1
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Zhou J, He H, Zhang JJ, Liu X, Yao W, Li C, Xu T, Yin SY, Wu DY, Dou CL, Li Q, Xiang J, Xiong WJ, Wang LY, Tang JM, Xue Z, Zhang X, Miao YL. ATG7-mediated autophagy facilitates embryonic stem cell exit from naive pluripotency and marks commitment to differentiation. Autophagy 2022; 18:2946-2968. [PMID: 35311460 PMCID: PMC9673953 DOI: 10.1080/15548627.2022.2055285] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Macroautophagy/autophagy is a conserved cellular mechanism to degrade unneeded cytoplasmic proteins and organelles to recycle their components, and it is critical for embryonic stem cell (ESC) self-renewal and somatic cell reprogramming. Whereas autophagy is essential for early development of embryos, no information exists regarding its functions during the transition from naive-to-primed pluripotency. Here, by using an in vitro transition model of ESCs to epiblast-like cells (EpiLCs), we find that dynamic changes in ATG7-dependent autophagy are critical for the naive-to-primed transition, and are also necessary for germline specification. RNA-seq and ATAC-seq profiling reveal that NANOG acts as a barrier to prevent pluripotency transition, and autophagy-dependent NANOG degradation is important for dismantling the naive pluripotency expression program through decommissioning of naive-associated active enhancers. Mechanistically, we found that autophagy receptor protein SQSTM1/p62 translocated into the nucleus during the pluripotency transition period and is preferentially associated with K63 ubiquitinated NANOG for selective protein degradation. In vivo, loss of autophagy by ATG7 depletion disrupts peri-implantation development and causes increased chromatin association of NANOG, which affects neuronal differentiation by competitively binding to OTX2-specific neuroectodermal development-associated regions. Taken together, our findings reveal that autophagy-dependent degradation of NANOG plays a critical role in regulating exit from the naive state and marks distinct cell fate allocation during lineage specification.Abbreviations: 3-MA: 3-methyladenine; EpiLC: epiblast-like cell; ESC: embryonic stem cell; PGC: primordial germ cell.
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Affiliation(s)
- Jilong Zhou
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, China
| | - Hainan He
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, China
| | - Jing-Jing Zhang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, China
| | - Xin Liu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, China
| | - Wang Yao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Chengyu Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Tian Xu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, China
| | - Shu-Yuan Yin
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, China
| | - Dan-Ya Wu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, China
| | - Cheng-Li Dou
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, China
| | - Qiao Li
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, China
| | - Jiani Xiang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, China
| | - Wen-Jing Xiong
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, China
| | - Li-Yan Wang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, China
| | - Jun-Ming Tang
- Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medicine Science, Hubei University of Medicine, Shiyan, Hubei, China
| | - Zhouyiyuan Xue
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, China
| | - Xia Zhang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, China
| | - Yi-Liang Miao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan, Hubei, China,Hubei Hongshan Laboratory, Wuhan, Hubei, China,CONTACT Yi-Liang Miao Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
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2
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Leung RF, George AM, Roussel EM, Faux MC, Wigle JT, Eisenstat DD. Genetic Regulation of Vertebrate Forebrain Development by Homeobox Genes. Front Neurosci 2022; 16:843794. [PMID: 35546872 PMCID: PMC9081933 DOI: 10.3389/fnins.2022.843794] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/14/2022] [Indexed: 01/19/2023] Open
Abstract
Forebrain development in vertebrates is regulated by transcription factors encoded by homeobox, bHLH and forkhead gene families throughout the progressive and overlapping stages of neural induction and patterning, regional specification and generation of neurons and glia from central nervous system (CNS) progenitor cells. Moreover, cell fate decisions, differentiation and migration of these committed CNS progenitors are controlled by the gene regulatory networks that are regulated by various homeodomain-containing transcription factors, including but not limited to those of the Pax (paired), Nkx, Otx (orthodenticle), Gsx/Gsh (genetic screened), and Dlx (distal-less) homeobox gene families. This comprehensive review outlines the integral role of key homeobox transcription factors and their target genes on forebrain development, focused primarily on the telencephalon. Furthermore, links of these transcription factors to human diseases, such as neurodevelopmental disorders and brain tumors are provided.
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Affiliation(s)
- Ryan F. Leung
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Ankita M. George
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
| | - Enola M. Roussel
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
| | - Maree C. Faux
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
| | - Jeffrey T. Wigle
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, MB, Canada
| | - David D. Eisenstat
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
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3
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Gibbs HC, Sarasamma S, Benavides OR, Green DG, Hart NA, Yeh AT, Maitland KC, Lekven AC. Quantifiable Intravital Light Sheet Microscopy. Methods Mol Biol 2022; 2440:181-196. [PMID: 35218540 DOI: 10.1007/978-1-0716-2051-9_11] [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] [Indexed: 06/14/2023]
Abstract
Live imaging of zebrafish embryos that maintains normal development can be difficult to achieve due to a combination of sample mounting, immobilization, and phototoxicity issues that, once overcome, often still results in image quality sufficiently poor that computer-aided analysis or even manual analysis is not possible. Here, we describe our mounting strategy for imaging the zebrafish midbrain-hindbrain boundary (MHB) with light sheet fluorescence microscopy (LSFM) and pilot experiments to create a study-specific set of parameters for semiautomatically tracking cellular movements in the embryonic midbrain primordium during zebrafish segmentation.
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Affiliation(s)
- Holly C Gibbs
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA.
