1
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Ahmadzadeh E, Bayin NS, Qu X, Singh A, Madisen L, Stephen D, Zeng H, Joyner AL, Rosello-Diez A. A collection of genetic mouse lines and related tools for inducible and reversible intersectional mis-expression. Development 2020; 147:dev.186650. [PMID: 32366677 DOI: 10.1242/dev.186650] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 04/16/2020] [Indexed: 12/30/2022]
Abstract
Thanks to many advances in genetic manipulation, mouse models have become very powerful in their ability to interrogate biological processes. In order to precisely target expression of a gene of interest to particular cell types, intersectional genetic approaches using two promoter/enhancers unique to a cell type are ideal. Within these methodologies, variants that add temporal control of gene expression are the most powerful. We describe the development, validation and application of an intersectional approach that involves three transgenes, requiring the intersection of two promoter/enhancers to target gene expression to precise cell types. Furthermore, the approach uses available lines expressing tTA/rTA to control the timing of gene expression based on whether doxycycline is absent or present, respectively. We also show that the approach can be extended to other animal models, using chicken embryos. We generated three mouse lines targeted at the Tigre (Igs7) locus with TRE-loxP-tdTomato-loxP upstream of three genes (p21, DTA and Ctgf), and combined them with Cre and tTA/rtTA lines that target expression to the cerebellum and limbs. Our tools will facilitate unraveling biological questions in multiple fields and organisms.
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Affiliation(s)
- Elham Ahmadzadeh
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800. Australia
| | - N Sumru Bayin
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Xinli Qu
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800. Australia
| | - Aditi Singh
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800. Australia
| | - Linda Madisen
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Daniel Stephen
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Alexandra L Joyner
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Alberto Rosello-Diez
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800. Australia
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2
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Daigle TL, Madisen L, Hage TA, Valley MT, Knoblich U, Larsen RS, Takeno MM, Huang L, Gu H, Larsen R, Mills M, Bosma-Moody A, Siverts LA, Walker M, Graybuck LT, Yao Z, Fong O, Nguyen TN, Garren E, Lenz GH, Chavarha M, Pendergraft J, Harrington J, Hirokawa KE, Harris JA, Nicovich PR, McGraw MJ, Ollerenshaw DR, Smith KA, Baker CA, Ting JT, Sunkin SM, Lecoq J, Lin MZ, Boyden ES, Murphy GJ, da Costa NM, Waters J, Li L, Tasic B, Zeng H. A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain-Cell-Type Targeting and Functionality. Cell 2019; 174:465-480.e22. [PMID: 30007418 DOI: 10.1016/j.cell.2018.06.035] [Citation(s) in RCA: 414] [Impact Index Per Article: 82.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 04/12/2018] [Accepted: 06/13/2018] [Indexed: 01/05/2023]
Abstract
Modern genetic approaches are powerful in providing access to diverse cell types in the brain and facilitating the study of their function. Here, we report a large set of driver and reporter transgenic mouse lines, including 23 new driver lines targeting a variety of cortical and subcortical cell populations and 26 new reporter lines expressing an array of molecular tools. In particular, we describe the TIGRE2.0 transgenic platform and introduce Cre-dependent reporter lines that enable optical physiology, optogenetics, and sparse labeling of genetically defined cell populations. TIGRE2.0 reporters broke the barrier in transgene expression level of single-copy targeted-insertion transgenesis in a wide range of neuronal types, along with additional advantage of a simplified breeding strategy compared to our first-generation TIGRE lines. These novel transgenic lines greatly expand the repertoire of high-precision genetic tools available to effectively identify, monitor, and manipulate distinct cell types in the mouse brain.
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Affiliation(s)
- Tanya L Daigle
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Linda Madisen
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Travis A Hage
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Ulf Knoblich
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Rylan S Larsen
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Marc M Takeno
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lawrence Huang
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hong Gu
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Rachael Larsen
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Maya Mills
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | - Miranda Walker
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Emma Garren
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Garreck H Lenz
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Mariya Chavarha
- Departments of Neurobiology and Bioengineering, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | | | | | - Julie A Harris
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Medea J McGraw
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | | | | | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Jérôme Lecoq
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Michael Z Lin
- Departments of Neurobiology and Bioengineering, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Edward S Boyden
- MIT Media Lab and McGovern Institute, Departments of Biological Engineering and Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gabe J Murphy
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Jack Waters
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Lu Li
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA.
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3
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Zimmerman CA, Huey EL, Ahn JS, Beutler LR, Tan CL, Kosar S, Bai L, Chen Y, Corpuz TV, Madisen L, Zeng H, Knight ZA. A gut-to-brain signal of fluid osmolarity controls thirst satiation. Nature 2019; 568:98-102. [PMID: 30918408 PMCID: PMC6483081 DOI: 10.1038/s41586-019-1066-x] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 03/04/2019] [Indexed: 12/03/2022]
Affiliation(s)
- Christopher A Zimmerman
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA.,Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA, USA.,Neuroscience Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Erica L Huey
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA.,Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA, USA.,Graduate Program in Neuroscience, Harvard Medical School, Boston, MA, USA
| | - Jamie S Ahn
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA.,Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA, USA.,California Northstate University College of Medicine, Elk Grove, CA, USA
| | - Lisa R Beutler
- Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Chan Lek Tan
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA.,Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA, USA.,Department of Neuroscience, Genentech Inc., South San Francisco, CA, USA
| | - Seher Kosar
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA.,Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA, USA
| | - Ling Bai
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA.,Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA, USA
| | - Yiming Chen
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA.,Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA, USA.,Neuroscience Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Timothy V Corpuz
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA.,Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA, USA
| | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Zachary A Knight
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA. .,Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA, USA. .,Neuroscience Graduate Program, University of California San Francisco, San Francisco, CA, USA. .,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA.
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4
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Tasic B, Yao Z, Graybuck LT, Smith KA, Nguyen TN, Bertagnolli D, Goldy J, Garren E, Economo MN, Viswanathan S, Penn O, Bakken T, Menon V, Miller J, Fong O, Hirokawa KE, Lathia K, Rimorin C, Tieu M, Larsen R, Casper T, Barkan E, Kroll M, Parry S, Shapovalova NV, Hirschstein D, Pendergraft J, Sullivan HA, Kim TK, Szafer A, Dee N, Groblewski P, Wickersham I, Cetin A, Harris JA, Levi BP, Sunkin SM, Madisen L, Daigle TL, Looger L, Bernard A, Phillips J, Lein E, Hawrylycz M, Svoboda K, Jones AR, Koch C, Zeng H. Shared and distinct transcriptomic cell types across neocortical areas. Nature 2018; 563:72-78. [PMID: 30382198 DOI: 10.1038/s41586-018-0654-5] [Citation(s) in RCA: 917] [Impact Index Per Article: 152.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 09/24/2018] [Indexed: 12/11/2022]
Abstract
The neocortex contains a multitude of cell types that are segregated into layers and functionally distinct areas. To investigate the diversity of cell types across the mouse neocortex, here we analysed 23,822 cells from two areas at distant poles of the mouse neocortex: the primary visual cortex and the anterior lateral motor cortex. We define 133 transcriptomic cell types by deep, single-cell RNA sequencing. Nearly all types of GABA (γ-aminobutyric acid)-containing neurons are shared across both areas, whereas most types of glutamatergic neurons were found in one of the two areas. By combining single-cell RNA sequencing and retrograde labelling, we match transcriptomic types of glutamatergic neurons to their long-range projection specificity. Our study establishes a combined transcriptomic and projectional taxonomy of cortical cell types from functionally distinct areas of the adult mouse cortex.
