Wataru Kobayashi
@wkobayashi.bsky.social
PI at the University of Dundee / Pre-implantation development / Genomics / TFs / Chromatin / Biochemistry / Cryo-EM
Postdoc: MPIB, IMBA
Ph.D: Waseda Univ.
Google Scholar: https://scholar.google.com/citations?hl=ja&user=tw4M2dgAAAAJ
Postdoc: MPIB, IMBA
Ph.D: Waseda Univ.
Google Scholar: https://scholar.google.com/citations?hl=ja&user=tw4M2dgAAAAJ
Pinned
Feed-forward loops by NR5A2 ensure robust gene activation during pre-implantation development
Pioneer transcription factors are crucial for regulating zygotic genome activation and cell differentiation during mouse pre-implantation development. However, how pioneer factors function collectivel...
journals.biologists.com
Excited to announce that our peer-reviewed manuscript is online in the Development journal @dev-journal.bsky.social. The manuscript was much improved through the peer-review process, and I am grateful to the reviewers for their valuable feedback.
journals.biologists.com/dev/article/...
journals.biologists.com/dev/article/...
NR5A2 overexpression improves SCNT efficiency and enhances ZGA by promoting H3K27ac deposition. Great work!
journals.plos.org/plosbiology/...
journals.plos.org/plosbiology/...
Overexpression of the pioneer transcription factor Nr5a2 promotes the development of mouse somatic cell nuclear transfer embryos
Somatic Cell Nuclear Transfer (SCNT) is an approach that enables the generation of an embryo from a somatic cell, but its efficiency remains low due to epigenetic barriers. This study shows that pione...
journals.plos.org
January 27, 2026 at 10:54 AM
NR5A2 overexpression improves SCNT efficiency and enhances ZGA by promoting H3K27ac deposition. Great work!
journals.plos.org/plosbiology/...
journals.plos.org/plosbiology/...
Reposted by Wataru Kobayashi
Happy New Year! Check out 👀our new protocol paper on the analysis of transcription factor-nucleosome interactions! Hope you find it useful 🔬🧬Was a pleasure to write up with you @wkobayashi.bsky.social and Kikuë Tachibana!
Happy to share a protocol for analysis of TF-nucleosome interactions and cryo-EM structure determination in STAR Protocols. I had a great opportunity to describe this protocol with @aliciakmichael.bsky.social. Thank you very much, all!
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination
Pioneer transcription factors (TFs) possess the ability to read out DNA motifs embedded within nucleosomes, driving changes in gene expression during …
www.sciencedirect.com
December 31, 2025 at 9:25 AM
Happy New Year! Check out 👀our new protocol paper on the analysis of transcription factor-nucleosome interactions! Hope you find it useful 🔬🧬Was a pleasure to write up with you @wkobayashi.bsky.social and Kikuë Tachibana!
Happy to share a protocol for analysis of TF-nucleosome interactions and cryo-EM structure determination in STAR Protocols. I had a great opportunity to describe this protocol with @aliciakmichael.bsky.social. Thank you very much, all!
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Protocol for integrative analysis of transcription factor-nucleosome interactions using SeEN-seq and cryo-EM structure determination
Pioneer transcription factors (TFs) possess the ability to read out DNA motifs embedded within nucleosomes, driving changes in gene expression during …
www.sciencedirect.com
December 29, 2025 at 9:11 PM
Happy to share a protocol for analysis of TF-nucleosome interactions and cryo-EM structure determination in STAR Protocols. I had a great opportunity to describe this protocol with @aliciakmichael.bsky.social. Thank you very much, all!
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Excited to announce that our peer-reviewed manuscript is online in the Development journal @dev-journal.bsky.social. The manuscript was much improved through the peer-review process, and I am grateful to the reviewers for their valuable feedback.
journals.biologists.com/dev/article/...
journals.biologists.com/dev/article/...
