Cell lineage tracing techniques

Site-specific recombinases (Cre/loxP, FLP/FRT, Dre/rox)

Used to stochastically flip/excise DNA cassettes → color codes (Brainbow/Confetti), mosaics (MADM/MARCM), or endogenous barcodes (Polylox).

  • Brainbow (multicolor FPs via Cre/lox variants). Livet et al., Nature 2007. Nature, PubMed
  • Confetti mouse (R26R-Confetti Cre reporter for clonal tracing). Snippert et al., Cell 2010. ScienceDirect, Hubrecht Institute
  • MADM (Cre-dependent interchromosomal recombination; twin-spot clonal analysis in mouse). Zong et al., Cell 2005. PubMed, Cell
  • MARCM (FLP/FRT mosaic labeling in fly). Lee & Luo, Neuron 1999; protocol follow-ups. PubMed
  • Polylox barcoding (Cre recombination of a synthetic lox array for endogenous barcodes). Pei et al., Nature 2017; PolyloxExpress, Cell Stem Cell 2020. PMC, PubMed

Integrases & transposases (Bxb1, ϕC31; PiggyBac/Sleeping Beauty)

Enable unidirectional recombination or insertion; used in some multicolor/“digital” Brainbow variants and for stable integration/barcoding.

  • Bxb1 integrase (high accuracy, unidirectional LSR used broadly in mammalian cells). Xu et al., BMC Biotechnol. 2013. BioMed Central
  • (Background on LSR vs tyrosine recombinases.) Durrant et al., Nat Biotechnol 2023. Nature

CRISPR/DNA-writing lineage recorders (“scarring” and beyond)

Cas9 (or base/prime/TdT-based) edits accumulate over time in arrays → read by scRNA-seq or in situ.

  • GESTALT (CRISPR scars in synthetic target arrays). McKenna et al., Science 2016. Science, PMC
  • scGESTALT (lineage + scRNA-seq). Raj et al., Science 2018. PubMed, PMC
  • LINNAEUS (CRISPR scars with scRNA-seq in zebrafish). Spanjaard et al., Nat Biotechnol 2018. Nature, PubMed
  • ScarTrace (whole-organism clone tracing). Alemany et al., Nature 2018. PubMed, Hubrecht Institute
  • CARLIN mouse (inducible CRISPR array repair). Bowling et al., Cell 2020. PubMed, ScienceDirect
  • MEMOIR/intMEMOIR (CRISPR recording read out in situ). Frieda et al., Nature 2017. PMC
  • CHYRON (ordered insertions with TdT). Loveless et al., Nat Biotechnol 2021. PubMed, PMC
  • DNA Typewriter (multi-symbol temporal recorder). Choi et al., Nature 2022. Nature

Multicolor “Brainbow-like” toolkits (beyond the original)

Many variants adapt the basic idea to more colors or other species.

  • Brainbow (mouse). Livet et al., Nature 2007. Nature
  • Confetti (four-color Cre reporter). Snippert et al., Cell 2010. ScienceDirect
  • (Plus Flybow/Tetbow/Bitbow variants in other systems; see the Brainbow paper & later method notes for context.) Nature

Viral combinatorics for connectome tracing

Use engineered viruses (rabies, HSV, AAV) and/or nucleotide barcodes to map inputs/outputs at scale; often combined with recombinase logic (TRIO/cTRIO) and sequencing.

Rabies/HSV/PRV trans-synaptic tracers

  • G-deleted rabies monosynaptic tracing (starter-cell restricted). Wickersham et al., Neuron 2007; protocol/review updates. Cell, Journal of Neuroscience
  • PRV Bartha (retrograde polysynaptic). Card & Enquist, J Vis Exp 2014; classic PRV studies. PMC, ASM Journals
  • HSV-1 H129 (anterograde; poly- or mono-synaptic variants). Yang et al., Mol Neurodegener 2022; reviews. BioMed Central, MDPI

AAV retro/anterograde and systemic capsids

  • AAV2-retro (efficient retrograde access). Tervo et al., Neuron 2016. PubMed
  • AAV-PHP.B / PHP.eB (broad CNS transduction in certain mouse strains). Chan et al., Nat Neurosci 2017; caveats on strain dependence. PMC, Cell

Sequencing-based “barcoded connectomics”

  • MAPseq (AAV RNA barcodes to map projections by sequencing). Kebschull et al., Neuron 2016. ScienceDirect
  • BARseq (in situ sequencing of barcodes for projections). Chen et al., Neuron 2019; Cell
  • BRICseq / related high-throughput projection sequencing. See Zador/Chen labs overviews (reviews/Cell 2022). Allen Institute, BioRxiv
  • SYNseq (pairing pre/post synaptic barcodes via engineered proteins + crosslinking). Concept review by Zador (2012). BioRxiv, PMC
  • RABID-seq / SBARRO (barcoded rabies to read synaptic relationships in scRNA-seq). Clark et al., Science 2021; Saunders et al., Nat Commun 2022; Science, Nature, PMC

Genetically encoded trans-synaptic labeling (nonviral or virus-assisted)

These label synaptic partners via protein complementation or synthetic signaling and this approach is often complementary to viral tracers.

  • GRASP / mGRASP (split-GFP reconstitution across synaptic partners). Feinberg et al., Neuron 2008; Kim et al., Nat Methods 2012. PubMed
  • trans-Tango (synthetic ligand→GPCR→proteolysis signaling to postsynaptic partners; Drosophila). Talay et al., Neuron 2017. PubMed
  • BLINC / iBLINC (BirA/AviTag proximity-dependent biotinylation across synapses). Liu et al., PLOS One 2013; Desbois et al., J Neurosci 2015. PLOS, PMC

Other

SpyTag/SpyCatcher is a peptide–protein pair that forms a covalent isopeptide bond, widely used to lock protein complexes or anchor labels. It’s not itself a mainstream lineage or connectome recorder, but it’s often used as a building block to stably decorate synaptic proteins or assemble modular reporters. Canonical reference: Zakeri et al., PNAS 2012. PubMed

See also

See mapseq and in situ sequencing.

See also DNA ticker tape memory for examples of real-time spatial transcriptomics using event-triggered real-time DNA writing to record information and DNA sequencing to later recover the information.

See gene editing for other plausible lineage tracing technologies that could be incorporated into cells in vivo.