Clemens Mauksch (he/him)

ATP-dependent remodeling of chromatin condensates reveals distinct mesoscale outcomes Adenosine triphosphate (ATP)–dependent chromatin remodeling enzymes mobilize nucleosomes, but how such mobilization affects chromatin condensation is unclear. We investigate effects of two major remod...

Today I am so pleased to present our work on how chromatin remodelers affect mesoscale chromatin organization.
www.science.org/doi/10.1126/...

Neues Polizeigesetz in Berlin: „Abkehr von der grundrechtsfreundlichen Politik“ Die schwarz-rote Berliner Landesregierung bastelt an einem neuen Polizeigesetz, das mehr Videoüberwachung, Staatstrojaner und viele weitere Befugnisse für die Polizei bereit hält. Dafür gab es…

Gesetzesnovelle von 700 Seiten: Grundrechtsfreundliche Politik vorbei. Nun biometrische Massenüberwachung & #Staatstrojaner für Polizei Berlin netzpolitik.org/2025/neues-p...

How do flexible regions of histone chaperones team up to handle histones? Together with Fred Winston’s lab
@harvardmed.bsky.social, we reveal new insights in our study just out in Mol Cell. Hats off to James Warner and Vanda Lux @iocbprague.bsky.social for their key contributions! dlvr.it/TNB145

Functional maps of a genomic locus reveal confinement of an enhancer by its target gene Genes are often activated by enhancers located at large genomic distances, and the importance of this positioning is poorly understood. By relocating promoter-reporter constructs into thousands of alt...

✨Exciting news: the main story of my PhD is out in Science!

Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation.

📖 Read the full story here: www.science.org/doi/10.1126/...

Functional maps of a genomic locus reveal confinement of an enhancer by its target gene Genes are often activated by enhancers located at large genomic distances, and the importance of this positioning is poorly understood. By relocating promoter-reporter constructs into thousands of alt...

Functional maps of a genomic locus reveal confinement of an enhancer by its target gene

www.science.org/doi/10.1126/...

Kinetic organization of the genome revealed by ultraresolution multiscale live imaging Genome function requires regulated genome motion. However, tools to directly observe this motion in vivo have been limited in coverage and resolution. Here we introduce an approach to tile mammalian c...

Congrats to my friends in the Boettiger lab for this really beautiful live imaging work. A big leap forward in understanding the dynamic side of genome organization. www.science.org/doi/10.1126/...

Grafik, welche die Entwicklung der Vermögensverteilung in Deutschland seit 2010 zeigt. Der Anteil des Vermögens der oberen zehn Prozent am Gesamtvermögen steigt kontinuierlich an. Aktuell besitzen die oberen zehn Prozent der Bevölkerung 11,4 Billionen Euro, die unteren 50 Prozent lediglich 0,48 Billionen Euro (Stand: 1. Quartal 2025, Quelle: EZB).

In kaum einem Land ist Vermögen so ungleich verteilt wie in Deutschland. Die reichsten zehn Prozent der Bevölkerung besitzen sagenhafte 11,4 Billionen Euro – und werden immer reicher. Sparen aber will die Regierung bei den Ärmsten.
www.t-online.de/nachrichten/...

PhD position in Gene Regulation Are you excited about studying the crucial process of transcription? Join our supportive, young and growing team!

As part of this grant, I have a vacancy out for a PhD student to join our super nice team. It closes on September 9 (Tuesday).
If you are or know a good prospective PhD student, excited about studying transcription, please (suggest them to) apply here: www.uu.nl/en/organisat...

Our new preprint is out!
We combined single-nucleosome imaging and 3D-SIM to reveal:
🔹 Euchromatin forms condensed domains, not open fibers
🔹Cohesin loss increases nucleosome mobility without decompaction
🔹Cohesin prevents neighboring domain mixing

Full story & movies👇

YouTube video by SWR Wissen Was ihr noch NICHT über den Eisprung wusstet! | SWR Wissen

Tabea Marx from the Department of Meiosis @schuhlab.bsky.social talks about the group’s ovulation research in the new SWR Wissen video (in German)! Why is ovulation research so challenging for scientists? What did the team find out? Watch the video to learn more👇
www.youtube.com/watch?v=UDz-...