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Affiliation(s)
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Emma Garren
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Michael N Economo
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Sarada Viswanathan
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Osnat Penn
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Vilas Menon
- Allen Institute for Brain Science, Seattle, WA, USA.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Kanan Lathia
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Michael Tieu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Eliza Barkan
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Sheana Parry
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | - Aaron Szafer
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nick Dee
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Ian Wickersham
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ali Cetin
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Loren Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Karel Svoboda
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
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5
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Roselló-Díez A, Madisen L, Bastide S, Zeng H, Joyner AL. Cell-nonautonomous local and systemic responses to cell arrest enable long-bone catch-up growth in developing mice. PLoS Biol 2018; 16:e2005086. [PMID: 29944650 PMCID: PMC6019387 DOI: 10.1371/journal.pbio.2005086] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 05/24/2018] [Indexed: 01/12/2023] Open
Abstract
Catch-up growth after insults to growing organs is paramount to achieving robust body proportions. In fly larvae, injury to individual tissues is followed by local and systemic compensatory mechanisms that allow the damaged tissue to regain normal proportions with other tissues. In vertebrates, local catch-up growth has been described after transient reduction of bone growth, but the underlying cellular responses are controversial. We developed an approach to study catch-up growth in foetal mice in which mosaic expression of the cell cycle suppressor p21 is induced in the cartilage cells (chondrocytes) that drive long-bone elongation. By specifically targeting p21 expression to left hindlimb chondrocytes, the right limb serves as an internal control. Unexpectedly, left-right limb symmetry remained normal, revealing deployment of compensatory mechanisms. Above a certain threshold of insult, an orchestrated response was triggered involving local enhancement of bone growth and systemic growth reduction that ensured that body proportions were maintained. The local response entailed hyperproliferation of spared left limb chondrocytes that was associated with reduced chondrocyte density. The systemic effect involved impaired placental function and IGF signalling, revealing bone-placenta communication. Therefore, vertebrates, like invertebrates, can mount coordinated local and systemic responses to developmental insults that ensure that normal body proportions are maintained.
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Affiliation(s)
- Alberto Roselló-Díez
- Developmental Biology Program, Sloan Kettering Institute, New York, New York, United States of America
| | - Linda Madisen
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Sébastien Bastide
- Developmental Biology Program, Sloan Kettering Institute, New York, New York, United States of America
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, Washington, United States of America
| | - Alexandra L. Joyner
- Developmental Biology Program, Sloan Kettering Institute, New York, New York, United States of America
- Biochemistry, Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, New York, United States of America
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6
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Hsiang JC, Johnson KP, Madisen L, Zeng H, Kerschensteiner D. Local processing in neurites of VGluT3-expressing amacrine cells differentially organizes visual information. eLife 2017; 6:31307. [PMID: 29022876 PMCID: PMC5653236 DOI: 10.7554/elife.31307] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/11/2017] [Indexed: 12/17/2022] Open
Abstract
Neurons receive synaptic inputs on extensive neurite arbors. How information is organized across arbors and how local processing in neurites contributes to circuit function is mostly unknown. Here, we used two-photon Ca2+ imaging to study visual processing in VGluT3-expressing amacrine cells (VG3-ACs) in the mouse retina. Contrast preferences (ON vs. OFF) varied across VG3-AC arbors depending on the laminar position of neurites, with ON responses preferring larger stimuli than OFF responses. Although arbors of neighboring cells overlap extensively, imaging population activity revealed continuous topographic maps of visual space in the VG3-AC plexus. All VG3-AC neurites responded strongly to object motion, but remained silent during global image motion. Thus, VG3-AC arbors limit vertical and lateral integration of contrast and location information, respectively. We propose that this local processing enables the dense VG3-AC plexus to contribute precise object motion signals to diverse targets without distorting target-specific contrast preferences and spatial receptive fields.
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Affiliation(s)
- Jen-Chun Hsiang
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, Saint Louis, United States.,Graduate Program in Neuroscience, Washington University School of Medicine, Saint Louis, United States
| | - Keith P Johnson
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, Saint Louis, United States.,Graduate Program in Neuroscience, Washington University School of Medicine, Saint Louis, United States
| | - Linda Madisen
- Allen Institute for Brain Science, Seattle, United States
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, United States
| | - Daniel Kerschensteiner
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, Saint Louis, United States.,Department of Neuroscience, Washington University School of Medicine, Saint Louis, United States.,Department of Biomedical Engineering, Washington University School of Medicine, Saint Louis, United States.,Hope Center for Neurological Disorders, Washington University School of Medicine, Saint Louis, United States
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7
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Jang S, Choubey S, Furchtgott L, Zou LN, Doyle A, Menon V, Loew EB, Krostag AR, Martinez RA, Madisen L, Levi BP, Ramanathan S. Dynamics of embryonic stem cell differentiation inferred from single-cell transcriptomics show a series of transitions through discrete cell states. eLife 2017; 6:20487. [PMID: 28296635 PMCID: PMC5352225 DOI: 10.7554/elife.20487] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/31/2017] [Indexed: 02/06/2023] Open
Abstract
The complexity of gene regulatory networks that lead multipotent cells to acquire different cell fates makes a quantitative understanding of differentiation challenging. Using a statistical framework to analyze single-cell transcriptomics data, we infer the gene expression dynamics of early mouse embryonic stem (mES) cell differentiation, uncovering discrete transitions across nine cell states. We validate the predicted transitions across discrete states using flow cytometry. Moreover, using live-cell microscopy, we show that individual cells undergo abrupt transitions from a naïve to primed pluripotent state. Using the inferred discrete cell states to build a probabilistic model for the underlying gene regulatory network, we further predict and experimentally verify that these states have unique response to perturbations, thus defining them functionally. Our study provides a framework to infer the dynamics of differentiation from single cell transcriptomics data and to build predictive models of the gene regulatory networks that drive the sequence of cell fate decisions during development. DOI:http://dx.doi.org/10.7554/eLife.20487.001
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Affiliation(s)
- Sumin Jang
- FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Sandeep Choubey
- FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Leon Furchtgott
- FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Biophysics Program, Harvard University, Cambridge, United States
| | - Ling-Nan Zou
- FAS Center for Systems Biology, Harvard University, Cambridge, United States
| | - Adele Doyle
- FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Vilas Menon
- Allen Institute for Brain Science, Seattle, United States
| | - Ethan B Loew
- FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | | | | | - Linda Madisen
- Allen Institute for Brain Science, Seattle, United States
| | - Boaz P Levi
- Allen Institute for Brain Science, Seattle, United States
| | - Sharad Ramanathan
- FAS Center for Systems Biology, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States.,Allen Institute for Brain Science, Seattle, United States.,School of Engineering and Applied Sciences, Harvard University, Cambridge, United States.,Harvard Stem Cell Institute, Harvard University, Cambridge, United States
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8
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Tasic B, Menon V, Nguyen TN, Kim TK, Jarsky T, Yao Z, Levi B, Gray LT, Sorensen SA, Dolbeare T, Bertagnolli D, Goldy J, Shapovalova N, Parry S, Lee C, Smith K, Bernard A, Madisen L, Sunkin SM, Hawrylycz M, Koch C, Zeng H. Adult mouse cortical cell taxonomy revealed by single cell transcriptomics. Nat Neurosci 2016; 19:335-46. [PMID: 26727548 PMCID: PMC4985242 DOI: 10.1038/nn.4216] [Citation(s) in RCA: 1052] [Impact Index Per Article: 131.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 12/03/2015] [Indexed: 12/13/2022]
Abstract
Nervous systems are composed of various cell types, but the extent of cell type diversity is poorly understood. Here, we construct a cellular taxonomy of one cortical region, primary visual cortex, in adult mice based on single cell RNA-sequencing. We identify 49 transcriptomic cell types including 23 GABAergic, 19 glutamatergic and seven non-neuronal types. We also analyze cell-type specific mRNA processing and characterize genetic access to these transcriptomic types by many transgenic Cre lines. Finally, we show that some of our transcriptomic cell types display specific and differential electrophysiological and axon projection properties, thereby confirming that the single cell transcriptomic signatures can be associated with specific cellular properties.
