iiinova — where your digital self keeps evolving

Teif lab @teiflab.bsky.social · 23/09/2026

Zeng et al, 2026. Transcription factors read a second regulatory code in chromatin www.biorxiv.org/content/10.6... "our findings establish that TFs interpret two complementary layers of genomic information: the primary DNA sequence and a second code written into the nucleosome architecture"

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Teif lab @teiflab.bsky.social · 30/08/2026

AlBawardi et al, 2026. Irregular nucleosome positioning governs a crystalline to liquid-like phase transition and tunes chromatin accessibility www.biorxiv.org/content/10.6... ▶️heterochromatin-like sequences produce compact fibres ▶️positional irregularity (>2-3 bp) triggers a state transition

Abstract: Chromatin must fold tightly enough to protect the genome while being sufficiently accessible for DNA dependent processes such as transcription. The physical rules that balance these competing roles remain unclear, as DNA sequence encodes both biochemical information such as transcription factor binding sites, and biophysical cues that shape chromatin structure. Here, using synthetic chromatin fibres assembled from physiologically relevant DNA sequences, we show that nucleosome positioning dictates the material state of chromatin. Heterochromatin-like sequences produce compact fibres stabilised by nucleosome stacking, whereas euchromatin-like sequences generate irregular nucleosome positioning that yields disrupted, heterogeneous, and mechanically deformable fibres. Quantitative polymer modelling reveals that these irregular arrays are highly dynamic, continually sampling a broad ensemble of conformations as nucleosome stacking breaks down. We identify two previously unrecognised thresholds encoded by nucleosome positioning: minimal positional irregularity (2–3 bp) triggers a transition from an ordered paracrystalline state to a liquid-like phase, whereas an order of magnitude greater irregularity (∼18 bp) is required to generate accessibility and mechanical fragility permissive for transcription factor binding. Euchromatin-like arrays reside at this accessibility threshold. These findings indicate that nucleosome positioning tunes chromatin toward or away from critical structural states that couple genome protection, chromatin dynamics, and transcriptional potential—providing a physical mechanism that helps connect DNA sequence to gene expression.

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Teif lab @teiflab.bsky.social · 18/08/2026

Luo et al, 2026 (review). The roles of chromatin remodeling and 3D genome organization in cancers: from mechanistic insights to emerging treatment options link.springer.com/article/10.1... 🤯548 references!

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Teif lab @teiflab.bsky.social · 26/07/2026

Woolfe et al, 2026. Decoding the mystery of ultra-conservation in developmental enhancers: a role for nucleosome positioning, DNA structure and transcription factor binding www.biorxiv.org/content/10.6... ▶️conserved non-coding elements ... favor nucleosome occupancy at their borders

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Teif lab @teiflab.bsky.social · 10/07/2026

Finally: nucleosome positioning as highlighting with a marker in a book. Just as highlighted words or sentences stand out differently, where nucleosomes sit can make parts of the genome easier or harder to read. This analogy took me a while to come up with! 4/4

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Teif lab @teiflab.bsky.social · 10/07/2026

Next: DNA methylation as accents on letters. In languages like French, an accent can change how a letter or word is read; methylation marks can change how cells read DNA, without changing the underlying sequence. Has anyone seen this analogy used before? 3/4

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Teif lab @teiflab.bsky.social · 10/07/2026

First: the genome as a book. DNA sequence is the text, written with four letters - A, T, G and C. This is a standard analogy, but it gives students a clear starting point before introducing gene regulation. 2/4

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Teif lab @teiflab.bsky.social · 07/07/2026

Chen et al 2026. Genome-wide rotational and translational phasing of nucleosomes with human transcription factors www.cell.com/molecular-ce... ▶️ In vivo nucleosome phasing measured on the same TF-bound DNA molecule ▶️ Phasing around CTCF sites is DNA encoded ▶️ FoxA and NFIA phase adjacent nucleosomes

