It’s a bit belated, but I am happy to share the latest work from our group, led by a very talented post doc in the lab, Tessa Popay @tessapopay with great support from the 4D Nucleome consortium, Rita Allen, and the Pew Biomedical Scholars.

The federal government’s demand of $1 billion from @UCLA would devastate the nation’s best public university, cut off life-saving care, halt tech and economic growth, and reduce educational access. Stand with UC to protect our students, staff, faculty and our vital mission:

1/10 Excited to share our latest - the first whole-body map of both DNA methylation and 3D genome at single-cell resolution.

Introducing RAEFISH, our lab's new flagship image-based spatial transcriptomics technology that simultaneously enables single-molecule spatial resolution and whole-genome level coverage of long and short, endogenous and engineered RNA species in cell cultures and intact tissues.

Lastly, the genes that fail to be established during mitotic exit are less affected when NIPBL is degraded in asynchronous cells, suggesting that loss of cohesin may be more impactful for establishing expression during mitotic exit rather than maintenance of expression.

During mitotic exit, loss of NIPBL affects the expression of ~500 genes, with a strong enrichment for genes linked to distal super enhancers. With prolonged NIPBL depletion the cells undergo obvious changes in their morphology and changes of epithelial-vs-mesenchymal identity.

What distinguishes these stable chromatin loops? The clearest determinant we can identify so far is chromatin state. One interesting class is associated with repressive H3K27me3 sites in the genome, and these can persist for hours in the absence of NIPBL.

While we are limited in terms of temporal resolution, we observe both chromatin loops that rapidly lost and loops that persist in the absence of NIPBL. The loops are cohesin dependent as they are lost if we degrade RAD21 and require NIPBL for their formation during mitotic exit.

Inspired by recent reports from Anders Hansen and Luca Giorgetti using imaging to show that loops persist for 5-20 minutes in vivo, we wondered whether all chromatin loops were equally as transient or if there were populations that could “persist” on chromatin without NIPBL.

In this study, we were interested in the role of NIPBL in regulating the dynamic formation of chromatin loops. NIPBL is essential for loop extrusion to occur in vitro, seemingly promoting the formation of chromatin loops before Cohesin is evicted from chromatin by WAPL.

Glad to share the peer-reviewed version of the @mgheffel manuscript now in @Nature. In collaboration with @lab_paredes , we studied the chromatin conformation and DNA methylation changes during human hippocampus and frontal cortex development.

Very excited and honored to be named a Pew Biomedical Scholar

📢 Calling all recent PhD or MD graduates 📢 Explore immunology frontiers from neuro-immunology to infectious disease, while launching your independent career! Benefit from a 5-year appointment, mentorship, and funding support @salkinstitute. Learn more: https://t.co/WnjwEOHydr

Thrilled to announce the launch of our pilot run for the inaugural DISCOVER Salk Postdoc Symposium, where we invite potential postdocs to visit @salkinstitute, meet faculty, take lab tours, join career development workshops and seed new collaborative opportunities that would be

In our first Fellow search, we hired @zhou_jingtian, a computational biologist at the forefront of studying the gene regulatory landscape of the mammalian brain. Come join Jingtian, @li_lingyin, @LukeGilbertSF, @SKonermann, @genophoria, and @BrianHie + our growing Arc community

It takes too long to start your own lab—the average R01 recipient is 42 y/o 😵. Want to start your independent research group out of grad school? Come to my @ArcInstitute Fellows Program info session next Wed (Nov 15, 12pm PT). You'll get a $250K/year research budget + salary.

Happy to report that this study is now out in Nature Communications https://t.co/r1NI2S41vC

.@Jesse_R_Dixon, Ye Zheng, Dong-Sung Lee & Zhi Liu discovered Foxp3 as the protein that determines regulatory #Tcells genome structure in mice–and that Foxp3 may be a good therapeutic target for regulating immunosuppression to treat #cancer @NatureComms https://t.co/3f4mTE9FN4

Attention Post-Docs!! We would love to invite you to The Salk Institute to give a talk about your research, meet Salk faculty, and create career-changing networks! The first ever Salk Rising Stars Symposium will be on April 10th. Apply here! Please RT! https://t.co/WX35cITcFp.

@zhou_jingtian joins as our first Science Fellow. Jingtian is a recent PhD graduate in Bioinformatics & Systems Biology from @UCSD and a former Salk Institute scientist. His pioneering work has developed new algorithms and insights into the epigenetic basis of brain development