Oscillatory pattern of chain extension and nucleosome self-association with variation in protein-free DNA linker length in simulated nucleosome-decorated DNA chains. Regular structures bearing 15 nucleosomes constructed from the mean rigid-body parameters between successive base pairs; nucleosomal cores depicted as wedge-shaped objects and color-coded to highlight the two- and three-start organization of the structures. Nucleosomal DNA constrained to the 147-bp pathway found in the best-resolved core particle structure, pdb_id 1kx5

Distortions in the average structures of simulated nucleosome-decorated DNA chains introduced by changes in the positioning of a singe nucleosome. A. Local opening and unpacking of a compact array introduced by a single 2-bp increment in the spacing between nucleosomes. B. Kinking of an extended array by a single 5-bp increment in nucleosome spacing.

Effects of the nucleosomal DNA pathway on the average configurations of simulated 12-nucleosome arrays. Average structures bearing the undertwisted DNA found in the best-resolved core particle structure, pdb_id 1kx5, compared to the overtwisted DNA found in the RCC1-nucleosome complex, pdb_id 3mvd. The regulatory protein is not included in the simulations. Upper views looking perpendicular to the chromatin axis and lower views down the axis

Molecular 'snapshots' illustrating the potential effects of chain length and nucleosome positioning on large-scale chromatin folding. A. Smoothly deformed array of 78 nucleosomes with uniform 177-bp spacing. B. 77-nucleosome chromatin 'copolymer' containing three stretches of nucleosomes with different spacings: a compact array of 26 nucleosomes (deep brown) with 172-bp spacing at the 5́-end of the chain; an extended array of 26 nucleosomes (light brown) with 177-bp spacing in the middle; an opened array of 25 nucleosomes (yellow) with 207-bp spacing and a nucleosome-free gap at the 3́-end of the chain. Note the more pronounced junction between ‘helical’ stretches when the spacing changes by roughly a half turn of DNA (172 – 177 = –5 bp) than when altered by a multiple of the double-helical repeat (207 – 177 = 30 bp). The presence of a nucleosome-free gap, within the stretch of nucleosomes spaced at 207-bp intervals, enhances the flexibility of the modeled structure, allowing the chain to bend in various directions

Contributions of local structural and energetic features of DNA to large-scale genomic organization [perspective by Wilma Olson & Co) www.sciencedirect.com/science/arti...

MLL2 facilitates long-range gene regulation through LINE1 elements Transcriptional regulation is tightly linked to chromatin organization, with H3K4me3 commonly marking both active and bivalent promoters. In embryonic stem cells (ESC), MLL2 is essential for H3K4me3 d...

#Preprint alert! 📣

We are thrilled to share the work led by Lara Zorro-Shahidian and Lucio di Filippo, in which we show that #MLL2 controls gene expression in both #ESC and upon #differentiation by facilitating the #enhancer like activity of #LINE1 elements

www.biorxiv.org/cgi/content/...

Synthetic engineering demonstrates that synergy among enhancers involves an increase in transcriptionally productive enhancer-gene contacts Enhancers are non-coding cis-regulatory elements that control the expression of distally located genes in a tissue- and time-specific manner. Recent studies indicate that enhancers can differ in their...

Excited to share the latest work from the lab led by @eharo84.bsky.social, in which we have used synthetic biology to explore the mechanisms by which different types of long-range enhancers ensure robust and precise developmental gene expression

www.biorxiv.org/content/10.1...

A novel deep learning-based framework reveals a continuum of chromatin sensitivities across transcription factors The genome-wide binding of many transcription factors (TFs) depends not only on the presence of their recognition motifs, but also on the surrounding chromatin context. This raises the question of how...

Excited to share our latest preprint. www.biorxiv.org/content/10.1.... Lead by Lukas, we investigated multiple ways of assessing a TF's sensitivity to chromatin based on genome-wide binding profiles. The developed methods allowed us to quantify chromatin sensitivity across tested TFs.

Excited to see this published with additional data following our preprint a while back. Cool combination (in our biased view) of controlled TF expression and machine learning to decode chromatin sensitivity. www.sciencedirect.com/science/arti....

Group Leader - Genome Biology Unit Are you ready to lead groundbreaking research in Genome Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group addressing exciting and original biological...

To all post-docs: The Genome Biology dept ‪@embl.org
has an Independent faculty position. Fantastic place to set up your lab –great package: core funding, fantastic Ph.D. students, cutting edge core facilities & great colleagues. Closing date Sept 19th
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...

cFOOT-seq maps chromatin accessibility, nucleosome occupancy, and TF footprints A. Schematic of the cFOOT-seq workflow. After cell permeabilization, dsDNA deaminases (blue) convert cytosine to uracil in accessible chromatin DNA (blue lines), but DNA occupied by nucleosomes or transcription factors (TFs) (gray lines) remains unconverted. The profile of DNA conversion rate defines nucleosome occupancy and TF footprints.