- Microscopy and Imaging Center, Texas A&M University, College Station, TX, USA.
| | - Sreeja Sarasamma
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
| | - Oscar R Benavides
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
| | - David G Green
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - Nathan A Hart
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
| | - Alvin T Yeh
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
| | - Kristen C Maitland
- Department of Biomedical Engineering, Texas A&M University, College Station, TX, USA
- Microscopy and Imaging Center, Texas A&M University, College Station, TX, USA
| | - Arne C Lekven
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
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4
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Zhang M, Niibe K, Kondo T, Limraksasin P, Okawa H, Miao X, Kamano Y, Yamada M, Jiang X, Egusa H. Rapid and efficient generation of cartilage pellets from mouse induced pluripotent stem cells by transcriptional activation of BMP-4 with shaking culture. J Tissue Eng 2022; 13:20417314221114616. [PMID: 35923173 PMCID: PMC9340412 DOI: 10.1177/20417314221114616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 07/04/2022] [Indexed: 11/15/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) offer an unlimited source for cartilage
regeneration as they can generate a wide spectrum of cell types. Here, we
established a tetracycline (tet) controlled bone morphogenetic
protein-4 (BMP-4) expressing iPSC
(iPSC-Tet/BMP-4) line in which transcriptional activation
of BMP-4 was associated with enhanced chondrogenesis. Moreover,
we developed an efficient and simple approach for directly guiding
iPSC-Tet/BMP-4 differentiation into chondrocytes in
scaffold-free cartilaginous pellets using a combination of transcriptional
activation of BMP-4 and a 3D shaking suspension culture system.
In chondrogenic induction medium, shaking culture alone significantly
upregulated the chondrogenic markers Sox9, Col2a1, and
Aggrecan in iPSCs-Tet/BMP-4 by day 21. Of
note, transcriptional activation of BMP-4 by addition of tet
(doxycycline) greatly enhanced the expression of these genes. The cartilaginous
pellets derived from iPSCs-Tet/BMP-4 showed an oval morphology
and white smooth appearance by day 21. After day 21, the cells presented a
typical round morphology and the extracellular matrix was stained intensively
with Safranin O, alcian blue, and type II collagen. In addition, the homogenous
cartilaginous pellets derived from iPSCs-Tet/BMP-4 with 28 days
of induction repaired joint osteochondral defects in immunosuppressed rats and
integrated well with the adjacent host cartilage. The regenerated cartilage
expressed the neomycin resistance gene, indicating that the newly formed
cartilage was generated by the transplanted iPSCs-Tet/BMP-4.
Thus, our culture system could be a useful tool for further investigation of the
mechanism of BMP-4 in regulating iPSC differentiation toward the chondrogenic
lineage, and should facilitate research in cartilage development, repair, and
osteoarthritis.
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Affiliation(s)
- Maolin Zhang
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
- Department of Prosthodontics, Ninth People’s Hospital affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Kunimichi Niibe
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
| | - Takeru Kondo
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
| | - Phoonsuk Limraksasin
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
| | - Hiroko Okawa
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
| | - Xinchao Miao
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
| | - Yuya Kamano
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
| | - Masahiro Yamada
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
| | - Xinquan Jiang
- Department of Prosthodontics, Ninth People’s Hospital affiliated to Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Hiroshi Egusa
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
- Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai, Miyagi, Japan
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5
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Pálfy M, Schulze G, Valen E, Vastenhouw NL. Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation. PLoS Genet 2020; 16:e1008546. [PMID: 31940339 PMCID: PMC6986763 DOI: 10.1371/journal.pgen.1008546] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 01/28/2020] [Accepted: 12/02/2019] [Indexed: 12/12/2022] Open
Abstract
In many organisms, early embryonic development is driven by maternally provided factors until the controlled onset of transcription during zygotic genome activation. The regulation of chromatin accessibility and its relationship to gene activity during this transition remain poorly understood. Here, we generated chromatin accessibility maps with ATAC-seq from genome activation until the onset of lineage specification. During this period, chromatin accessibility increases at regulatory elements. This increase is independent of RNA polymerase II-mediated transcription, with the exception of the hypertranscribed miR-430 locus. Instead, accessibility often precedes the transcription of associated genes. Loss of the maternal transcription factors Pou5f3, Sox19b, and Nanog, which are known to be required for zebrafish genome activation, results in decreased accessibility at regulatory elements. Importantly, the accessibility of regulatory regions, especially when established by Pou5f3, Sox19b and Nanog, is predictive for future transcription. Our results show that the maternally provided transcription factors Pou5f3, Sox19b, and Nanog open up chromatin and prime genes for activity during zygotic genome activation in zebrafish.
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Affiliation(s)
- Máté Pálfy
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Gunnar Schulze
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Eivind Valen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
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6
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Hsieh YC, Chiang MC, Huang YC, Yeh TH, Shih HY, Liu HF, Chen HY, Wang CP, Cheng YC. Pparα deficiency inhibits the proliferation of neuronal and glial precursors in the zebrafish central nervous system. Dev Dyn 2018; 247:1264-1275. [DOI: 10.1002/dvdy.24683] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 09/12/2018] [Accepted: 10/16/2018] [Indexed: 12/28/2022] Open
Affiliation(s)
- Yen-Che Hsieh
- Graduate Institute of Biomedical Sciences, College of Medicine; Chang Gung University; Taoyuan Taiwan
| | - Ming-Chang Chiang
- Department of Life Science; Fu Jen Catholic University; New Taipei City Taiwan
| | - Yin-Cheng Huang
- College of Medicine; Chang Gung University; Taoyuan Taiwan
- Department of Neurosurgery; Chang Gung Memorial Hospital; Linkou, Taoyuan Taiwan
| | - Tu-Hsueh Yeh
- College of Medicine; Chang Gung University; Taoyuan Taiwan
- Neuroscience Research Center, Chang Gung Memorial Hospital; Linkou, Taoyuan Taiwan
- Section of Movement Disorders, Department of Neurology; Chang Gung Memorial Hospital; Linkou, Taoyuan Taiwan
- Department of Neurology; Taipei Medical University Hospital; Taipei Taiwan
| | - Hung-Yu Shih