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Affiliation(s)
- Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Vilas Menon
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Tae Kyung Kim
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Tim Jarsky
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Boaz Levi
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Lucas T Gray
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Tim Dolbeare
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Jeff Goldy
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Sheana Parry
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Changkyu Lee
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Kimberly Smith
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Amy Bernard
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Linda Madisen
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Susan M Sunkin
- Allen Institute for Brain Science, Seattle, Washington, USA
| | | | - Christof Koch
- Allen Institute for Brain Science, Seattle, Washington, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, Washington, USA
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9
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Madisen L, Garner AR, Shimaoka D, Chuong AS, Klapoetke NC, Li L, van der Bourg A, Niino Y, Egolf L, Monetti C, Gu H, Mills M, Cheng A, Tasic B, Nguyen TN, Sunkin SM, Benucci A, Nagy A, Miyawaki A, Helmchen F, Empson RM, Knöpfel T, Boyden ES, Reid RC, Carandini M, Zeng H. Transgenic mice for intersectional targeting of neural sensors and effectors with high specificity and performance. Neuron 2015; 85:942-58. [PMID: 25741722 DOI: 10.1016/j.neuron.2015.02.022] [Citation(s) in RCA: 687] [Impact Index Per Article: 76.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 01/08/2015] [Accepted: 02/11/2015] [Indexed: 12/25/2022]
Abstract
UNLABELLED An increasingly powerful approach for studying brain circuits relies on targeting genetically encoded sensors and effectors to specific cell types. However, current approaches for this are still limited in functionality and specificity. Here we utilize several intersectional strategies to generate multiple transgenic mouse lines expressing high levels of novel genetic tools with high specificity. We developed driver and double reporter mouse lines and viral vectors using the Cre/Flp and Cre/Dre double recombinase systems and established a new, retargetable genomic locus, TIGRE, which allowed the generation of a large set of Cre/tTA-dependent reporter lines expressing fluorescent proteins, genetically encoded calcium, voltage, or glutamate indicators, and optogenetic effectors, all at substantially higher levels than before. High functionality was shown in example mouse lines for GCaMP6, YCX2.60, VSFP Butterfly 1.2, and Jaws. These novel transgenic lines greatly expand the ability to monitor and manipulate neuronal activities with increased specificity. VIDEO ABSTRACT
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Affiliation(s)
- Linda Madisen
- Allen Institute for Brain Science, 551 N 34(th) Street, Seattle, WA 98103, USA
| | - Aleena R Garner
- Allen Institute for Brain Science, 551 N 34(th) Street, Seattle, WA 98103, USA
| | - Daisuke Shimaoka
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London, EC1V 9EL, UK
| | - Amy S Chuong
- MIT Media Lab and McGovern Institute, Massachusetts Institute of Technology, 20 Ames Street, Cambridge, MA 02139, USA
| | - Nathan C Klapoetke
- MIT Media Lab and McGovern Institute, Massachusetts Institute of Technology, 20 Ames Street, Cambridge, MA 02139, USA
| | - Lu Li
- Allen Institute for Brain Science, 551 N 34(th) Street, Seattle, WA 98103, USA
| | - Alexander van der Bourg
- Brain Research Institute, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Yusuke Niino
- Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama 351-0198, Japan
| | - Ladan Egolf
- Brain Research Institute, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Claudio Monetti
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Hong Gu
- Allen Institute for Brain Science, 551 N 34(th) Street, Seattle, WA 98103, USA
| | - Maya Mills
- Allen Institute for Brain Science, 551 N 34(th) Street, Seattle, WA 98103, USA
| | - Adrian Cheng
- Allen Institute for Brain Science, 551 N 34(th) Street, Seattle, WA 98103, USA
| | - Bosiljka Tasic
- Allen Institute for Brain Science, 551 N 34(th) Street, Seattle, WA 98103, USA
| | - Thuc Nghi Nguyen
- Allen Institute for Brain Science, 551 N 34(th) Street, Seattle, WA 98103, USA
| | - Susan M Sunkin
- Allen Institute for Brain Science, 551 N 34(th) Street, Seattle, WA 98103, USA
| | - Andrea Benucci
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London, EC1V 9EL, UK; Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama 351-0198, Japan
| | - Andras Nagy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Atsushi Miyawaki
- Brain Science Institute, RIKEN, 2-1 Hirosawa, Wako-city, Saitama 351-0198, Japan
| | - Fritjof Helmchen
- Brain Research Institute, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Ruth M Empson
- Department of Physiology, Brain Health Research Centre, University of Otago, PO Box 913, Dunedin 9054, New Zealand
| | - Thomas Knöpfel
- The Division of Brain Sciences, Department of Medicine, Imperial College London, 160 DuCane Road, London, W12 0NN, UK
| | - Edward S Boyden
- MIT Media Lab and McGovern Institute, Massachusetts Institute of Technology, 20 Ames Street, Cambridge, MA 02139, USA
| | - R Clay Reid
- Allen Institute for Brain Science, 551 N 34(th) Street, Seattle, WA 98103, USA
| | - Matteo Carandini
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London, EC1V 9EL, UK
| | - Hongkui Zeng
- Allen Institute for Brain Science, 551 N 34(th) Street, Seattle, WA 98103, USA.
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10
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Pieraut S, Gounko N, Sando R, Dang W, Rebboah E, Panda S, Madisen L, Zeng H, Maximov A. Experience-dependent remodeling of basket cell networks in the dentate gyrus. Neuron 2015; 84:107-122. [PMID: 25277456 DOI: 10.1016/j.neuron.2014.09.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2014] [Indexed: 11/19/2022]
Abstract
The structural organization of neural circuits is strongly influenced by experience, but the underlying mechanisms are incompletely understood. We found that, in the developing dentate gyrus (DG), excitatory drive promotes the somatic innervation of principal granule cells (GCs) by parvalbumin (PV)-positive basket cells. In contrast, presynaptic differentiation of GCs and interneuron subtypes that inhibit GC dendrites is largely resistant to loss of glutamatergic neurotransmission. The networks of PV basket cells in the DG are regulated by vesicular release from projection entorhinal cortical neurons and, at least in part, by NMDA receptors in interneurons. Finally, we present evidence that glutamatergic inputs and NMDA receptors regulate these networks through a presynaptic mechanism that appears to control the branching of interneuron axons. Our results provide insights into how cortical activity tunes the inhibition in a subcortical circuit and reveal new principles of interneuron plasticity.
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Affiliation(s)
- Simon Pieraut
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA; The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Natalia Gounko
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA; The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Richard Sando
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA; The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA; The Kellogg School of Science and Technology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Westley Dang
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA; The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA; The Kellogg School of Science and Technology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Elisabeth Rebboah
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA; The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Satchidananda Panda
- Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Linda Madisen
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98103, USA
| | - Anton Maximov
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, CA 92037, USA; The Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, CA 92037, USA.
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11
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Harris JA, Hirokawa KE, Sorensen SA, Gu H, Mills M, Ng LL, Bohn P, Mortrud M, Ouellette B, Kidney J, Smith KA, Dang C, Sunkin S, Bernard A, Oh SW, Madisen L, Zeng H. Anatomical characterization of Cre driver mice for neural circuit mapping and manipulation. Front Neural Circuits 2014; 8:76. [PMID: 25071457 PMCID: PMC4091307 DOI: 10.3389/fncir.2014.00076] [Citation(s) in RCA: 272] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 06/18/2014] [Indexed: 01/26/2023] Open
Abstract
Significant advances in circuit-level analyses of the brain require tools that allow for labeling, modulation of gene expression, and monitoring and manipulation of cellular activity in specific cell types and/or anatomical regions. Large-scale projects and individual laboratories have produced hundreds of gene-specific promoter-driven Cre mouse lines invaluable for enabling genetic access to subpopulations of cells in the brain. However, the potential utility of each line may not be fully realized without systematic whole brain characterization of transgene expression patterns. We established a high-throughput in situ hybridization (ISH), imaging and data processing pipeline to describe whole brain gene expression patterns in Cre driver mice. Currently, anatomical data from over 100 Cre driver lines are publicly available via the Allen Institute's Transgenic Characterization database, which can be used to assist researchers in choosing the appropriate Cre drivers for functional, molecular, or connectional studies of different regions and/or cell types in the brain.
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Affiliation(s)
| | | | | | - Hong Gu
- Allen Institute for Brain Science Seattle, WA, USA
| | - Maya Mills
- Allen Institute for Brain Science Seattle, WA, USA
| | - Lydia L Ng
- Allen Institute for Brain Science Seattle, WA, USA
| | - Phillip Bohn
- Allen Institute for Brain Science Seattle, WA, USA
| | | | | | | | | | - Chinh Dang
- Allen Institute for Brain Science Seattle, WA, USA
| | - Susan Sunkin
- Allen Institute for Brain Science Seattle, WA, USA
| | - Amy Bernard
- Allen Institute for Brain Science Seattle, WA, USA
| | | | | | - Hongkui Zeng
- Allen Institute for Brain Science Seattle, WA, USA
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12
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Lee H, Kim DW, Remedios R, Anthony TE, Chang A, Madisen L, Zeng H, Anderson DJ. Scalable control of mounting and attack by Esr1+ neurons in the ventromedial hypothalamus. Nature 2014; 509:627-32. [PMID: 24739975 PMCID: PMC4098836 DOI: 10.1038/nature13169] [Citation(s) in RCA: 304] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 02/21/2014] [Indexed: 12/17/2022]
Abstract
Social behaviours, such as aggression or mating, proceed through a series of appetitive and consummatory phases that are associated with increasing levels of arousal. How such escalation is encoded in the brain, and linked to behavioural action selection, remains an unsolved problem in neuroscience. The ventrolateral subdivision of the murine ventromedial hypothalamus (VMHvl) contains neurons whose activity increases during male-male and male-female social encounters. Non-cell-type-specific optogenetic activation of this region elicited attack behaviour, but not mounting. We have identified a subset of VMHvl neurons marked by the oestrogen receptor 1 (Esr1), and investigated their role in male social behaviour. Optogenetic manipulations indicated that Esr1(+) (but not Esr1(-)) neurons are sufficient to initiate attack, and that their activity is continuously required during ongoing agonistic behaviour. Surprisingly, weaker optogenetic activation of these neurons promoted mounting behaviour, rather than attack, towards both males and females, as well as sniffing and close investigation. Increasing photostimulation intensity could promote a transition from close investigation and mounting to attack, within a single social encounter. Importantly, time-resolved optogenetic inhibition experiments revealed requirements for Esr1(+) neurons in both the appetitive (investigative) and the consummatory phases of social interactions. Combined optogenetic activation and calcium imaging experiments in vitro, as well as c-Fos analysis in vivo, indicated that increasing photostimulation intensity increases both the number of active neurons and the average level of activity per neuron. These data suggest that Esr1(+) neurons in VMHvl control the progression of a social encounter from its appetitive through its consummatory phases, in a scalable manner that reflects the number or type of active neurons in the population.
