Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Enhancer viruses and a transgenic platform for combinatorial cell subclass-specific labeling

View ORCID ProfileLucas T. Graybuck, View ORCID ProfileTanya L. Daigle, View ORCID ProfileAdriana E. Sedeño-Cortés, View ORCID ProfileMiranda Walker, View ORCID ProfileBrian Kalmbach, View ORCID ProfileGarreck H. Lenz, View ORCID ProfileThuc Nghi Nguyen, Emma Garren, View ORCID ProfileTae Kyung Kim, View ORCID ProfileLa’ Akea Siverts, View ORCID ProfileJacqueline L. Bendrick, Thomas Zhou, Marty Mortrud, View ORCID ProfileShenqin Yao, View ORCID ProfileAli H. Cetin, Rachael Larsen, Luke Esposito, Bryan Gore, Eric Szelenyi, View ORCID ProfileElyse Morin, View ORCID ProfileJohn K. Mich, View ORCID ProfileNick Dee, View ORCID ProfileJeff Goldy, View ORCID ProfileKimberly Smith, View ORCID ProfileZizhen Yao, View ORCID ProfileViviana Gradinaru, View ORCID ProfileSusan M. Sunkin, View ORCID ProfileEd Lein, View ORCID ProfileBoaz P. Levi, Jonathan T. Ting, View ORCID ProfileHongkui Zeng, View ORCID ProfileBosiljka Tasic
doi: https://doi.org/10.1101/525014
Lucas T. Graybuck
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Lucas T. Graybuck
Tanya L. Daigle
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Tanya L. Daigle
Adriana E. Sedeño-Cortés
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Adriana E. Sedeño-Cortés
Miranda Walker
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Miranda Walker
Brian Kalmbach
1Allen Institute for Brain Science, Seattle, WA
2Department of Physiology and Biophysics, University of Washington, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Brian Kalmbach
Garreck H. Lenz
1Allen Institute for Brain Science, Seattle, WA
8University of California, Davis, CA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Garreck H. Lenz
Thuc Nghi Nguyen
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Thuc Nghi Nguyen
Emma Garren
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Tae Kyung Kim
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Tae Kyung Kim
La’ Akea Siverts
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for La’ Akea Siverts
Jacqueline L. Bendrick
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jacqueline L. Bendrick
Thomas Zhou
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Marty Mortrud
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Shenqin Yao
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Shenqin Yao
Ali H. Cetin
1Allen Institute for Brain Science, Seattle, WA
3Department of Biological Structure, University of Washington, Seattle, WA
7Stanford University, Stanford, CA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Ali H. Cetin
Rachael Larsen
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Luke Esposito
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Bryan Gore
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Eric Szelenyi
1Allen Institute for Brain Science, Seattle, WA
3Department of Biological Structure, University of Washington, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Elyse Morin
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Elyse Morin
John K. Mich
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for John K. Mich
Nick Dee
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Nick Dee
Jeff Goldy
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jeff Goldy
Kimberly Smith
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Kimberly Smith
Zizhen Yao
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Zizhen Yao
Viviana Gradinaru
4Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Viviana Gradinaru
Susan M. Sunkin
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Susan M. Sunkin
Ed Lein
1Allen Institute for Brain Science, Seattle, WA
5Department of Neurological Surgery, University of Washington, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Ed Lein
Boaz P. Levi
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Boaz P. Levi
Jonathan T. Ting
1Allen Institute for Brain Science, Seattle, WA
2Department of Physiology and Biophysics, University of Washington, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Hongkui Zeng
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Hongkui Zeng
Bosiljka Tasic
1Allen Institute for Brain Science, Seattle, WA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Bosiljka Tasic
  • For correspondence: bosiljkat@alleninstitute.org
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Summary