- Graduate Institute of Biomedical Sciences, College of Medicine; Chang Gung University; Taoyuan Taiwan
| | - Han-Fang Liu
- Graduate Institute of Biomedical Sciences, College of Medicine; Chang Gung University; Taoyuan Taiwan
| | - Hao-Yuan Chen
- Graduate Institute of Biomedical Sciences, College of Medicine; Chang Gung University; Taoyuan Taiwan
| | - Chien-Ping Wang
- School of Medicine, College of Medicine, Chang Gung University; Taoyuan Taiwan
| | - Yi-Chuan Cheng
- Graduate Institute of Biomedical Sciences, College of Medicine; Chang Gung University; Taoyuan Taiwan
- College of Medicine; Chang Gung University; Taoyuan Taiwan
- Neuroscience Research Center, Chang Gung Memorial Hospital; Linkou, Taoyuan Taiwan
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7
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Kesavan G, Chekuru A, Machate A, Brand M. CRISPR/Cas9-Mediated Zebrafish Knock-in as a Novel Strategy to Study Midbrain-Hindbrain Boundary Development. Front Neuroanat 2017; 11:52. [PMID: 28713249 PMCID: PMC5492657 DOI: 10.3389/fnana.2017.00052] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/19/2017] [Indexed: 11/13/2022] Open
Abstract
The midbrain-hindbrain boundary (MHB) acts as an organizer and controls the fate of neighboring cells to develop into either mesencephalic (midbrain) or metencephalic (hindbrain) cells by secreting signaling molecules like Wnt1 and Fgf8. The zebrafish is an excellent vertebrate model for studying MHB development due to the ease of gene manipulation and the possibility of following cellular dynamics and morphogenetic processes using live imaging. Currently, only very few reporter and/or Cre-driver lines are available to study gene expression at the MHB, hampering the understanding of MHB development, and traditional transgenic technologies using promoter/enhancer fragments or bacterial artificial chromosome (BAC)-mediated transgenesis often do not faithfully recapitulate endogenous expression patterns. In contrast, CRISPR/Cas9-mediated genome editing technology now provides a great opportunity to efficiently knock-in or knock-out genes. We have generated four CRISPR/Cas9-based knock-in fluorescent reporter lines for two crucial genes involved in MHB development, namely otx2 and pax2a. The coding sequences of the reporters were knocked-in upstream of the corresponding ATG and are, thus, under the control of the endogenous promoter/enhancer elements. Interestingly, this strategy does not disturb endogenous gene expression. Using the fast maturing fluorescent protein reporter, Venus, enabled us to follow MHB development using cell tracking and live imaging. In addition, we show that these reporter lines label various neuronal and glial cell types in the adult zebrafish brain, making them highly suitable for investigating embryonic and adult midbrain, hindbrain, and MHB development.
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Affiliation(s)
- Gokul Kesavan
- Biotechnology Center and DFG-Research Center for Regenerative Therapies Dresden, Technische Universität DresdenDresden, Germany
| | - Avinash Chekuru
- Biotechnology Center and DFG-Research Center for Regenerative Therapies Dresden, Technische Universität DresdenDresden, Germany
| | - Anja Machate
- Biotechnology Center and DFG-Research Center for Regenerative Therapies Dresden, Technische Universität DresdenDresden, Germany
| | - Michael Brand
- Biotechnology Center and DFG-Research Center for Regenerative Therapies Dresden, Technische Universität DresdenDresden, Germany
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8
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Li WH, Zhou L, Li Z, Wang Y, Shi JT, Yang YJ, Gui JF. Zebrafish Lbh-like Is Required for Otx2-mediated Photoreceptor Differentiation. Int J Biol Sci 2015; 11:688-700. [PMID: 25999792 PMCID: PMC4440259 DOI: 10.7150/ijbs.11244] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 04/11/2015] [Indexed: 12/12/2022] Open
Abstract
The homeobox transcription factor orthodenticle homolog 2 (otx2) is supposed as an organizer that orchestrates a transcription factor network during photoreceptor development. However, its regulation in the process remains unclear. In this study, we have identified a zebrafish limb bud and heart-like gene (lbh-like), which is expressed initially at 30 hours post fertilization (hpf) in the developing brain and eyes. Lbh-like knockdown by morpholinos specifically inhibits expression of multiple photoreceptor-specific genes, such as opsins, gnat1, gnat2 and irbp. Interestingly, otx2 expression in the morphants is not significantly reduced until 32 hpf when lbh-like begins to express, but its expression level in 72 hpf morphants is higher than that in wild type embryos. Co-injection of otx2 and its downstream target neuroD mRNAs can rescue the faults in eyes of Lbh-like morphants. Combined with the results of promoter-reporter assay, we suggest that lbh-like is a new regulator of photoreceptor differentiation directly through affecting otx2 expression in zebrafish. Furthermore, knockdown of lbh-like increases the activity of Notch pathway and perturbs the balance among proliferation, differentiation and survival of photoreceptor precursors.
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Affiliation(s)
- Wen-Hua Li
- 1. State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, ; 2. Graduate University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Li Zhou
- 1. State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences
| | - Zhi Li
- 1. State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences
| | - Yang Wang
- 1. State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences
| | - Jian-Tao Shi
- 1. State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences
| | - Yan-Jing Yang
- 1. State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, ; 2. Graduate University of the Chinese Academy of Sciences, Wuhan 430072, China
| | - Jian-Fang Gui
- 1. State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences
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9
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HEB associates with PRC2 and SMAD2/3 to regulate developmental fates. Nat Commun 2015; 6:6546. [PMID: 25775035 DOI: 10.1038/ncomms7546] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 02/05/2015] [Indexed: 11/09/2022] Open
Abstract
In embryonic stem cells, extracellular signals are required to derepress developmental promoters to drive lineage specification, but the proteins involved in connecting extrinsic cues to relaxation of chromatin remain unknown. We demonstrate that the helix-loop-helix (HLH) protein, HEB, directly associates with the Polycomb repressive complex 2 (PRC2) at a subset of developmental promoters, including at genes involved in mesoderm and endoderm specification and at the Hox and Fox gene families. While we show that depletion of HEB does not affect mouse ESCs, it does cause premature differentiation after exposure to Activin. Further, we find that HEB deposition at developmental promoters is dependent upon PRC2 and independent of Nodal, whereas HEB association with SMAD2/3 elements is dependent of Nodal, but independent of PRC2. We suggest that HEB is a fundamental link between Nodal signalling, the derepression of a specific class of poised promoters during differentiation, and lineage specification in mouse ESCs.
