Taro Kitazawa
@kitazawa-taro.bsky.social
Group Leader at DANDRITE Nordic-EMBL/Aarhus Univ.
ERC Research, FensKavli Scholar.
Molecular basis of neuroplasticity.
New genomics technologies.
https://www.kitazawa-lab.com/home
ERC Research, FensKavli Scholar.
Molecular basis of neuroplasticity.
New genomics technologies.
https://www.kitazawa-lab.com/home
Pinned
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...
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...
Reposted by Taro Kitazawa
Send us nominations for the FKNE Mentoring Prize 2026!The award will be presented at FENS Forum 2026 in Barcelona to a scientist who has demontrated leadership in fostering the careers of neuroscientists. Deadline: 15 February 2026 2cm.es/1gh-m
February 4, 2026 at 7:41 AM
Send us nominations for the FKNE Mentoring Prize 2026!The award will be presented at FENS Forum 2026 in Barcelona to a scientist who has demontrated leadership in fostering the careers of neuroscientists. Deadline: 15 February 2026 2cm.es/1gh-m
If you’re a young PI (or senior postdoc) heading to FENS, this one’s for you! It’ll be a lot of fun—and honestly, I can’t think of a better moment in one’s career to have a strong peer network.
📣 Our website is live and registration is NOW OPEN for the Young PI Symposium 2026 - the day prior to FENS Barcelona!
Navigate challenges, sharpen leadership skills, make a roadmap together for generations of neuroscientists!
youngpisymposium2026.com
Check out our program and join us!
Navigate challenges, sharpen leadership skills, make a roadmap together for generations of neuroscientists!
youngpisymposium2026.com
Check out our program and join us!
January 16, 2026 at 3:34 PM
Reposted by Taro Kitazawa
Call for junior or mid-career group leaders in neuroscience! Apply by 30 Jan to join the FENS-Kavli Network. We are looking for excellent and engaged future scholars who are committed to exchanging scientific ideas & improve neuroscience in Europe. fenskavlinetwork.org/who-we-are/a...
November 17, 2025 at 11:21 AM
Call for junior or mid-career group leaders in neuroscience! Apply by 30 Jan to join the FENS-Kavli Network. We are looking for excellent and engaged future scholars who are committed to exchanging scientific ideas & improve neuroscience in Europe. fenskavlinetwork.org/who-we-are/a...
Reposted by Taro Kitazawa
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!
Our lab is now applying HisTrac to study id specification and plasticity (e.g., memory) and we look forward to sharing exciting results soon!
August 16, 2025 at 7:15 AM
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!
Our lab is now applying HisTrac to study id specification and plasticity (e.g., memory) and we look forward to sharing exciting results soon!
Reposted by Taro Kitazawa
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...
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...
August 16, 2025 at 7:15 AM
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...
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...
Reposted by Taro Kitazawa
#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...
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
August 19, 2025 at 12:01 AM
#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...
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...
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!
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!
August 18, 2025 at 8:59 PM
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!
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!
Thank you so much!!
August 16, 2025 at 11:00 AM
Thank you so much!!
Reposted by Taro Kitazawa
Whole-genome single-cell multimodal history tracing to reveal cell identity transition #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.1101/2025.08.12.669973v1
https://www.biorxiv.org/content/10.1101/2025.08.12.669973v1
August 16, 2025 at 7:00 AM
Whole-genome single-cell multimodal history tracing to reveal cell identity transition #SingleCell 🧪🧬🖥️
https://www.biorxiv.org/content/10.1101/2025.08.12.669973v1
https://www.biorxiv.org/content/10.1101/2025.08.12.669973v1
Thank you so much, Oliver!
August 16, 2025 at 7:25 AM
Thank you so much, Oliver!
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.
August 16, 2025 at 7:15 AM
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.
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!
Our lab is now applying HisTrac to study id specification and plasticity (e.g., memory) and we look forward to sharing exciting results soon!
August 16, 2025 at 7:15 AM
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!
Our lab is now applying HisTrac to study id specification and plasticity (e.g., memory) and we look forward to sharing exciting results soon!
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.
August 16, 2025 at 7:15 AM
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.
Such abrupt identity jumps were previously unobservable with current single-cell technologies, as trajectory inference relies on continuity between single-cell snapshots.
August 16, 2025 at 7:15 AM
Such abrupt identity jumps were previously unobservable with current single-cell technologies, as trajectory inference relies on continuity between single-cell snapshots.
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.
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.
August 16, 2025 at 7:15 AM
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.
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.
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).
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).
August 16, 2025 at 7:15 AM
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).
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).
We also achieved sample multiplexing within the 10x Genomics microfluidics, dramatically reducing single-cell library preparation costs to just $0.04 per cell.
August 16, 2025 at 7:15 AM
We also achieved sample multiplexing within the 10x Genomics microfluidics, dramatically reducing single-cell library preparation costs to just $0.04 per cell.
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.
August 16, 2025 at 7:15 AM
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.
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!
This captured neonatal epigenome and transcriptome in the adult brain, demonstrating that HisTrac-seq remains effective for at least two months in vivo!
August 16, 2025 at 7:15 AM
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!
This captured neonatal epigenome and transcriptome in the adult brain, demonstrating that HisTrac-seq remains effective for at least two months in vivo!
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.
In addition, we extended the validation to the mesodermal cardiomyocyte lineage.
August 16, 2025 at 7:15 AM
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.
In addition, we extended the validation to the mesodermal cardiomyocyte lineage.
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.
August 16, 2025 at 7:15 AM
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.
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.
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.
August 16, 2025 at 7:15 AM
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.
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.
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.
August 16, 2025 at 7:15 AM
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.