Scott Berry

This fun project was driven by the talented and rigorous Alex Gillis @cftbla.bsky.social, in wonderful collaboration with Ana Tufegdžić Vidaković's @anatv.bsky.social lab!

@singmolsci.bsky.social
@unswrna.bsky.social

Hierarchical buffering of cellular RNA polymerase II pools maintains transcriptional homeostasis RNA polymerase II (Pol II) abundance and transcriptional output are coordinated across diverse conditions to maintain mRNA homeostasis. To determine whether Pol II acts as a limiting factor for transc...

What happens when you suddenly remove half of an essential enzyme from cells? 🤔

We watched in real-time as cells deploy multiple backup strategies to buffer against changes in RNA Pol II abundance.

Our lab's new preprint 👇

bit.ly/4pyPgax

Stalling of elongating Pol II triggers Ser7 phosphorylation in trans to drive transcription recovery DNA is scattered with obstacles that stall RNA polymerase II (Pol II) and block the production of full-length transcripts. Two mechanisms are known to resolve stalled Pol II: transcription-coupled nuc...

Happy to share a new preprint from our lab, uncovering "spooky action at a distance" - for RNA Polymerase II:
www.biorxiv.org/content/10.6...

🎉 𝙒𝙝𝙖𝙩 𝙖 𝙙𝙖𝙮! 🎉

On Thursday we held our inaugural EMCR Mini Symposium, bringing together six in-person nodes plus online attendees from across Australasia. It was fantastic to see our community come together to share science, build connections, and finish 2025 strong.

#EMCR #AEpiA #epigenetics

Oh! Would have been great to see you (I live in Wollongong now). But I am off to Korea tomorrow! Enjoy the gong. Hope the weather improves. 🤞

Optimised nanobody-based quenchbodies for enhanced protein detection - Communications Biology Optimised nanobody-based quenchbodies are developed through rational design and in vitro evolution, enabling improved protein detection with up to 2.4-fold fluorescence increase and 2 nM sensitivity f...

Optimised nanobody-based quenchbodies are developed through rational design and in vitro evolution, enabling improved protein detection with up to 2.4-fold fluorescence increase @haiboyu.bsky.social
@lisannes.bsky.social @molecularhorizons.bsky.social
www.nature.com/articles/s42...

🌟 𝐈𝐧𝐭𝐫𝐨𝐝𝐮𝐜𝐢𝐧𝐠 𝐄𝐌𝐂𝐑 𝐌𝐢𝐧𝐢 𝐒𝐲𝐦𝐩𝐨𝐬𝐢𝐮𝐦 𝐂𝐚𝐫𝐞𝐞𝐫 𝐏𝐚𝐧𝐞𝐥𝐥𝐢𝐬𝐭 – 𝐃𝐫 𝐋𝐮𝐤𝐞 𝐈𝐬𝐛𝐞𝐥 🌟

We’re excited to spotlight Dr Luke Isbel, one of our inspiring career development panellists for the upcoming Australasian Epigenetics Alliance 𝐄𝐌𝐂𝐑 𝐌𝐢𝐧𝐢 𝐒𝐲𝐦𝐩𝐨𝐬𝐢𝐮𝐦!

aepia.org.au/emcr-symposium

A purpose built solution to Australia’s biomedical funding crisis….. release the #MRFF = invest in our future scientists & their discoveries. #DiscoveriesNeedDollars www.smh.com.au/politics/fed...

The Asia RNA Club Symposium will be happening in Seoul in Nov 3-5, bringing together RNA scientists from the Asia-Pacific region. Excellent speakers and a great opportunity to connect! Abstract submission by Sept 5 asiarnaclub.org

Great list! Can I be added too please?

Research The immune system is a spatially distributed, whole-body sensory-reactive system that monitors, reacts, and adapts to various stress signals (e.g., tissue

We have some news to share: The Kueh lab is moving to ‪Yale this fall!‬ We will be joining the Yale Center for Systems and Engineering Immunology ‪@yalecsei.bsky.social‬ and the Department of Immunobiology.

medicine.yale.edu/systems-engi...

Extensible Immunofluorescence (ExIF) accessibly generates high-plexity datasets by integrating standard 4-plex imaging data Nature Communications - Gunawan et al. propose an Extensible Immunofluorescence (ExIF) strategy that integrates distinct 4-plex image panels from routine fluorescence microscopy into multiplexed...