Feed-forward loops by NR5A2 ensure robust gene activation during pre-implantation development
Pioneer transcription factors are crucial for regulating zygotic genome activation and cell differentiation during mouse pre-implantation development. However, how pioneer factors function collectivel...
journals.biologists.com
December 8, 2025 at 5:57 PM
Excited to announce that our peer-reviewed manuscript is online in the Development journal @dev-journal.bsky.social. The manuscript was much improved through the peer-review process, and I am grateful to the reviewers for their valuable feedback.
journals.biologists.com/dev/article/...
journals.biologists.com/dev/article/...
Reposted by Wataru Kobayashi
Our first cell-free DNA paper is now published! Thank you to all co-authors and collaborators for their contributions.
Officially published in Communications Biology!
In this study, we developed an open chromatin-guided, interpretable machine learning pipeline to uncover cancer-specific nucleosomal fragment patterns directly from cell-free DNA.
📄 Published article: doi.org/10.1038/s420...
In this study, we developed an open chromatin-guided, interpretable machine learning pipeline to uncover cancer-specific nucleosomal fragment patterns directly from cell-free DNA.
📄 Published article: doi.org/10.1038/s420...
November 13, 2025 at 6:01 AM
Our first cell-free DNA paper is now published! Thank you to all co-authors and collaborators for their contributions.
I'm looking forward to presenting at the Third Scottish Cryo-EM Symposium tomorrow. A nice opportunity to meet cryo-EM folks in Scotland.
September 1, 2025 at 2:03 PM
I'm looking forward to presenting at the Third Scottish Cryo-EM Symposium tomorrow. A nice opportunity to meet cryo-EM folks in Scotland.
It was extremely challenging to identify transcription factor binding profiles using mouse pre-implantation embryos due to the limited availability of material. I was fortunate to establish an optimised CUT&Tag protocol for this purpose in 2020.
May 30, 2025 at 2:01 PM
It was extremely challenging to identify transcription factor binding profiles using mouse pre-implantation embryos due to the limited availability of material. I was fortunate to establish an optimised CUT&Tag protocol for this purpose in 2020.
This method chapter describes the CUT&Tag approach for profiling transcription factors during murine ZGA. I hope it will be helpful for others studying TF binding profiles in similar contexts.
link.springer.com/protocol/10....
link.springer.com/protocol/10....
CUT&Tag for Transcription Factor Binding Profiles During Mammalian Zygotic Genome Activation
Zygotic genome activation (ZGA) triggered by transcription factors (TFs) is a critical event to facilitate subsequent embryonic development. However, the paucity of material poses a challenge for mapp...
link.springer.com
May 30, 2025 at 2:01 PM
This method chapter describes the CUT&Tag approach for profiling transcription factors during murine ZGA. I hope it will be helpful for others studying TF binding profiles in similar contexts.
link.springer.com/protocol/10....
link.springer.com/protocol/10....
Thank you very much!
April 24, 2025 at 10:43 AM
Thank you very much!
Thank you, Johanna! See you at the conference!
April 22, 2025 at 5:52 PM
Thank you, Johanna! See you at the conference!
Combining expertise with low-input genomics, biochemistry, and cryo-EM analysis, my group cross the scale to understand this fundamental question.
Dundee is a surprisingly sunny spot in Scotland, and I’m looking forward to enjoying life in the UK, surrounded by its beautiful nature!
Dundee is a surprisingly sunny spot in Scotland, and I’m looking forward to enjoying life in the UK, surrounded by its beautiful nature!
April 22, 2025 at 3:10 PM
Combining expertise with low-input genomics, biochemistry, and cryo-EM analysis, my group cross the scale to understand this fundamental question.
Dundee is a surprisingly sunny spot in Scotland, and I’m looking forward to enjoying life in the UK, surrounded by its beautiful nature!
Dundee is a surprisingly sunny spot in Scotland, and I’m looking forward to enjoying life in the UK, surrounded by its beautiful nature!
I’m pleased to announce that I have now officially started my research group at the University of Dundee, UK. My laboratory focus on how transcription factors orchestrate epigenetic reprogramming in mammalian embryos.
