Why can't we explain enhancer action despite 2 decades of chromosome conformation technologies? 😬 Our new study spearheaded by Leonid Mirny's group points to a flaw in our assumptions, and to a solution from physical principles By @timothyfoldes.bsky.social 💻& @karissalhansen.bsky.social 🧪 🧵👇

Our lab is proud to present our latest work harnessing Bridge Recombinase for genome-scale editing in diverse bacteria, microbiome editing, and programmable horizontal gene transfer.

Faculty search at the Institute for Human Genetics at UCSF. Come be my colleague! aprecruit.ucsf.edu/JPF06052

Excited to share our discovery of a new programmable RNA-guided DNA-targeting system hiding inside bacteriophages that predates CRISPR. We call it VIPR (Viral Interference Programmable Repeat), and it uses an entirely new logic to find its targets. Thread + link below.

Harvey Yang and I were fortunate to contribute polymer simulations to this paper from @nicholas-aboreden.bsky.social Zhao... Zhang, Blobel showing that most CRE loops can form de novo after mitosis without loop extrusion www.nature.com/articles/s41...

A short Bluetorial on plots of NIH application success rates as a function of percentile. 1/20

We are also considering postdoc candidates with deep perspectives on transcription factor / chromatin biology, and would like to tackle such topics using high-throughput synthetic biology approaches.

Been working on a really strange retron bacterial immune system, here's the preprint: www.biorxiv.org/content/10.1... Type VI retrons are unlike any other. Phage infection triggers reverse transcription of a DNA fragment that activates translation of a toxin to kill the infected cell.

Bay Area Chromatin Club today at UCSF Mission Bay. Great mechanistic talks from UCSF, Berkeley, Stanford, UCSC, and Genentech. High attendance, awesome posters, many great questions and interactions. (Photo credit to Active Motif, who generously support this awesome series). See you at the next one!

I am absolutely holding Fisher Scientific to what is printed on this order.

Delighted to see this published: H3K115 acetylation is associated with fragile nucleosomes at CpG island promoters and active regulatory sites. Great work from all contributors; Yatendra Kumar, @illingworth-lab.bsky.social @eliasfriman.bsky.social @helink.bsky.social doi.org/10.7554/eLif...

postdoc recruitment still open!

Thanks to New Scientist for coverage of exciting new work from Doudna Lab & first author Wayne Ngo — self-amplifying #GeneEditing for targeting hard-to-target organs like the brain. Read the article: https://ow.ly/fYu650YfseV Or the preprint: https://ow.ly/hfb850YfseT

新年快乐 happy new year!

Ucsf faculty search for a genome editing delivery expert, come be my colleague!

Sign on and share the letter honoring Dr. Jane Ying Wu's memory today! The deadline has been extended to Tuesday, Feb. 3rd at 12 pm ET. Join nearly 850 and help us reach 1,000. Let us be united, standing up for fairness, transparency, and dignity. Sign on: buff.ly/u656wy3

Blog post: Chance favors the (theoretically) prepared mind Data is big, machines are learning, so what good is theory anyway? Isn't most discovery driven by serendipity anyway, with theory mostly a "post-mortem"? I argue that this view discounts the value of theory. open.substack.com/pub/arjunraj...

Blog post: Just quit Quitting projects in science is hard, but we should be doing a lot more of it. open.substack.com/pub/arjunraj...

Excited to share our new preprint from the Klose lab, where we investigate how SET1/MLL complexes shape H3K4me3 and regulate transcription in mouse ES cells. www.biorxiv.org/content/10.6...

Updated job posting description for our postdoc recruitment to include interest in immuno-oncology

My lab at UCSF is recruiting postdoc candidates interested in CRISPR synthetic biology and functional genomics approaches to study and engineer tissue injury responses! hsiunglab.org

So awesome to have this great paper from Sam Reffsin and Sara Cherry out! In it, we use retrospective clone tracing to show that there are particular single cell states that are more susceptible to viral infection (both SARS-CoV-2 and flu)! www.cell.com/cell/fulltex...

biology is so cool because like every week someone is like "Dr. Smith is coming to campus! She is the world expert in blargyblarg!" And i'm like A) never heard of blargyblarg, B) look it up, it's super important and interesting

(3/n) Do mitotic microcompartments have a transcriptional function? Prior work from @chrishsiung.bsky.social Gerd Blobel discovered 'mitotic transcriptional spiking', where ~half of genes transcriptionally spike in mitosis. We now show that microcompartment dot number and strength predicts spiking

Really excited to share our latest work led by @mattiaubertini.bsky.social and @nesslfy.bsky.social: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication. www.biorxiv.org/content/10.1... A🧵👇

Another paper bluetorial! Today: how does the spatial location of genes influence their function? (1/n) www.nature.com/articles/s41...

What do GWAS and rare variant burden tests discover, and why? Do these studies find the most IMPORTANT genes? If not, how DO they rank genes? Here we present a surprising result: these studies actually test for SPECIFICITY! A 🧵on what this means... (🧪🧬) www.biorxiv.org/content/10.1...

New preprint! We solve a mystery you didn't know existed. Mitotic cells lack new transcription but require ongoing translation. Interphase mRNA half life is only 2-4 hrs. So how do cells arrest in mitosis for hours without depleting their transcriptomes? www.biorxiv.org/content/10.1...

EPIGENETIC HULK READY TO SMASH AGAIN! GET IN LOSERS!

#FragileNucleosome seminar happening tomorrow!

Looking forward to sharing our work in the #FragileNucleosome series!

We're still recruiting!

We've successfully recruited one postdoc. We are still looking to recruit one more postdoc especially candidates with wet/dry lab hybrid background in genome regulation and/or interests in functional genomics approaches in novel human tissue biology models.

Excited to share James Jusuf's preprint: By integrating Micro-C with SuperRes Live-Imaging we can calibrate genomics&imaging to perform absolute quantification of looping (e.g. this loop is present 3%) We quantify mESC 36k loops: <loops> are generally rare (2.3%) www.biorxiv.org/content/10.1...

Happy new year! Our lab (hsiunglab.org) at UCSF is moving forward to next stages in our search for postdoc candidates. The positions are still open -- if interested please apply soon!

A little fun with numbers on this Sunday, showing just how successful DNA really is. First, here's what DNA looks like. I'll draw your attention to the "rise" in DNA, that is, the distance between two basepairs, which is 3.4 Angstroms, also known as 3.4x10^-10 meters...

My lab at UCSF (hsiunglab.org) is looking to recruit multiple postdocs across the spectrum of wet/dry lab interests to contribute to our research in synthetic gene regulation, combinatorial genetics, and tissue biology (including liver biology and immuno-oncology).