Wataru Kobayashi

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...

NR5A2 overexpression improves SCNT efficiency and enhances ZGA by promoting H3K27ac deposition. Great work!

journals.plos.org/plosbiology/...

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!

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 …

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...

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...

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/...

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.

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.

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...

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....

Thank you very much!

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!

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.

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...

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

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.

Thank you, Ana!

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)

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)

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)

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 ...

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)

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)

We previously found that NR5A2 targets cell-type specific (putative) enhancers between 2-cell embryos (totipotency) and ESCs (pluripotency). We hypothesized that NR5A2 may cooperate with other TFs to control distinct transcriptional networks during totipotency-to-pluripotency transition. (3/n)

Nucleosome-bound NR5A2 structure reveals pioneer factor mechanism by DNA minor groove anchor competition - Nature Structural & Molecular Biology The authors determined a cryo-EM structure of the pioneer factor NR5A2 bound to a nucleosome. NR5A2 releases nucleosomal DNA from histones by DNA minor anchor groove competition, providing a mechanism...

NR5A2 is a pioneer transcription factor essential for pre-implantation development in mice. We recently reported that NR5A2 facilitates gene expression by unwrapping nucleosomal DNA through minor groove anchor competition. (2/n)
www.nature.com/articles/s41...

🚀Excited to share preprint as my last work in the Tachibana lab! Our study shows how the pioneer factor NR5A2 ensures robust gene activation through feed-forward regulatory loops with lineage-determining factors. A quick summary follows (1/n)
www.biorxiv.org/content/10.1...