Sudarshan Pinglay

nature.comWhy a synthetic human genome is still worth buildingA decade on from the launch of an ambitious project, it’s time to revisit the reasons for constructing a human genome from scratch.

How much of the human genome is essential? Two pieces out today from our lab: 1) a method to map essential genomic intervals at gigabase scale, and 2) an argument that it's time to consider synthesizing a minimal human genome. biorxiv.org/content/10.6... nature.com/articles/d41...

nature.comHighly multiplexed mammalian metabolic engineering with a shotgun approach - Nature BiotechnologyMetabolic engineering of mammalian cells is simplified and scaled by screening ‘shotgun’ modifications.

Excited to share Shotgun Genetic Engineering, developed by @julietrolle.bsky.social out now @natbiotech.nature.com! Read on to learn how Julie enabled mammalian cells to grow without 2 essential amino acids for the first time in >500 million years using highly multiplexed metabolic engineering!

Nature Biotechnology@natbiotech.nature.com

Highly multiplexed mammalian metabolic engineering with a shotgun approach - @sudpinglay.bsky.social @jefboeke.bsky.social www.nature.com/articles/s41...

nature.comWhy a synthetic human genome is still worth buildingA decade on from the launch of an ambitious project, it’s time to revisit the reasons for constructing a human genome from scratch.

pinglay-lab.comPinglay Lab

Looking forward to engaging further with the community on these ideas. If you're excited about working in these areas, we are hiring! www.pinglay-lab.com

huge thank you to all the co-authors and in particular, @jonaskoeppel.bsky.social and @jshendure.bsky.social for helping to lead this effort! also big thanks to @brotmanbaty.bsky.social, @biohub.org, NIH @genometdcc.org, NIH Common Fund and DARPA for funding!

nature.comWhy a synthetic human genome is still worth buildingA decade on from the launch of an ambitious project, it’s time to revisit the reasons for constructing a human genome from scratch.

2. Bio-manufacturing/bio-medicine: the vast majority of a CHO cell or CAR-T cell genome is not an asset but a liability: silenced viruses that can reactivate, transposons that drive instability, unexpressed DNA to maintain and the pull towards unwanted cellular states.

3. Genome synthesis: smaller genomes are cheaper and easier to synthesize. The first minimal genome built becomes the foundation every future synthetic genome can be built from, bringing the cost of every subsequent project down with it.

nature.comWhy a synthetic human genome is still worth buildingA decade on from the launch of an ambitious project, it’s time to revisit the reasons for constructing a human genome from scratch.

DNA synthesis, long-read sequencing, AI models for DNA design, and programmable methods for DNA delivery and integration, all of which are critical for genome design and synthesis have all come a long way since 2016. A minimal genome is the right target for a few reasons:

1. Fundamental biology: minimizing genomes reveals which combinations of genetic elements are sufficient to support the function of any cell. Importantly, any minimization is useful! We don't have to build the entire genome to learn something. We learn at each step.

nature.comWhy a synthetic human genome is still worth buildingA decade on from the launch of an ambitious project, it’s time to revisit the reasons for constructing a human genome from scratch.

We're excited to scale Shred-seq to saturating coverage, genome-wide and across multiple cell states, to fully map essentiality in the human genome. Knowing what's essential is the first step toward knowing what we'd actually need to build, which brings us to the second piece.

nature.comWhy a synthetic human genome is still worth buildingA decade on from the launch of an ambitious project, it’s time to revisit the reasons for constructing a human genome from scratch.

In a Nature World View, I mark the ten-year anniversary of GP-write, a project that set out to synthesize a human genome in cells. I argue that the conditions are right to try again, with a sharper target: a minimal human genome. www.nature.com/articles/d41...

nature.comWhy a synthetic human genome is still worth buildingA decade on from the launch of an ambitious project, it’s time to revisit the reasons for constructing a human genome from scratch.

Surviving deletions are depleted not just for known essential genes, but some non-coding regions as well, giving us a direct, annotation-agnostic measure of what's essential in the genome of one human cell line. We are able to put empirical bounds on dispensability of 50-96%!

