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 cartoon says hey everybody an old man 's talking while bart simpson looks on ALT: a cartoon says hey everybody an old man 's talking while bart simpson looks on

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!

250 liters of DNA molecular weight ladder costs $171.93

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

Would love to be added!

Starter pack links dont seem to be working

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

Chance favors the (theoretically) prepared mind In defense of the role of theory in innovation

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...

Just quit Quitting projects in science is hard, but we should be doing a lot more of it.

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...

SET1/MLL complexes control transcription independently of H3K4me3 Histone H3 lysine 4 trimethylation (H3K4me3) at gene promoters is thought to play a central role in gene transcription. H3K4 methylation is deposited by the SET1 (A/B) and MLL (1-4) multi-protein comp...

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

👋 add me !

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

Single-cell susceptibility to viral infection is driven by variable cell states Not all cells that can be infected by a virus become infected with that virus. Single-cell clone tracing reveals intrinsic cell states with variable expression patterns that increase susceptibility to...

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

Thanks for highlighting the relevance to our prior work....Can't wait to see what more this line of discoveries leads to!

(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🧵👇

The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fate - Nature Cell Biology Marin et al. report the role of lamin proteins and the lamin B receptor (LBR) in chromatin positioning at the nuclear periphery. Knockout of all lamins and LBR in mouse embryonic stem cells leads to h...

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

Specificity, length, and luck: How genes are prioritized by rare and common variant association studies Standard genome-wide association studies (GWAS) and rare variant burden tests are essential tools for identifying trait-relevant genes. Although these methods are conceptually similar, we show by anal...

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...

...........

Global inhibition of deadenylation stabilizes the transcriptome in mitotic cells In the presence of cell division errors, mammalian cells can pause in mitosis for tens of hours with little to no transcription, while still requiring continued translation for viability. These unique...

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...

we are very interested using our recently developed combinatorial Cas12a CRISPRi platform. happy to chat!