Teif lab
LightNews LightNews
banner
teiflab.bsky.social
Teif lab
@teiflab.bsky.social
2.9K followers 1K 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
Posts Replies Media Videos
Reposted by Teif lab
karsten-rippe.bsky.social
1/ 🎄 We got our Christmas present today: "Two distinct chromatin modules regulate proinflammatory gene expression" is now published @natcellbio.nature.com doi.org/10.1038/s415.... Our study introduces a scATAC-seq-based framework for genome-wide analysis of gene regulation features.
December 24, 2025 at 10:44 PM
Reposted by Teif lab
jobdekker.bsky.social
A major output of the 4D Nucleome project appeared today. This is the joint effort of many scientists working together and (publicly) sharing data and results for several years. We hope this is of interest to many genome biologists!

www.nature.com/articles/s41...
An integrated view of the structure and function of the human 4D nucleome - Nature
The 4D Nucleome Project demonstrates the use of genomic assays and computational methods to measure genome folding and then predict genomic structure from DNA sequence, facilitatin...
www.nature.com
December 17, 2025 at 8:59 PM
Reposted by Teif lab
nucleosomepolice.bsky.social
Confused by all the histones that are cropping up in organisms that are decidedly NOT eukaryotes? check out our review - fantastic work by team NucEvo in the #Lugerlab
The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms - www.annualreviews.org/content/jour...
December 9, 2025 at 3:14 PM
Reposted by Teif lab
rcollepardo.bsky.social
Our Science paper is out!

Huge congratulations to @huabin-zhou.bsky.social, Mike Rosen, and the brilliant @janhuemar.bsky.social @juliamaristany.bsky.social and @kieran-russell.bsky.social from our group

News: bit.ly/4avnkAr and bit.ly/3XBGVHS

Great perspective by @vram142.bsky.social +K Zhang
December 5, 2025 at 9:47 AM
teiflab.bsky.social
Rudnizky et al., 2025. Ultrafast CTCF dynamics control cohesin barrier function www.biorxiv.org/content/10.1...
December 4, 2025 at 6:50 PM
Reposted by Teif lab
mspivakov.bsky.social
I'm guest-editing a collection on "Enhancer-promoter interactions" at Genome Biology. Please send us your exciting stories!

link.springer.com/collections/...
Enhancer-promoter interactions
Genome Biology is calling for submissions to our Collection on enhancer-promoter interactions. Enhancer–promoter interactions are central to the regulation ...
link.springer.com
November 25, 2025 at 10:55 AM
teiflab.bsky.social
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. Different cell-free DNA (cfDNA) methylation detection methods. (A) Normal and tumor cells have different methylation profiles, which are detectable in the bloodstream. Several strategies for cfDNA methylation quantification exist, each with their own strengths (+) and limitations (−). (B) Bisulfite conversion is the gold standard of methylation profiling; however, it is limited by high DNA degradation requiring a high input content. (C) As an alternative to bisulfite, enzymatic methyl sequencing (EM-seq) preserves the DNA integrity while providing single base-pair (bp) resolution of 5-methylcytosine (5mC) with higher coverage and less GC bias than bisulfite conversion. (D) Two separate 5mC cfDNA enrichment strategies exist, cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP–seq) and T7-MBD-seq. cfMeDIP utilizes anti-5mC-DNA antibodies to isolate methylated cfDNA fragments, whereas T7-MBD-seq uses methyl-binding domain 2 protein (MBD2) to enrich for 5mC. Precipitated cfDNA is sequenced, generating a coverage profile representing the genomic region's methylation status. (E) 6-letter sequencing with Duet is one of the more recently developed methods and enables quantification of 5mC and 5-hydroxymethylcytosine (5hmC) at single-bp resolution. (F) Native cfDNA is sequenced with long reads using nanopore technology, generating both an epigenetic and genetic profile at single-bp resolution. Fragmentomics of active and inactive genes. (A) Stable regions in the genome result in cell-free DNA (cfDNA) coverage peaks and valleys corresponding to the underlying chromatin structure. Regions with more dynamic chromatin result in a flatter cfDNA coverage profile. (B) Inactive genes are enriched for 5-methylcytosine (5mC) and do not have a structured cfDNA coverage profile around the transcript start site (TSS). cfDNA fragments from inactive genes have a peak at approximately 165 bp corresponding to caspase-activated DNase (CAD) cleavage in internucleosomal regions, leading to distinct fragment end motifs (FEMs). (C) Active genes are depleted of nucleosomes around the TSS, leading to distinct cfDNA coverage profiles. cfDNA fragments from active genes are shorter, with approximately 10-bp oscillations. Gene activity is also characterized by hypomethylation, causing the DNA to be more loosely bound to the nucleosome, allowing for internucleosomal CAD cleavage and altered FEM frequencies.
November 24, 2025 at 11:24 AM
teiflab.bsky.social
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...
November 24, 2025 at 10:21 AM
Reposted by Teif lab
zeitlingerlab.bsky.social
We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below:

