Fine-scale chromatin mapping uncovers principles of cis-regulatory element interactions. #NBThighlight www.cell.com/cell/fulltex...
Mapping chromatin structure at base-pair resolution unveils a unified model of cis-regulatory element interactions
Li et al. apply base-pair resolution Micro Capture-C ultra to map chromatin contacts
between individual motifs within cis-regulatory elements and reveal a unified model
of biophysically mediated enhan...
www.cell.com
November 10, 2025 at 8:58 AM
Fine-scale chromatin mapping uncovers principles of cis-regulatory element interactions. #NBThighlight www.cell.com/cell/fulltex...
Third day of Genome Informatics #GI2025 began with an exciting session on “AI, ML and Integrative Genomics” chaired by Irene Kaplow & Thomas Pierrot.
The first talk, by Irene Kaplow, focused on Challenges in Predicting Enhancer Activity Differences Between Species
doi.org/10.1186/s12864-022-08450-7
The first talk, by Irene Kaplow, focused on Challenges in Predicting Enhancer Activity Differences Between Species
doi.org/10.1186/s12864-022-08450-7
![OCR Ortholog Open Chromatin Status Prediction Framework Overview. a We trained a convolutional neural network (CNN) for predicting brain open chromatin using sequences underlying brain open chromatin region (OCR) orthologs in a small number of species and used the CNN to predict brain OCR ortholog open chromatin status across the species in the Zoonomia Consortium. Specifically, we used the sequences underlying the orthologs for which we have brain open chromatin data to train a CNN for predicting open chromatin. Then, we used the CNN to predict the probability of brain open chromatin for all brain OCR orthologs; predictions are illustrated on the right. Animals for which we do not have open chromatin data are in dark gray instead of black to indicate that their brain open chromatin is imputed. While we cannot evaluate the accuracy of most of our predictions, obtaining open chromatin data from most tissues in most species is infeasible, so predictions might be the best OCR annotations that we can obtain. b To demonstrate that our models can accurately predict whether sequence differences between species are associated with open chromatin differences, in addition to the evaluations described in previous work [57], we evaluated our performance on species-specific open chromatin for a species not used in model training and clade-specific open and closed chromatin for clades not used in model training. Since such regions often comprise a minority of OCR orthologs, models could obtain good overall performance while obtaining poor performance on such regions. We also evaluated our performance on tissue-specific open and closed chromatin for a tissue not used in model training, where we expect models to predict 0 if model learns sequence signatures related to the tissue used in training. c Full mouse test set and lineage-specific OCR accuracy evaluations for mouse sequence-only brain model, illustrating that, even for the best of these models,](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:jkd2l647lviezhenqed454lh/bafkreicgkhegfuippjqhdt2tkku6dr74stuf5znohmtovfk5zojt5w7xkq@jpeg)
November 7, 2025 at 2:28 PM
Third day of Genome Informatics #GI2025 began with an exciting session on “AI, ML and Integrative Genomics” chaired by Irene Kaplow & Thomas Pierrot.
The first talk, by Irene Kaplow, focused on Challenges in Predicting Enhancer Activity Differences Between Species
doi.org/10.1186/s12864-022-08450-7
The first talk, by Irene Kaplow, focused on Challenges in Predicting Enhancer Activity Differences Between Species
doi.org/10.1186/s12864-022-08450-7
The Closing Scientific Retreat of @spp2202.bsky.social is under way in Goettingen with Gerd Blobel delivering the first Keynote lecture on LDB11-mediated looping of chromatin.
November 10, 2025 at 2:51 PM
The Closing Scientific Retreat of @spp2202.bsky.social is under way in Goettingen with Gerd Blobel delivering the first Keynote lecture on LDB11-mediated looping of chromatin.
Julie Ahringer from @gurdoninstitute.bsky.social @geneticscam.bsky.social @cam.ac.uk gives talk on decoding genome regulation during development. Exploring how chromatin accessibility changes throughout development enable single cells to become multicellular organisms.
November 7, 2025 at 1:48 PM
Julie Ahringer from @gurdoninstitute.bsky.social @geneticscam.bsky.social @cam.ac.uk gives talk on decoding genome regulation during development. Exploring how chromatin accessibility changes throughout development enable single cells to become multicellular organisms.
Our latest paper has just been published in Cell!
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
November 5, 2025 at 5:20 PM
Our latest paper has just been published in Cell!
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
doi.org/10.1016/j.ce...
We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
CRISPR live-cell imaging reveals chromatin dynamics and enhancer interactions at multiple non-repetitive loci - @tsinghuauniversity.bsky.social go.nature.com/49EhzA4
CRISPR live-cell imaging reveals chromatin dynamics and enhancer interactions at multiple non-repetitive loci - Nature Biotechnology
Multiplexed DNA imaging uncovers promoter−enhancer interaction dynamics and effects of epigenetic modifications.
go.nature.com
November 6, 2025 at 5:26 PM
CRISPR live-cell imaging reveals chromatin dynamics and enhancer interactions at multiple non-repetitive loci - @tsinghuauniversity.bsky.social go.nature.com/49EhzA4
CRISPR live-cell imaging reveals chromatin dynamics and enhancer interactions at multiple non-repetitive loci
www.nature.com/articles/s41...
www.nature.com/articles/s41...
