# 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](https://www.nature.com/articles/nature06293?utm_source=chatgpt.com), [PubMed](https://pubmed.ncbi.nlm.nih.gov/17972876/?utm_source=chatgpt.com)
* **Confetti mouse** (R26R-Confetti Cre reporter for clonal tracing). Snippert et al., *Cell* 2010. [ScienceDirect](https://www.sciencedirect.com/science/article/pii/S0092867410010640?utm_source=chatgpt.com), [Hubrecht Institute](https://www.hubrecht.eu/app/uploads/2017/11/PIIS0092867410010640.pdf?utm_source=chatgpt.com)
* **MADM** (Cre-dependent interchromosomal recombination; twin-spot clonal analysis in mouse). Zong et al., *Cell* 2005. [PubMed](https://pubmed.ncbi.nlm.nih.gov/15882628/?utm_source=chatgpt.com), [Cell](https://www.cell.com/fulltext/S0092-8674%2805%2900157-1?utm_source=chatgpt.com)
* **MARCM** (FLP/FRT mosaic labeling in fly). Lee & Luo, *Neuron* 1999; protocol follow-ups. [PubMed](https://pubmed.ncbi.nlm.nih.gov/10197526/?utm_source=chatgpt.com)
* **Polylox barcoding** (Cre recombination of a synthetic lox array for endogenous barcodes). Pei et al., *Nature* 2017; PolyloxExpress, *Cell Stem Cell* 2020. [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC5905670/?utm_source=chatgpt.com), [PubMed](https://pubmed.ncbi.nlm.nih.gov/32783885/?utm_source=chatgpt.com)

## 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](https://bmcbiotechnol.biomedcentral.com/articles/10.1186/1472-6750-13-87?utm_source=chatgpt.com)
* (Background on LSR vs tyrosine recombinases.) Durrant et al., *Nat Biotechnol* 2023. [Nature](https://www.nature.com/articles/s41587-022-01494-w?utm_source=chatgpt.com)

## 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](https://www.science.org/doi/10.1126/science.aaf7907?utm_source=chatgpt.com), [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC4967023/?utm_source=chatgpt.com)
* **scGESTALT** (lineage + scRNA-seq). Raj et al., *Science* 2018. [PubMed](https://pubmed.ncbi.nlm.nih.gov/29608178/?utm_source=chatgpt.com), [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC5938111/?utm_source=chatgpt.com)
* **LINNAEUS** (CRISPR scars with scRNA-seq in zebrafish). Spanjaard et al., *Nat Biotechnol* 2018. [Nature](https://www.nature.com/articles/nbt.4124?utm_source=chatgpt.com), [PubMed](https://pubmed.ncbi.nlm.nih.gov/29644996/?utm_source=chatgpt.com)
* **ScarTrace** (whole-organism clone tracing). Alemany et al., *Nature* 2018. [PubMed](https://pubmed.ncbi.nlm.nih.gov/29590089/?utm_source=chatgpt.com), [Hubrecht Institute](https://www.hubrecht.eu/app/uploads/2017/11/vanOudenaarden_Key_2018_Alemany_Whole-organism-clone-tracing-using-single-cell-sequencing.pdf?utm_source=chatgpt.com)
* **CARLIN mouse** (inducible CRISPR array repair). Bowling et al., *Cell* 2020. [PubMed](https://pubmed.ncbi.nlm.nih.gov/32413320/?utm_source=chatgpt.com), [ScienceDirect](https://www.sciencedirect.com/science/article/pii/S0092867420305547?utm_source=chatgpt.com)
* **MEMOIR/intMEMOIR** (CRISPR recording read out **in situ**). Frieda et al., *Nature* 2017. [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC6487260/?utm_source=chatgpt.com)
* **CHYRON** (ordered insertions with TdT). Loveless et al., *Nat Biotechnol* 2021. [PubMed](https://pubmed.ncbi.nlm.nih.gov/33753928/?utm_source=chatgpt.com), [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC8891441/?utm_source=chatgpt.com)
* **DNA Typewriter** (multi-symbol temporal recorder). Choi et al., *Nature* 2022. [Nature](https://www.nature.com/articles/s41586-022-04922-8?utm_source=chatgpt.com)

## 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](https://www.nature.com/articles/nature06293?utm_source=chatgpt.com)
* **Confetti** (four-color Cre reporter). Snippert et al., *Cell* 2010. [ScienceDirect](https://www.sciencedirect.com/science/article/pii/S0092867410010640?utm_source=chatgpt.com)
* (Plus Flybow/Tetbow/Bitbow variants in other systems; see the Brainbow paper & later method notes for context.) [Nature](https://www.nature.com/articles/nature06293?utm_source=chatgpt.com)