How transcription factors (TFs) and their binding sites organize and engage nucleosomes at natural genomic locations remains poorly understood. Here, we develop Benzonase-seq to measure the rotational phasing of nucleosomes in human cells and enhance chromatin immunoprecipitation (ChIP)-exo (v6) to measure rotational phasing on the same DNA molecule bound by a TF. Unbound CTCF sites were found to be rotationally accessible on nucleosomes, and this rotational accessibility is encoded by classical dinucleotide periodicities. CTCF binding results in nucleosome displacement to adjacent DNA phasing sequences. Upon examining 40 TF classes, unbound sites were found to be phased either inward or outward or to lack phasing. In all examined cases, TF binding (e.g., NFIA and FoxA) results in adjacent rotational and translational phasing, which is not dinucleotide encoded. Benzonase-seq also more robustly maps nucleosome and subnucleosome positions in hard-to-map CpG islands. These findings provide a clearer view of how TFs engage and position nucleosomes to shape the natural chromatin landscape.

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Teif lab @teiflab.bsky.social · 12/06/2026

Great preprint by @vram142.bsky.social & Co www.biorxiv.org/content/10.6... "fiber homotypy," where chromatin fibers with similar nucleosome spacing interact more frequently in 3D --> Related to our previous "nucleosome homology recognition" in chromatin royalsocietypublishing.org/rsif/article...

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Teif lab @teiflab.bsky.social · 10/06/2026

Come celebrate Professor Leo Schalkwyk with us! We’re holding a one-day symposium to mark Leo's remarkable career and many contributions to genomics. 📆26 June 2026 📍University of Essex, Colchester Details and registration: schalkwykfest.essex.ac.uk There will be a BBQ as well!

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Teif lab @teiflab.bsky.social · 04/06/2026

Sun et al, 2026. NuRD-enabled CTCF-TET crosstalk orchestrates epigenome reprogramming and genome architecture www.cell.com/molecular-ce...

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Teif lab @teiflab.bsky.social · 15/05/2026

The +1 nucleosome functions in Pol II transcription initiation and the transition to elongation www.biorxiv.org/content/10.6... [Yumeng Zhan, Julio Abril-Garrido, Frauke Grabbe, Paulina Seweryn, Ute Neef, Christian Dienemann, Patrick Cramer]

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Teif lab @teiflab.bsky.social · 03/05/2026

Very interesting analogy to micelle! Reminded me visually about this model www.cell.com/biophysj/ful...

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Teif lab @teiflab.bsky.social · 09/03/2026

Adhireksan et al, 2026. Linker histones consolidate heterogenous nucleosome fiber contacts by linking together multiple nucleosomes www.nature.com/articles/s41...

The consensus mode for linker histone (H1) association coincides with ‘on-dyad’ binding to an individual nucleosome, making it challenging to rationalize the chromatin dynamics and compacting activities of H1 in the context of a highly heterogeneous structural scaffold. Here, we investigate the activity of the somatic H1 variants by conducting crystallographic analysis of nucleosomal assemblies and characterization of nucleosome array condensates, which recapitulate long-range nucleosome fiber interactions in chromatin. H1 is observed to associate variant-dependently with nucleosomes through a diversity of binding modes that include linking multiple nucleosomes/fibers together. Binding versatility is facilitated by the proclivity of the H1 globular domain to recognize DNA structural motifs, which are similar between an individual nucleosome and specific niches within clusters of nucleosomes. We propose that linker histones support a structurally and functionally complex repertoire for chromatin regulation by assuming a variety of context-and variant-dependent DNA binding modes.

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Teif lab @teiflab.bsky.social · 05/03/2026

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

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/)).

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Teif lab @teiflab.bsky.social · 08/02/2026

I found another paper where whole-chromosomes have been coloured in lymphocytes journals.plos.org/plosone/arti... Here the positions of chromosomes 9 and 22 are not far but not convincingly close. It would be cool to find a figure with territories of all chromosomes coloured as in the one above

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Teif lab @teiflab.bsky.social · 08/02/2026

Probably this one can work haematologica.org/article/view...

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Teif lab @teiflab.bsky.social · 08/02/2026

The closest image I found is this relative spatial positioning of chromosomes between GM12878 and K562 cell lines link.springer.com/article/10.1.... But I am looking for a more direct visualisation in the style of chromosome territories, and ideally not in cancer cells

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Teif lab @teiflab.bsky.social · 08/02/2026

Preparing a lecture about cancer genomics. Looking for a 3D map of human chromatin to show chromosomes 22 and 9 close to each other to demonstrate Philadelphia chromosome translocation. Chromosome territories like the one below don't show them together. Any other visualisations in this style?