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10
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Engerer P, Yoshimatsu T, Suzuki SC, Godinho L. CentrinFish permit the visualization of centrosome dynamics in a cellular context in vivo. Zebrafish 2014; 11:586-7. [PMID: 25387243 DOI: 10.1089/zeb.2014.1503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Peter Engerer
- 1 Institute of Neuronal Cell Biology, Technische Universität München , Munich, Germany
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11
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Oonuma K, Hirose D, Takatori N, Saiga H. Analysis of the Transcription Regulatory Mechanism of Otx During the Development of the Sensory Vesicle in Ciona intestinalis. Zoolog Sci 2014; 31:565-72. [DOI: 10.2108/zs140060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Kouhei Oonuma
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachiohji, Tokyo 192-0397, Japan
| | - Dan Hirose
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachiohji, Tokyo 192-0397, Japan
| | - Naohito Takatori
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachiohji, Tokyo 192-0397, Japan
| | - Hidetoshi Saiga
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, 1-1 Minamiohsawa, Hachiohji, Tokyo 192-0397, Japan
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12
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Kurokawa D, Ohmura T, Sakurai Y, Inoue K, Suda Y, Aizawa S. Otx2 expression in anterior neuroectoderm and forebrain/midbrain is directed by more than six enhancers. Dev Biol 2014; 387:203-13. [PMID: 24457099 DOI: 10.1016/j.ydbio.2014.01.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 01/12/2014] [Accepted: 01/14/2014] [Indexed: 11/25/2022]
Abstract
Otx2 plays essential roles in each site at each step of head development. We previously identified the AN1 enhancer at 91kb 5' upstream for the Otx2 expressions in anterior neuroectoderm (AN) at neural plate stage before E8.5, and the FM1 enhancer at 75kb 5' upstream and the FM2 enhancer at 122kb 3' downstream for the expression in forebrain/midbrain (FM) at brain vesicle stage after E8.5. The present study identified a second AN enhancer (AN2) at 88kb 5' upstream; the AN2 enhancer also recapitulates the endogenous Otx2 expression in choroid plexus, cortical hem and choroidal roof. However, the enhancer mutants indicated the presence of another AN enhancer. The study also identified a third FM enhancer (FM3) at 153kb 5' upstream. Thus, the Otx2 expressions in anterior neuroectoderm and forebrain/midbrain are regulated by more than six enhancers located far from the coding region. The enhancers identified are differentially conserved among vertebrates; none of the AN enhancers has activities in caudal forebrain and midbrain at brain vesicle stage after E8.5, nor do any of the FM enhancers in anterior neuroectoderm at neural plate stage before E8.5.
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Affiliation(s)
- Daisuke Kurokawa
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology (CDB), RIKEN Kobe, 2-2-3 Minatojima Minami-machi, Chuo-Ku, Kobe, Hyogo 650-0047, Japan; Misaki Marine Biological Station, Graduate School of Science, The University of Tokyo, 1024 Koajiro, Misaki, Miura, Kanagawa 238-0225, Japan
| | - Tomomi Ohmura
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology (CDB), RIKEN Kobe, 2-2-3 Minatojima Minami-machi, Chuo-Ku, Kobe, Hyogo 650-0047, Japan
| | - Yusuke Sakurai
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology (CDB), RIKEN Kobe, 2-2-3 Minatojima Minami-machi, Chuo-Ku, Kobe, Hyogo 650-0047, Japan
| | - Kenichi Inoue
- Laboratory for Animal Resources and Genetic Engineering, Center for Developmental Biology (CDB), RIKEN Kobe, 2-2-3 Minatojima Minami-machi, Chuo-Ku, Kobe, Hyogo 650-0047, Japan
| | - Yoko Suda
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology (CDB), RIKEN Kobe, 2-2-3 Minatojima Minami-machi, Chuo-Ku, Kobe, Hyogo 650-0047, Japan
| | - Shinichi Aizawa
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology (CDB), RIKEN Kobe, 2-2-3 Minatojima Minami-machi, Chuo-Ku, Kobe, Hyogo 650-0047, Japan; Laboratory for Animal Resources and Genetic Engineering, Center for Developmental Biology (CDB), RIKEN Kobe, 2-2-3 Minatojima Minami-machi, Chuo-Ku, Kobe, Hyogo 650-0047, Japan.
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Evolutionary growth process of highly conserved sequences in vertebrate genomes. Gene 2012; 504:1-5. [PMID: 22580082 DOI: 10.1016/j.gene.2012.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 04/27/2012] [Accepted: 05/02/2012] [Indexed: 11/22/2022]
Abstract
Genome sequence comparison between evolutionarily distant species revealed ultraconserved elements (UCEs) among mammals under strong purifying selection. Most of them were also conserved among vertebrates. Because they tend to be located in the flanking regions of developmental genes, they would have fundamental roles in creating vertebrate body plans. However, the evolutionary origin and selection mechanism of these UCEs remain unclear. Here we report that UCEs arose in primitive vertebrates, and gradually grew in vertebrate evolution. We searched for UCEs in two teleost fishes, Tetraodon nigroviridis and Oryzias latipes, and found 554 UCEs with 100% identity over 100 bps. Comparison of teleost and mammalian UCEs revealed 43 pairs of common, jawed-vertebrate UCEs (jUCE) with high sequence identities, ranging from 83.1% to 99.2%. Ten of them retain lower similarities to the Petromyzon marinus genome, and the substitution rates of four non-exonic jUCEs were reduced after the teleost-mammal divergence, suggesting that robust conservation had been acquired in the jawed vertebrate lineage. Our results indicate that prototypical UCEs originated before the divergence of jawed and jawless vertebrates and have been frozen as perfect conserved sequences in the jawed vertebrate lineage. In addition, our comparative sequence analyses of UCEs and neighboring regions resulted in a discovery of lineage-specific conserved sequences. They were added progressively to prototypical UCEs, suggesting step-wise acquisition of novel regulatory roles. Our results indicate that conserved non-coding elements (CNEs) consist of blocks with distinct evolutionary history, each having been frozen since different evolutionary era along the vertebrate lineage.
