Zukai Liu

A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording - Nature Biotechnology Prime editing in mammalian cells benefits from a comprehensive list of genetic parts.

A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording - @jshendure.bsky.social @troymcdiarmid.bsky.social @uwgenome.bsky.social go.nature.com/49eTPCu

Stoked to share our latest work entitled: “Large-scale discovery of neural enhancers for cis-regulation therapies”

shorturl.at/H3Qww

This is an enormous team effort that I had the honour of spearheading with Nick Page and Florence Chardon.

Bluetorial below.

Thrilled to share I’ve started my lab at Dartmouth’s Geisel School of Medicine! We focus on mapping cellular trajectories & TF networks in development and Mendelian disorders, exploring new therapies. Join us—postdocs, grads, and scientists welcome! sites.dartmouth.edu/qiulab/

Super excited about first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to the brilliant Chase Suiter (not here) & @greenahn.bsky.social on the work! Preprint here:
www.biorxiv.org/content/10.1...

Dual-patterned pluripotent stem cells self-organize into a human embryo model with extended anterior-posterior patterning Human gastruloids are a powerful class of stem cell derived models that recapitulate key features of early embryonic development, including symmetry breaking and the emergence of three germ layers. Ho...

Thank you for pointing this out! Absolutely amazing work on the mouse HAP gastruloids! We updated our preprint here www.biorxiv.org/content/10.1...

Gag proteins encoded by endogenous retroviruses are required for zebrafish development | PNAS Transposable elements (TEs) make up the bulk of eukaryotic genomes and examples abound of TE-derived sequences repurposed for organismal function. ...

💥🥳 At long last, our latest paper is out!

Gag proteins of endogenous retroviruses are required for zebrafish development

www.pnas.org/doi/10.1073/...

Led heroically by Sylvia Chang & @jonowells.bsky.social

A study which has changed the way I think of #transposons! No less! 🧵 1/n

4/n This is absolutely a teamwork and it would not be done without the support from Robson Lab and Cell Engineering Lab at JAX. My deepest gratitude goes to my mentor @paulrobson.bsky.social for his amazing guidance, support and encouragement along this journey!

3/n As an example of EvoDevo, the ExMC only shows up in peri implementation embryos in apes not in other mammals, making it difficult to be studied. Our hiPSC-based model not only uncovered the molecular basis of this species difference, but provide a powerful tool to study human ExMC.

2/n as a young TE, LTR2B was evolved 40 million years ago with around 300 copies across human genome. Then we precisely deleted a single copy of LTB2B and found it is sufficient to down regulate the expression of ANKS1A, a key marker of human ExMC and thus impair the cell specification.

1/n Wondering how transposable elements shape the evolution of cell lineage specification in embryogenesis? Please check this out! We found that human specific LTR2B can be bound by HAND1, transcribed and spliced into neighboring genes, most of which are human specific ExMC marker genes.

Great work from @zukailiu.bsky.social defining the first mesenchymal cells in human development as trophoblast-derived, and adding to the examples of evolutionary co-option of viral sequences contributing to our uniquely ape/human features. #hiPSC #MorPhiC #EvoDevo
doi.org/10.1016/j.ce...

Our genome encodes > 7000 microproteins that have been previously ignored in genome annotations. How do these microproteins impact tissue function? Here, we use an in vivo single-cell CRISPR screen to systematically explore microprotein function in the mouse epidermis. 1/9

I can highly recommend the YEN 2025 meeting for students and postdocs working on 'anything embryo' - a fantastic meeting organized by students and postdocs for you!

Brief PSA for the functional genomics community: if you are profiling complex libraries with >1 internal components (e.g., enhancer+barcodes in MPRAs) delivered via AAVs, be aware that there might be substantial unlinking within your libraries if you packaged as a pool! doi.org/10.1101/2025...

Wonderful work! Congrats, Ryan!