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Teif lab @teiflab.bsky.social · 21/01/2026

Today we had very nice interactions in the University of North Dakota (remotely)! Thank you very much @adhasarathy.bsky.social, Motoki Takaku & Co for the invitation to give this talk and hosting the visit!

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Teif lab @teiflab.bsky.social · 14/01/2026

Congratulations to Negin Behboodi on successfully passing your PhD viva! We are so proud of you! Keep an eye out for Negin's upcoming big papers! And thank you to the kind examiners @mspivakov.bsky.social and @amarcobio.bsky.social!

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Teif lab @teiflab.bsky.social · 11/01/2026

Schaepe et al, 2026. Thermodynamic principles link in vitro transcription factor affinities to single-molecule chromatin states in cells www.cell.com/cell/fulltex...

The molecular details governing transcription factor (TF) binding and the formation of accessible chromatin are not yet quantitatively understood—including how sequence context modulates affinity, how TFs search DNA, the kinetics of TF occupancy, and how motif grammars coordinate binding. To resolve these questions for a human TF, erythroid Krüppel-like factor (eKLF/KLF1), we quantitatively compare, in high throughput, in vitro TF binding rates and affinities with in vivo single-molecule TF and nucleosome occupancies and in vivo-derived deep learning models. We find that 40-fold flanking sequence effects on affinity are consistent with distal flanks tuning TF search parameters and captured by a linear energy model. Motif recognition probability, rather than time in the bound state, drives affinity changes, and in vitro and in nuclei measurements exhibit consistent, minutes-long TF residence times. Finally, in vitro biophysical parameters predict in vivo sequence preferences and single-molecule chromatin states for unseen motif grammars.

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Teif lab @teiflab.bsky.social · 07/01/2026

Structural organization and function of telomeric chromatin [Review by Ruben van der Lugt & Jacqueline Jacobs] www.nature.com/articles/s41...

Fig. 1: Schematic of the human telomeric chromatin architecture. The human telomere is made up of TTAGGG repeats arranged into nucleosomes, bound by a six-subunit shelterin complex (comprising TRF1, TRF2, RAP1, TIN2, TPP1 and POT1). Some complexes are depicted without TPP1 and POT1, which it has been suggested are less abundant than the other subunits. Recent in vitro structural analyses of telomeric chromatin revealed a columnar stacking of histones on TTAGGG repeats, characterized by face-to-face nucleosome arrangements, as well as an alternative open configuration where two histone octamers are oriented at a nearly 90° angle. These in vitro columnar arrays exhibit an NRL of approximately 130 bp. In vivo, however, the telomeric NRL is 157 bp, longer than the NRL of the proposed columnar histone arrangement, but shorter than the ~197-bp NRL of bulk chromatin. To reconcile this, we depict here a model in which shelterin remodels the telomeric chromatin to integrate features of a columnar nucleosome organization with the nucleosome periodicity observed in vivo. At the telomere terminus, a 3′ single-stranded overhang of TTAGGG repeats invades the duplex telomeric DNA to form a lariat structure known as the T-loop. This loop structure serves a protective function by preventing the telomere from being recognized as damaged DNA. The size of the T-loop is variable and may differ between telomeres, contributing to the structural heterogeneity of the telomere. The extent to which nucleosomes are present within the T-loop remains unclear.

Fig. 2: Impact of the TPE on the local and distal chromatin environment. Telomere elongation results in the repression of genes in the vicinity of telomeres, a phenomenon known as the TPE. a, Schematic of the repression of telomere-proximal genes via the classical TPE that has been shown at telomere-adjacent artificial reporter genes in human cells. Upon elongation, telomeres accumulate repressive histone modifications (indicated in red) through the activity of a histone methyltransferase (HMT) and HP1. The repressive heterochromatin environment of elongated telomeres spreads to nearby subtelomeric genes (indicated with red and orange DNA strands), resulting in transcriptional repression. The strength of silencing diminishes as the distance from the telomere increases (indicated with fading arrows). Conversely, upon telomere shortening, the human TPE (at telomere-adjacent transgenes) is characterized by loss of the repressive histone modification H3K9me3 and gain of the activating modification H3K9ac. In contrast to telomere-adjacent artificial reporter genes, at natural subtelomeres, spreading of repressive histone modifications from telomeres is not consistently observed, probably due to the presence of boundary elements. b, Schematic of telomere-mediated repression of telomere-distal genes via TPE-OLD. Elongated telomeres acquire the ability to form long-distance loops between telomeres and interstitial telomere sequences (ITSs; that is, sequences of TTAGGG repeats outside of the telomeres). Looping requires binding of shelterin to an ITS and results in transcriptional repression of the affected gene.

