeneration have become a hot topic, and gene knockout mice have become a valuable tool in this field of research. With the development of science and technology, constitutive gene knockout mice can be constructed using homologous recombination, zinc finger nuclease, transcription activator-like effector nuclease technology and clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9) system, and conditional gene knockout mice can be constructed using the Cre/LoxP system. The gene-edited mice using these techniques have been widely used in the studies on disc degeneration. This paper reviews the development process and principles of these technologies, functions of the edited genes in disc degeneration, advantages, and disadvantages of different methods and possible targets of the specific Cre recombinase in intervertebral discs. Recommendations for the choice of suitable gene-edited model mice are presented. At the same time, possible technological improvements in the future are also discussed.
Collapse
Affiliation(s)
- Ze‐Yu Lu
- Spine Center Xinhua Hospital, Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Peng‐Bo Chen
- Spine Center Xinhua Hospital, Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Qing‐Yin Xu
- Spine Center Xinhua Hospital, Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Bo Li
- Spine Center Xinhua Hospital, Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Sheng‐Dan Jiang
- Spine Center Xinhua Hospital, Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Lei‐Sheng Jiang
- Spine Center Xinhua Hospital, Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Xin‐Feng Zheng
- Spine Center Xinhua Hospital, Shanghai Jiao Tong University School of Medicine Shanghai China
| |
Collapse
|
11
|
Ferran JL, Irimia M, Puelles L. Is There a Prechordal Region and an Acroterminal Domain in Amphioxus? BRAIN, BEHAVIOR AND EVOLUTION 2022; 96:334-352. [PMID: 35034027 DOI: 10.1159/000521966] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/03/2022] [Indexed: 12/16/2022]
Abstract
This essay re-examines the singular case of the supposedly unique rostrally elongated notochord described classically in amphioxus. We start from our previous observations in hpf 21 larvae [Albuixech-Crespo et al.: PLoS Biol. 2017;15(4):e2001573] indicating that the brain vesicle has rostrally a rather standard hypothalamic molecular configuration. This correlates with the notochord across a possible rostromedian acroterminal hypothalamic domain. The notochord shows some molecular differences that specifically characterize its pre-acroterminal extension beyond its normal rostral end under the mamillary region. We explored an alternative interpretation that the putative extension of this notochord actually represents a variant form of the prechordal plate in amphioxus, some of whose cells would adopt the notochordal typology, but would lack notochordal patterning properties, and might have some (but not all) prechordal ones instead. We survey in detail the classic and recent literature on gastrulation, prechordal plate, and notochord formation in amphioxus, compare the observed patterns with those of some other vertebrates of interest, and re-examine the literature on differential gene expression patterns in this rostralmost area of the head. We noted that previous literature failed to identify the amphioxus prechordal primordia at appropriate stages. Under this interpretation, a consistent picture can be drawn for cephalochordates, tunicates, and vertebrates. Moreover, there is little evidence for an intrinsic capacity of the early notochord to grow rostralwards (it normally elongates caudalwards). Altogether, we conclude that the hypothesis of a prechordal nature of the elongated amphioxus notochord is consistent with the evidence presented.
Collapse
Affiliation(s)
- José Luis Ferran
- Department of Human Anatomy and Psychobiology, Faculty of Medicine, University of Murcia, Murcia, Spain.,Institute of Biomedical Research of Murcia - IMIB, Virgen de la Arrixaca University Hospital, Murcia, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Luis Puelles
- Department of Human Anatomy and Psychobiology, Faculty of Medicine, University of Murcia, Murcia, Spain.,Institute of Biomedical Research of Murcia - IMIB, Virgen de la Arrixaca University Hospital, Murcia, Spain
| |
Collapse
|
12
|
Romero-Morales AI, Gama V. Revealing the Impact of Mitochondrial Fitness During Early Neural Development Using Human Brain Organoids. Front Mol Neurosci 2022; 15:840265. [PMID: 35571368 PMCID: PMC9102998 DOI: 10.3389/fnmol.2022.840265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial homeostasis -including function, morphology, and inter-organelle communication- provides guidance to the intrinsic developmental programs of corticogenesis, while also being responsive to environmental and intercellular signals. Two- and three-dimensional platforms have become useful tools to interrogate the capacity of cells to generate neuronal and glia progeny in a background of metabolic dysregulation, but the mechanistic underpinnings underlying the role of mitochondria during human neurogenesis remain unexplored. Here we provide a concise overview of cortical development and the use of pluripotent stem cell models that have contributed to our understanding of mitochondrial and metabolic regulation of early human brain development. We finally discuss the effects of mitochondrial fitness dysregulation seen under stress conditions such as metabolic dysregulation, absence of developmental apoptosis, and hypoxia; and the avenues of research that can be explored with the use of brain organoids.
