Surfin' NuRD

Drinking in The Dolphin. If you know, you know.

Developmental origins of paediatric cancer symposium A one-day event showcasing the latest cutting-edge research on the modelling, biology and treatment of paediatric cancers in the context of their developmental origins.

Abstract deadline extended to 20 March for our @cclguk.bsky.social @biologists.bsky.social-DMM
symposium on the developmental origins of paediatric cancers (8 June, @crick.ac.uk)-short talk slots still available.

See: www.cclg.org.uk/information-...

Please RT!

Figure 1.(A) Classical gel electrophoresis experiments showing mono-, di-, tri-, tetra-, and further multinucleosome bands upon chromatin digestion. (B) The nucleosome repeat length (NRL) is defined as the genomic distance between the centres of two neighbouring nucleosomes.

Figure 2.Nucleosome mapping using MNase-seq versus ATAC-seq. (A) In MNase-seq, nucleosomes in both open and tightly packed genomic regions are accessible to digestion. MNase preferentially cleaves DNA between nucleosomes and digests DNA until it encounters a histone octamer, which provides a footprint of nucleosome-protected DNA regions. (B) Bulk MNase-seq results in averaged maps across millions of cells, effectively capturing all possible nucleosome positioning configurations. (C) Single-cell MNase-seq (scMNase-seq) results in a noisier and sparser signal. The resulting footprints still represent nucleosome-protected regions, but not all nucleosomes are represented. (D) In ATAC-seq, open regions can be accessed by the enzyme Tn5 transposase, which can insert primers in regions free from the binding of nucleosomes and transcription factors (TFs). (E) For open chromatin regions, nucleosome maps can be obtained from ATAC-seq similar to MNase-seq. (F) Closed, tightly packed chromatin regions may be less represented in ATAC-seq nucleosome maps.

Figure 5.Molecular mechanisms affecting nucleosome spacing. (A) Linker histones H1 and nonhistone chromatin proteins which compete with H1s and modulate nucleosome spacing through structural and electrostatic mechanisms. (B) Chromatin remodellers actively reposition nucleosomes following context-dependent rules. (C) Cell state-dependent chromatin boundaries formed by CTCF and other structural proteins, as well as associated recruitment of chromatin remodellers which space nucleosomes. (D) Gene activity associated with remodeller action and RNA polymerases transcribing through the nucleosomes, leading to smaller distances between nucleosomes in regulatory regions and gene bodies. (E) DNA sequence repeats of different types.

Figure 6. Examples of NRL changes in biological systems. (A) Cell differentiation leads to NRL changes between different cell types, e.g. mouse dorsal root ganglia neurons (NRL ∼165 bp) versus cortical astrocytes (NRL ∼183 bp) [175]. Schematic cell shapes are adapted from an image created in BioRender (https://BioRender.com/89trj2t). (B) Paired normal versus tumour breast tissues show NRL shortening in cancer (figure adapted from [36] under the CC BY 4.0 licence (https://creativecommons.org/licenses/by/4.0/)). (C) Nucleosome positioning derived from cfDNA of human volunteers shows NRL increase with age (figure reprinted from [79] under the CC BY 4.0 licence (https://creativecommons.org/licenses/by/4.0/)).

Nucleosome aficionados! Our new review "Nucleosome spacing across cell types, diseases, and ages" is out in NAR: academic.oup.com/nar/article/...

A huge effort to pull together what we’ve learned about nucleosome spacing in many systems. Enjoy!
@milena-bikova.bsky.social @chrsclrksn.bsky.social

Incredibly proud to share our new preprint, lead by the Incomparable Rithika Sankar.
Here we temporally dissect the role of FACT in mES cells, finding that FACT loss drives progressive deterioration of chromatin architecture, leading to transcriptional collapse.
www.biorxiv.org/content/10.6...

Great to see our paper on light-intensity dependent swimming patterns in #Chlamydomonas out now in Phys Rev Lett. as an Editors' suggestion! With a nice commentary by @philipcball.bsky.social.

Chlamy actively modulate the beat planes of their #cilia!
journals.aps.org/prl/abstract... #protistsonsky

📢📢📢Lectureships at Bristol!📢📢📢

We're hiring 3 x lecturers (=assistant professor) in Biological Sciences, across the discipline.