Fig. 3: Heterogeneity of (sub)telomeric chromatin and its reorganization upon telomere elongation. a, Telomeric and subtelomeric chromatin are organized into distinct domains. The subtelomeric TAR1 site acts as a TSS for the telomeric non-coding RNA TERRA (depicted in red for UUAGGG and in orange for subtelomere-derived RNA). The canonical TERRA promoter contains a high density of CpG dinucleotides, regulated by the DNA methyltransferases DNMT1 and DNMT3B. In contrast, certain subtelomeres (variable across cell lines) contain non-canonical TERRA promoters that lack CpG-rich regions and escape regulation by DNA methylation. Binding of CTCF and cohesin to the centromeric side of TAR1 maintains transcriptionally competent chromatin at the TSS and facilitates the recruitment of RNA polymerase II. The telomeric tract itself displays a bivalent pattern of histone modifications, with both activating (H3K4me3 and H3K27ac) and repressive marks (H3K9me3, H3K27me3 and H4K20me3). TERRA modulates this environment through the formation of RNA:DNA hybrids (R-loops) and G4s. Furthermore, RNA- or G4-binding chromatin remodellers, including Suv39H1, ORC1, NoRC, PRC2 and FUS, are recruited by TERRA and alter the epigenetic landscape. G4-binding proteins, including CTCF and YY1, mediate long-range interactions between distal G4s, contributing to higher-order chromatin organization. The telomeric shelterin complex itself is heterogeneous and probably assembles into subcomplexes (for example, TRF1–TIN2–TPP1–POT1 or TRF2–RAP1). TRF2 is essential for formation of the terminal T-loop, which requires direct interaction between TRF2 and nucleosomes. TRF2-mediated stabilization of nucleosomes may prevent branch migration at the base of the loop, which would result in cleavage of the loop by resolvases. b, TERT-mediated elongation alters the chromatin of telomeres. The length of TERRA molecules is proportional to the telomere length, allowing increased recruitment of chromatin-modifying enzymes…

Fig. 4: Schematic of the ALT pathway. ALT is a telomerase-independent, cancer-specific mechanism of telomere maintenance enabled by alterations to the telomeric chromatin. Between 10 and 15% of cancers activate the ALT pathway to maintain telomere length in a telomerase-independent manner. ALT+ cancers frequently display loss of ATRX–DAXX histone chaperone activity, resulting in reduced deposition of the histone variant H3.3 at telomeres and, consequentially, progressive decompaction of the telomeres. This chromatin disruption promotes increased TERRA transcription, leading to accumulation of R-loops and G4s. ALT+ telomeres also display increased levels of the repressive histone mark H3K9me3, partially due to additional mutations such as those encoding the G34R substitution in H3.3 and the R132H substitution in IDH1, which inhibit the histone demethylase KDM4B. The combined effect of R-loops, G4s and decreased nucleosome occupancy cause persistent replication stress, ultimately giving rise to telomeric breaks. Broken telomeres are further enriched in H3K9me3 due to the break-induced recruitment of the CHAMP1–POGZ–HP1 complex. These telomeric breaks are clustered in APBs, membrane-less condensates formed through HP1- and PML-dependent phase separation. Within APBs, broken telomeres invade homologous telomeric templates to initiate HDR-mediated extension. Invasion of the broken strand is stimulated by RAD51AP1, which promotes the switch from TERRA R-loops to stable telomeric D-loops, where telomere elongation takes place.