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Gbx2 directly restricts Otx2 expression to forebrain and midbrain, competing with class III POU factors. Mol Cell Biol 2012; 32:2618-27. [PMID: 22566684 DOI: 10.1128/mcb.00083-12] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Otx2 plays essential roles in rostral brain development, and its counteraction with Gbx2 has been suggested to determine the midbrain-hindbrain boundary (MHB) in vertebrates. We previously identified the FM enhancer that is conserved among vertebrates and drives Otx2 transcription in forebrain/midbrain from the early somite stage. In this study, we found that the POU homeodomain of class III POU factors (Brn1, Brn2, Brn4, and Oct6) associates with noncanonical target sequence TAATTA in the FM enhancer. MicroRNA-mediated knockdown of Brn2 and Oct6 diminished the FM enhancer activity in anterior neural progenitor cells (NPCs) differentiated from P19 cells. The class III POU factors associate with the FM enhancer in forebrain and midbrain but not in hindbrain. We also demonstrated that the Gbx2 homeodomain recognizes the same target TAATTA in the FM enhancer, and Gbx2 associates with the FM enhancer in hindbrain. Gbx2 misexpression in the anterior NPCs repressed the FM enhancer activity and inhibited Brn2 association with the enhancer, whereas Gbx2 knockdown caused ectopic Brn2 association in the posterior NPCs. These results suggest that class III POU factors and Gbx2 share the same target site, TAATTA, in the FM enhancer and that their region-specific binding restricts Otx2 expression at the MHB.
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15
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Immunoglobulin from Antarctic fish species of Rajidae family. Mar Genomics 2012; 5:35-41. [DOI: 10.1016/j.margen.2011.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 09/06/2011] [Accepted: 09/07/2011] [Indexed: 11/17/2022]
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16
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Parker HJ, Piccinelli P, Sauka-Spengler T, Bronner M, Elgar G. Ancient Pbx-Hox signatures define hundreds of vertebrate developmental enhancers. BMC Genomics 2011; 12:637. [PMID: 22208168 PMCID: PMC3261376 DOI: 10.1186/1471-2164-12-637] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 12/30/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene regulation through cis-regulatory elements plays a crucial role in development and disease. A major aim of the post-genomic era is to be able to read the function of cis-regulatory elements through scrutiny of their DNA sequence. Whilst comparative genomics approaches have identified thousands of putative regulatory elements, our knowledge of their mechanism of action is poor and very little progress has been made in systematically de-coding them. RESULTS Here, we identify ancient functional signatures within vertebrate conserved non-coding elements (CNEs) through a combination of phylogenetic footprinting and functional assay, using genomic sequence from the sea lamprey as a reference. We uncover a striking enrichment within vertebrate CNEs for conserved binding-site motifs of the Pbx-Hox hetero-dimer. We further show that these predict reporter gene expression in a segment specific manner in the hindbrain and pharyngeal arches during zebrafish development. CONCLUSIONS These findings evoke an evolutionary scenario in which many CNEs evolved early in the vertebrate lineage to co-ordinate Hox-dependent gene-regulatory interactions that pattern the vertebrate head. In a broader context, our evolutionary analyses reveal that CNEs are composed of tightly linked transcription-factor binding-sites (TFBSs), which can be systematically identified through phylogenetic footprinting approaches. By placing a large number of ancient vertebrate CNEs into a developmental context, our findings promise to have a significant impact on efforts toward de-coding gene-regulatory elements that underlie vertebrate development, and will facilitate building general models of regulatory element evolution.
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Affiliation(s)
- Hugo J Parker
- Division of Systems Biology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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17
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Kurokawa D, Ohmura T, Akasaka K, Aizawa S. A lineage specific enhancer drives Otx2 expression in teleost organizer tissues. Mech Dev 2011; 128:653-61. [PMID: 22108260 DOI: 10.1016/j.mod.2011.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Revised: 10/01/2011] [Accepted: 11/07/2011] [Indexed: 10/15/2022]
Abstract
In mouse Otx2 plays essential roles in anterior-posterior axis formation and head development in anterior visceral endoderm and anterior mesendoderm. The Otx2 expression in these sites is regulated by VE and CM enhancers at the 5' proximal to the translation start site, and we proposed that these enhancers would have been established in ancestral sarcoptergians after divergence from actinopterigians for the use of Otx2 as the head organizer gene (Kurokawa et al., 2010). This would make doubtful an earlier proposal of ours that a 1.1 kb fragment located at +14.4 to +15.5 kb 3' (3'En) of fugu Otx2a gene harbors enhancers phylogenetically and functionally homologous to mouse VE and CM enhancers (Kimura-Yoshida et al., 2007). In the present study, we demonstrate that fugu Otx2a is not expressed in the dorsal margin of blastoderm, shield and early anterior mesendoderm, and that the fugu Otx2a 3'En do not exhibit activities at these sites of fugu embryos. We conclude that the fugu Otx2a 3'En does not harbor an organizer enhancer, but encodes an enhancer for the expression in later anterior mesendodermal tissues. Instead, in fugu embryos Otx2b is expressed in the dorsal margin of blastoderm at blastula stage and shield at 50% epiboly, and this expression is directed by an enhancer, 5'En, located at -1000 to -800 bp, which is uniquely conserved among teleost Otx2b orthologues.