Collapse
Affiliation(s)
| | - Vivian Gama
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Center for Stem Cell Biology, Vanderbilt University, Nashville, TN, United States
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, United States
| |
Collapse
|
13
|
Wu Y, Devotta A, José-Edwards DS, Kugler JE, Negrón-Piñeiro LJ, Braslavskaya K, Addy J, Saint-Jeannet JP, Di Gregorio A. Xbp1 and Brachyury establish an evolutionarily conserved subcircuit of the notochord gene regulatory network. eLife 2022; 11:e73992. [PMID: 35049502 PMCID: PMC8803312 DOI: 10.7554/elife.73992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Abstract
Gene regulatory networks coordinate the formation of organs and structures that compose the evolving body plans of different organisms. We are using a simple chordate model, the Ciona embryo, to investigate the essential gene regulatory network that orchestrates morphogenesis of the notochord, a structure necessary for the proper development of all chordate embryos. Although numerous transcription factors expressed in the notochord have been identified in different chordates, several of them remain to be positioned within a regulatory framework. Here, we focus on Xbp1, a transcription factor expressed during notochord formation in Ciona and other chordates. Through the identification of Xbp1-downstream notochord genes in Ciona, we found evidence of the early co-option of genes involved in the unfolded protein response to the notochord developmental program. We report the regulatory interplay between Xbp1 and Brachyury, and by extending these results to Xenopus, we show that Brachyury and Xbp1 form a cross-regulatory subcircuit of the notochord gene regulatory network that has been consolidated during chordate evolution.
Collapse
Affiliation(s)
- Yushi Wu
- Department of Molecular Pathobiology, New York University College of DentistryNew YorkUnited States
| | - Arun Devotta
- Department of Molecular Pathobiology, New York University College of DentistryNew YorkUnited States
| | - Diana S José-Edwards
- Department of Molecular Pathobiology, New York University College of DentistryNew YorkUnited States
| | - Jamie E Kugler
- Department of Molecular Pathobiology, New York University College of DentistryNew YorkUnited States
| | - Lenny J Negrón-Piñeiro
- Department of Molecular Pathobiology, New York University College of DentistryNew YorkUnited States
| | - Karina Braslavskaya
- Department of Molecular Pathobiology, New York University College of DentistryNew YorkUnited States
| | - Jermyn Addy
- Department of Molecular Pathobiology, New York University College of DentistryNew YorkUnited States
| | | | - Anna Di Gregorio
- Department of Molecular Pathobiology, New York University College of DentistryNew YorkUnited States
| |
Collapse
|
14
|
Schwaner MJ, Hsieh ST, Braasch I, Bradley S, Campos CB, Collins CE, Donatelli CM, Fish FE, Fitch OE, Flammang BE, Jackson BE, Jusufi A, Mekdara PJ, Patel A, Swalla BJ, Vickaryous M, McGowan CP. Future Tail Tales: A Forward-Looking, Integrative Perspective on Tail Research. Integr Comp Biol 2021; 61:521-537. [PMID: 33999184 PMCID: PMC8680820 DOI: 10.1093/icb/icab082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Synopsis Tails are a defining characteristic of chordates and show enormous diversity in function and shape. Although chordate tails share a common evolutionary and genetic-developmental origin, tails are extremely versatile in morphology and function. For example, tails can be short or long, thin or thick, and feathered or spiked, and they can be used for propulsion, communication, or balancing, and they mediate in predator-prey outcomes. Depending on the species of animal the tail is attached to, it can have extraordinarily multi-functional purposes. Despite its morphological diversity and broad functional roles, tails have not received similar scientific attention as, for example, the paired appendages such as legs or fins. This forward-looking review article is a first step toward interdisciplinary scientific synthesis in tail research. We discuss the importance of tail research in relation to five topics: (1) evolution and development, (2) regeneration, (3) functional morphology, (4) sensorimotor control, and (5) computational and physical models. Within each of these areas, we highlight areas of research and combinations of long-standing and new experimental approaches to move the field of tail research forward. To best advance a holistic understanding of tail evolution and function, it is imperative to embrace an interdisciplinary approach, re-integrating traditionally siloed fields around discussions on tail-related research.