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Affiliation(s)
- Hyosang Lee
- 1] Division of Biology and Biological Engineering 156-29, California Institute of Technology, Pasadena, California 91125, USA [2] Howard Hughes Medical Institute, Pasadena, California 91125, USA
| | - Dong-Wook Kim
- Computation and Neural Systems, California Institute of Technology, Pasadena, California 91125, USA
| | - Ryan Remedios
- Division of Biology and Biological Engineering 156-29, California Institute of Technology, Pasadena, California 91125, USA
| | - Todd E Anthony
- Division of Biology and Biological Engineering 156-29, California Institute of Technology, Pasadena, California 91125, USA
| | - Angela Chang
- Division of Biology and Biological Engineering 156-29, California Institute of Technology, Pasadena, California 91125, USA
| | - Linda Madisen
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - David J Anderson
- 1] Division of Biology and Biological Engineering 156-29, California Institute of Technology, Pasadena, California 91125, USA [2] Howard Hughes Medical Institute, Pasadena, California 91125, USA [3] Computation and Neural Systems, California Institute of Technology, Pasadena, California 91125, USA
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13
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Abstract
A major challenge in neuroscience is to understand how universal behaviors, such as sensation, movement, cognition, and emotion, arise from the interactions of specific cells that are present within intricate neural networks in the brain. Dissection of such complex networks has typically relied on disturbing the activity of individual gene products, perturbing neuronal activities pharmacologically, or lesioning specific brain regions, to investigate the network's response in a behavioral output. Though informative for many kinds of studies, these approaches are not sufficiently fine-tuned for examining the functionality of specific cells or cell classes in a spatially or temporally restricted context. Recent advances in the field of optogenetics now enable researchers to monitor and manipulate the activity of genetically defined cell populations with the speed and precision uniquely afforded by light. Transgenic mice engineered to express optogenetic tools in a cell type-specific manner offer a powerful approach for examining the role of particular cells in discrete circuits in a defined and reproducible way. Not surprisingly then, recent years have seen substantial efforts directed toward generating transgenic mouse lines that express functionally relevant levels of optogenetic tools. In this chapter, we review the state of these efforts and consider aspects of the current technology that would benefit from additional improvement.
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Affiliation(s)
- Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA.
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14
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Zariwala HA, Madisen L, Ahrens KF, Bernard A, Lein ES, Jones AR, Zeng H. Visual tuning properties of genetically identified layer 2/3 neuronal types in the primary visual cortex of cre-transgenic mice. Front Syst Neurosci 2011; 4:162. [PMID: 21283555 PMCID: PMC3028542 DOI: 10.3389/fnsys.2010.00162] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 12/20/2010] [Indexed: 11/29/2022] Open
Abstract
The putative excitatory and inhibitory cell classes within the mouse primary visual cortex V1 have different functional properties as studied using recording microelectrode. Excitatory neurons show high selectivity for the orientation angle of moving gratings while the putative inhibitory neurons show poor selectivity. However, the study of selectivity of the genetically identified interneurons and their subtypes remain controversial. Here we use novel Cre-driver and reporter mice to identify genetic subpopulations in vivo for two-photon calcium dye imaging: Wfs1(+)/Gad1(−) mice that labels layer 2/3 excitatory cell population and Pvalb(+)/Gad1(+) mice that labels a genetic subpopulation of inhibitory neurons. The cells in both mice were identically labeled with a tdTomato protein, visible in vivo, using a Cre-reporter line. We found that the Wfs1(+) cells exhibited visual tuning properties comparable to the excitatory population, i.e., high selectivity and tuning to the angle, direction, and spatial frequency of oriented moving gratings. The functional tuning of Pvalb(+) neurons was consistent with previously reported narrow-spiking interneurons in microelectrode studies, exhibiting poorer selectivity than the excitatory neurons. This study demonstrates the utility of Cre-transgenic mouse technology in selective targeting of subpopulations of neurons and makes them amenable to structural, functional, and connectivity studies.
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15
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Madisen L, Zwingman TA, Sunkin SM, Oh SW, Zariwala HA, Gu H, Ng LL, Palmiter RD, Hawrylycz MJ, Jones AR, Lein ES, Zeng H. A robust and high-throughput Cre reporting and characterization system for the whole mouse brain. Nat Neurosci 2009; 13:133-40. [PMID: 20023653 PMCID: PMC2840225 DOI: 10.1038/nn.2467] [Citation(s) in RCA: 4643] [Impact Index Per Article: 309.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Accepted: 11/06/2009] [Indexed: 11/09/2022]
Abstract
The Cre/lox system is widely used in mice to achieve cell-type-specific gene expression. However, a strong and universal responding system to express genes under Cre control is still lacking. We have generated a set of Cre reporter mice with strong, ubiquitous expression of fluorescent proteins of different spectra. The robust native fluorescence of these reporters enables direct visualization of fine dendritic structures and axonal projections of the labeled neurons, which is useful in mapping neuronal circuitry, imaging and tracking specific cell populations in vivo. Using these reporters and a high-throughput in situ hybridization platform, we are systematically profiling Cre-directed gene expression throughout the mouse brain in a number of Cre-driver lines, including novel Cre lines targeting different cell types in the cortex. Our expression data are displayed in a public online database to help researchers assess the utility of various Cre-driver lines for cell-type-specific genetic manipulation.
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Affiliation(s)
- Linda Madisen
- Allen Institute for Brain Science, Seattle, Washington, USA
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16
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Zeng H, Horie K, Madisen L, Pavlova MN, Gragerova G, Rohde AD, Schimpf BA, Liang Y, Ojala E, Kramer F, Roth P, Slobodskaya O, Dolka I, Southon EA, Tessarollo L, Bornfeldt KE, Gragerov A, Pavlakis GN, Gaitanaris GA. An inducible and reversible mouse genetic rescue system. PLoS Genet 2008; 4:e1000069. [PMID: 18464897 PMCID: PMC2346557 DOI: 10.1371/journal.pgen.1000069] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Accepted: 04/10/2008] [Indexed: 12/13/2022] Open
Abstract
Inducible and reversible regulation of gene expression is a powerful approach for uncovering gene function. We have established a general method to efficiently produce reversible and inducible gene knockout and rescue in mice. In this system, which we named iKO, the target gene can be turned on and off at will by treating the mice with doxycycline. This method combines two genetically modified mouse lines: a) a KO line with a tetracycline-dependent transactivator replacing the endogenous target gene, and b) a line with a tetracycline-inducible cDNA of the target gene inserted into a tightly regulated (TIGRE) genomic locus, which provides for low basal expression and high inducibility. Such a locus occurs infrequently in the genome and we have developed a method to easily introduce genes into the TIGRE site of mouse embryonic stem (ES) cells by recombinase-mediated insertion. Both KO and TIGRE lines have been engineered for high-throughput, large-scale and cost-effective production of iKO mice. As a proof of concept, we have created iKO mice in the apolipoprotein E (ApoE) gene, which allows for sensitive and quantitative phenotypic analyses. The results demonstrated reversible switching of ApoE transcription, plasma cholesterol levels, and atherosclerosis progression and regression. The iKO system shows stringent regulation and is a versatile genetic system that can easily incorporate other techniques and adapt to a wide range of applications. We describe a technology for the creation of inducible and reversible gene inactivation in mice. It combines two genetically modified mouse lines: a knock-out line with a tetracycline transactivator replacing the endogenous target gene, and a line in which a tetracycline-inducible cDNA of the target gene has been inserted into a specific genomic locus. A critical component of this system is the unique chromosomal loci we have identified and engineered that offer a platform for easy insertion of any gene of interest for tightly controlled expression. Because of its simple binary nature, allowing independent modification of each of the two components and possibility of use in a high-throughput mode, we believe that our system will be useful for multiple applications, such as introducing mutant or humanized form of the target gene as well as functional manipulating tools. We have applied this technology to the Apolipoprotein E (ApoE) gene and have demonstrated that: a) the expression of ApoE is strictly dependent on the presence of doxycycline, a tetracycline group antibiotic, in the mouse diet, b) in the absence of doxycycline (ApoE repressed) atherosclerotic plaques are formed, confirming the importance of ApoE in the process, and c) upon re-induction of ApoE in the animals with doxicyclin, atherosclerosis regressed.