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Affiliation(s)
- Daisuke Kurokawa
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology, RIKEN Kobe, 2-2-1 Minatojima Minami-machi, Chuo-ku, Kobe 650-0047, Japan
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18
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Lang M, Hadzhiev Y, Siegel N, Amemiya CT, Parada C, Strähle U, Becker MB, Müller F, Meyer A. Conservation of shh cis-regulatory architecture of the coelacanth is consistent with its ancestral phylogenetic position. EvoDevo 2010; 1:11. [PMID: 21047394 PMCID: PMC2992049 DOI: 10.1186/2041-9139-1-11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 11/03/2010] [Indexed: 12/17/2022] Open
Abstract
Background The modern coelacanth (Latimeria) is the extant taxon of a basal sarcopterygian lineage and sister group to tetrapods. Apart from certain apomorphic traits, its morphology is characterized by a high degree of retention of ancestral vertebrate structures and little morphological change. An insight into the molecular evolution that may explain the unchanged character of Latimeria morphology requires the analysis of the expression patterns of developmental regulator genes and their cis-regulatory modules (CRMs). Results We describe the comparative and functional analysis of the sonic hedgehog (shh) genomic region of Latimeria menadoensis. Several putative enhancers in the Latimeria shh locus have been identified by comparisons to sarcopterygian and actinopterygian extant species. Specific sequence conservation with all known actinopterygian enhancer elements has been detected. However, these elements are selectively missing in more recently diverged actinopterygian and sarcopterygian species. The functionality of the putative Latimeria enhancers was confirmed by reporter gene expression analysis in transient transgenic zebrafish and chick embryos. Conclusions Latimeria shh CRMs represent the ancestral set of enhancers that have emerged before the split of lobe-finned and ray-finned fishes. In contrast to lineage-specific losses and differentiations in more derived lineages, Latimeria shh enhancers reveal low levels of sequence diversification. High overall sequence conservation of shh conserved noncoding elements (CNE) is consistent with the general trend of high levels of conservation of noncoding DNA in the slowly evolving Latimeria genome.
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Affiliation(s)
- Michael Lang
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany.,Development and Neurobiology Program, Jacques Monod Institute, 75013 Paris, France
| | - Yavor Hadzhiev
- Department of Medical and Molecular Genetics, University of Birmingham, Birmingham B15 2TT, UK
| | - Nicol Siegel
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany.,Medical University of Vienna, Medical Genetics, 1090 Vienna, Austria
| | - Chris T Amemiya
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA
| | - Carolina Parada
- Developmental Biology Group, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003 Barcelona, Spain.,Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90030, USA
| | - Uwe Strähle
- Karlsruhe Institute of Technology, Institute for Toxicology and Genetics, 76021 Karlsruhe, Germany
| | - May-Britt Becker
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany.,Exzellenzcluster CellNetworks, INF 267, 69120 Heidelberg, Germany
| | - Ferenc Müller
- Department of Medical and Molecular Genetics, University of Birmingham, Birmingham B15 2TT, UK.,Karlsruhe Institute of Technology, Institute for Toxicology and Genetics, 76021 Karlsruhe, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
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Sakurai Y, Kurokawa D, Kiyonari H, Kajikawa E, Suda Y, Aizawa S. Otx2 and Otx1 protect diencephalon and mesencephalon from caudalization into metencephalon during early brain regionalization. Dev Biol 2010; 347:392-403. [PMID: 20816794 DOI: 10.1016/j.ydbio.2010.08.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 08/24/2010] [Accepted: 08/25/2010] [Indexed: 10/19/2022]
Abstract
Otx2 is expressed in each step and site of head development. To dissect each Otx2 function we have identified a series of Otx2 enhancers. The Otx2 expression in the anterior neuroectoderm is regulated by the AN enhancer and the subsequent expression in forebrain and midbrain later than E8.5 by FM1 and FM2 enhancers; the Otx1 expression takes place at E8.0. In telencephalon later than E9.5 Otx1 continues to be expressed in the entire pallium, while the Otx2 expression is confined to the most medial pallium. To determine the Otx functions in forebrain and midbrain development we have generated mouse mutants that lack both FM1 and FM2 enhancers (DKO: Otx2(ΔFM1ΔFM2/ΔFM1ΔFM2)) and examined the TKO (Otx1(-/-)Otx2(ΔFM1ΔFM2/ΔFM1ΔFM2)) phenotype. The mutants develop normally until E8.0, but subsequently by E9.5 the diencephalon, including thalamic eminence and prethalamus, and the mesencephalon are caudalized into metencephalon consisting of isthmus and rhombomere 1; the caudalization does not extend to rhombomere 2 and more caudal rhombomeres. In rostral forebrain, neopallium, ganglionic eminences and hypothalamus in front of prethalamus develop; we propose that they become insensitive to the caudalization with the switch from the Otx2 expression under the AN enhancer to that under FM1 and FM2 enhancers. In contrast, the medial pallium requires Otx1 and Otx2 for its development later than E9.5, and the Otx2 expression in diencepalon and mesencephalon later than E9.5 is also directed by an enhancer other than FM1 and FM2 enhancers.
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Affiliation(s)
- Yusuke Sakurai
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology, RIKEN Kobe, 2-2-3 Minatojima Minamimachi, Chuo-ku, Kobe 650-0047, Japan
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20
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Kurokawa D, Ohmura T, Ogino H, Takeuchi M, Inoue A, Inoue F, Suda Y, Aizawa S. Evolutionary origin of the Otx2 enhancer for its expression in visceral endoderm. Dev Biol 2010; 342:110-20. [PMID: 20353765 DOI: 10.1016/j.ydbio.2010.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 03/15/2010] [Accepted: 03/16/2010] [Indexed: 11/27/2022]
Abstract
In the mouse, the Otx2 gene has been shown to play essential roles in the visceral endoderm during anterior-posterior axis formation and head induction. While these are primary processes in vertebrate embryogenesis, the visceral endoderm is a tissue unique to mammals. Two enhancers (VE and CM) have been previously found to direct Otx2 expression during early embryogenesis. This study demonstrates that in anterior visceral endoderm the CM enhancer does not have an activity by itself, but enhances the activity of the VE enhancer. These two enhancers also cooperate for the activities in anterior mesendoderm and cephalic mesenchyme. Comparative studies suggest that VE enhancer function was most likely established before the divergence of sarcopterygians into Actinistia, Dipnoi and tetrapods, while the nucleotide sequence corresponding to the VE enhancer was already present in the last common ancestor of bony fishes. The CM enhancer sequence and function would have been also established in ancestral sarcopterygians. The VE/CM enhancers and their gene cascades in the ancestral sarcopterygian head organizer would then have been co-opted by amphibian deep endoderm cells and mammalian visceral endoderm cells for the head development.
