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teiflab.bsky.social
Teif lab
@teiflab.bsky.social
2.9K followers 990 following 310 posts
Teif lab at the University of Essex. We work on gene regulation in chromatin and applications to liquid biopsies, using approaches of genomics, biophysics, bioinformatics & AI. Our focus is nucleosomics, TF binding, CTCF, cfDNA. https://generegulation.org
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teiflab.bsky.social
October 31, 2025 at 4:45 PM
teiflab.bsky.social
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.
October 26, 2025 at 2:25 PM
teiflab.bsky.social
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...
October 26, 2025 at 10:56 AM
teiflab.bsky.social
October 16, 2025 at 11:34 AM
teiflab.bsky.social
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...
October 7, 2025 at 9:43 AM
teiflab.bsky.social
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.
October 7, 2025 at 9:35 AM
teiflab.bsky.social
October 6, 2025 at 2:56 PM
teiflab.bsky.social
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.
October 6, 2025 at 11:24 AM
teiflab.bsky.social
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...
October 4, 2025 at 7:01 PM
teiflab.bsky.social
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
September 28, 2025 at 1:29 PM
teiflab.bsky.social
Aging by the clock and yet without a program [perspective by David Meyer, Alexei Maklakov & Björn Schumacher] www.nature.com/articles/s43...
September 19, 2025 at 10:45 AM
teiflab.bsky.social
Hsu et al., 2025. MNase stratification reveals heterogeneous 5hmC in naive B cells www.biorxiv.org/content/10.1...
September 16, 2025 at 8:21 AM
teiflab.bsky.social
my target price remains 200 for this one
September 8, 2025 at 7:05 PM
teiflab.bsky.social
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
August 23, 2025 at 11:33 AM
teiflab.bsky.social
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
August 19, 2025 at 9:43 AM
teiflab.bsky.social
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
Transcription factors create accessibility through distinct mechanisms involving nucleosome sliding and eviction. A) Estimation of nucleosome-free (NFR) and nucleosomal fragment probabilities using ATAC-seq fragment size distributions. B) Example genomic locus showing ATAC insertion profile, nucleosome occupancy scores, and dyad positions inferred from NucleoATAC.
July 27, 2025 at 12:31 PM
teiflab.bsky.social
Wang et al, 2025. Genome-Wide Investigation of Transcription Factor Occupancy and Dynamics Using cFOOT-seq www.biorxiv.org/content/10.1...
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.
July 22, 2025 at 8:55 AM
teiflab.bsky.social
This graph shows no correlation woth GBP/USD
July 10, 2025 at 10:57 AM
teiflab.bsky.social
May 25, 2025 at 1:23 PM
teiflab.bsky.social
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
May 10, 2025 at 7:42 PM
teiflab.bsky.social
Kable et al., 2025. Compromised 2-start zigzag chromatin folding in immature mouse retina cells driven by irregularly spaced nucleosomes with short DNA linkers www.biorxiv.org/content/10.1...
▶️In mature retina cells, the fraction of short-linker nucleosomes is lower -> stronger chromatin compaction.
The formation of condensed heterochromatin is critical for establishing cell-specific transcriptional programs. To reveal structural transitions underlying heterochromatin formation in maturing mouse rod photoreceptors, we apply cryo-EM tomography, AI-assisted deep denoising, and molecular modeling. We find that chromatin isolated from immature retina cells contains many closely apposed nucleosomes with extremely short or absent nucleosome linkers, which are inconsistent with the typical two-start zigzag chromatin folding. In mature retina cells, the fraction of short-linker nucleosomes is much lower, supporting stronger chromatin compaction. By Cryo-EM-assisted nucleosome interaction capture we observe that chromatin in immature retina is enriched with i±1 interactions while chromatin in mature retina contains predominantly i±2 interactions typical of the two-start zigzag. By mesoscale modeling and computational simulation, we clarify that the unusually short linkers typical of immature retina are sufficient to inhibit the two-start zigzag and chromatin compaction by the interference of very short linkers with linker DNA stems. We propose that this short linker composition renders nucleosome arrays more open in immature retina and that, as the linker DNA length increases in mature retina, chromatin fibers become globally condensed via tight zigzag folding. This mechanism may be broadly utilized to introduce higher chromatin folding entropy for epigenomic plasticity.
May 5, 2025 at 12:52 PM
teiflab.bsky.social
Ultrastable and versatile multimeric ensembles of FoxP3 on microsatellites www.cell.com/molecular-ce...
▶️FoxP3 recognizes a variety of TnG repeat microsatellites
▶️FoxP3 multimers are ultrastable, can bridge 2–4 DNA duplexes
▶️Nucleosomes can facilitate FoxP3 assembly by inducing local DNA bending
Microsatellites are essential genomic components increasingly linked to transcriptional regulation. FoxP3, a transcription factor critical for regulatory T cell (Treg) development, recognizes TTTG repeat microsatellites by forming multimers along DNA. However, FoxP3 also binds a broader range of TnG repeats (n = 2–5), often at the edges of accessible chromatin regions. This raises questions about how FoxP3 adapts to sequence variability and the potential role of nucleosomes. Using cryoelectron microscopy and single-molecule analyses, we show that murine FoxP3 assembles into various distinct supramolecular structures, depending on DNA sequence. This structural plasticity enables FoxP3 to bridge 2–4 DNA duplexes, forming ultrastable structures that coordinate multiple genomic loci. Nucleosomes further facilitate FoxP3 assembly by inducing local DNA bending, creating a nucleus that recruits distal DNA elements through multiway bridging. Our findings thus reveal FoxP3’s unusual ability to shapeshift to accommodate evolutionarily dynamic microsatellites and its potential to reinforce chromatin boundaries and three-dimensional genomic architecture.
April 5, 2025 at 9:54 PM
teiflab.bsky.social
Miloshev et al., 2025, Linker Histones Maintain Genome Stability and Drive the Process of Cellular Ageing [review] www.imrpress.com/journal/FBL/...

Interesting figure: we did observe NRL increase with ageing (onlinelibrary.wiley.com/doi/10.1111/...). Not sure about about loop sizes, to be checked
April 1, 2025 at 10:08 AM
teiflab.bsky.social
Evolutionary divergence in CTCF-mediated chromatin topology drives transcriptional innovation in humans www.nature.com/articles/s41...
Human vs macaque:
▶️2133 gained (2.7%), 2418 lost (3.1%) CTCF loops in B-cells
▶️5873 gained (7.3%), 6708 lost (8.3%) in neurons
▶️implications for ASD and immunity
March 30, 2025 at 2:19 PM
teiflab.bsky.social
Do et al., 2025. Binding domain mutations provide insight into CTCF’s relationship with chromatin and its contribution to gene regulation www.cell.com/cell-genomic...
March 23, 2025 at 7:55 AM