We demonstrate that Shred-seq is compatible with single-cell RNA-seq readout, enabling deletions to be linked to more complex phenotypes across thousands of cells. This could provide the kind of training data for genomic AI models that Perturb-seq has for coding regions.

nature.comWhy a synthetic human genome is still worth buildingA decade on from the launch of an ambitious project, it’s time to revisit the reasons for constructing a human genome from scratch.

Shred-seq, led by the incredible @jonaskoeppel.bsky.social, couples CRISPR-Cas3 with phage polymerase genotyping to enable gigabase-scale deletion scans. We generated >36,000 overlapping deletions ranging from 100bp to 500kb, covering ~14% of the genome! bsky.app/profile/jona...

Jonas Koeppel@jonaskoeppel.bsky.social

1/n What fraction of the human genome is essential for cells? Excited to share our preprint that explores this question by combining an unusual CRISPR system, phage promoters, and thousands of deletion launchpads. @sudpinglay.bsky.social @jshendure.bsky.social www.biorxiv.org/content/10.6...

Sudarshan Pinglay reposted

Carl de Boer

@carldeboer.bsky.social

25 Feb

We wrote a perspective "How to build the regulatory genome: a constructionist guide to the cis-regulatory code", out in Development yesterday. Title says it all. Find it here: journals.biologists.com/dev/article/...

wd5.myworkdaysite.comResearch Scientist/Engineer 2, SeaHubJob Description The Department of Genome Sciences has an outstanding opportunity for a Research Scientist Engineer 2 to join the team. About this Opportunity Reporting to the Principal Investigator, t...

6 Feb

We are hiring a staff member to support various projects in our lab. Please reach out with questions! wd5.myworkdaysite.com/recruiting/u...

sciencedirect.comMammalian genome writing: Unlocking new length scales for genome engineeringThe ability to design and engineer mammalian genomes across arbitrary length scales would transform biology and medicine. Such capabilities would enab…

Happy to share that our review on mammalian genome writing with Jack Atwater, Ran Brosh, Jef Boeke, @jshendure.bsky.social and Matt Maurano is now out in @cellpress.bsky.social! www.sciencedirect.com/science/arti...

We also discuss current bottlenecks for mammalian genome writing (mainly throughput and size), mechanisms to address them, and future directions for the technology. We think it is particularly poised to revolutionize generating training data for genomic AI models.

t.cohttps://www.pinglay-lab.com/

if you are excited about these areas, come join our lab @uwgenome.bsky.social and the Seattle Hub for Synthetic Biology! We are hiring at all levels. t.co/wAehoBsJ5F

Engineering mammalian cells with large synthetic DNA payloads promises to be highly enabling for understanding mammalian gene regulation, dissecting GWAS haplotypes, engineering better animal models for human disease, and encoding multi-gene functions for cell therapy and biotech

Sudarshan Pinglay reposted

25 Oct 2025

Please 🔁! #MASSIV will be held in Vancouver from January 19-22, 2026. 4-day meeting on #synbio x #tissueengineering. Some trainee-focused events. >50 talks (10 from abstracts), posters, panel & publishing insights sessions. www.massivconference.com Abstract deadline: Nov 14

Sudarshan Pinglay reposted

@nobuhamazaki.bsky.social

18 Oct 2025

Please RP! A 4-day synbio and tissue engineering conference #MASSIV to transform biology and medicine together. Couldn't list all amazing speakers, so please check out this 👉https://www.massivconference.com/ Poster due is Nov 7, but will be extended. With @stemcellnetwork.ca and JST.

Sudarshan Pinglay reposted

Nobu Hamazaki

26 Sept 2025

New paper from my lab and @jshendure.bsky.social lab! Led by the brilliant @zukailiu.bsky.social and @cxqiu.bsky.social. We tackled how anterior and posterior progenitor cells cooperate to self-organize into an embryonic structure (termed AP-gastruloid). (1/n) www.biorxiv.org/content/10.1...

alleninstitute.orgJobsWe are working to solve the biggest mysteries in bioscience.

13 Aug 2025

We are hiring a scientist to lead our 'Build' team at the Seattle Hub for Synthetic Biology. @alleninstitute.org Job posting below: alleninstitute.org/careers/jobs... Please reach out if you have any questions!