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Affiliation(s)
- Hongkui Zeng
- Omeros Corporation, Seattle, Washington, United States of America
| | - Kyoji Horie
- Human Retrovirus Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Linda Madisen
- Omeros Corporation, Seattle, Washington, United States of America
| | - Maria N. Pavlova
- Omeros Corporation, Seattle, Washington, United States of America
| | - Galina Gragerova
- Omeros Corporation, Seattle, Washington, United States of America
| | - Alex D. Rohde
- Omeros Corporation, Seattle, Washington, United States of America
| | - Brian A. Schimpf
- Omeros Corporation, Seattle, Washington, United States of America
| | - Yuqiong Liang
- Omeros Corporation, Seattle, Washington, United States of America
| | - Ethan Ojala
- Omeros Corporation, Seattle, Washington, United States of America
| | - Farah Kramer
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Patricia Roth
- Human Retrovirus Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Olga Slobodskaya
- Human Retrovirus Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Io Dolka
- Human Retrovirus Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Eileen A. Southon
- Neural Development Section, Mouse Cancer Genetics Program, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Lino Tessarollo
- Neural Development Section, Mouse Cancer Genetics Program, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
| | - Karin E. Bornfeldt
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | | | - George N. Pavlakis
- Human Retrovirus Section, Vaccine Branch, Center for Cancer Research, National Cancer Institute-Frederick, Frederick, Maryland, United States of America
- * E-mail: (GGA); (GNP)
| | - George A. Gaitanaris
- Omeros Corporation, Seattle, Washington, United States of America
- * E-mail: (GGA); (GNP)
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17
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Gragerov A, Horie K, Pavlova M, Madisen L, Zeng H, Gragerova G, Rhode A, Dolka I, Roth P, Ebbert A, Moe S, Navas C, Finn E, Bergmann J, Vassilatis DK, Pavlakis GN, Gaitanaris GA. Large-scale, saturating insertional mutagenesis of the mouse genome. Proc Natl Acad Sci U S A 2007; 104:14406-11. [PMID: 17720809 PMCID: PMC1964832 DOI: 10.1073/pnas.0700608104] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We describe the construction of a large-scale, orderly assembly of mutant ES cells, generated with retroviral insertions and having mutational coverage in >90% of mouse genes. We also describe a method for isolating ES cell clones with mutations in specific genes of interest from this library. This approach, which combines saturating random mutagenesis with targeted selection of mutations in the genes of interest, was successfully applied to the gene families of G protein-coupled receptors (GPCRs) and nuclear receptors. Mutant mouse strains in 60 different GPCRs were generated. Applicability of the technique for the GPCR genes, which on average represent fairly small targets for insertional mutagenesis, indicates the general utility of our approach for the rest of the genome. The method also allows for increased scale and automation for the large-scale production of mutant mice, which could substantially expedite the functional characterization of the mouse genome.
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Affiliation(s)
- Alexander Gragerov
- Omeros Corporation, 1420 Fifth Avenue, Suite 2600, Seattle, WA 98101, USA.
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18
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Krumm A, Madisen L, Yang XJ, Goodman R, Nakatani Y, Groudine M. Long-distance transcriptional enhancement by the histone acetyltransferase PCAF. Proc Natl Acad Sci U S A 1998; 95:13501-6. [PMID: 9811829 PMCID: PMC24848 DOI: 10.1073/pnas.95.23.13501] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Enhancers are defined by their ability to stimulate gene activity from remote sites and their requirement for promoter-proximal upstream activators to activate transcription. Here we demonstrate that recruitment of the p300/CBP-associated factor PCAF to a reporter gene is sufficient to stimulate promoter activity. The PCAF-mediated stimulation of transcription from either a distant or promoter-proximal position depends on the presence of an upstream activator (Sp1). These data suggest that acetyltransferase activity may be a primary component of enhancer function, and that recruitment of polymerase and enhancement of transcription are separable. Transcriptional activation by PCAF requires both its acetyltransferase activity and an additional activity within its N terminus. We also show that the simian virus 40 enhancer and PCAF itself are sufficient to counteract Mad-mediated repression. These results are compatible with recent models in which gene activity is regulated by the competition between deacetylase-mediated repression and enhancer-mediated recruitment of acetyltransferases.
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Affiliation(s)
- A Krumm
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave North, Seattle, WA 98109, USA.
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19
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Madisen L, Krumm A, Hebbes TR, Groudine M. The immunoglobulin heavy chain locus control region increases histone acetylation along linked c-myc genes. Mol Cell Biol 1998; 18:6281-92. [PMID: 9774645 PMCID: PMC109215 DOI: 10.1128/mcb.18.11.6281] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In chromosome translocations characteristic of Burkitt lymphomas (BL) and murine plasmacytomas, c-myc genes become juxtaposed to immunoglobulin heavy-chain (IgH) sequences, resulting in aberrant c-myc transcription. Translocated c-myc alleles that retain the first exon exhibit increased transcription from the normally minor c-myc promoter, P1, and increased transcriptional elongation through inherent pause sites proximal to the major c-myc promoter, P2. We recently demonstrated that a cassette derived from four DNase I-hypersensitive sites (HS1234) in the 3'Calpha region of the IgH locus functions as an enhancer-locus control region (LCR) and directs a similar pattern of deregulated expression of linked c-myc genes in BL and plasmacytoma cell lines. Here, we report that the HS1234 enhancer-LCR mediates a widespread increase in histone acetylation along linked c-myc genes in Raji BL cells. Significantly, the increase in acetylation was not restricted to nucleosomes within the promoter region but also was apparent upstream and downstream of the transcription start sites as well as along vector sequences. Histone hyperacetylation of control c-myc genes, which was induced by the deacetylase inhibitor trichostatin A, mimics the effect of the HS1234 enhancer on expression from the c-myc P2 promoter, but not that from the P1 promoter. These results suggest that the HS1234 enhancer stimulates transcription of c-myc by a combination of mechanisms. Whereas HS1234 activates expression from the P2 promoter through a mechanism that includes increased histone acetylation, a general increase in histone acetylation is not sufficient to explain the HS1234-mediated activation of transcription from P1.
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Affiliation(s)
- L Madisen
- Fred Hutchinson Cancer Research Center, University of Washington School of Medicine, Seattle, Washington, USA
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20
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Muto A, Hoshino H, Madisen L, Yanai N, Obinata M, Karasuyama H, Hayashi N, Nakauchi H, Yamamoto M, Groudine M, Igarashi K. Identification of Bach2 as a B-cell-specific partner for small maf proteins that negatively regulate the immunoglobulin heavy chain gene 3' enhancer. EMBO J 1998; 17:5734-43. [PMID: 9755173 PMCID: PMC1170901 DOI: 10.1093/emboj/17.19.5734] [Citation(s) in RCA: 147] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Maf family transcription factors are important regulators in various differentiation systems. Putative Maf recognition elements (MAREs) are found in the 3' enhancer region of the immunoglobulin heavy chain (IgH) gene. These elements are bound in B-cell extracts by a heterodimeric protein complex containing both Bach2 and a small Maf protein. Analysis of normal hematopoietic cells revealed that Bach2 is specifically expressed in B cells. Bach2 is abundantly expressed in the early stages of B-cell differentiation and turned off in terminally differentiated cells. Bach2 acts together with MafK as a negative effector of the IgH 3' enhancer and binds to the co-repressor SMRT (silencing mediator of retinoid and thyroid receptor). Hence the Bach2-small-Maf heterodimer may represent the first example of a B-cell lineage, and of a developmental stage-restricted negative effector of the MARE in the IgH 3' enhancer region.
