CONCLUSIONS:
To promote the best science being done, we need to look at the incentives of science publishing and funding. Long-term funding produces better science. Short-term and topical agendas encourages irreproducibility.
Funding model organisms generates science we can build on! 🪰🪱🦠🐠🐁🐸
6/6 🧵
- We found the chromatin signal is predictive of the activity of transcription factors (master regulators of cell identity).
Our datasets and tools are available open-source. I think there are many interesting results worth a deeper follow-up to further understand embryonic development.
Very important work #epigenomics, as we almost never image the cells when performing CnR/CnT experiments
With @burgesslab.bsky.social, not one, but TWO freshly caught T2T zebrafish reference genomes for the Tübingen and AB strains 🎣 🎣 🎉
It's well known that genes in different cell types are "bookmarked" on the DNA via active or silencing epigenetic modifications. But how does this cell-type specific bookmarking and gene activity take shape, when all our cells originally come from the same single stem cell?
Using developing zebrafish embryos as a model system, our team went on to catch this epigenetic landscaping happening "in action", by applying an single-cell multiomics technology we call "whole-organism T-ChIC".
- We found that the chromatin "syncs-up" with gene activity as cells mature during embryo development.
- We saw a spreading and de-methylation dynamics of repressive chromatin that associate with switching off of developmental genes.
This project is part of my postdoc work in van Oudenaarden lab at @hubrechtinstitute.bsky.social. Big thanks to my co-authors and former colleagues: @agriffa.bsky.social, Peter Zeller, Helena Viñas Gaza & Alexander van Oudenaarden for their crucial contribution.
Our research work on using #singlecell co-mapping to study early embryonic development is now published: doi.org/10.7554/eLif....
A new #zebrafish reference genome assembly (GRCz12tu) has been posted at GenBank! Special thanks to @burgesslab.bsky.social, NCBI, and the GRC for their immeasurable work 🔥 It is not yet annotated, but that will be forthcoming. www.ncbi.nlm.nih.gov/datasets/gen... h/t Monte Westerfield on ZR! Slack
Vivek Bhardwaj
Mark A. Hanson
A robust and quantitative map links chromatin modification and gene expression of cells during zebrafish embryogenesis.
🎉 Excited to share our new preprint presenting a complete de novo assembly of the zebrafish genome; a major advance for zebrafish genomics and research! 🧬
Full paper: www.biorxiv.org/content/10.1...
@zebrafishrock.bsky.social @izfs.bsky.social @zfinmod.bsky.social @modelzebrafish.bsky.social