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Teif lab @teiflab.bsky.social · 04/01/2026

The famous "It takes two to think" by @itaiyanai.bsky.social and martinlercher.bsky.social (www.nature.com/articles/s41...) may have some ramifications in the era of AI :)

Four-panel black-and-white stick-figure cartoon comparing work styles. Panel 1, “Boss”: one person sits on a cart full of books and points forward while three others pull the cart. Panel 2, “Leader”: four people pull the cart together, with the front person pointing the direction while still pulling. Panel 3, “Introvert”: a single person pulls the cart alone. Panel 4, “Introvert with AI”: the same person walks easily while a small robot pulls two book-filled carts behind them.

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Teif lab @teiflab.bsky.social · 04/12/2025

Rudnizky et al., 2025. Ultrafast CTCF dynamics control cohesin barrier function www.biorxiv.org/content/10.1...

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Teif lab @teiflab.bsky.social · 24/11/2025

Maansson et al., 2025. Liquid biopsy epigenetics: establishing a molecular profile based on cell-free DNA [review] febs.onlinelibrary.wiley.com/doi/full/10....

Various analytes of liquid biopsies. Cancer cells shed various analytes into the bloodstream, all of which can be analyzed in liquid biopsies. (A) Extracellular vesicles contain various molecules, including DNA, RNA, and proteins representing the biology of the tumor. (B) Several types of cell-free RNA (cfRNA) molecules can be found in plasma, including noncoding micro-RNA (miRNA), long noncoding RNA (lncRNA), messenger RNA (mRNA), and tumor-derived RNA fusions. (C) Circulating tumor cells (CTCs) from primary tumors or metastatic sites directly represent cancer biology at the site of origin. CTCs can group together with healthy cells, creating CTC clusters. (D) Many features of cell-free DNA (cfDNA) provide great insights into tumor biology. These features include fragmentomics focusing on cfDNA fragment lengths and fragment end motifs (FEMs), 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) patterns and post-translational modifications (PTMs) of circulating histones. In addition, somatic variants, such as single-nucleotide variants (SNVs), insertions and deletions (indels), and copy number alterations (CNAs) are detectable in liquid biopsies.

$Origin of cell-free DNA (cfDNA) in healthy individuals and various diseases. (A) In a healthy population, the tissue of origin of cfDNA can be traced to hematopoietic (90%) and nonhematopoietic cells (10%). Of circulating peripheral blood mononuclear cells (PBMCs), monocytes (yellow) and granulocytes (green) are the main contributors to the cfDNA pool. Erythroblasts (pink) and megakaryocytes (blue) are the main contributors from the bone marrow. Nonhematopoietic cfDNA primarily originates from endothelial and liver cells (red). (B, C) Pathological conditions can alter the origin of cfDNA; however, most of the cfDNA still originates from healthy tissues shown in (A) (gray). Patients with acute myocardial infarction (AMI) have increased cfDNA from cardiac (purple) cells (B). Similarly, cancer patients have an increased fraction of cfDNA from the organ of the primary tumor and the metastatic site (C). This is illustrated with an increased fraction of colon (orange) and neuron (brown) cfDNA in a colorectal cancer (CRC) patient with a brain metastasis.$

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Teif lab @teiflab.bsky.social · 24/11/2025

Some refs on nucleosome-mediated cooperativity in TF binding: ▶️Concept suggested by Polach & Widom, 1996: www.sciencedirect.com/science/arti... ▶️Our first single-bp resolution model, 2010: www.cell.com/biophysj/ful... ▶️Its application to TFs at enhancers, 2011: iopscience.iop.org/article/10.1...

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Teif lab @teiflab.bsky.social · 18/11/2025

Congratulations to Amishasingh Beeharry for successfully passing the MSD viva! You are the best, Amisha! Thank you very much to the examiners, Abdenour Soufi and Toni Marco!