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Affiliation(s)
- A Muto
- Department of Biochemistry, Tohoku University School of Medicine, Seiryo-machi, Aoba-ku, Sendai 980-8575, USA
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21
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Madisen L, Groudine M. Identification of a locus control region in the immunoglobulin heavy-chain locus that deregulates c-myc expression in plasmacytoma and Burkitt's lymphoma cells. Genes Dev 1994; 8:2212-26. [PMID: 7958890 DOI: 10.1101/gad.8.18.2212] [Citation(s) in RCA: 213] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In murine plasmacytoma and human Burkitt's lymphoma cells, one allele of c-myc is translocated into one of the immunoglobulin loci, resulting in a characteristic pattern of deregulated c-myc transcription. Translocation events between c-myc and the IgH locus segregate c-myc and the IgH intron enhancer to different reciprocal products in all plasmacytomas and in most Burkitt's lymphoma cells, suggesting that an additional element(s) capable of affecting c-myc expression over a large and variable distance must exist in the IgH locus. The region 3' of the IgH C alpha gene contains four tissue-specific and cell stage-specific DNase I hypersensitive sites (HSs), two of which map to the late B cell-specific 3' C alpha enhancer. We report here that DNA sequences comprising the two other 3' C alpha HSs contain potential protein-binding motifs for trans-activators commonly associated with immunoglobulin enhancers and that these sites can function as cell stage-specific enhancers in transient B cell assays. A DNA fragment containing all four HSs (HS1234) synergistically activates c-myc transcription in plasmacytoma and Burkitt's lymphoma cells in transient assays and induces high-level transcription, a promoter shift from P2 to P1, and an increase in readthrough transcription in stable transfections. Furthermore, plasmacytoma clones stably transfected with a HS1234-linked c-myc construct express c-myc in a position-independent, copy number-dependent manner. These results suggest that HS1234 may function as a locus control region (LCR), deregulating c-myc expression in t(15;12) plasmacytomas, as well as potentially contributing to aspects of normal IgH chain expression.
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Affiliation(s)
- L Madisen
- Hutchinson Cancer Center, University of Washington School of Medicine, Seattle 98104
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Brunner AM, Lioubin MN, Marquardt H, Malacko AR, Wang WC, Shapiro RA, Neubauer M, Cook J, Madisen L, Purchio AF. Site-directed mutagenesis of glycosylation sites in the transforming growth factor-beta 1 (TGF beta 1) and TGF beta 2 (414) precursors and of cysteine residues within mature TGF beta 1: effects on secretion and bioactivity. Mol Endocrinol 1992; 6:1691-700. [PMID: 1448117 DOI: 10.1210/mend.6.10.1448117] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The transforming growth factor-beta 1 (TGF beta 1) and -beta 2 (414) precursors both contain three predicted sites of N-linked glycosylation within their pro regions. These are located at amino acid residues 72, 140, and 241 for the TGF beta 2 (414) precursor and at residues 82, 136, and 176 for the TGF beta 1 precursor; both proteins contain mannose-6-phosphate (M-6-P) residues. The major sites of M-6-P addition are at Asn (82) and Asn (136), the first two sites of glycosylation, for the TGF beta 1 precursor. We now show that the major site of M-6-P addition within the TGF beta 2 (414) precursor is at Asn241, the third glycosylation site. To determine the importance of N-linked glycosylation to the secretion of TGF beta 1 and -beta 2, site-directed mutagenesis was used to change the Asn residues to Ser residues; the resulting DNAs were transfected into COS cells, and their supernatants were assayed for TGF beta activity. Substitution of Asn (241) of the TGF beta 2 (414) precursor resulted in an 82% decrease in secreted TGF beta 2 bioactivity. Mutation at Asn72 resulted in a 44% decrease, while mutation at Asn140 was without effect. Elimination of all three glycosylation sites resulted in undetectable levels of TGF beta 2. These results were compared with similar mutations made in the cDNA encoding the TGF beta 1 precursor. Mutagenesis of the two M-6-P-containing sites (Asn82 and Asn136) resulted in an 83% decrease in secreted TGF beta 1; replacement of Asn82 and Asn136 with Ser individually resulted in 85% and 42% decreases in activity, respectively. Substitution of Asn176 with Ser was without effect, while substitution of all three sites of glycosylation resulted in undetectable levels of TGF beta 1 activity, similar to the results obtained with TGF beta 2. The nine Cys residues within the mature region of TGF beta 1 were mutated to serine, and their effects on TGF beta 1 secretion were evaluated. Mutation of most Cys residues resulted in undetectable levels of TGF beta 1 protein or activity in conditioned medium. Mutation of Cys (355) led to the secretion of inactive TGF beta 1 monomers, suggesting that this residue is either directly involved in dimer formation or required for correct interchain disulfide bond formation.
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Affiliation(s)
- A M Brunner
- Bristol-Myers Squibb Pharmaceutical Research Institute, Seattle, Washington 98121
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Skonier J, Neubauer M, Madisen L, Bennett K, Plowman GD, Purchio AF. cDNA cloning and sequence analysis of beta ig-h3, a novel gene induced in a human adenocarcinoma cell line after treatment with transforming growth factor-beta. DNA Cell Biol 1992; 11:511-22. [PMID: 1388724 DOI: 10.1089/dna.1992.11.511] [Citation(s) in RCA: 389] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Transforming growth factor-beta (TGF-beta) is capable of affecting the proliferation of many cell types. To identify novel genes whose protein products may mediate cellular responses to this factor, a cDNA library was made from mRNA isolated from a human lung adenocarcinoma cell line (A549) that had been treated for 3 days with TGF-beta. The library was screened by differential hybridization and a cDNA clone, beta ig-h3, was isolated. This gene was induced up to 20-fold in A549 cells after 2 days of treatment with TGF-beta 1. It was also induced in several other cell lines, including PC-3 and H2981. DNA sequence analysis of beta ig-h3 indicated that it encoded a novel protein, beta IG-H3, of 683 amino acids, which contained an amino-terminal secretory sequence and a carboxy-terminal Arg-Gly-Asp (RGD) sequence that can serve as a ligand recognition site for several integrins. beta IG-H3 also contained short amino acid regions homologous to similar regions in Drosophila fasciclin-I and four homologous internal domains, which can be folded into a potential bivalent structure and could act as a bridge between cells expressing the appropriate ligand. beta ig-h3 RNA was detected in several cell lines and tissues. COS cells transfected with plasmids encoding beta IG-H3 secreted a major 68-kD protein that was detected by immunoblotting using antipeptide antibodies. Since beta ig-h3 is induced in several cell lines whose proliferation is affected by TGF-beta 1, it may be involved in mediating some of the signals of this multifunctional growth modulator.
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Affiliation(s)
- J Skonier
- Bristol Myers Squibb, Seattle, WA 98121
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Abstract
Serum-free medium conditioned by BSC-40 cells was analyzed for the presence of transforming growth factor-beta 2 (TGF beta 2)-related proteins. Western blot analysis was performed using site-specific antipeptide antibodies directed against the pro- and mature regions of the TGF beta 2 precursor. When conditioned medium was analyzed by polyacrylamide gel electrophoresis under reducing conditions, proteins with mol wt of 53 kDa (containing both mature and proregion sequences), 34-38 kDa (containing proregion sequences only), and 12 kDa (containing mature sequences) were detected. Under nonreducing conditions, complexes of 60- to 80-kDa, 160- to 200-kDa, as well as 24-kDa mature dimers were seen. Cleavage of mature TGF beta 2 from its precursor was inhibited by monensin and chloroquin, but not by ammonium chloride or methylamine. Two peaks of bioactivity were detected after fractionation on a TSK column corresponding to mol wt of 130 and 400 kDa. These peaks contained TGF beta 2 and pro-TGF beta 2 proteins. Partial purification of the 130-kDa complex followed by N-glyconase digestion indicated that the pro-TGF beta 2 proteins were glycosylated. These data demonstrate that BSC-40 cells secrete mature TGF beta 2 complexed with proregion-containing proteins and suggest that this association may contribute to the latency phenomena observed with respect to this growth regulator.