Our #AI #research @natcomms.nature.com uses #multiomics data integration concepts to fuse 4-channel imaging data into unlimitedly multiplexed image datasets via generative deep learning to interrogate complex cell biology, like #EMT. Multiplexing made easy! rdcu.be/emtBc @singmolsci.bsky.social

Fantastic to see this short film about A/Prof Lawrence Lee who is a Group Leader in UNSW Single Molecule Science and the founding CEO of the exciting startup, SWAN Genomics 🧬🔬

Join our group (www.luginbuehllab.com) at @camplantsci.bsky.social! Are you excited about mycorrhiza, (single-cell) transcriptomics, carbon physiology, and the model crop rice? We have a 2-year postdoc position available, starting ASAP. Closing date 23rd May 2025!

www.jobs.cam.ac.uk/job/51214/

We have had multiple discussions about why people have not previously observed the very dramatic reduction in transcription upon PNUTS depletion. So I looked at our own TT-seq data and analysed it without including the spike-in. The numbers speak for themselves! Spike-in calibration is important!

Cartoon showing two people working at a conveyer belt which is processing Pol II complexes. Aberrant Pol II complexes are being removed from the conveyer belt and placed in recycling or rubbish bins. This represents the checkpoint formed by CRL3ARMC5 ubiquitin ligase and Integrator phosphatase which controls the quality and quantity of transcription complexes on genes.

Mechanism of quality control of gene expression revealed by @anatv.bsky.social & @scottbscience.bsky.social’s groups in study of Pol II molecules.
Read more about the work, led by Roberta Cacioppo, Alexander Gillis, Iván Shlamovitz & Andrew Zeller: www2.mrc-lmb.cam.ac.uk/newly-identi...
#LMBResearch

Was a pleasure working with @anatv.bsky.social on this!

Redundant pathways for removal of defective RNA polymerase II complexes at a promoter-proximal pause checkpoint The biological purpose of Integrator and RNA polymerase II (RNAPII) promoter-proximal pausing remains uncertain. Here, we show that loss of INTS6 in h…

Also take a look at complementary work from Jesper Svejstrup's lab:
sciencedirect.com/science/arti...

Thanks to support from @singmolsci.bsky.social @unswrna.bsky.social

When both ARMC5 and INTS8 are depleted, excess Pol II is released into genes but often fails to transcribe the full transcription unit, resulting in major gene expression changes. There is lots more in the paper, of course!

This finding pushed us to try to understand what stops Pol II from entering the elongation phase and actually making more RNA. We found that ARMC5 and Integrator phosphatase play complementary roles in this process.

ARMC5 also regulates Pol II levels during normal cell growth - seemingly responsible for around half the cell’s Pol II turnover. But the extra Pol II that accumulates in cells upon ARMC5 loss doesn’t lead to more Pol II in gene bodies: it is mostly in the free pool or in the proximal promoter.

However, using live-cell imaging and cellular fractionation, we found that this excess Pol II mostly accumulates off-chromatin.

It has long been known that Pol II is degraded when transcription is inhibited - either with small molecules or if specific cofactors are depleted. We now know the ubiquitin ligase responsible is CUL3-ARMC5. When we remove ARMC5, Pol II is no longer lost upon inhibition.

Building on our previous work on RNA concentration homeostasis doi.org/10.1016/j.ce..., we were interested to understand how global levels of Pol II are controlled. We teamed up with @anatv.bsky.social's lab who delve deep into mechanisms of ubiquitin-mediated regulation of the transcription cycle.

CRL3ARMC5 ubiquitin ligase and Integrator phosphatase form parallel mechanisms to control early stages of RNA Pol II transcription Cacioppo, Gillis, Shlamovitz, Zeller, et al. show that CRL3ARMC5 ubiquitylates RNA Pol II at early stages of transcription as part of a major homeostatic RNA Pol II turnover mechanism. CRL3ARMC5 and the Integrator phosphatase act as complementary pathways, monitoring the quantity and quality of RNA Pol II complexes before they are licensed into elongation.

📣 New paper from the lab!

In a fantastic new collaboration with @anatv.bsky.social lab, we characterise a major Pol II homeostasis pathway in human cells. Congratulations Roberta, Alex, Ivan, and Andrew.

www.cell.com/molecular-ce...

The PNUTS phosphatase complex controls transcription pause release Kelley et al. discover that the PNUTS phosphatase complex plays an essential role in gene transcription by controlling RNA polymerase II pause release. PNUTS achieves this through its TND, which recog...

Very excited that our paper describing a critical role for the PNUTS-PP1 phosphatase complex in transcription pause release is up online! This was a massive team effort with @edimitrova.bsky.social and the rest of the @robklose.bsky.social lab www.cell.com/molecular-ce... A short thread: (1/8)