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Reposted by Taro Kitazawa

Taro Kitazawa @kitazawa-taro.bsky.social · Aug 16

Please RP.
We are thrilled to announce that our lab’s first preprint is out!
”Whole-genome single-cell multimodal history tracing to reveal cell identity transition”

We report HisTrac-seq, a multiomic single-cell molecular recording platform.
www.biorxiv.org/content/10.1...

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Reposted by Taro Kitazawa

neuroradio.bsky.social @neuroradio.bsky.social · Aug 19

#94 Timestamping academic life events onto podcast sequels – Part 4
定期ゲスト北沢太郎さん(@kitazawa_taro) 回。直近に公開した自身のHisTrac-seqプレプリントと(と競合LagTagプレプリントの)解説回
#NeuroRadio
neuroradio.tokyo/2025/08/19/9...

#94 Timestamping academic life events onto podcast sequels – Part 4 - NeuroRadio

定期ゲスト北沢太郎さん(@kitazawa_taro) 回。直近に公開した自身のHisTrac-seqプレプリントと(と競合LagTagプレプリントの)解説回 (8/17 収録) Show Notes: Editoria...

neuroradio.tokyo

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Taro Kitazawa @kitazawa-taro.bsky.social · Aug 18

Thanks, Marek!
Indeed, your nanobody-Tn5 protocol is AMAZING!
We actually put some modifications, like sample-bcd implementation, as well as replacement of enzyme for 10x reaction, which may be interesting for you.
I look forward to discussing with you again!

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Taro Kitazawa @kitazawa-taro.bsky.social · Aug 16

Thanks Moritz!

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Taro Kitazawa @kitazawa-taro.bsky.social · Aug 16

Thank you so much!!

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Reposted by Taro Kitazawa

#SingleCell preprints @prepub-singlecell.bsky.social · Aug 16

Whole-genome single-cell multimodal history tracing to reveal cell identity transition #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.1101/2025.08.12.669973v1

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Taro Kitazawa @kitazawa-taro.bsky.social · Aug 16

Thank you so much, Oliver!

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Taro Kitazawa @kitazawa-taro.bsky.social · Aug 16

This work was carried out by our super talented postdocs Yumiko K Kawamura and Valentina Khalil with generous supports of ‪@dandrite.bsky.social‬, ‪@erc.europa.eu‬, ‪@lundbeckfonden.bsky.social‬, ‪@novo-nordisk.bsky.social‬, JST, and Aarhus University.‬‬‬‬

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Taro Kitazawa @kitazawa-taro.bsky.social · Aug 16

In summary, we established whole-genome, multimodal single-cell history tracing, applicable to a wide range of experimental systems.
Our lab is now applying HisTrac to study id specification and plasticity (e.g., memory) and we look forward to sharing exciting results soon!

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Taro Kitazawa @kitazawa-taro.bsky.social · Aug 16

We next explored the mechanisms underlying this hidden layer of developmental plasticity and found that identity jumps are associated with precocious activation of maturation programs, altered cell–cell interactions and downstream signaling, and resolution of enhancer bivalency.

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Taro Kitazawa @kitazawa-taro.bsky.social · Aug 16

Such abrupt identity jumps were previously unobservable with current single-cell technologies, as trajectory inference relies on continuity between single-cell snapshots.

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Taro Kitazawa @kitazawa-taro.bsky.social · Aug 16

Time for biology:
Using scHisTrac-seq to profile transcriptome, chromatin accessibility, and bivalency during neurodifferentiation, we analyzed over 90,000 single cells and uncovered drastic cell identity transitions—namely “identity jumps.

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Taro Kitazawa @kitazawa-taro.bsky.social · Aug 16

So far, so good—perhaps too good.
For the final form, we developed scHisTrac-seq, enabling simultaneous profiling of past and present multiomic states from the same single cells via a nanobody-mediated dual scCUT&Tag protocol (past = m6A, present = H3K27ac, transcription marker).