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Affiliation(s)
- Daisuke Kurokawa
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology, RIKEN Kobe, 2-2-3 Minatojima Minamimachi, Chuou-ku, Kobe 650-0047, Japan
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21
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McEwen GK, Goode DK, Parker HJ, Woolfe A, Callaway H, Elgar G. Early evolution of conserved regulatory sequences associated with development in vertebrates. PLoS Genet 2009; 5:e1000762. [PMID: 20011110 PMCID: PMC2781166 DOI: 10.1371/journal.pgen.1000762] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Accepted: 11/10/2009] [Indexed: 01/22/2023] Open
Abstract
Comparisons between diverse vertebrate genomes have uncovered thousands of highly conserved non-coding sequences, an increasing number of which have been shown to function as enhancers during early development. Despite their extreme conservation over 500 million years from humans to cartilaginous fish, these elements appear to be largely absent in invertebrates, and, to date, there has been little understanding of their mode of action or the evolutionary processes that have modelled them. We have now exploited emerging genomic sequence data for the sea lamprey, Petromyzon marinus, to explore the depth of conservation of this type of element in the earliest diverging extant vertebrate lineage, the jawless fish (agnathans). We searched for conserved non-coding elements (CNEs) at 13 human gene loci and identified lamprey elements associated with all but two of these gene regions. Although markedly shorter and less well conserved than within jawed vertebrates, identified lamprey CNEs are able to drive specific patterns of expression in zebrafish embryos, which are almost identical to those driven by the equivalent human elements. These CNEs are therefore a unique and defining characteristic of all vertebrates. Furthermore, alignment of lamprey and other vertebrate CNEs should permit the identification of persistent sequence signatures that are responsible for common patterns of expression and contribute to the elucidation of the regulatory language in CNEs. Identifying the core regulatory code for development, common to all vertebrates, provides a foundation upon which regulatory networks can be constructed and might also illuminate how large conserved regulatory sequence blocks evolve and become fixed in genomic DNA. Recent comparative analyses of vertebrate genomes has resulted in the identification of highly conserved non-coding sequences near genes that coordinate early development. Many of these sequences can activate gene expression and are thought to be important regulatory elements. Surprisingly, a large set of these long, near-identical sequences is found in every jawed vertebrate, including sharks, yet almost completely absent in non-vertebrates. This study looks for this set of sequences in the lamprey, a representative of our most distant vertebrate relatives, in order to determine when and how such a large set of important non-coding regulatory sequences became established in the genome. Although the lamprey divergence is only a little older than the divergence of cartilaginous fish (including sharks), relatively few, and considerably shorter, conserved non-coding sequences are identifiable. Nevertheless, these shorter lamprey sequences are capable of driving gene expression in a precise spatial pattern in zebrafish embryos in the same way as the equivalent human elements. This analysis has shed light on the emergence of these regulatory sequences during early vertebrate evolution, at a time of whole-genome duplications and considerable morphological variation, consistent with a role for these sequences in directing gene regulatory networks for vertebrate development.
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Affiliation(s)
- Gayle K. McEwen
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Debbie K. Goode
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Hugo J. Parker
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Adam Woolfe
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Heather Callaway
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Greg Elgar
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
- * E-mail:
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23
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Elgar G. Pan-vertebrate conserved non-coding sequences associated with developmental regulation. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 8:256-65. [DOI: 10.1093/bfgp/elp033] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Ogino H, Ochi H. Resources and transgenesis techniques for functional genomics in Xenopus. Dev Growth Differ 2009; 51:387-401. [PMID: 19382936 DOI: 10.1111/j.1440-169x.2009.01098.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Recent developments in genomic resources and high-throughput transgenesis techniques have allowed Xenopus to 'metamorphose' from a classic model for embryology to a leading-edge experimental system for functional genomics. This process has incorporated the fast-breeding diploid frog, Xenopus tropicalis, as a new model-system for vertebrate genomics and genetics. Sequencing of the X. tropicalis genome is nearly complete, and its comparison with mammalian sequences offers a reliable guide for the genome-wide prediction of cis-regulatory elements. Unique cDNA sets have been generated for both X. tropicalis and X. laevis, which have facilitated non-redundant, systematic gene expression screening and comprehensive gene expression analysis. A variety of transgenesis techniques are available for both X. laevis and X. tropicalis, and the appropriate procedure may be chosen depending on the purpose for which it is required. Effective use of these resources and techniques will help to reveal the overall picture of the complex wiring of gene regulatory networks that control vertebrate development.
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Affiliation(s)
- Hajime Ogino
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, Japan.
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25
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Coolen M, Menuet A, Chassoux D, Compagnucci C, Henry S, Lévèque L, Da Silva C, Gavory F, Samain S, Wincker P, Thermes C, D'Aubenton-Carafa Y, Rodriguez-Moldes I, Naylor G, Depew M, Sourdaine P, Mazan S. The Dogfish Scyliorhinus canicula: A Reference in Jawed Vertebrates. Cold Spring Harb Protoc 2008; 2008:pdb.emo111. [PMID: 21356737 DOI: 10.1101/pdb.emo111] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
INTRODUCTIONDue to their large size and long generation times, chondrichthyans have been largely ignored by geneticists. However, their key phylogenetic position makes them ideal subjects to study the molecular bases of the important morphological and physiological innovations that characterize jawed vertebrates. Such analyses are crucial to understanding the origin of the complex genetic mechanisms unraveled in osteichthyans. The small spotted dogfish Scyliorhinus canicula, a representative of the largest order of extant sharks, presents a number of advantages in this context. Due to its relatively small size among sharks, its abundance, and easy maintenance, the dogfish has been an important model in comparative anatomy and physiology for more than a century. Recently, revived interest has occurred with the development of large-scale transcriptomic and genomic resources, together with the establishment of facilities allowing massive egg and embryo production. These new tools open the way to molecular analyses of the elaborate physiological and sensory systems used by sharks. They also make it possible to take advantage of unique characteristics of these species, such as organ zonation, in analyses of cell proliferation and differentiation. Finally, they offer important perspectives to evolutionary developmental biology that will provide a better understanding of the origin and diversifications of jawed vertebrates. The dogfish whole-genome sequence, which may shortly become accessible, should establish this species as an essential shark reference, complementary to other chondrichthyan models. These analyses are likely to reveal an organism of an underestimated complexity, far from the primitive prototypical gnathostome anticipated in gradistic views.