CRISPR live-cell imaging reveals chromatin dynamics and enhancer interactions at multiple non-repetitive loci - Nature Biotechnology
Multiplexed DNA imaging uncovers promoter−enhancer interaction dynamics and effects of epigenetic modifications.
www.nature.com
November 7, 2025 at 12:56 PM
CRISPR live-cell imaging reveals chromatin dynamics and enhancer interactions at multiple non-repetitive loci
www.nature.com/articles/s41...
www.nature.com/articles/s41...
New @natgenet.nature.com paper from the brilliant @eszterlakatos.bsky.social presents evidence that chromatin alterations disrupt antigen presentation & neoantigens in colorectal cancer. Also that immune escape is part of the "Big Bang", at the outset of CRC growth. www.nature.com/articles/s41...
Epigenetically driven and early immune evasion in colorectal cancer evolution - Nature Genetics
This study nominates immune escape as an early event in colorectal cancer and shows how this can be driven through both genetic and epigenetic changes.
www.nature.com
November 5, 2025 at 4:36 PM
New @natgenet.nature.com paper from the brilliant @eszterlakatos.bsky.social presents evidence that chromatin alterations disrupt antigen presentation & neoantigens in colorectal cancer. Also that immune escape is part of the "Big Bang", at the outset of CRC growth. www.nature.com/articles/s41...
PLAMseq enables performance of genomics and proteomics of chromatin-associated proteins and protein interactions simultaneously
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
November 7, 2025 at 9:31 PM
PLAMseq enables performance of genomics and proteomics of chromatin-associated proteins and protein interactions simultaneously
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Discover SlimVar! Track single molecules in Arabidopsis roots up to 30 μm depth. See chromatin regulation like never before with high precision and speed! PMID:40890105, Nat Commun 2025, @NatureComms https://doi.org/10.1038/s41467-025-63108-8 #Medsky #Pharmsky #RNA #ASHG #ESHG 🧪
SlimVar for rapid in vivo single-molecule tracking of chromatin regulators in plants | Nature Communications
Epigenetic regulation occurs over many rounds of cell division in higher organisms. However, visualisation of the regulators in vivo is limited by imaging dynamic molecules deep in tissue. We report a technology—Variable-angle Slimfield microscopy (SlimVar)—that enables tracking of single fluorescent reporters to 30 µm depth through multiple Arabidopsis thaliana root tip cell layers. SlimVar uses rapid photobleaching to resolve tracked particles to molecular steps in intensity. By modifying widefield microscopy to minimise optical aberrations and robustly post-process few-photon signals, SlimVar mitigates performance losses at depth. We use SlimVar to quantify chromatin-protein assemblies in nuclei, finding that two homologous proteins key to epigenetic switching at FLOWERING LOCUS C (FLC) —cold-induced VERNALISATION INSENSITIVE3 (VIN3) and constitutively expressed VERNALISATION 5 (VRN5)—exhibit dynamic assemblies during FLC silencing. Upon cold exposure, the number of assembly molecul
doi.org
November 8, 2025 at 5:10 AM
Epigenetics Update - Repair of DNA double-strand breaks leaves heritable impairment to genome function bit.ly/4oVUjC8
Susanne Bantele and Jiri Lukas reporting in Science
#Epigenetics #DNAdamage #Chromatin
Perfect for cancer, immunology, and aging research; epigenometech.com
Susanne Bantele and Jiri Lukas reporting in Science
#Epigenetics #DNAdamage #Chromatin
Perfect for cancer, immunology, and aging research; epigenometech.com
Repair of DNA double-strand breaks leaves heritable impairment to genome function
Upon DNA breakage, a genomic locus undergoes alterations in three-dimensional chromatin architecture to facilitate signaling and repair. Although cells possess mechanisms to repair damaged DNA, it is ...
bit.ly
November 7, 2025 at 11:17 AM
Epigenetics Update - Repair of DNA double-strand breaks leaves heritable impairment to genome function bit.ly/4oVUjC8
Susanne Bantele and Jiri Lukas reporting in Science
#Epigenetics #DNAdamage #Chromatin
Perfect for cancer, immunology, and aging research; epigenometech.com
Susanne Bantele and Jiri Lukas reporting in Science
#Epigenetics #DNAdamage #Chromatin
Perfect for cancer, immunology, and aging research; epigenometech.com
Base-pair resolution Micro Capture-C ultra to map chromatin contacts between individual motifs within cis-regulatory elements and reveal a unified model of biophysically mediated enhancer-promoter communication @cellcellpress.bsky.social
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
November 6, 2025 at 3:03 AM
Base-pair resolution Micro Capture-C ultra to map chromatin contacts between individual motifs within cis-regulatory elements and reveal a unified model of biophysically mediated enhancer-promoter communication @cellcellpress.bsky.social
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Not from Tron or a psychedelic wallpaper. This exquisite pic reveals chromatin at base-pair resolution, captured by #ListerFellow James Davies and collaborators🤩
"For the first time, we can see how the genome's control switches are physically arranged inside cells." @jojdavies.bsky.social
"For the first time, we can see how the genome's control switches are physically arranged inside cells." @jojdavies.bsky.social
November 5, 2025 at 4:50 PM
Not from Tron or a psychedelic wallpaper. This exquisite pic reveals chromatin at base-pair resolution, captured by #ListerFellow James Davies and collaborators🤩
"For the first time, we can see how the genome's control switches are physically arranged inside cells." @jojdavies.bsky.social
"For the first time, we can see how the genome's control switches are physically arranged inside cells." @jojdavies.bsky.social
Large-scale chromatin accessibility profiling (ATAC-seq) of neurons and non-neurons from 2 human neocortical regions from 469 unique donors, comprising controls and individuals diagnosed with schizophrenia and bipolar disorder
www.nature.com/articles/s41...
