RF1 - Tasic 1RF1MH121274-01

Cell class- or type-specific viruses for brain-wide labeling and neural circuit examination

Three distinct cell classes labeled by three different enhancer viruses in a mouse carrying a novel 3-color reporter transgene. A combination of viruses engineered to target two distinct excitatory cell classes or all inhibitory cells were injected retroorbitally into the reporter animal, revealing a largely mutually exclusive labeling pattern in the primary visual cortex.


Our goal is to develop a suite of enhancer viruses that can provide access to specific brain cell classes, subclasses or types when delivered by retroorbital injections to the whole brain. The viruses will be endowed with specificity by enhancers defined experimentally from the combination of single-cell RNA-seq and single cell ATAC-seq data. The viruses will be screened for specificity by several methods including whole-brain imaging, single-cell RNA-seq and multiplex FISH. Intersectional genetic approaches to further refine specificity and enable functional interrogation of specific cell types will also be established. DNA constructs, virus packaging techniques, recommended titers, and whole-brain expression data will be made publicly available. The research consists of the following major components:

  • Selection of enhancers with potential cell type- or class-specific activity by joint analysis of brain-wide single-cell RNA-seq and single-cell ATAC-seq data
  • Generation and screening of enhancer-driven viruses for cell type-specific labeling
  • Establishment of intersectional approaches to label more than one cell type, refine cell type-specific labeling, and enable functional studies

Project Leadership

Bosiljka Tasic, Ph.D. (Principal Investigator)
Director, Molecular Genetics
Allen Institute for Brain Science, Seattle, WA, USA


Tanya Daigle, Ph.D. (Co-Investigator)
Senior Scientist
Allen Institute for Brain Science, Seattle, WA, USA


Hongkui Zeng, Ph.D. (Co-Investigator)
Executive Director, Structured Science
Allen Institute for Brain Science, Seattle, WA, USA

Project Data Types

  • A collection of enhancer elements with potential for cell class-, subclass- or type-specific activity
  • A collection of enhancer-driven adeno-associated viruses (AAVs) that express an exogenous recombinase or transcription factor
  • Whole-brain expression pattern characterization for AAVs delivered retro-orbitally
  • Specificity of AAVs evaluated by single-cell RNA sequencing and multiplex FISH (mFISH) on infected brain cells
  • Combinatorial approaches utilizing AAVs and transgenic mice to refine genetic access and probe the function of more than one cell class or type

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