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Affiliation(s)
- Marion Coolen
- CNRS UMR 6218 Immunologie et Embryologie Moléculaires, Université Sciences et Techniques d'Orléans, 45071 Orléans, France
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26
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Hall BK. Evolutionary Origins of the Neural Crest and Neural Crest Cells. Evol Biol 2008. [DOI: 10.1007/s11692-008-9033-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Suda Y, Kurokawa D, Takeuchi M, Kajikawa E, Kuratani S, Amemiya C, Aizawa S. Evolution of Otx paralogue usages in early patterning of the vertebrate head. Dev Biol 2008; 325:282-95. [PMID: 18848537 DOI: 10.1016/j.ydbio.2008.09.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Revised: 09/10/2008] [Accepted: 09/12/2008] [Indexed: 11/17/2022]
Abstract
To assess evolutional changes in the expression pattern of Otx paralogues, expression analyses were undertaken in fugu, bichir, skate and lamprey. Together with those in model vertebrates, the comparison suggested that a gnathostome ancestor would have utilized all of Otx1, Otx2 and Otx5 paralogues in organizer and anterior mesendoderm for head development. In this animal, Otx1 and Otx2 would have also functioned in specification of the anterior neuroectoderm at presomite stage and subsequent development of forebrain/midbrain at somite stage, while Otx5 expression would have already been specialized in epiphysis and eyes. Otx1 and Otx2 functions in anterior neuroectoderm and brain of the gnathostome ancestor would have been differentially maintained by Otx1 in a basal actinopterygian and by Otx2 in a basal sarcopterygian. Otx5 expression in head organizer and anterior mesendoderm seems to have been lost in the teleost lineage after divergence of bichir, and also from the amniotes after divergence of amphibians as independent events. Otx1 expression was lost from the organizer in the tetrapod lineage. In contrast, in a teleost ancestor prior to whole genome duplication, Otx1 and Otx2 would have both been expressed in the dorsal margin of blastoderm, embryonic shield, anterior mesendoderm, anterior neuroectoderm and forebrain/midbrain, at respective stages of head development. Subsequent whole genome duplication and the following genome changes would have caused different Otx paralogue usages in each teleost lineage. Lampreys also have three Otx paralogues; their sequences are highly diverged from gnathostome cognates, but their expression pattern is well related to those of skate Otx cognates.
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Affiliation(s)
- Yoko Suda
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology, RIKEN Kobe, Chuo-ku, Kobe 650-0047, Japan
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Takasaki N, Kurokawa D, Nakayama R, Nakayama JI, Aizawa S. Acetylated YY1 regulates Otx2 expression in anterior neuroectoderm at two cis-sites 90 kb apart. EMBO J 2007; 26:1649-59. [PMID: 17332747 PMCID: PMC1829384 DOI: 10.1038/sj.emboj.7601619] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2006] [Accepted: 01/23/2007] [Indexed: 11/09/2022] Open
Abstract
The mouse homeobox gene Otx2 plays essential roles at each step and in every tissue during head development. We have previously identified a series of enhancers that are responsible for driving the Otx2 expression in these contexts. Among them the AN enhancer, existing 92 kb 5' upstream, directs Otx2 expression in anterior neuroectoderm (AN) at the headfold stage. Analysis of the enhancer mutant Otx2(DeltaAN/-) indicated that Otx2 expression under the control of this enhancer is essential to the development of AN. This study demonstrates that the AN enhancer is promoter-dependent and regulated by acetylated YY1. YY1 binds to both the AN enhancer and promoter region. YY1 is acetylated in the anterior head, and only acetylated YY1 can bind to the sequence in the enhancer. Moreover, YY1 binding to both of these two sites is essential to Otx2 expression in AN. These YY1 binding sites are highly conserved in AN enhancers in tetrapods, coelacanth and skate, suggesting that establishment of the YY1 regulation coincides with that of OTX2 function in AN development in an ancestral gnathostome.
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Affiliation(s)
- Nobuyoshi Takasaki
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology (CDB), RIKEN Kobe, Chuo-ku, Kobe, Japan
| | - Daisuke Kurokawa
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology (CDB), RIKEN Kobe, Chuo-ku, Kobe, Japan
| | - Rika Nakayama
- Laboratory for Animal Resources and Genetic Engineering, Center for Developmental Biology (CDB), RIKEN Kobe, Chuo-ku, Kobe, Japan
| | - Jun-ichi Nakayama
- Laboratory for Chromatin Dynamics, Center for Developmental Biology (CDB), RIKEN Kobe, Chuo-ku, Kobe, Japan
| | - Shinichi Aizawa
- Laboratory for Vertebrate Body Plan, Center for Developmental Biology (CDB), RIKEN Kobe, Chuo-ku, Kobe, Japan
- Laboratory for Animal Resources and Genetic Engineering, Center for Developmental Biology (CDB), RIKEN Kobe, Chuo-ku, Kobe, Japan
- Laboratory for Vertebrate Body Plan, RIKEN Kobe, 2-2-3, Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan. Tel.: +81783063149; Fax: +81783063148; E-mail:
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