## 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](https://www.cell.com/neuron/fulltext/S0896-6273%2807%2900078-5?utm_source=chatgpt.com), [Journal of Neuroscience](https://www.jneurosci.org/content/jneuro/35/24/8979.full.pdf?utm_source=chatgpt.com)
* **PRV Bartha** (retrograde polysynaptic). Card & Enquist, *J Vis Exp* 2014; classic PRV studies. [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC4165084/?utm_source=chatgpt.com), [ASM Journals](https://journals.asm.org/doi/10.1128/jvi.73.5.4350-4359.1999?utm_source=chatgpt.com)
* **HSV-1 H129** (anterograde; poly- or mono-synaptic variants). Yang et al., *Mol Neurodegener* 2022; reviews. [BioMed Central](https://molecularneurodegeneration.biomedcentral.com/articles/10.1186/s13024-021-00508-6?utm_source=chatgpt.com), [MDPI](https://www.mdpi.com/1422-0067/21/16/5937?utm_source=chatgpt.com)

**AAV retro/anterograde and systemic capsids**

* **AAV2-retro** (efficient retrograde access). Tervo et al., *Neuron* 2016. [PubMed](https://pubmed.ncbi.nlm.nih.gov/27720486/?utm_source=chatgpt.com)
* **AAV-PHP.B / PHP.eB** (broad CNS transduction in certain mouse strains). Chan et al., *Nat Neurosci* 2017; caveats on strain dependence. [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC5529245/?utm_source=chatgpt.com), [Cell](https://www.cell.com/molecular-therapy-family/methods/fulltext/S2329-0501%2820%2930215-1?utm_source=chatgpt.com)

**Sequencing-based “barcoded connectomics”**

* **MAPseq** (AAV RNA barcodes to map projections by sequencing). Kebschull et al., *Neuron* 2016. [ScienceDirect](https://www.sciencedirect.com/science/article/pii/S0092867419310748?utm_source=chatgpt.com)
* **BARseq** (in situ sequencing of barcodes for projections). Chen et al., *Neuron* 2019; [Cell](https://www.cell.com/neuron/fulltext/S0896-6273%2807%2900078-5?utm_source=chatgpt.com)
* **BRICseq** / related high-throughput projection sequencing. See Zador/Chen labs overviews (reviews/Cell 2022). [Allen Institute](https://alleninstitute.org/division/brain-science/brain-science-management-team/barcoded-connectomics/?utm_source=chatgpt.com), [BioRxiv](https://www.biorxiv.org/content/10.1101/2020.04.07.030593v2?utm_source=chatgpt.com)
* **SYNseq** (pairing pre/post synaptic barcodes via engineered proteins + crosslinking). Concept review by Zador (2012). [BioRxiv](https://www.biorxiv.org/content/10.1101/099093v2.full.pdf?utm_source=chatgpt.com), [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC3479097/?utm_source=chatgpt.com)
* **RABID-seq** / **SBARRO** (barcoded rabies to read synaptic relationships in scRNA-seq). Clark et al., *Science* 2021; Saunders et al., *Nat Commun* 2022; [Science](https://www.science.org/doi/10.1126/science.abf1230?utm_source=chatgpt.com), [Nature](https://www.nature.com/articles/s41467-022-34334-1?utm_source=chatgpt.com), [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC10055146/?utm_source=chatgpt.com)

## 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](https://pubmed.ncbi.nlm.nih.gov/18255029/?utm_source=chatgpt.com)
* **trans-Tango** (synthetic ligand→GPCR→proteolysis signaling to postsynaptic partners; Drosophila). Talay et al., *Neuron* 2017. [PubMed](https://pubmed.ncbi.nlm.nih.gov/29107518/?utm_source=chatgpt.com)
* **BLINC / iBLINC** (BirA/AviTag proximity-dependent biotinylation across synapses). Liu et al., *PLOS One* 2013; Desbois et al., *J Neurosci* 2015. [PLOS](https://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0052823&utm_source=chatgpt.com), [PMC](https://pmc.ncbi.nlm.nih.gov/articles/PMC4512537/?utm_source=chatgpt.com)

## 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](https://pubmed.ncbi.nlm.nih.gov/22855427/?utm_source=chatgpt.com)

## 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.