Sudarshan Pinglay reposted

Abby Buchwalter

@abbybuch.bsky.social

21 July 2025

The nuclear lamina strengthens the nucleus and organizes the genome. So what happens when you acutely degrade it in living cells? Not what we thought! (1/n) www.molbiolcell.org/doi/10.1091/...

molbiolcell.orgLamin B1 and LAP2β resist cytoskeletal force to maintain lamin A/C meshwork organization and preserve nuclear integrity | Molecular Biology of the CellThe nuclear lamins are extremely long-lived proteins in most cell types. As a consequence, lamin function cannot be effectively dissected with temporal precision using standard knock-down approaches. ...

doi.orgA shotgun approach for highly multiplexed mammalian metabolic engineeringMammalian metabolic engineering is critical to advancing basic biology, bioproduction, and cell therapy. However, as pathway complexity increases, so does the size of both the combinatorial design spa...

Excited to share our work with @julietrolle.bsky.social & Jef Boeke. We developed a 'shotgun' method to screen millions of synthetic metabolic pathways to enable mammalian cells to grow without two essential nutrients for the first time in >500 million years! doi.org/10.1101/2025... Thread...

pinglay-lab.comPinglay Lab

A big thank you to all co-authors - looking forward to seeing where we can take this approach. If you are interested in joining us on this effort, check out our website: www.pinglay-lab.com

biorxiv.orgA shotgun approach for highly multiplexed mammalian metabolic engineeringMammalian metabolic engineering is critical to advancing basic biology, bioproduction, and cell therapy. However, as pathway complexity increases, so does the size of both the combinatorial design spa...

Here's a link to the preprint if you made it this far: www.biorxiv.org/content/10.1... any feedback would be highly appreciated!

SGE is generalizable across cell types. We engineer T-cells (Jurkat) to grow without valine. We believe a similar strategy could help create more resilient T-cells for therapy, capable of surviving and functioning in the metabolically depleted environments of tumors. Hopefully more here soon!

Finally, we demonstrate that data resulting from SGE is compatible with training predictive machine learning models. We are very excited about using SGE to generate the synthetic data needed to train the next generation of models for biological design.

Using SGE, we screened millions of pathway combinations in a single experiment to engineer CHO cells that grew at WT rate (~1.1 day/doubling) in valine-free medium. Intriguingly, the best clones all employed mitochondrial localization of pathway components, not cytoplasm as in our prev. design.

We then used SGE to engineer CHO cells to grow without isoleucine, a feat we could not achieve via rational design and delivery of entire synthetic pathways. Again, mitochondrial localization was favored, with individual clones reflecting ~40-50kb of integrated DNA!

As a test case, we used SGE to engineer essential amino acid prototrophy in mammalian cells, a behavior last seen over 500 million years ago. Unlike E. coli, which can make all 20 proetinogenic amino acids, mammals lack the pathways for 9 “essential” ones and must obtain them through the diet.

doi.orgResurrecting essential amino acid biosynthesis in mammalian cellsMammalian cells were engineered to synthesize valine, a metabolic capacity that had been lost from the lineage of higher eukaryotes for >500 million years.

In collaboration with Harris Wang’s lab, we previously engineered cells to grow without valine by importing 4 genes from E.coli. However, the cells grew 4x slower than normal - and we could not extend this strategy to enable any other amino acid prototrophies. doi.org/10.7554/eLif...

To address this, we developed Shotgun Genetic Engineering (SGE), which leverages the fact that building and delivering many small, barcoded transcription units - each with a gene, promoter and localization signal - is exponentially easier than delivering a single large construct to a mammalian cell.

In SGE, we clone and deliver a TU library at high MOI so that each cell gets a random mix, assembling a unique synthetic metabolic pathway per cell. Cells with the desired phenotype (e.g., survival or fluorescence) are selected, and TU barcodes are sequenced to identify functional combinations.

nature.comRange extender mediates long-distance enhancer activity - NatureThe REX element is associated with long-range enhancer–promoter interactions.