(TLDR; low-affinity motifs matter as pioneers!)
Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs
Low-affinity transcription factor (TF) motifs are an important element of the cis-regulatory code, yet they are notoriously difficult to map and mechanistically incompletely understood, limiting our a...
www.biorxiv.org
November 19, 2025 at 8:57 PM
teiflab.bsky.social
Circular DNA has a ticket to ride chromosomes www.nature.com/articles/d41...
Circular DNA has a ticket to ride chromosomes
How circular extrachromosomal DNA is inherited during cell division is a puzzle. Key sequences enabling this DNA to journey with chromosomes have been identified.
www.nature.com
November 23, 2025 at 4:36 PM
teiflab.bsky.social
A new £2.5 million Government-funded laboratory is set to open at the University of Essex to train workplace-ready scientists for the NHS and the life-sciences sector www.essex.ac.uk/news/2025/11...
Essex to train workplace-ready NHS scientists in new lab | University of Essex
www.essex.ac.uk
November 19, 2025 at 4:47 PM
teiflab.bsky.social
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!
November 18, 2025 at 4:20 PM
Reposted by Teif lab
jojdavies.bsky.social
Finally, we propose a model in which chromatin is self-organising based on histone acetylation and nucleosome depletion. We hypothesise that active cis-regulatory elements may contact one another at or above a layer of acetylated nucleosomes.
November 5, 2025 at 5:20 PM
teiflab.bsky.social
October 31, 2025 at 4:45 PM
Reposted by Teif lab
maxvcg.bsky.social
Spread the word! There is a professor position opening at our University @upcite.bsky.social. There are several possible (great) labs to join, but if you are interested in DNA methylation and epigenetics in mammals, don't hesitate to contact me directly!
ijmonod.bsky.social Institut Jacques Monod @ijmonod.bsky.social · Oct 28
#JobOffer

💼 Un poste susceptible d’être vacant de Professeur en stabilité des génomes devrait s’ouvrir pour la rentrée 2026 au sein de l’Institut Jacques Monod

➡️ Informations concernant ce poste et la procédure de candidature 🔗 www.ijm.fr/poste-de-pro...
October 28, 2025 at 1:51 PM
teiflab.bsky.social
Since 2020, we were running a practical introducing year 2 students to a hypothetical situation requiring to diagnose a patient placed in ICU based on real-time analysis of cfDNA. This new paper shows that it works in actual ICU at a bedside-relevant sequencing depth www.nature.com/articles/s41...
Nanopore sequencing enables tissue-of-origin and pathogen detection in plasma cell-free DNA from critically ill patients - Cell Death Discovery
Cell Death Discovery - Nanopore sequencing enables tissue-of-origin and pathogen detection in plasma cell-free DNA from critically ill patients
www.nature.com
October 27, 2025 at 9:29 AM
Reposted by Teif lab
akhiad.bsky.social
Do we need LLMs to predict epigenomes from DNA—or is biophysics enough? 🧬
IceQream (IQ) is a biophysics-based framework that predicts epigenomes with SOTA-level accuracy—and is fully explainable.
@NatureComms: www.nature.com/articles/s41...
Thread 🧵👇
1/
October 17, 2025 at 8:31 AM
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
We lack clear guidelines for AI use by our students. My attempt:

Encouraged (when used responsibly):
✅Exploration, brainstorming and troubleshooting
✅Controlled software development and debugging

Discouraged (in most cases):
🚫Writing or "improving" academic texts
🚫Creating academic illustrations
October 26, 2025 at 10:41 AM
teiflab.bsky.social
October 16, 2025 at 11:34 AM
Reposted by Teif lab
guertin.bsky.social
we are recruiting a postdoc with interest in using genomics and molecular biology to study transcription factors. We have an R35 to fund the project/salary.
October 15, 2025 at 4:00 PM
Reposted by Teif lab
odedrechavi.bsky.social
BIG ANNOUNCEMENT📣: I haven’t been this excited to be part of something new in 15 years… Thrilled to reveal the passion project I’ve been working on for the past year and a half!🙀🥳 (thread 👇)
October 15, 2025 at 12:22 PM
teiflab.bsky.social
Just received a notification that our university is renegotiating #openaccess agreements with the “big five” publishers (Springer, Elsevier, etc), and it is highly likely that we will lose some of these agreements. If we do, this will be a big problem since we do not have budgets to pay OA fees
October 15, 2025 at 8:48 AM
Reposted by Teif lab
alexis-verger.cpesr.fr
Remember this paper "Low overlap
of transcription factor DNA binding and regulatory targets" ? (www.nature.com/articles/s41...)

well, well, well 🍿

⬇️

www.biorxiv.org/content/10.1...
On the overlap of transcription factor binding and regulatory targets: functional and regulatory coherence of top-bound targets is masked by weakly bound ones
A recent study that systematically mapped genomic bindings and regulatory effects of transcription factors (TFs) reported a surprisingly low overlap between TF binding and regulatory targets in Saccha...
www.biorxiv.org
October 14, 2025 at 12:00 PM
Reposted by Teif lab
sproullab.bsky.social
Sequencing advice sought:
Anyone have any experience of Element AVITI sequencing for methylation profiling by WGBS or EM-sequencing?
Useful to know what other people's experience is as local facility have one and cheaper than Illumina for short read sequencing.
Please share 🙏
#epigenetics
October 8, 2025 at 9:41 AM