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Abstract
Functional biological assays were performed using a hybrid molecule of Transforming Growth Factor-Beta (TGF-5 beta) where nine amino acids near the cleavage site of TGF-beta 1 were substituted with nine amino acids located in the identical position of TGF-beta 2. Bovine aortic endothelial and smooth muscle cells as well as rat epididymal fat pad microvascular endothelia were studied in three distinct bioassays examining proliferation, migration and angiogenesis. The data suggested TGF-5 beta elicited results that do not differ significantly from the TGF-beta 1 isoform, while TGF-beta 2 expressed unique characteristics. We have also shown that these amino acid substitutions to TGF-beta 1 do not, in fact, alter the biological functions of the growth factor.
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Affiliation(s)
- J R Merwin
- Pathology Department, Yale University, New Haven, CT 06413
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Abstract
Analysis of cDNA clones encoding transforming growth factor (TGF)-beta 2 predicts two different precursor proteins derived by alternative mRNA splicing; a 414 amino acid precursor [TGF-beta 2(414)] and a 442 amino acid precursor [TGF-beta 2(442)]. The two proteins differ by a 28 amino acid insertion within the pro-region of TGF-beta 2(442). In order to characterize the TGF-beta 2-related proteins encoded by the TGF-beta 2(442) cDNA and determine whether it could, in fact, direct the synthesis of active growth factor, we have expressed this gene in Chinese hamster ovary (CHO) cells and, after amplification with methotrexate, obtained stable clones secreting TGF-beta 2(442). The TGF-beta 2 secreted by these cells was latent as acidification was necessary to detect optimal biological activity. In addition to mature TGF-beta 2, high molecular weight pro-region containing proteins were also secreted as analyzed by immunoblotting using site-specific anti-peptide antibodies. These proteins migrated differently than those secreted by CHO cells transfected with cDNA encoding TGF-beta 2(414), indicating that structural differences exist between the two complexes. An anti-peptide antiserum was produced in rabbits against the 28 amino acid insert region of TGF-beta 2(442). This sera was then used to detect the presence of TGF-beta 2(442) in serum-free media conditioned by BSC-40 cells. Since the TGF-beta 2(442) precursor is produced and secreted by a non-recombinant cell line, this suggests that it may play a physiological role in regulating the activity of TGF-beta 2.
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Affiliation(s)
- L Madisen
- Bristol-Myers Squibb Pharmaceutical Research Institute, Seattle, WA 98121
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Lioubin MN, Madisen L, Marquardt H, Roth R, Kovacina KS, Purchio AF. Characterization of latent recombinant TGF-beta 2 produced by Chinese hamster ovary cells. J Cell Biochem 1991; 45:112-21. [PMID: 1848562 DOI: 10.1002/jcb.240450118] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Latent recombinant transforming growth factor-beta 2 (LrTGF-beta 2) complex has been purified from serum-free media conditioned by Chinese hamster ovary cells transfected with a plasmid encoding the TGF-beta 2 (414) precursor. Under neutral conditions, LrTGF-beta 2 had an apparent molecular weight of 130 kDa. The complex contained both mature and pro-region sequences. Acidification of LrTGF-beta 2 resulted in the release of mature 24 kDa TGF-beta 2 from the high molecular weight pro-region-containing complex, suggesting that TGF-beta 2 was non-covalently associated with this complex. These results were confirmed by crosslinking experiments performed on partially purified LrTGF-beta 2. Protein sequence analysis of the purified TGF-beta 2 pro-region indicated that signal peptide cleavage occurred between ser(20) and leu(21). The pro-region, which previously was found to contain mannose-6-phosphate, bound to the mannose-6-phosphate receptor. Proteolytic cleavage of mature TGF-beta 2 from pro-TGF-beta 2 was inhibited by monensin and chloroquine suggesting that binding to this receptor and subsequent transport to acidic vesicles may be involved in the processing of rTGF-beta 2 precursor.
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Madisen L, Neubauer M, Plowman G, Rosen D, Segarini P, Dasch J, Thompson A, Ziman J, Bentz H, Purchio AF. Molecular cloning of a novel bone-forming compound: osteoinductive factor. DNA Cell Biol 1990; 9:303-9. [PMID: 2372374 DOI: 10.1089/dna.1990.9.303] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
cDNA clones encoding osteoinductive factor (OIF) have been isolated from a bovine osteoblast library. Sequence analysis of these clones indicated that the 105-amino-acid OIF is synthesized as a larger 299-amino-acid precursor, the carboxyl terminus of which is cleaved to yield the mature protein. Northern blot analysis of bovine osteoblast mRNA revealed two OIF-specific transcripts of 1.9 and 2.4 kb. The polymerase chain reaction was used to obtain clones coding for human OIF from the osteosarcoma cell line, MG-63. The human OIF cDNA encodes a precursor of 298 amino acids that exhibits 94% identity to the bovine protein. Northern blot analysis of various cell lines and tissues indicated that expression of OIF transcripts is limited and may be restricted to cells of bone lineage.
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Madisen L, Lioubin MN, Farrand AL, Brunner AM, Purchio AF. Analysis of proteolytic cleavage of recombinant TGF-beta 1: production of hybrid molecules with increased processing efficiency. Ann N Y Acad Sci 1990; 593:7-25. [PMID: 2197963 DOI: 10.1111/j.1749-6632.1990.tb16096.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Abstract
Chinese hamster ovary (CHO) clones secreting high levels of transforming growth factor-beta 2 (TGF-beta 2) were obtained after transfection with a cDNA clone coding for the 414-amino acid TGF-beta 2 precursor and subsequent amplification with methotrexate. The TGF-beta 2 was secreted in a latent form since acidification was necessary for detection of maximal levels of bioactivity. Amino- and carboxy-terminal sequencing of purified recombinant TGF-beta 2 indicated that correct processing of mature TGF-beta 2 had occurred. In addition to mature TGF-beta 2, the recombinant CHO clones secreted larger proteins having molecular weights of 85, 105, and 130 kD, which consisted of both mature and pro-region sequences when analyzed by immunoblotting using site-specific anti-peptide antibodies. Analysis of serum- and cell-free media from recombinant CHO cells metabolically labeled with [3H]glucosamine and [32P]orthophosphate indicated that pro-TGF-beta 2 was glycosylated and phosphorylated. Two-dimensional electrophoretic analysis of acid hydrolysates showed that the 32P was incorporated into mannose-6-phosphate.
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Bascom CC, Wolfshohl JR, Coffey RJ, Madisen L, Webb NR, Purchio AR, Derynck R, Moses HL. Complex regulation of transforming growth factor beta 1, beta 2, and beta 3 mRNA expression in mouse fibroblasts and keratinocytes by transforming growth factors beta 1 and beta 2. Mol Cell Biol 1989; 9:5508-15. [PMID: 2586525 PMCID: PMC363721 DOI: 10.1128/mcb.9.12.5508-5515.1989] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Regulation of transforming growth factor beta 1 (TGF beta 1), TGF beta 2, and TGF beta 3 mRNAs in murine fibroblasts and keratinocytes by TGF beta 1 and TGF beta 2 was studied. In quiescent AKR-2B fibroblasts, in which TGF beta induces delayed stimulation of DNA synthesis, TGF beta 1 autoregulation of TGF beta 1 expression was observed as early as 1 h, with maximal induction (25-fold) after 6 to 12 h. Increased expression of TGF beta 1 mRNA was accompanied by increased TGF beta protein production into conditioned medium of AKR-2B cells. Neither TGF beta 2 nor TGF beta 3 mRNA, however, was significantly induced, but both were apparently down regulated at later times by TGF beta 1. Protein synthesis was not required for autoinduction of TGF beta 1 mRNA in AKR-2B cells. Nuclear run-on analyses and dactinomycin experiments indicated that autoregulation of TGF beta 1 expression is complex, involving both increased transcription and message stabilization. In contrast to TGF beta 1, TGF beta 2 treatment of quiescent AKR-2B cells increased expression of TGF beta 1, TGF beta 2, and TGF beta 3 mRNAs, but with different kinetics. Autoinduction of TGF beta 2 mRNA occurred rapidly with maximal induction at 1 to 3 h, enhanced TGF beta 3 mRNA levels were observed after 3 h, and increased expression of TGF beta 1 occurred later, with maximal mRNA levels obtained after 12 to 24 h. Nuclear run-on analyses indicated that TGF beta 2 regulation of TGF beta 2 and TGF beta 3 mRNA levels is transcriptional, while TGF beta 2 induction of TGF beta 1 expression most likely involves both transcriptional and posttranscriptional controls. In BALB/MK mouse keratinocytes, minimal autoinduction of TGF beta 1 occurred at only the 12- and 24-h time points and protein synthesis was required for this autoinduction. The results of this study provide an example in which TGF beta 1 and TGF beta 2 elicit different responses and demonstrate that expression of TGF beta 1, and TGF beta 3 are regulated differently. The physiological relevance of TGF beta 1 autoinduction in the context of wound healing is discussed.