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Teif lab @teiflab.bsky.social · 26/10/2025

Bercovich et al., 2025. IceQream: Quantitative chromosome accessibility analysis using physical TF models www.nature.com/articles/s41... ▶️spatially integrates sequences and localises them relative to the target locus ▶️infers effective TF concentrations ▶️supplements with pairwise TF interactions

Schematic of the IceQream (IQ) workflow: (i) Single-cell ATAC raw counts are transformed into estimated access probabilities (AP). (ii) The IQ model incorporates transcription factor (TF) models, epigenomic context variables, and pairwise interactions of TF models. Each TF model integrates contributions from strong and weak affinity sequences, weighted by spatial preferences around the accessible hotspot, which are transformed into dose-response-like spatial binding preference curves using pre-defined non-linear functions. (iii) Model initialization involves scanning candidate TF models from PSSM (position-specific scoring matrix) databases and de novo motif regression. (iv) An integrated IQ model predicts differential AP (dAP) across a selected manifold trajectory. (v) IQ models from multiple trajectories are fused to create a manifold-wide set of common TF motif models.

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Teif lab @teiflab.bsky.social · 26/10/2025

It seems that it was not introduced by Google Scholar. It is a third-party add-on project.iith.ac.in/sharmaglab/g... addons.mozilla.org/en-US/firefo...

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Teif lab @teiflab.bsky.social · 07/10/2025

This is consistent with our observations, where in many cases statistically significant (and biologically informative) differences that occur between different states are just about 1-2bp or few bps that do not round to 5 (e.g. figure below from Piroeva et al., 2023) genome.cshlp.org/content/33/1...

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Teif lab @teiflab.bsky.social · 07/10/2025

When NRL is defined as a single genome-average value, it is usually not expected to be quantized. For example, this distribution of linker sizes from Voong et al, 2006 shows 10-bp quantization of preferred sizes, but the average of this distribution is expected to be a non-quantized value.

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Teif lab @teiflab.bsky.social · 06/10/2025

IT as a whole may be moved just about 100% up on this graph, but a sub-sector devoted to AI moved about 1000% up, so it might be interesting to repeat that earnings vs valuations analysis specifically for AI companies.

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Teif lab @teiflab.bsky.social · 04/10/2025

Interesting paper from Gernot Längst & Co. They calculated nucleosome repeat length in Plasmodium falciparum, the malaria-causing parasite, and showed that it follows a smooth continuous function of time (the numbers on the X axis below are hours post-invasion) www.biorxiv.org/content/10.1...

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Teif lab @teiflab.bsky.social · 28/09/2025

Polletti et al, 2025. Control of myeloid lineage fidelity and response to stimuli by ISWI-enforced nucleosome phasing www.cell.com/immunity/abs... ▶️PU.1 can form strongly phased nucleosome arrays similar to CTCF

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Teif lab @teiflab.bsky.social · 19/09/2025

Aging by the clock and yet without a program [perspective by David Meyer, Alexei Maklakov & Björn Schumacher] www.nature.com/articles/s43...

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Teif lab @teiflab.bsky.social · 16/09/2025

Hsu et al., 2025. MNase stratification reveals heterogeneous 5hmC in naive B cells www.biorxiv.org/content/10.1...

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Teif lab @teiflab.bsky.social · 08/09/2025

my target price remains 200 for this one

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Teif lab @teiflab.bsky.social · 23/08/2025

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

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

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Teif lab @teiflab.bsky.social · 19/08/2025

Saunders et al., 2025. HMGB1 deforms nucleosomal DNA to generate a dynamic chromatin environment counteracting the effects of linker histone www.science.org/doi/full/10.... ▶️HMGB1 sites are away from where H1 binds ▶️HMGB1 increases nucleosomal DNA accessibility without displacing H1

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Teif lab @teiflab.bsky.social · 27/07/2025

Liu et al., 2025. An automated ATAC-seq method reveals sequence determinants of transcription factor dose response in the open chromatin www.biorxiv.org/content/10.1... ▶️RoboATAC - automated ATAC-seq ▶️Deep learning models: motif orientation, spacing, flanking bases ▶️Nucleosome positioning analysis

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Teif lab @teiflab.bsky.social · 22/07/2025

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

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Teif lab @teiflab.bsky.social · 10/07/2025

This graph shows no correlation woth GBP/USD

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Teif lab @teiflab.bsky.social · 10/05/2025

Native nucleosomes intrinsically encode genome organization principles www.nature.com/articles/s41... ▶️Condensed purified native mononucleosomes with polyamines ▶️Nucleosomes from A compartments have low condensability and those from B compartments have high condensability

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