Charlotte Soneson @csoneson

Remodeling Activity of ChAHP Restricts Transcription Factor Access to Chromatin Transcription in eukaryotes is regulated by chromatin-based mechanisms that control nucleosome occupancy, chromatin modifications, and transcription factor binding. We have previously shown that the transcription factor ADNP forms the ChAHP complex with the chromatin remodeler CHD4 and HP1 proteins, acting as a site-specific regulator of transcription and antagonist of CTCF binding. However, the molecular basis of these functions remained unclear. Here, we demonstrate that the CHD4 subunit is essential to antagonize CTCF and silence transcription of transposons, while HP1 proteins are dispensable. Although the remodeling activity of CHD4 is not required for ChAHP chromatin association, it is critical for both transposon repression and CTCF antagonism. Our findings support a model wherein ADNP recruits chromatin remodeling activity in a sequence-specific manner, enabling transcriptional control and local modulation of chromatin architecture. ### Competing Interest Statement The Friedrich Miescher Institute for Biomedical Research (FMI) receives significant financial contributions from the Novartis Research Foundation. Published research reagents from the FMI are shared with the academic community under a Material Transfer Agreement (MTA) having terms and conditions corresponding to those of the UBMTA (Uniform Biological Material Transfer Agreement). Novartis Research Foundation, n.a. Swiss National Science Foundation, grant 310030_188835

preprint alert: www.biorxiv.org/content/10.1...

06.07.2025 11:55 — 👍 41 🔁 10 💬 1 📌 2

EuroBioC2025 late-breaking poster abstract submission Please fill the form below before the end of Friday July 11th, 2025, to submit an abstract for a poster to be considered for presentation at EuroBioC2025 in Barcelona on September 17-19, 2025…

📣 Late-breaking poster call for #EuroBioC2025 is now open!

Submit by July 11 to present your work in Barcelona this September.
🔗 forms.gle/ewTGdKzB2xyE...
📅 Notifications by July 15

#Bioconductor #Bioinformatics

20.06.2025 19:44 — 👍 9 🔁 12 💬 0 📌 0

If you look for an easy way to plot OME-zarr images in your scripts, I hope the ez-zarr python package will be useful:

18.05.2025 07:30 — 👍 7 🔁 6 💬 0 📌 0

Learning and teaching biological data science in the Bioconductor community Modern biological research is increasingly data-intensive, leading to a growing demand for effective training in biological data science. In this article, we provide an overview of key resources and…

🎓 New Publication!

Our 1st paper on Bioconductor training from the Bioconductor Training Committee is now published in PLOS Comp Biol. We're pleased to share our work with the community.

Read here: journals.plos.org/ploscompbiol...

Thank you to everyone involved for your contributions!

24.04.2025 18:01 — 👍 6 🔁 2 💬 0 📌 0

Participate in the Bioconductor community by sharing your work in a meeting designed to maximize interactivity and productivity at the seafront of Barcelona! 👩‍💻🏖️🧬 #EuroBiocC2025

22.04.2025 16:51 — 👍 5 🔁 4 💬 0 📌 0

Bioconductor - Bioconductor 3.21 Released The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and…

Bioconductor 3.21 is released!

A huge thank you to all developers and community members for your contributions.
Explore what’s new in the full release announcement:
bioconductor.org/news/bioc_3_...

#Bioconductor #RStats

16.04.2025 20:35 — 👍 22 🔁 13 💬 0 📌 0

Eleven quick tips for writing a Bioconductor package

From @csoneson.bsky.social , @mramos148.bsky.social, @jorainer.bsky.social & colleagues in @plos.org #Computational #Biology | Eleven quick tips for writing a #Bioconductor package | #Bioinformatics #Education #Rstats #PLOSCBQT 🧬 🖥️ 🧪 🔓
⬇️
journals.plos.org/ploscompbiol...

20.03.2025 11:53 — 👍 9 🔁 6 💬 0 📌 1

Eleven quick tips for writing a Bioconductor package

Eleven (!) quick tips for writing a Bioconductor package from @csoneson.bsky.social et al. from @fmiscience.bsky.social

journals.plos.org/ploscompbiol...

20.03.2025 09:49 — 👍 21 🔁 7 💬 1 📌 0

This work is not only an amazing resource for the community, it is also a total masterclass in code reusability, data FAIRness and reproducibility. Hopefully, this is the future!

26.02.2025 16:58 — 👍 14 🔁 5 💬 0 📌 0

A comprehensive Schizosaccharomyces pombe atlas of physical transcription factor interactions with proteins and chromatin Transcription factors (TFs) are key regulators of gene expression, yet many of their targets and modes of action remain unknown. In Schizosaccharomyce…

www.sciencedirect.com/science/arti...

I am very excited to share our latest work on the protein and chromatin interactomes of transcription factors! 🧬

Huge thanks to everyone who contributed, especially @csoneson.bsky.social and @mbstadler.bsky.social for driving this story with me! 🙌

26.02.2025 16:41 — 👍 21 🔁 11 💬 2 📌 1

CSAMA 2025 flyer

Do you want to learn more about the statistical analysis of proteomics, metabolomics, single-cell and spatial transcriptomics? Do you want to up your game with R and Bioconductor? All of this while enjoying summer in the beautiful Italian Alps? Join us for the 21st edition of CSAMA July 6-11!

27.01.2025 08:16 — 👍 27 🔁 15 💬 1 📌 3

📣 Please share: We’re hiring a tenure-track Group Leader in Multicellular Systems to explore the molecular and cellular mechanisms driving the formation, maintenance, or destabilization of tissues, organs and organisms. Apply at: www.fmi.ch/education-ca...

16.12.2024 11:50 — 👍 110 🔁 118 💬 4 📌 7

The tidyomics ecosystem: enhancing omic data analyses - Nature Methods tidyomics offers a software ecosystem for omic data manipulation and analysis that bridges Bioconductor with the tidyverse framework.

#tidyomics made it to #NatureMethods! "The tidyomics ecosystem: Enhancing omic data analyses", 👏🏽 Will, Timothy, and Team!

32 researchers | 26 institutes | 10 countries | 4 continents

A #crowd/#community-research success

nature.com/articles/s41...

#CZI, Thanks @mikelove.bsky.social !

17.06.2024 01:20 — 👍 13 🔁 9 💬 0 📌 2

This is great @lcolladotor.bsky.social! Maybe one link to add to the document would be the iSEE-verse website: isee.github.io

15.04.2024 06:43 — 👍 1 🔁 0 💬 1 📌 0

[2024-04-12] A user perspective on using iSEE interactive websites

For more information on Leonardo Collado-Torres, check https://twitter.com/lcolladotor.For more information about the materials discussed in this video, chec... [2024-04-12] A user perspective on using iSEE interactive websites

New: "A user perspective on using #iSEE interactive websites" for @LIBDrstats

📽️ youtu.be/i5I_mFOsGks
📓 docs.google.com/document/d/1...

#rstats #Bioconductor #RNAseq #datavis @federicomarini.bsky.social @csoneson.bsky.social

13.04.2024 18:21 — 👍 3 🔁 5 💬 1 📌 0

Charlotte Soneson

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