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Taro Kitazawa @kitazawa-taro.bsky.social · Aug 16

We also achieved sample multiplexing within the 10x Genomics microfluidics, dramatically reducing single-cell library preparation costs to just $0.04 per cell.

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Taro Kitazawa @kitazawa-taro.bsky.social · Aug 16

To fully leverage history tracing, we developed a single-cell m6A detection method on the 10x Genomics platform. By targeting Tn5 transposase via the m6A-tracer, we captured in vivo sc profiles with 5–10K unique reads—among the highest quality achieved for 10x-based assays.

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Taro Kitazawa @kitazawa-taro.bsky.social · Aug 16

We next validated HisTrac-seq in vivo, pulse-labeling the neonatal brain and harvesting in adulthood (8 weeks).
This captured neonatal epigenome and transcriptome in the adult brain, demonstrating that HisTrac-seq remains effective for at least two months in vivo!

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Taro Kitazawa @kitazawa-taro.bsky.social · Aug 16

We first demonstrated bulk HisTrac-seq in vitro, showing that transient Dam–POI activation in immature neurons beautifully reproduced their profiles after maturation!
In addition, we extended the validation to the mesodermal cardiomyocyte lineage.

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Taro Kitazawa @kitazawa-taro.bsky.social · Aug 16

By transiently activating Dam fused to POIs (proteins of interest), HisTrac-seq can record whole-genome multiomic profiles, including transcriptome, open chromatin, LAD-heterochromatin, Trithorax, Polycomb, and even bivalency.

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Taro Kitazawa @kitazawa-taro.bsky.social · Aug 16

We used Dam (DNA adenine methyltransferase) to label DNA with m6A, a mark absent from our genome.
Because previously shown that m6A can persist for several hours until the next DNA replication, we expected it to serve as a long-term ”bookmark” in neurons, potentially for months.

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Taro Kitazawa @kitazawa-taro.bsky.social · Aug 16

While single-cell sequencing such as scRNA-seq are powerful, they inherently capture only static snapshots, and trajectory inference can only approximate dynamic processes. This has created a long-standing need for sc observations across multiple time points—history tracing.

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Taro Kitazawa @kitazawa-taro.bsky.social · Aug 16

This approach revealed previously unseen, drastic cell identity transitions, namely “identity jumps” in the Waddington landscape, during neurodifferentiation.

Following threads will elaborate on HisTrac-seq and and our findings.

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Taro Kitazawa @kitazawa-taro.bsky.social · Aug 16

Please RP.
We are thrilled to announce that our lab’s first preprint is out!
”Whole-genome single-cell multimodal history tracing to reveal cell identity transition”

We report HisTrac-seq, a multiomic single-cell molecular recording platform.
www.biorxiv.org/content/10.1...

2 41 77

Taro Kitazawa @kitazawa-taro.bsky.social · Aug 1

Federation of European Neuroscience Societies - FENS @fens.org · Aug 1

🚨 #FENS2026 NEW DATES 🚨

First, Formula 1 sent us from Madrid to #Barcelona. Now the Tour de France Grand Départ has us switching gears again—we're updating our dates to 6-10 July 2026! 🗓️

Find out more 👉: https://loom.ly/zMkMKcA

🔔 Stay tuned!

Taro Kitazawa @kitazawa-taro.bsky.social · Jul 24

Wow congratz!

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Taro Kitazawa @kitazawa-taro.bsky.social · Jun 21

Only a few days left before the extdnded deadline (23 June).

Do not forget to submit your abstracts!

Taro Kitazawa @kitazawa-taro.bsky.social · Apr 15

Thrilled to announce @dandrite.bsky.social Symposium: Gene Expression in Brain (20-21 August 2025)!

World-class plenaries Mike Greenberg, Elly Nedivi, Anne Schaefer, Alex Schier + more speakers.

Why don't you travel to Denmark this summer? Travel grants prepared.
dandrite.au.dk/news/events/...