Julia Zeitlinger

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

Congratulations to Investigator @juliazeitlinger.bsky.social, Ph.D., who has been named a 2026 NextGen Leader by the Kansas City Business Journal! 🎉

The award recognizes emerging leaders across the #KansasCity region who are making an impact in their fields and in the community.

🔗 bit.ly/4rbNAEE

Excited to share @suminkim.bsky.social and @mileshuseyin.bsky.social 's new Current Opinion review on how Polycomb complexes mediate 3D genome interactions including mechanistic models and potential roles in gene regulation:
www.sciencedirect.com/science/arti...

Acute NIPBL depletion reveals in vivo dynamics of loop extrusion and its role in transcription activation - Nature Genetics Acute depletion of NIPBL reveals a class of chromatin loops that are independent of NIPBL for their maintenance but not their establishment and that NIPBL is necessary for the expression of lineage-de...

Very excited to share my postdoc research in the @jesserdixon.bsky.social lab at @salkinstitute.bsky.social, out online at @natgenet.nature.com today! www.nature.com/articles/s41... We investigated the function of the cohesin accessory protein NIPBL, making two particularly interesting findings:

Deadline: 28 Feb!

Want to interpret DNA sequence-to-function models to understand the underlying molecular mechanisms? Then this is a must read!

The abstract submission deadline is March 6.

AlphaGenome is out in @nature.com today along with model weights! 🧬

📄 Paper: www.nature.com/articles/s41...

💻 Weights: github.com/google-deepm...

Getting here wasn’t a straight path. We discussed the story behind the model, paper & API in the following roundtable: youtu.be/V8lhUqKqzUc

Ziga, congrats again to you and your team!

Today @nature.com, it's #AlphaGenome, to decipher and determine functionality of the regulatory (very challenging) variants in our genome.
Another big step of AI for advancing life science
nature.com/articles/s41...

Sonic hedgehog is not a limb morphogen but acts as a trigger to specify all digits in mice Limb patterning by Sonic hedgehog (Shh), via either graded spatial or temporal signal integration, is a paradigm for “morphogen” function, yet how Shh…

Finally had a chance to read this beautiful paper from Susan Mackem's lab. It's interesting that even well-established paradigms, like Sonic Hedgehog's role as a traditional morphogen in limb development, can be proven wrong over time.
www.sciencedirect.com/science/arti...

Thanks to
@ferhatay.bsky.social
and Aly Khan, we’re excited to announce a new chapter for RECOMB-RSG 2026. After years with ISCB/DREAM, we are transitioning to an official RECOMB satellite meeting (May 25 in Thessaloniki). recomb-rsg.github.io

Our work on TFIID is finally out as preprint!

Don't miss Bing Ren (@columbiauniversity.bsky.social) as the keynote speaker for #SRCKC26! Ren's work in #epigenomics and gene regulation continues to transform our understanding of #genome function. Organized by: @saukaspengler.bsky.social, @juliazeitlinger.bsky.social, Neşet Özel

🔗 bit.ly/4rMvVoI

Interested in spending the summer doing #science? Don't miss your chance to apply for the #StowersGrad Summer Scholars program! Applications close 1/16. ⬇️

A SWI/SNF-specific Ig-like domain, SWIFT, is a transcription factor binding platform Mammalian SWI/SNF chromatin remodeling complexes modulate DNA accessibility and gene expression; however, their genomic targeting mechanisms remain incompletely understood. Here, we identify SWIFT (SW...

🧬 @science.org A SWI/SNF-specific Ig-like domain, SWIFT, is a transcription factor binding platform | Science www.science.org/doi/10.1126/... @ckadoch.bsky.social @danafarber.bsky.social @harvardmed.bsky.social @broadinstitute.org @hhmi-science.bsky.social 🔬 #chromatin #transcription #cancer 🧫

Stowers Research Conferences: Development, Regulatory Genomics & AI Organized by Julia Zeitlinger, Ph.D., Neşet Özel, Ph.D., and Tatjana Sauka-Spengler, Ph.D.

“Development, regulatory genomics & AI on April 22-24 www.stowers.org/events/stowe...

Please consider attending and RT. Great lineup of speakers!

Allele Frequencies at Recessive Disease Genes are Mainly Determined by Pleiotropic Effects in Heterozygotes The classic theory of mutation-selection balance predicts the equilibrium frequency of genetic variation under negative selection. The model predicts a simple relationship between the total frequency ...

Our latest preprint revisits the classic model of mutation-selection balance.

Do human recessive genes fit Haldane's 100-year old model?

This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io

www.biorxiv.org/content/10.6...

Very proud of our new paper! Great job @mweilert.bsky.social, our experimentalists and modeling collaborator Rosa Martinez-Corral. It was fun to see the story grow and get feedback from various experts. Thank you all!

It's always special when you find your own paper in the table of contents of the journal 😍

"The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube" -> Now out in its final form

www.cell.com/developmenta...

Nice to see this out. This was a completely new research direction for me 7 years ago. I am so grateful for all the people who made this possible!

Promoter-proximal gatekeepers restrict pleiotropic enhancer inputs to achieve tissue specificity Developmental enhancers are central regulatory elements that can activate multiple genes, yet how they selectively regulate one gene over its neighbours remains unclear. Using the Drosophila twist E3 ...

Ever wondered what drives enhancer-promoter specificity? Why would an enhancer activate one gene rather than another neighboring one?

Check our latest preprint, led by @mmasoura.bsky.social, to find out!
www.biorxiv.org/content/10.1...

Emergence of activation or repression in transcriptional control under a fixed molecular context | PNAS Transcription factors (TFs) can be both activators and repressors of gene transcription. This can manifest as “duality,” where the transcriptional ...

Emergence of activation or repression in transcriptional control under a fixed molecular context www.pnas.org/doi/10.1073/...

Excited to share another new preprint from our lab in which we developed a cluster-based phasing strategy using long read nano-NOMe-seq data to link distinct CTCF binding states—captured at the single molecule level—to the transcriptional status of genes: biorxiv.org/content/10.1...

bioRxiv - An unbiased survey of distal element-gene regulatory interactions with direct-capture targeted Perturb-seq

New preprint from our lab!

What can we learn about the properties of gene regulatory elements by CRISPR’ing a random set of accessible sites in human cells?

Find out here: www.biorxiv.org/content/10.1...

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It is my pleasure to share with you the latest from @jsvejstrup.bsky.social lab, where we look at how the reduction of RNAPII levels has a severe, yet organized transcriptional response in the cell.

Very nice talk on this at CSH Mechanisms of Eukaryotic Transcription. Elegant approach!

Happy to see my lab here, too! Please follow if you are passionate about regulatory genomics and deep learning.

Abstract deadline for CSH Asia meeting on Systems Biology of Gene Regulation and Genome Editing is extended to September 5th.