April 22, 2025 at 3:09 PM
I’m pleased to announce that I have now officially started my research group at the University of Dundee, UK. My laboratory focus on how transcription factors orchestrate epigenetic reprogramming in mammalian embryos.
Reposted by Wataru Kobayashi
Our study with Anjana Rao's lab was just published at NSMB 🥳 Shows how OGT prevents TET proteins from activating retrotransposons, particularly those in heterochromatin. Paper has 6-base and ONT sequencing data from OGT iKO mESCs, and also interesting OGT inhibitor data 👀.
rdcu.be/efuho
rdcu.be/efuho
OGT prevents DNA demethylation and suppresses the expression of transposable elements in heterochromatin by restraining TET activity genome-wide
Nature Structural & Molecular Biology - Here the authors show that the disruption of OGT expression in mouse embryonic stem cells unleashes TET activity, causing genome-wide decreases in DNA...
rdcu.be
March 28, 2025 at 11:43 AM
Our study with Anjana Rao's lab was just published at NSMB 🥳 Shows how OGT prevents TET proteins from activating retrotransposons, particularly those in heterochromatin. Paper has 6-base and ONT sequencing data from OGT iKO mESCs, and also interesting OGT inhibitor data 👀.
rdcu.be/efuho
rdcu.be/efuho
Reposted by Wataru Kobayashi
Our second cell-free DNA manuscript is here! In collaboration with Dr. Takada’s group, we explore how abemaciclib treatment response in metastatic breast cancer can be monitored via circulating chromatin fragments: www.researchsquare.com/article/rs-5...
Exploring Mechanism of Action of Abemaciclib in Breast Cancer Through Circulating Chromatin Fragment
Cell free DNA (cfDNA) analysis has a large potential for cancer patient diagnosis. Given the evidence that cfDNA partially preserves chromatin architecture of tumor cells, it potentially allows the de...
www.researchsquare.com
March 24, 2025 at 4:34 AM
Our second cell-free DNA manuscript is here! In collaboration with Dr. Takada’s group, we explore how abemaciclib treatment response in metastatic breast cancer can be monitored via circulating chromatin fragments: www.researchsquare.com/article/rs-5...
Thank you very much. I moved to UK yesterday. It’s gonna be slow starting.
February 20, 2025 at 12:51 PM
Thank you very much. I moved to UK yesterday. It’s gonna be slow starting.
Thank you, Ana!
February 20, 2025 at 9:41 AM
Thank you, Ana!
Reposted by Wataru Kobayashi
Feed-forward loops by NR5A2 ensure robust gene activation during pre-implantation development https://www.biorxiv.org/content/10.1101/2025.02.14.638292v1
February 20, 2025 at 12:30 AM
Feed-forward loops by NR5A2 ensure robust gene activation during pre-implantation development https://www.biorxiv.org/content/10.1101/2025.02.14.638292v1
Finally, this work is a great collaboration within the Tachibana lab!
🎉 Huge thanks to:
Chad for all bioinformatic analysis. Eda (a talented student!) helped CUT&Tag and biochemistry. Adarsh helped testing KD. (11/n)
🎉 Huge thanks to:
Chad for all bioinformatic analysis. Eda (a talented student!) helped CUT&Tag and biochemistry. Adarsh helped testing KD. (11/n)
February 20, 2025 at 7:43 AM
Finally, this work is a great collaboration within the Tachibana lab!
