A homing CRISPR mouse resource for barcoding and lineage tracing

Reza Kalhor, Kian Kalhor, Kathleen Leeper, Amanda Graveline, Prashant Mali, George M. Church

Research output: Contribution to journalArticlepeer-review


Cellular barcoding using nuclease-induced genetic mutations is an effective approach that is emerging for recording biological information, including developmental lineages. We have previously introduced the homing CRISPR system as a promising methodology for generating such barcodes with scalable diversity and without crosstalk. Here, we present a mouse line (MARC1) with multiple genomically-integrated and heritable homing guide RNAs (hgRNAs). We determine the genomic locations of these hgRNAs, their activity profiles during gestation, and the diversity of their mutants. We apply the line for unique barcoding of mouse embryos and differential barcoding of embryonic tissues. We conclude that this mouse line can address the unique challenges associated with in vivo barcoding in mammalian model organisms and is thus an enabling platform for recording and lineage tracing applications in a mammalian model system.

Original languageEnglish (US)
JournalUnknown Journal
StatePublished - Mar 12 2018
Externally publishedYes


  • Cas9
  • Cas9 mouse
  • cellular barcoding
  • DNA barcodes
  • evolving barcodes
  • hgRNA mouse
  • homing CRISPR
  • homing guide RNA
  • lineage tracing
  • MARC1 mouse line
  • NHEJ

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • Immunology and Microbiology(all)
  • Neuroscience(all)
  • Pharmacology, Toxicology and Pharmaceutics(all)

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