Fluorescent protein ticker tape (FPTT): Multiplexed recording of transcriptional dynamics in living cells and in vivo.

Overview

1. School of Mathematical Sciences, Peking University, Beijing, China
2. School of Life Sciences, Westlake University, Hangzhou, China
3. Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
4. Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
5. Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Medicine and School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
6. School of Engineering, Westlake University, Hangzhou, Zhejiang 310030, China
7. College of Life Sciences, Zhejiang University, Hangzhou, China

Abstract

Recording and real-time imaging of promoter activities are critical for deciphering signaling cross-talk, but technologies for simultaneously capturing multiple transient events in living cells are lacking. Here, we design fluorescent protein–based ticker tapes (FPTT) for multiplexed, scalable, longitudinal recording of single-cell physiological activities by integrating multispectral monomeric fluorescent proteins with self-assembling protein fibers. FPTT logged dose-dependent, reversible endogenous cFos transcriptional histories in hippocampal neurons at 3-hour resolution over 8 days. We engineered FPTT variants for human nuclear factor κB (NF-κB), Janus kinase/signal transducer and activator of transcription 3 (STAT3), mechanistic target of rapamycin (mTOR), nuclear factor of activated T cells (NFAT), and adenosine 3′,5′-monophosphate (cAMP) signaling. This expanded toolset enabled quantification of cFos and NF-κB cross-talk in neurons, tracking of STAT3/cAMP dynamics during mouse liver injury, discovery of unexpected NFAT/STAT3 cross-talk, and characterization of cell cycle–dependent oscillating mTOR dynamics. Last, we achieved simultaneous analysis of four major pathways during T cell activation. FPTT provides a versatile platform to investigate transcriptional histories and signaling interplay, with broad applications in developmental biology and disease modeling.

Reproduced under the paper's license (CC BY-NC), from the paper cited above.

Code

No file of the authors' code could be read here: it is described below, and read at its source.

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

• 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
• 0 scripts, each with its path and the digest of its content;
• no match between paragraphs and code yet;
• neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data, code, and materials availability

All data and code needed to evaluate and reproduce the results in the paper are present in the paper and/or the Supplementary Materials. Raw image files with metadata, source data, raw RNA-seq datasets, and custom VBA macro scripts are publicly accessible on Zenodo (https://doi.org/10.5281/zenodo.20259137). All plasmids used in this study can be obtained from WeKwikGene (https://wekwikgene.wllsb.edu.cn/publications/0000470) under standard material transfer agreement.

Reproduced under the paper's license (CC BY-NC), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 5 authors, 12 MeSH terms, 3 funders, 86 references.

Cite

This paper

Li, Z., Liu, T., Wang, Y., Xie, M., & Piatkevich, K. D. (2026). Fluorescent protein ticker tape (FPTT): Multiplexed recording of transcriptional dynamics in living cells and in vivo. Science advances, 12(36), eaef9406. https://doi.org/10.1126/sciadv.aef9406

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

Similar papers

The papers with a page that share the most with this one: the tools found in their code, their categories, datasets, cited references and authors, the rarest counting most.

[1] doi:10.1038/s41586-026-10156-9 [code]

Scalable and multiplexed recorders of gene regulation dynamics across weeks.

Journal: Nature

In common: mouse, cellular / molecular, 5 references

[2] doi:10.1038/s41586-026-10323-y [code]

Genetically encoded assembly recorder temporally resolves cellular history.

Journal: Nature

In common: mouse, cellular / molecular, 5 references

[3] doi:10.1242/dev.203102

Barcoding Notch signaling in the developing brain.

Journal: Development (Cambridge, England)

In common: 4 references

[4] doi:10.1371/journal.pbio.3003048 [code]

A sensitive soma-localized red fluorescent calcium indicator for in vivo imaging of neuronal populations at single-cell resolution.

Journal: PLoS biology

In common: mouse, 1 reference, author Kiryl D. Piatkevich

[5] doi:10.1016/j.crmeth.2026.101471 [code]

Development of far-red fluorescent proteins for temporal domain multiplexing and super-resolution imaging.

Journal: Cell reports methods

In common: mouse, cellular / molecular, author Kiryl D. Piatkevich

[6] doi:10.1371/journal.pbio.3002993

Sensitive red fluorescent indicators for real-time visualization of potassium ion dynamics in vivo.

Journal: PLoS biology

In common: mouse, cellular / molecular, author Kiryl D. Piatkevich

[7] doi:10.1038/s41467-022-34824-2 [code]

Spatially resolved proteomics via tissue expansion.

Journal: Nature communications

In common: mouse, author Kiryl D. Piatkevich

[8] doi:10.1186/s12950-025-00464-8

Loss of tuberous sclerosis complex 2 confers inflammation via dysregulation of nuclear factor kappa-light-chain-enhancer of activated B cells.

Journal: Journal of inflammation (London, England)

In common: cellular / molecular, 3 references

[9] doi:10.1038/s41586-024-08282-3

Synthetic GPCRs for programmable sensing and control of cell behaviour.

Journal: Nature

In common: mouse, cellular / molecular, 2 references

[10] doi:10.1038/s41587-022-01586-7 [code]

Recording of cellular physiological histories along optically readable self-assembling protein chains.

Journal: Nature biotechnology

In common: mouse, cellular / molecular, 2 references

Contribute

The authors of this paper can claim it, correct its record and validate its tracing map, and the maintainers of its code (its owner, or a public member of its organization) correct what it says of their repository; anyone signed in can ask for its removal. Every request goes to OSCR's own machine, which answers it; your account page follows them.

<!-- oscr-badge:start -->
[![OSCR](https://openscicode.org/badge/doi/10.1126/sciadv.aef9406.svg)](https://openscicode.org/badge/doi/10.1126/sciadv.aef9406)
<!-- oscr-badge:end -->

.. oscr-badge:start

.. image:: https://openscicode.org/badge/doi/10.1126/sciadv.aef9406.svg
   :target: https://openscicode.org/badge/doi/10.1126/sciadv.aef9406
   :alt: OSCR

.. oscr-badge:end

<!-- oscr-badge:start -->
<a href="https://openscicode.org/badge/doi/10.1126/sciadv.aef9406"><img src="https://openscicode.org/badge/doi/10.1126/sciadv.aef9406.svg" alt="OSCR"></a>
<!-- oscr-badge:end -->

Request its removal

To ask OSCR to remove this record, the copies of its authors' scripts or its tracing map, use the removal request page: signed in, you say who you are, what to remove and why, then review and confirm the request. Published rules decide every request (how).

Discussion: code errors and mismatches between the code and the paper about this paper and its code, from readers and its authors, beside the paper and its tracing map.

Report a mismatch between the code and the paper · Report a code error (signed in)

Reproductions: reports from readers who ran the authors' code and did not get the paper's result, what they ran, with which environment, commit and data.

Report a reproduction failure (signed in)

Activity: what happens around this paper: new versions of its record, its map's validation, discussions and reproductions. It opens with sign-in.