The rapid pace of cell type identification by new single-cell analysis methods has not been met with efficient experimental access to the newly discovered types. To enable flexible and efficient access to specific neural populations in the mouse cortex, we collected chromatin accessibility data from individual cells and clustered the single-cell data to identify enhancers specific for cell classes and subclasses. When cloned into adeno-associated viruses (AAVs) and delivered to the brain by retro-orbital injections, these enhancers drive transgene expression in specific cell subclasses in the cortex. We characterize several enhancer viruses in detail to show that they result in labeling of different projection neuron subclasses in mouse cortex, and that one of them can be used to label the homologous projection neuron subclass in human cortical slices. To enable the combinatorial labeling of more than one cell type by enhancer viruses, we developed a three-color Cre-, Flp- and Nigri-recombinase dependent reporter mouse line, Ai213. The delivery of three enhancer viruses driving these recombinases via a single retroorbital injection into a single Ai213 transgenic mouse results in labeling of three different neuronal classes/subclasses in the same brain tissue. This approach combines unprecedented flexibility with specificity for investigation of cell types in the mouse brain and beyond.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • This preprint has been updated from original biorXiv submission. The following are major changes: Version 3: 1.Characterization of triple-reporter mouse line Ai213. 2.Description and characterization of additional viral constructs: enhanced versions of mscRE4-based constructs, additional L6-targeted enhancers, additional high-specificity L5 PT-targeted enhancers. 3.Viral infection experiments in human slice culture demonstrating cross-species functionality of L5 PT enhancers. 4.RNAscope experiments to validate specificity and completeness of several enhancer viruses 5.Removal of coembedding analyses with Cusanovich, Hill, et al. (2018) data. It's a great dataset, but fit less with the theme of the manuscript as we shift more towards additional genetic tools. Version 2: 1.Correction of GM12878 cell culturing and collection methods. GM12878 is a suspension cell line, not adherent. Thanks to Darren Cusanovich for identifying this error. 2.Addition of GM12878 data from Pliner, et al. (2018) to Supp Fig 4 and updates to some calculations. This better shows the high quality of current sci-ATAC-seq methods. Thanks to Jay Shendure and Darren Cusanovich for recommending this addition. 3.Updated analysis of Cusanovich, Hill, et al. (2018) data in Supp Fig 7 by changing the label metadata column selected. Thanks to Andrew Hill for recommending these higher-resolution labels. 4.Proper citation of Cusanovich, Hill et al. (2018), and discussion of the prior work in Drosophila in Cusanovich, Reddington, Garfield et al. (2018). Thanks to Jay Shendure for identifying these omissions. 5.Listing of R packages used for analysis.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Back to top
PreviousNext
Posted April 21, 2020.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Enhancer viruses and a transgenic platform for combinatorial cell subclass-specific labeling
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Enhancer viruses and a transgenic platform for combinatorial cell subclass-specific labeling
Lucas T. Graybuck, Tanya L. Daigle, Adriana E. Sedeño-Cortés, Miranda Walker, Brian Kalmbach, Garreck H. Lenz, Thuc Nghi Nguyen, Emma Garren, Tae Kyung Kim, La’ Akea Siverts, Jacqueline L. Bendrick, Thomas Zhou, Marty Mortrud, Shenqin Yao, Ali H. Cetin, Rachael Larsen, Luke Esposito, Bryan Gore, Eric Szelenyi, Elyse Morin, John K. Mich, Nick Dee, Jeff Goldy, Kimberly Smith, Zizhen Yao, Viviana Gradinaru, Susan M. Sunkin, Ed Lein, Boaz P. Levi, Jonathan T. Ting, Hongkui Zeng, Bosiljka Tasic
bioRxiv 525014; doi: https://doi.org/10.1101/525014
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Enhancer viruses and a transgenic platform for combinatorial cell subclass-specific labeling
Lucas T. Graybuck, Tanya L. Daigle, Adriana E. Sedeño-Cortés, Miranda Walker, Brian Kalmbach, Garreck H. Lenz, Thuc Nghi Nguyen, Emma Garren, Tae Kyung Kim, La’ Akea Siverts, Jacqueline L. Bendrick, Thomas Zhou, Marty Mortrud, Shenqin Yao, Ali H. Cetin, Rachael Larsen, Luke Esposito, Bryan Gore, Eric Szelenyi, Elyse Morin, John K. Mich, Nick Dee, Jeff Goldy, Kimberly Smith, Zizhen Yao, Viviana Gradinaru, Susan M. Sunkin, Ed Lein, Boaz P. Levi, Jonathan T. Ting, Hongkui Zeng, Bosiljka Tasic
bioRxiv 525014; doi: https://doi.org/10.1101/525014

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Neuroscience
Subject Areas
All Articles
  • Animal Behavior and Cognition (4115)
  • Biochemistry (8818)
  • Bioengineering (6522)
  • Bioinformatics (23466)
  • Biophysics (11792)
  • Cancer Biology (9212)
  • Cell Biology (13326)
  • Clinical Trials (138)
  • Developmental Biology (7439)
  • Ecology (11416)
  • Epidemiology (2066)
  • Evolutionary Biology (15155)
  • Genetics (10439)
  • Genomics (14045)
  • Immunology (9173)
  • Microbiology (22160)
  • Molecular Biology (8814)
  • Neuroscience (47582)
  • Paleontology (350)
  • Pathology (1429)
  • Pharmacology and Toxicology (2492)
  • Physiology (3731)
  • Plant Biology (8082)
  • Scientific Communication and Education (1437)
  • Synthetic Biology (2221)
  • Systems Biology (6039)
  • Zoology (1253)