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Affiliation(s)
- C C Bascom
- Department of Cell Biology, Vanderbilt University, Nashville, Tennessee 37232
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Madisen L, Farrand AL, Lioubin MN, Marzowski J, Knox LB, Webb NR, Lim J, Purchio AF. Expression and characterization of recombinant TGF-beta 2 proteins produced in mammalian cells. DNA 1989; 8:205-12. [PMID: 2721369 DOI: 10.1089/dna.1.1989.8.205] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Recombinant DNA plasmids coding for transforming growth factor beta 2 (TGF-beta 2) precursor and a hybrid TGF-beta 1(NH2)/beta 2(COOH) molecule consisting of the amino-terminal precursor portion of transforming growth factor-beta 1 (TGF-beta 1) linked in phase to the carboxyl terminus of mature TGF-beta 2 were constructed and transfected into COS cells. Both plasmids directed the synthesis of active TGF-beta 2 which was secreted into the supernatants of transfected cells. The TGF-beta 2 was secreted in a latent form, as an acidification step was required to demonstrate optimal biological activity. Using site-specific anti-peptide antibodies, we show that precursor and mature forms of TGF-beta 2 are produced. A stable Chinese hamster ovary (CHO) cell line expressing the hybrid TGF-beta 1(NH2)/beta 2(COOH) protein was isolated. This cell line secreted both precursor and mature forms of TGF-beta 1(NH2)/beta 2(COOH); acidification was required to demonstrate biological activity. Protein sequence analysis of recombinant TGF-beta 2 produced by this CHO clone demonstrated that correct proteolytic cleavage had occurred, suggesting that the processing signals contained within the TGF-beta 1 amino portion can function in producing mature TGF-beta 2. Receptor binding studies showed that TGF-beta 2 specifically bound predominantly to type III receptors on the surface of human palatal mesenchymal cells. The availability of active TGF-beta 2 should aid in determining its potential therapeutic use as a growth modulator.
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Affiliation(s)
- L Madisen
- Department of Entomology, Texas A&M University, College Station 77843
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Webb NR, Madisen L, Rose TM, Purchio AF. Structural and sequence analysis of TGF-beta 2 cDNA clones predicts two different precursor proteins produced by alternative mRNA splicing. DNA 1988; 7:493-7. [PMID: 2850146 DOI: 10.1089/dna.1.1988.7.493] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Analysis of cDNA clones coding for human and simian transforming growth factor-beta 2 (TGF-beta 2) revealed the existence of two types of TGF-beta 2 precursor proteins of 414 amino acids (TGF-beta 2,414) and 442 amino acids (TGF-beta 2,442) in length. TGF-beta 2,442 contains a 29-amino-acid insertion in the amino terminus of the precursor region that replaces an Asn residue located at position 116 in TGF-beta 2,414. Of these 29 amino acids, three are cysteines, suggesting a more extensive disulfide-bond mediated secondary structure for TGF-beta 2,442 than for TGF-beta 2,414. Northern blot analysis using probes specific for the insert in TGF-beta 2,442 indicated that this protein is encoded by a minor 5.1-kb mRNA species present in human and simian cells. Since the DNA sequences flanking the insert are identical between clones coding for the two precursor protein, we suggest mRNAs coding for these proteins arise via differential splicing. Evidence is also presented that indicates that additional TGF-beta 2 mRNA heterogeneity is due to alternate polyadenylation. We propose that the 414-amino-acid precursor be referred to as TGF-beta 2a and the 442-amino-acid precursor be referred to as TGF-beta 2b.
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Madisen L, Webb NR, Rose TM, Marquardt H, Ikeda T, Twardzik D, Seyedin S, Purchio AF. Transforming growth factor-beta 2: cDNA cloning and sequence analysis. DNA 1988; 7:1-8. [PMID: 3162414 DOI: 10.1089/dna.1988.7.1] [Citation(s) in RCA: 170] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We have obtained a cDNA clone coding for human transforming growth factor (TGF)-beta 2. The clone was isolated from a tamoxifen-treated human prostatic adenocarcinoma cell line (PC-3) using oligonucleotide probes based on the partial amino acid sequence of purified TGF-beta 2. The cDNA sequence predicts that TGF-beta 2 is synthesized as a 442-amino-acid polypeptide precursor from which the mature 112-amino-acid TGF-beta 2 subunit is derived by proteolytic cleavage. The proteins coded for by the human TGF-beta 1 and TGF-beta 2 cDNAs show an overall homology of 41%. The mature and amino-terminal precursor regions show 71% and 31% homology, respectively. Northern blot analysis identified TGF-beta 2 transcripts of 4.1, 5.1, and 6.5 kb using mRNA from several different sources. Analysis of polyadenylated RNA from tamoxifen-treated PC-3 cells showed that these cells contain higher numbers of transcripts for TGF-beta 1 than for TGF-beta 2, although they produce more TGF-beta 2 protein than TGF-beta 1. This suggests that there is a post-transcriptional level of regulation for the production of these proteins.
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Madisen L, Hoar DI, Holroyd CD, Crisp M, Hodes ME. DNA banking: the effects of storage of blood and isolated DNA on the integrity of DNA. Am J Med Genet 1987; 27:379-90. [PMID: 3605221 DOI: 10.1002/ajmg.1320270216] [Citation(s) in RCA: 202] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Long-term storage of DNA is required for a number of genetic studies; prior to extraction, blood samples may be subject to elevated temperatures for variable intervals. We have studied the effect of temperatures ranging from -70 degrees C to +65 degrees C on human blood and on DNA extracted from it. DNA in solution stored at ambient temperatures up to 37 degrees C for 6 months was digestible by three different restriction endonucleases, whereas storage at 45 degrees C is deleterious after 6-7 weeks. DNA can be extracted from blood samples stored at -70 degrees C for at least 2 months or at 23 degrees C for a week or more, but blood stored at these temperatures may yield less high-molecular-weight DNA. Cell pellets from which plasma has been removed also can serve as a source of DNA. Isolated DNA stored dry for years (up to 30) is difficult to dissolve and may appear degraded, but a sample stored dry for 13 years and then in solution at -20 degrees C for 7 years appeared to be intact.
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Abstract
Regions of the gag-pol gene of human immunodeficiency virus (HIV), the causative agent of AIDS, have been cloned into the polyhedrin gene of the baculovirus Autographa californica nuclear polyhedrosis virus. When these recombinant viruses were used to infect insect cells, the cells produced gag-related proteins which could be immunoprecipitated with serum from AIDS patients. The major proteins produced by Acgag1, which contained the entire gag gene and a small portion of the pol gene, had molecular weights of 55,000 and 40,000 Da. Acgag2, which contained a larger portion of the pol gene in addition to the gag coding sequences, produced a major protein of 24,000 Da and only minor amounts of the 55,000- and 40,000-Da proteins. The implications of these results with respect to proteolytic processing of HIV gag proteins as well as the potential diagnostic use of this system are discussed.
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Purchio AF, Twardzik DR, Bruce AG, Wizental L, Madisen L, Ranchalis JE, Hu SL, Todaro G. Synthesis of an active hybrid growth factor (GF) in bacteria: transforming GF-alpha/vaccinia GF fusion protein. Gene 1987; 60:175-82. [PMID: 3327748 DOI: 10.1016/0378-1119(87)90225-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
A hybrid gene encoding for a polypeptide consisting of the first 33 N-terminal amino acid (aa) residues of transforming growth factor-alpha (TGF-alpha) and a C terminus consisting of 20 aa residues of vaccinia growth factor (VGF) was chemically synthesized and expressed as a fusion protein in Escherichia coli. The primary structure of the hybrid gene product maintained the same positioning of the three disulfide bonds found in each parent molecule thus conserving the first two loop regions of TGF-alpha and the third loop region of VGF. After cleavage with CNBr its renatured biological activity was found to be comparable to TGF-alpha and VGF with respect to binding to the epidermal growth factor receptor, stimulation of DNA synthesis and induction of anchorage-independent growth of NRK cells in the presence of TGF-beta. Thus, we suggest that similar domains can be interchanged within the same family of molecules and equivalent functionality maintained.
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