Collapse
Affiliation(s)
- M J Schwaner
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA
| | - S T Hsieh
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - I Braasch
- Department of Integrative Biology and Program in Ecology, Evolution, and Behavior (EEB), Michigan State University, East Lansing, MI 48824, USA
| | - S Bradley
- Department of Biomedical Science, University of Guelph, Guelph N1G 2W1, Canada
| | - C B Campos
- Department of Biological Sciences, Sacramento State University, Sacramento, CA 95819, USA
| | - C E Collins
- Department of Biological Sciences, Sacramento State University, Sacramento, CA 95819, USA
| | - C M Donatelli
- Department of Biology, University of Ottawa, Ontario K1N 6N5, Canada
| | - F E Fish
- Department of Biology, West Chester University, West Chester, PA 19383, USA
| | - O E Fitch
- Department of Integrative Biology and Program in Ecology, Evolution, and Behavior (EEB), Michigan State University, East Lansing, MI 48824, USA
| | - B E Flammang
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - B E Jackson
- Department of Biological and Environmental Sciences, Longwood University, Farmville, VA 23909, USA
| | - A Jusufi
- Max Planck Institute for Intelligent Systems, Stuttgart 70569, Germany
| | - P J Mekdara
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - A Patel
- Department of Electrical Engineering, University of Cape Town, Cape Town 7701, South Africa
| | - B J Swalla
- Department of Biology, University of Washington, Seattle, WA 98195, USA
| | - M Vickaryous
- Department of Biomedical Science, University of Guelph, Guelph N1G 2W1, Canada
| | - C P McGowan
- Department of Integrative Anatomical Sciences, University of Southern California, Los Angeles, CA 90033, USA
| |
Collapse
|
15
|
Zhang J, Wei J, Yu H, Dong B. Genome-Wide Identification, Comparison, and Expression Analysis of Transcription Factors in Ascidian Styela clava. Int J Mol Sci 2021; 22:4317. [PMID: 33919240 PMCID: PMC8122590 DOI: 10.3390/ijms22094317] [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: 01/15/2021] [Revised: 03/09/2021] [Accepted: 04/06/2021] [Indexed: 11/29/2022] Open
Abstract
Tunicates include diverse species, as they are model animals for evolutionary developmental biology study. The embryonic development of tunicates is known to be extensively regulated by transcription factors (TFs). Styela clava, the globally distributed invasive tunicate, exhibits a strong capacity for environmental adaptation. However, the TFs were not systematically identified and analyzed. In this study, we reported 553 TFs categorized into 60 families from S. clava, based on the whole genome data. Comparison of TFs analysis among the tunicate species revealed that the gene number in the zinc finger superfamily displayed the most significant discrepancy, indicating this family was under the highly evolutionary selection and might be related to species differentiation and environmental adaptation. The greatest number of TFs was discovered in the Cys2His2-type zinc finger protein (zf-C2H2) family in S. clava. From the point of temporal view, more than half the TFs were expressed at the early embryonic stage. The expression correlation analysis revealed the existence of a transition for TFs expression from early embryogenesis to the later larval development in S. clava. Eight Hox genes were identified to be located on one chromosome, exhibiting different arrangement and expression patterns, compared to Ciona robusta (C. intestinalis type A). In addition, a total of 23 forkhead box (fox) genes were identified in S. clava, and their expression profiles referred to their potential roles in neurodevelopment and sensory organ development. Our data, thus, provides crucial clues to the potential functions of TFs in development and environmental adaptation in the leathery sea squirt.
Collapse
Affiliation(s)
- Jin Zhang
- Sars-Fang Centre, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (J.Z.); (J.W.)
| | - Jiankai Wei
- Sars-Fang Centre, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (J.Z.); (J.W.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Haiyan Yu
- Sars-Fang Centre, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (J.Z.); (J.W.)
| | - Bo Dong
- Sars-Fang Centre, MoE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (J.Z.); (J.W.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| |
Collapse
|
16
|
Fodor A, Liu J, Turner L, Swalla BJ. Transitional chordates and vertebrate origins: Tunicates. Curr Top Dev Biol 2021; 141:149-171. [DOI: 10.1016/bs.ctdb.2020.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
17
|
Transcription Factors of the bHLH Family Delineate Vertebrate Landmarks in the Nervous System of a Simple Chordate. Genes (Basel) 2020; 11:genes11111262. [PMID: 33114624 PMCID: PMC7693978 DOI: 10.3390/genes11111262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 10/12/2020] [Indexed: 02/07/2023] Open
Abstract
Tunicates are marine invertebrates whose tadpole-like larvae feature a highly simplified version of the chordate body plan. Similar to their distant vertebrate relatives, tunicate larvae develop a regionalized central nervous system and form distinct neural structures, which include a rostral sensory vesicle, a motor ganglion, and a caudal nerve cord. The sensory vesicle contains a photoreceptive complex and a statocyst, and based on the comparable expression patterns of evolutionarily conserved marker genes, it is believed to include proto-hypothalamic and proto-retinal territories. The evolutionarily conserved molecular fingerprints of these landmarks of the vertebrate brain consist of genes encoding for different transcription factors, and of the gene batteries that they control, and include several members of the bHLH family. Here we review the complement of bHLH genes present in the streamlined genome of the tunicate Ciona robusta and their current classification, and summarize recent studies on proneural bHLH transcription factors and their expression territories. We discuss the possible roles of bHLH genes in establishing the molecular compartmentalization of the enticing nervous system of this unassuming chordate.
Collapse
|