Great department, great colleagues, great building, great city

Details here:
www.bristol.ac.uk/jobs/find/de...

child on ipad with headphones: maybe we should stop worrying about the screens kids are on adult driving looking at phone AND START WORRYING ABOUT THE SCREENS ADULTS ARE ON One thing leads to another.

Screen Time.

Good luck. 30 mins into my Zwift today I just felt like I couldn't be bothered. Before long 90 mins had passed and I felt much better.

But the coffee thing...man. That's rough!

Cheers Carla! Hope all's well witchoo.

Thanks Aleksander!

Thanks Kashyap!

Thanks Duncan!

Thanks Rob!

The chromatin remodeller CHD4 regulates transcription factor binding to both prevent activation of silent enhancers and maintain active regulatory elements CHD4 directly limits transcription factor binding to chromatin, which prevents activation of silent or cryptic enhancers but facilitates activity of active enhancers.

Our @elife.bsky.social reviewers were class:
informed, constructive, helpful reviews.

And Reviewer 3 is correct: I can’t be certain that things happening 30 mins post depletion are direct effects!

4/4.
elifesciences.org/articles/109...

You’ll miss a lot if you only focus on “peaks of enrichment”.

You’ll miss a lot if you only use ATAC-seq to assess accessible/inaccessible chromatin.
3/n

CHD4/NuRD removes fragile nucleosomes from active and inactive enhancers.
These activities serve to both promote activity of active enhancers and prevent activity of inactive enhancers. While it might have been known remodellers can both activate and repress for, we now show HOW THIS WORKS.
2/n

The chromatin remodeller CHD4 regulates transcription factor binding to both prevent activation of silent enhancers and maintain active regulatory elements CHD4 directly limits transcription factor binding to chromatin, which prevents activation of silent or cryptic enhancers but facilitates activity of active enhancers.

Final version of our paper now published.
elifesciences.org/articles/109...

Take homes:
CHD4/NuRD directly limits transcription factor residence times. At active enhancers this keeps them working efficiently. At inactive enhancers it prevents TFs from getting a foothold and causing activation. 1/n

Rack of 1.5 ml tubes with smiles in their bug cultures

Doing happy mini preps today.

Wait until they find out what solutions im about to put in them.

Potholes are not the problem – it’s our obsession with cars We need a shift away from thinking that using these vehicles is the only way to get around

www.telegraph.co.uk/news/2026/01...

Tour de France reveals plans for six UK stages with historic 2027 Grands Départs Men’s race will visit Edinburgh, Carlisle, Keswick, Liverpool, Welshpool and Cardiff, while women will head from Leeds to Manchester, then to Sheffield and also includes a central London stage

Once again I'm more than happy to accept invitations to talk in Edinburgh and the North of England in July 2027. In fact, let's get a group together to tour all of these towns. Who's in? #TourdeTourdeFrance

www.theguardian.com/sport/2026/j...

Exeter named one of the worst UK cities for traffic It confirms what many motorists stuck on Exe Bridges or Bridge Road have long thought

Is it LTNs? No wait! Bike Lanes, right?

Of course it can't be due to TOO MANY FEKKIN CARS!

Source: Devon Live
search.app/XxSnu

‘Oh my gosh, they’re all from London and Cambridge’: York University’s northerners fight back Lucy Morville, from Burnley, thought most students would be from the north and felt ‘culture shock’ surrounded by southerners

What an absurd article. I'm all for preservation of and education about local cultures, but if you go to a world class Uni like York, don't be surprised if the student population is made up of a large number of people from outside Yorkshire.
www.theguardian.com/education/20...

Poster featuring an illustration of three bikes in different colors with the text, "This Year ride a bicycle."

Here's an idea for 2026...

And time for a Japanese Negroni. Thanks, Maya!

Not for me. Was doing fine then got Whammed 3x in one day at the weekend. Not enough shopping online I guess.

Oh my giddy aunt this is amazing. I'm in awe of the avocado.

Check it, kids.

@anzymiller.bsky.social has taken dTAG-mediated protein expression control to the next level.

Pre-sunrise above Exeter Cathedral.

Morning, kids.

What, after hours of listening to that playlist I'm still good? I assumed i was more than WHAMMED.