Wang et al, 2025. Genome-Wide Investigation of Transcription Factor Occupancy and Dynamics Using cFOOT-seq www.biorxiv.org/content/10.1...

Epigenetic priming of mammalian embryonic enhancer elements coordinates developmental gene networks - Genome Biology Background Embryonic development requires the accurate spatiotemporal execution of cell lineage-specific gene expression programs, which are controlled by transcriptional enhancers. Developmental enha...

🚨 New paper alert 🚨
I am excited to share our new work on epigenetic enhancer priming in early mammalian development
genomebiology.biomedcentral.com/articles/10....
Fantastic collaboration with Wolf Reik’s team, with key contributions from many others, led by the excellent Chris Todd.
Short 🧵

How do chromatin remodelers use #IDRs to find TF binding partners? In our new Molecular Cell paper, we show that β-catenin is an adaptor that links SWI/SNF (cBAF) subunit ARID1A with binding partners via IDR-domain interactions.
www.cell.com/molecular-ce...

🎉 Join us at the upcoming GfG Symposium "Epigenetics & Chromatin" in Giessen, Sept 24–26, 2025!
Amazing speakers, low registration fee, € 300 prizes for best poster & short talk, + free GfG membership for non-members.

Please RT!

express.converia.de/frontend/ind...

Our paper is now out in Molecular Cell!

Check the thread in this former post:

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

The evolution of high-order genome architecture revealed from 1,000 species www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/xjtu-omics/H...

I'm proud to announce the latest release of 🧬 #Oxbow 🏹, with new features to make NGS data analysis more powerful, efficient, and "composable".

Learn more at: oxbow.readthedocs.io

(1/n) New preprint from @claricehongky.bsky.social
Fan Fang Varshini Ramanathan in collab w Jie Liu.

Q: How do we get ultra-high-res 3D genome maps?

A: New deep learning model, Cleopatra.

Cleo trains on Micro-C, fine-tunes on RCMC, and predicts genome-wide 3D maps at ultra-high resolution.

PSA: We just finished processing nearly all public ATAC-seq datasets from SRA (about 22,000 datasets). (Not?) Surprisingly, we had to throw-out nearly ~50% because they were low-quality (low signal-to-noise, duplicate rate, etc.). Check quality before analysis (TSS-enrichment is not sufficient!).

Single-cell Micro-C profiles 3D genome structures at high resolution and characterizes multi-enhancer hubs - Nature Genetics scMicro-C is a new method that provides high-resolution maps of the 3D genome. scMicro-C identifies structures called ‘promoter stripes’, which link a gene promoter to multiple downstream enhancers.

📢OUT TODAY @natgenet.nature.com

📰Single-cell Micro-C profiles 3D genome structures at high resolution and characterizes multi-enhancer hubs.

By Honggui Wu, @Xiaoliang Sunney Xie and colleagues.

⬇️

www.nature.com/articles/s41...

Image of Marie Sklodowska-Curie together with the text "€404.3 million to support postdoctoral researchers". The image of Sklodowska-Curie is in brown monochrome like an old photo and superimosed are modern images of four people, presumably postdoctoral researchers, in colour. They are holding rucksacks and walking down a corridor with arches and pillars, presumably a university or research centre.

Are you ready to boost your research career? Apply with @uniGoettingen for an #MSCA postdoctoral fellowship!

We’ll gladly support your application, so get in touch asap: www.uni-goettingen.de/en/671766.html

#EarlyCareerResearcher #PostdocCareers #Mobility #WeAreInternational Deadline 10 Sept.

It sounds hyperbolic, I know, but I genuinely believe that wikipedia incorporating LLM-produced article summaries, or sanctioning LLM-produced articles, would signal the end of the internet as we've known it.

URGENT: FlyBase has lost practically all its funding overnight; even user fees are tied up in denied grant funding. 🤬🤯

Any lab using @flybase.bsky.social please donate using the link in post below.

This incredible community, on whose backs our #Drosophila labs depend, can't be left out to dry.

We currently have a call for support that has gone out to European labs, to support FlyBase-UK. We are asking our colleagues from labs in the US and other countries to wait for a similar call to them that will go out in the near future, to support the US sites. We thank you for your patience.