Cited by 6,907Neuroscience and Neuropharmacology ResearchNeurogenesis and neuroplasticity mechanismsAnimal Genetics and Reproduction

A robust and high-throughput Cre reporting and characterization system for the whole mouse brain

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Madisen, Linda, Zwingman, Theresa A, Sunkin, Susan M, Oh, Seung Wook, Zariwala, Hatim A, Gu, Hong, Ng, Lydia L, Palmiter, Richard D +4 more·2010·Nature Neuroscience

Abstract

The Cre/lox system is widely used in mice to achieve cell-type-specific gene expression. However, a strong and universally 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 several Cre-driver lines, including new 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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Crossref · 10.1038/nn.2467

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  • Genes whose expression peaks at low maturation score tend to be expressed more highly in the ventricular zone, and as maturation score rank rises expression shifts to the subventricular zone and then to the mantle zone.

    “The trend overall shows that genes with peak expression at low MS tend to have higher expression in the VZ, and as MS rank increases the expression pattern shifts to the subventricular zone (SVZ) and then to the MZ”
  • The authors used many transgenic mouse lines to cover excitatory and inhibitory classes across cortical layers, target rare populations, and connect with other approaches like transcriptomic characterization.

    “A diverse set of transgenic mouse lines14–18 were used to ensure broad coverage of excitatory and inhibitory classes across all cortical layers, to enable selective targeting of rare cell populations, and to link our study with other experimental approaches, such as transcriptomic characterization19.”
  • The authors previously established a standardized Cre-reporter system in which transgene expression was driven by a strong, ubiquitous CAG promoter targeted to the Rosa26 locus, expressing fluorescent proteins, calcium sensor GCaMP3, and optogenetic activator ChR2(H134R) and silencers Arch and eNpHR3.0.

    “We previously establish a standardized Cre-reporter system in which transgene expression was driven by a strong, ubiquitous CAG promoter targeted to the Rosa26 locus (Madisen et al., 2010; Muzumdar et al., 2007), expressing fluorescent proteins, calcium sensor GCaMP3, and optogenetic activator ChR2(H134R) and silencers Arch and eNpHR3.0 (Madisen et al., 2012; Madisen et al., 2010; Zariwala et al.,”
  • In mice, the Cre/lox recombination system is the most widely used approach to access specific cell types, utilizing gene promoters or loci with specific expression patterns.

    “In mice, the Cre/lox recombination system is the most widely used approach to access specific cell types, utilizing gene promoters or loci with specific expression patterns (Gerfen et al., 2013; Gong et al., 2007; Madisen et al., 2010; Taniguchi et al., 2011).”
  • The EGFP reporter line Ai82 exhibited superior cytoplasmic labeling over previous Rosa-CAG reporter Ai3 and Snap25-LSL-2A-GFP.

    “The EGFP reporter line (Ai82) exhibited superior cytoplasmic labeling (Fig. 4A) over previous Rosa-CAG reporter Ai3 (Madisen et al., 2010) and Snap25-LSL-2A-GFP (Fig. 1D).”

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Research works printed but not linked: 2

  1. [28]Dong HW The Allen Reference Atlas: a Digital Color Brain Atlas of the C57BL/6J Male Mouse John Wiley & Sons 2008
  2. [45]Tsai PS Frostig RD Principle, design and construction of a two photon laser-scanning microscope for in vitro and in vivo brain imaging In vivo optical imaging of brain function 113 172 CRC Press 2002

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Authors
Madisen, L., Zwingman, T. A., Sunkin, S. M., Oh, S. W., Zariwala, H. A., Gu, H., Ng, L. L., Palmiter, R. D., Hawrylycz, M. J., Jones, A. R., Lein, E. S., & Zeng, H.
Affiliations
  • Allen Institute for Brain Science (US)
  • Howard Hughes Medical Institute (US)
Corresponding author
Zeng, Hongkui
Venue
Nature Neuroscience
Published
2009-12-20
Volume
13
Issue
1
Pages
133-140
ISSN
  • 1097-6256 (ISSN-L)
  • 1546-1726
OpenAlex
W2104135721
Cited by
6,907
References
43
Citations by year
2026: 484 · 2025: 644 · 2024: 623 · 2023: 664 · 2022: 568 · 2021: 595 · 2020: 582 · 2019: 555 · 2018: 465 · 2017: 396 · 2016: 328 · 2015: 311 · 2014: 247 · 2013: 231 · 2012: 110
FWCI
28.55
Type
journal article
Language
en
Open access
Locations
  • Nature Neuroscience (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • National Institutes of Health
  • National Institute of Mental Health (MH085500, R01MH085500)
Topics
  • Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
  • Life Sciences › Neuroscience › Developmental Neuroscience › Neurogenesis and neuroplasticity mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Animal Genetics and Reproduction
Keywords
Cre reporter mice, Rosa26, Cre-loxP system, fluorescent protein expression, mouse brain, cell type-specific gene expression, neuronal circuit mapping, axonal projections, cortical cell types
MeSH terms
Animals, Bacterial Proteins, Brain, Dendrites, Luminescent Proteins, Mice, Inbred C57BL, Mice, Transgenic, Neurons, Promoter Regions, Genetic, Recombination, Genetic, Regulatory Sequences, Nucleic Acid, Tamoxifen, Tissue Distribution, Viral Proteins, Gene Transfer Techniques, Microscopy, Confocal, Integrases, Mice

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