NGS Analysis Center at the University of Regensburg

Deciphering chromatin architecture and dynamics in Plasmodium falciparum using the nucDetective pipeline High-resolution analysis of cellular chromatin structure is crucial for uncovering developmental and cell-type-specific regulatory networks. We developed the nucDetective pipeline to provide a comprehensive evaluation of chromatin organisation. This involves assessing nucleosome positioning, occupancy, fuzziness, and array regularity. The pipeline was benchmarked by analysing the chromatin structure of the malaria-causing parasite Plasmodium falciparum ( Pf ) during its erythrocytic development cycle. Pf is characterised by a unique chromatin landscape, exhibiting unstable nucleosomes and a genomic AT-content exceeding 80%, which presents challenges for standard MNase-seq analysis of chromatin. The nucDetective pipeline provides specific, high-resolution nucleosome profiles for the different asexual stages of Pf , monitoring the dynamics of individual nucleosomes. In contrast to the current view, suggesting an irregular chromatin structure and lack of nucleosomal DNA, we demonstrate that the transcription start sites exhibit typical eukaryotic features, including +1 nucleosomes, nucleosome-free regions upstream, and phased nucleosome arrays downstream of the TSSs. The global mean nucleosome repeat length varies from 176 bp to 185 bp depending on the developmental stage. Stage specific changes in nucleosome positioning occur locally in intergenic regulatory regions, which are characterized by specific histone modifications and variants. Dynamic nucleosomes correlate with DNA accessibility, gene expression and determine the access to transcription factor binding sites in Pf . The highly regular chromatin structure, with stage-specific structural alterations, emphasises the important role of epigenetic mechanisms in regulating the complex life cycles of Pf. ### Competing Interest Statement The authors have declared no competing interest. Deutsche Forschungsgemeinschaft, 534335380

Here is the preprint:

www.biorxiv.org/cont...
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🚀 Checkout our new #nextflow MNase-pipeline nucDetective

Features:
✅ MNase QC analysis
✅ high resolution nucleosome maps
✅ detect nucleosome dynamics
✅ multi-condition comparison
✅ nucleosme-repeat-length

Try it here: github.com/uschwartz...
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What a great list 🤗. Please add me!

Our results highlight how nucleosome organisation and dynamics shape the parasite’s complex life cycle.

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🔹 +1 nucleosome & upstream nucleosome-free regions
🔹 Phased nucleosome arrays at promoters
🔹 Nucleosome repeat length varies (176–185 bp) over the life cycle
🔹 Stage-specific nucleosome dynamics linked to DNA accessibility & gene expression
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Deciphering chromatin architecture and dynamics in Plasmodium falciparum using the nucDetective pipeline High-resolution analysis of cellular chromatin structure is crucial for uncovering developmental and cell-type-specific regulatory networks. We developed the nucDetective pipeline to provide a comprehensive evaluation of chromatin organisation. This involves assessing nucleosome positioning, occupancy, fuzziness, and array regularity. The pipeline was benchmarked by analysing the chromatin structure of the malaria-causing parasite Plasmodium falciparum ( Pf ) during its erythrocytic development cycle. Pf is characterised by a unique chromatin landscape, exhibiting unstable nucleosomes and a genomic AT-content exceeding 80%, which presents challenges for standard MNase-seq analysis of chromatin. The nucDetective pipeline provides specific, high-resolution nucleosome profiles for the different asexual stages of Pf , monitoring the dynamics of individual nucleosomes. In contrast to the current view, suggesting an irregular chromatin structure and lack of nucleosomal DNA, we demonstrate that the transcription start sites exhibit typical eukaryotic features, including +1 nucleosomes, nucleosome-free regions upstream, and phased nucleosome arrays downstream of the TSSs. The global mean nucleosome repeat length varies from 176 bp to 185 bp depending on the developmental stage. Stage specific changes in nucleosome positioning occur locally in intergenic regulatory regions, which are characterized by specific histone modifications and variants. Dynamic nucleosomes correlate with DNA accessibility, gene expression and determine the access to transcription factor binding sites in Pf . The highly regular chromatin structure, with stage-specific structural alterations, emphasises the important role of epigenetic mechanisms in regulating the complex life cycles of Pf. ### Competing Interest Statement The authors have declared no competing interest. Deutsche Forschungsgemeinschaft, 534335380

🧬 New preprint about chromatin architecture in Plasmodium falciparum using our new #nextflow MNase-seq pipeline nucDetective!

📄 Read here: www.biorxiv.org/cont...

Plasmodium falciparum's chromatin is not irregular—it shows classical eukaryotic features.
👇 A short thread
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Interested in this technology? Come join us on 28.07.25 at the Single-Molecule Mini Symposium and C-Trap Launch event!

I was thinking of:
1) Contact the corresponding author
2) Contact the journal
3) Reanalyse the study myself

I discovered that in one study, samples were mixed up in one out of three replicates. The study pooled all three replicates for analysis, without showing any consistency. Getting the replicates right would be consistent with the trend of the study, but change some findings. What would you do next?

Always on the Move: Overview on Chromatin Dynamics within Nuclear Processes Our genome is organized into chromatin, a dynamic and modular structure made of nucleosomes. Chromatin organization controls access to the DNA sequence, playing a fundamental role in cell identity and...

Want to learn more about chromatin and its dynamics? Read this review by Charlotte and Jolijn in our lab, aimed at giving an overview on this and the ways this is dealt with during transcription, replication and damage repair. Thanks to Biochemistry for inviting us! doi.org/10.1021/acs....

Here is a growing list of conferences and schools in gene regulation for 2025 generegulation.org/conferences-.... You can order/filter this list by the date, deadline, location. Please reply here to suggest new events*

*should be specific to gene regulation

Great topic and working group. Apply!
krb-sjobs.brassring.com/TGnewUI/Sear...

Nextflow Training Week (2025-Q1) 🚀 Nextflow Training Week is a new quarterly self-paced online training designed for accessibility and flexibility. Featuring on-demand walkthrough videos and near real-time support via the community f...

🚀 Introducing #Nextflow Training Week!

A free, self-paced online training designed to help beginners get started with Nextflow.

📅 March 10-14, 2025
🎥 On-demand videos and real-time support
💬 Ask questions in our community forum

Learn more and join us: hubs.la/Q038kTQm0