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Wataru Kobayashi

@wkobayashi.bsky.social

PI at the University of Dundee / Wellcome CDA holder / Pre-implantation development / Genomics / TFs / Chromatin / Biochemistry / Cryo-EM Postdoc: MPIB, IMBA Ph.D: Waseda Univ. Lab website: https://sites.dundee.ac.uk/wataru-kobayashi-group/

32 Posts118 Follower168 Folgt
Karolin Luger@nucleosomepolice.bsky.social · 2mo ago

someone in the lab needs to use the PrepCell and apparently i am the last person to have used it 🙃. Needless to say there is a lot of sceptisism. But i have the receipts! Had to explain about degassing polyacrylamide, and analog recorders! lets see whether we can get this puppy to work.

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Wataru Kobayashi@wkobayashi.bsky.social · 5mo ago

I am excited to have been awarded a Wellcome Trust CDA fellowship. This award allows us to dissect the mechanistic basis for trophectoderm lineage commitment across scales, from atoms to embryos. I will start the recruitment for several positions. Stay tuned! www.dundee.ac.uk/news/wellcom...

Wellcome Career Development Awards awarded to Dr Wataru Kobayashi

Dr Wataru Kobayashi has been awarded £ 2.16M from the Wellcome Trust to study the earliest step of mammalian development

dundee.ac.uk

Wataru Kobayashi@wkobayashi.bsky.social · 6mo ago

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

Alicia Michael@aliciakmichael.bsky.social · 7mo ago

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!

Wataru Kobayashi@wkobayashi.bsky.social · 7mo ago

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...

Wataru Kobayashi@wkobayashi.bsky.social · 7mo ago

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...

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 …

sciencedirect.com

Wataru Kobayashi@wkobayashi.bsky.social · 8mo ago

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/...

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

Wataru Kobayashi@wkobayashi.bsky.social · last yr.

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....

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

Wataru Kobayashi@wkobayashi.bsky.social · last yr.

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.

Geoff Faulkner@faulknerlab.bsky.social · last yr.

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

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

Takaku Lab@takakulab.bsky.social · last yr.

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...

researchsquare.com