Mammalian metabolic engineering is key to advancing bioproduction, cell therapy, and rejuvenation. But as pathway complexity grows, so does the combinatorial design space! However, delivering large DNA constructs to mammalian cells is inefficient, making large unbiased screens intractable.

Sudarshan Pinglay reposted

Evgeny Kvon

@evgenykvon.bsky.social

2 July 2025

Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/

Sudarshan Pinglay reposted

20 June 2025

CAGT was fun! Thanks @carldeboer.bsky.social @sudpinglay.bsky.social and the de Boer lab for organizing! Folks from Seattle, Oregon, and other places. Great community. Arman gave a usual super talk, and Sanchit and Dayag won poster prizes☺️

Sudarshan Pinglay reposted

nature.comA multi-kingdom genetic barcoding system for precise clone isolation - Nature BiotechnologyA barcoded CRISPR base editing system isolates target clones from complex mammalian, yeast and bacterial populations.

21 May 2025

CloneSelect published in Nature Biotechnology @natbiotech.nature.com. This retrospective clone isolation method using CRISPR base editors is a powerful tool in broad biology. A history of Soh in the Yachie lab. www.nature.com/articles/s41...

Sudarshan Pinglay reposted

Dave Truong

@davidmtruong.bsky.social

11 Apr 2025

Need a site-specific, dox-inducible system for human cells? Low leakage, silencing-resistant, and modular? It’s here in the first paper from my lab, led by Tomoki Yanagi MD, PhD. Bonus: forward programming of TEC-like cells from hiPSCs. tinyurl.com/trunod01

tinyurl.comTermination sequence between an inducible promoter and ubiquitous chromatin opening element (UCOE) reduces gene expression leakage and silencing - Journal of Biological EngineeringBackground Inducible gene expression circuits enable precise control over target gene activation and are widely used in direct reprogramming. However, their usability is often compromised by DNA methy...

alleninstitute.orgJobsWe are working to solve the biggest mysteries in bioscience.

28 Mar 2025

We are hiring a person to join our team at the Seattle Hub for Synthetic Biology. Please share the word! Link to apply: alleninstitute.org/careers/jobs...

Sudarshan Pinglay reposted

Carl de Boer

@carldeboer.bsky.social

26 Mar 2025

Join us June 19-20, 2025 in Vancouver BC for the Cascadia Advanced Genomic Technologies meeting! Featuring Keynote speaker Calin Plesa @calin.bsky.social Abstract deadline April 30🔔, but registration is capped so don't wait! 😱 de-boer-lab.github.io/CAGT_meeting/

de-boer-lab.github.ioCAGT: Cascadia Advanced Genomic TechnologiesJune 19-20 2025, Vancouver, BC, Canada

de-boer-lab.github.ioCAGT: Cascadia Advanced Genomic TechnologiesJune 19-20 2025, Vancouver, BC, Canada

25 Mar 2025

Join us at the Cascadia Advanced Genomic Technologies conference in beautiful Vancouver this summer. Registration is FREE at the link below! de-boer-lab.github.io/CAGT_meeting/

youtu.beShuffling Mammalian GenomesYouTube video by GenomeTDCC

24 Feb 2025

Check out this video explainer of our recent paper on shuffling mammalian genomes. Thanks to Jeremy @genometdcc.bsky.social for putting this together!

GenomeTDCC@genometdcc.org

🧪🧬🖥️ #STS @sudpinglay.bsky.social describes how Genome-Shuffle-seq enables multiplex generation, mapping, and characterization of structural variants by leveraging barcoded "shuffle cassettes" with site-specific recombination and novel barcode pairings for genome-wide mapping 📽️ 👇 youtu.be/rW8AFhq1Pys

Sudarshan Pinglay reposted

Di Jiang

@dijiang319.bsky.social

1 Feb 2025

@science.org Genome recombination on demand | Science www.science.org/doi/10.1126/... a Perspective by @seczmarta.bsky.social Lars Steinmetz @stanford.edu on two studies bit.ly/4hzFRMg + bit.ly/4jyT4Hf that generate large genome rearrangements in mammalian cells @ unprecedented scale #synbio #genome

science.orgGenome recombination on demandLarge genome rearrangements in mammalian cells can be generated at scale