🎉 Huge thanks to:
Chad for all bioinformatic analysis. Eda (a talented student!) helped CUT&Tag and biochemistry. Adarsh helped testing KD. (11/n)
🎉 Huge thanks to:
Chad for all bioinformatic analysis. Eda (a talented student!) helped CUT&Tag and biochemistry. Adarsh helped testing KD. (11/n)
This work represents technical culmination in my postdoc, combining embryology, genomics, biochemistry, and cryo-EM. Huge thanks to Kikuë and the fantastic core facilities at @MPI_Biochem ! (10/n)
February 20, 2025 at 7:43 AM
This work represents technical culmination in my postdoc, combining embryology, genomics, biochemistry, and cryo-EM. Huge thanks to Kikuë and the fantastic core facilities at @MPI_Biochem ! (10/n)
Taken togther, NR5A2 regulates the expression of KLF5 and GATA6, which in turn function as NR5A2 co-regulators to ensures robust gene activation through feed-forward loops. (9/n)
February 20, 2025 at 7:43 AM
Taken togther, NR5A2 regulates the expression of KLF5 and GATA6, which in turn function as NR5A2 co-regulators to ensures robust gene activation through feed-forward loops. (9/n)
Biochemical data further revealed that NR5A2 co-binds to nucleosomes with KLF5 and GATA6 in vitro, providing strong support that these pioneer factors simultaneously engage with chromatin to drive transcriptional activation in vivo. (8/n)
February 20, 2025 at 7:43 AM
Biochemical data further revealed that NR5A2 co-binds to nucleosomes with KLF5 and GATA6 in vitro, providing strong support that these pioneer factors simultaneously engage with chromatin to drive transcriptional activation in vivo. (8/n)
Surprisingly, Xist was down-regulated upon Nr5a2 KD. We found that NR5A2 regulates Gata1 and Gata6 expression and further binds Xist enhancers with GATA6, indicating that NR5A2 directly or indirectly regulates X-chromosome inactivation. Please also see www.nature.com/articles/s41... (7/n)
GATA transcription factors drive initial Xist upregulation after fertilization through direct activation of long-range enhancers - Nature Cell Biology
Through a CRISPR-activation screen, Ravid Lustig et al. show that GATA transcription factors activate long-range Xist enhancers to upregulate Xist expression and initiate X chromosome inactivation in ...
www.nature.com
February 20, 2025 at 7:43 AM
Surprisingly, Xist was down-regulated upon Nr5a2 KD. We found that NR5A2 regulates Gata1 and Gata6 expression and further binds Xist enhancers with GATA6, indicating that NR5A2 directly or indirectly regulates X-chromosome inactivation. Please also see www.nature.com/articles/s41... (7/n)
Perturbation of both Nr5a2 and Klf5 caused severe developmental defects compared to that of Nr5a2 alone, highlighting synergistic roles of NR5A2 and KLF5. Mechanistically, NR5A2 promotes chromatin accessibility and facilitates H3K27ac deposition in cooperation with KLF5. (6/n)
February 20, 2025 at 7:43 AM
Perturbation of both Nr5a2 and Klf5 caused severe developmental defects compared to that of Nr5a2 alone, highlighting synergistic roles of NR5A2 and KLF5. Mechanistically, NR5A2 promotes chromatin accessibility and facilitates H3K27ac deposition in cooperation with KLF5. (6/n)
Thus, NR5A2 acts upstream of these factors. Interestingly, these three TFs co-occupancy correlated with the gain of H3K27ac levels at the morula stage. We then addressed how NR5A2 functions together with KLF5 or GATA6. (5/n)
February 20, 2025 at 7:43 AM
Thus, NR5A2 acts upstream of these factors. Interestingly, these three TFs co-occupancy correlated with the gain of H3K27ac levels at the morula stage. We then addressed how NR5A2 functions together with KLF5 or GATA6. (5/n)
We determined NR5A2 chromatin binding profiles from 2-cell to morula stage and identified KLF and GATA families as potential NR5A2 co-regulators. Klf5 and Gata6 were highly expressed in later developmental stages with their expression partially regulated by NR5A2. (4/n)
February 20, 2025 at 7:43 AM
We determined NR5A2 chromatin binding profiles from 2-cell to morula stage and identified KLF and GATA families as potential NR5A2 co-regulators. Klf5 and Gata6 were highly expressed in later developmental stages with their expression partially regulated by NR5A2. (4/n)