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Josh Brickman

@josh-brickman.bsky.social

Developmental and Stem Cell Biologist, interested in all things gene regulation. Transcription, lineage specification, potency and plasticity.

29 Posts963 Follower942 Folgt
Josh Brickman@josh-brickman.bsky.social · 12mo ago

Very happy to see this nice collaboration with @niakanlab.bsky.social bear fruit. Beautiful work by @clairesimon.bsky.social culturing human embryos in the presence of FGF/ERK stimulation/inhibition. www.nature.com/articles/s41...

Suppression of ERK signalling promotes pluripotent epiblast in the human blastocyst - Nature Communications

The authors show human embryo lineage specification in the blastocyst is driven by differential FGF/ERK signaling, which segregates yolk sac-fated hypoblast and embryonic epiblast. They establish naïv...

nature.com

Josh Brickman@josh-brickman.bsky.social · last yr.

Why combat aging with enhancers at 11? Why not just make 10 louder? It wouldn't be 11. For transcription, all the other processes (translation, splicing etc) are on ten, on ten, etc…where do they go? For Enhancers, everything on ten, the transcription factors deacetylate and go one higher, 11.

The EMBO Journal@embojournal.org · last yr.

Issue 11 N&V: fibroblast dynamics during mammary oncogenesis RIPK1 oligomers at core of CD95 necrosomes Autophagosomes as hub for AKAP regulation of neuronal PKA Centipede neurotoxin reveals new mode of Nav channel modulation Cover: @josh-brickman.bsky.social et al www.embopress.org/toc/14602075...

This cover highlights the article Altering metabolism programs cell identity via NAD+-dependent deacetylation by Robert A. Bone, Joshua M. Brickman and colleagues. The front cover illustration depicts an audience of embryonic stem cells consuming galactose, silencing background epigenetic noise, so that they can better “hear” the signal from the “Transcription Factors”. The band (key transcription factors) are deacetylated (their leather jackets are removed) by sirtuins (the roadies) to amplify the lineage-specific enhancer signal, at the same time as deacetylation of histones to reduce the availability of non-specific enhancer sequences. The state of both lineage-specific and non-specific “Enhancers” is indicated by their output (via the amplifier). The net result is that cellular instructions are better discernable, and the audience becomes energized. Cover concept by the authors, scientific illustration by SciStories
Josh Brickman@josh-brickman.bsky.social · last yr.

Very nice paper - all principles at the heart of molecular biology although the logic with which evolution implements them was a mystery.

Lars Velten@larsplus.bsky.social · last yr.

Out in Cell @cp-cell.bsky.social: Design principles of cell-state-specific enhancers in hematopoiesis 🧬🩸 screen of fully synthetic enhancers in blood progenitors 🤖 AI that creates new cell state specific enhancers 🔍 negative synergies between TFs lead to specificity! www.cell.com/cell/fulltex... 🧵

Josh Brickman@josh-brickman.bsky.social · last yr.

Alba Redo Riveiro - an amazing PhD student. One chapter in her PhD is described here. It was a great paper and a very long evolving story - www.cell.com/stem-cell-re...

Transcription factor co-expression mediates lineage priming for embryonic and extra-embryonic differentiation

Brickman and colleagues show that an unsegregated ICM-like population arises spontaneously in naive ESC culture in KOSR media. These cells resemble the E3.5 ICM and can contribute to both epiblast and...

cell.com

Stem Cell Reports@stemcellreports.bsky.social · last yr.

The Stem Cell Reports Best Of 2024-2025 issue is out now! Read the full issue to explore the most notable papers published over the last year. stemcellreports-bestof2024-2025.elsevierdigitaledition.com @isscr.org @cellpress.bsky.social @gairdnerawards.bsky.social @sickkidsvs.bsky.social

Josh Brickman@josh-brickman.bsky.social · last yr.

How does metabolism act through generic chromatin modifiers promote specific cellular states? Simultaneous modification of transcription factors and chromatin, enhancing epigenetic signal to noise ratios. www.embopress.org/doi/full/10....

Altering metabolism programs cell identity via NAD+-dependent deacetylation | The EMBO Journal

imageimageHow alterations in cell metabolism translate into specific developmental gene programs remains a major question. This study shows that forcing OXPHOS metabolism reprograms mouse embryonic stem cells (ESCs) to a more inner cell mass (ICM)-...

embopress.org

Josh Brickman@josh-brickman.bsky.social · last yr.

Really looking forward to a day in Sheffield - one of the first places In the world to work with human pluripotent cells!

Development, Regeneration and Neurophysiology@drn-sheffield.bsky.social · last yr.

Today we welcome Josh Brickman @josh-brickman.bsky.social from reNEW at the University of Copenhagen, who will present his work on transcription factors and cellular memory. Alfred Denny Conference Room, 1 pm. All welcome! Host: Anestis Tsakiridis @tsakiridis.bsky.social

Bart Deplancke@bartdeplancke.bsky.social · 2y ago

Superb work by Wouter @Zouters & @OlgaPushkarev developing ChromatinHD, two scale-adaptive #machinelearning models & interpretation tools that use #scRNAseq + #scATACseq data to better understand how chromatin accessibility relates to gene expression doi.org/10.1038/s414... Happy 2025 everyone 🎆 !

ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning - Nature Communications

Functional chromatin changes occur at different scales. Here, the authors introduce ChromatinHD, a method that characterises differential and predictive chromatin accessibility changes in a scale-adap...

doi.org

Josh Brickman@josh-brickman.bsky.social · 2y ago

Browsing through the literature as things calm down, thinking about posting now that the twittersphere has turned blue, I discover the next step change in chromatin analysis....an incredible data deluge! www.nature.com/articles/s41...

ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics

ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...

nature.com