www.nature.com/articles/s41...
The neuronal chromatin landscape in brains from individuals with schizophrenia is linked to early fetal development - Nature Neuroscience
This study maps chromatin accessibility in neurons and glia in schizophrenia, revealing fetal-like regulatory patterns in adult neurons enriched for genetic risk variants, linking early brain developm...
www.nature.com
November 5, 2025 at 12:22 PM
Large-scale chromatin accessibility profiling (ATAC-seq) of neurons and non-neurons from 2 human neocortical regions from 469 unique donors, comprising controls and individuals diagnosed with schizophrenia and bipolar disorder
www.nature.com/articles/s41...
www.nature.com/articles/s41...
We then collaborated with Lothar Schermelleh to undertake super-resolution microscopy of chromatin acetylation. In keeping with his previous work we find that histone acetylation maps to regions of chromatin that are adjacent to the interchromatin compartment.
November 5, 2025 at 5:20 PM
We then collaborated with Lothar Schermelleh to undertake super-resolution microscopy of chromatin acetylation. In keeping with his previous work we find that histone acetylation maps to regions of chromatin that are adjacent to the interchromatin compartment.
Excited to receive the Best Poster Award at the 9th Asian chromatin meeting 2025 in IISER Pune! Huge thanks to my mentor Srimonta for his guidance. Thanks to organizers of #ACM2025 for this wonderful opportunity!
#iiscbangalore #EMBO
#iiscbangalore #EMBO
November 7, 2025 at 5:44 AM
Excited to receive the Best Poster Award at the 9th Asian chromatin meeting 2025 in IISER Pune! Huge thanks to my mentor Srimonta for his guidance. Thanks to organizers of #ACM2025 for this wonderful opportunity!
#iiscbangalore #EMBO
#iiscbangalore #EMBO
A highlight of my summer was this collab w/
@twangmdphd.bsky.social ! CRISPR base editors are driving several clinical trials, but it's hard to quantify off-target edits and their effects. Tong developed a sequencing assay to identify off-targets *in primary cells* 🧬🖥️🧪 #genomics #chromatin #CRISPR
@twangmdphd.bsky.social ! CRISPR base editors are driving several clinical trials, but it's hard to quantify off-target edits and their effects. Tong developed a sequencing assay to identify off-targets *in primary cells* 🧬🖥️🧪 #genomics #chromatin #CRISPR
1/ Happy to share our preprint from the Greenleaf Lab: beCasKAS, our method to directly detect CRISPR base editor off-targets in primary cells. We additionally show how non-coding edits can be triaged for epigenetic dysregulation using deep learning.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
November 7, 2025 at 6:38 PM
A highlight of my summer was this collab w/
@twangmdphd.bsky.social ! CRISPR base editors are driving several clinical trials, but it's hard to quantify off-target edits and their effects. Tong developed a sequencing assay to identify off-targets *in primary cells* 🧬🖥️🧪 #genomics #chromatin #CRISPR
@twangmdphd.bsky.social ! CRISPR base editors are driving several clinical trials, but it's hard to quantify off-target edits and their effects. Tong developed a sequencing assay to identify off-targets *in primary cells* 🧬🖥️🧪 #genomics #chromatin #CRISPR
Are 3D chromatin changes after DNA repair tied to 𝘄𝗲𝗮𝗸𝗲𝗻𝗲𝗱 𝗥𝗡𝗔 𝗵𝘂𝗯𝘀?
Using RNA FISH at the c-MYC locus, we found they are — local RNA compartments stay compromised even after repair, mirroring structural chromatin changes. 10/n
Using RNA FISH at the c-MYC locus, we found they are — local RNA compartments stay compromised even after repair, mirroring structural chromatin changes. 10/n
November 6, 2025 at 11:05 PM
Are 3D chromatin changes after DNA repair tied to 𝘄𝗲𝗮𝗸𝗲𝗻𝗲𝗱 𝗥𝗡𝗔 𝗵𝘂𝗯𝘀?
Using RNA FISH at the c-MYC locus, we found they are — local RNA compartments stay compromised even after repair, mirroring structural chromatin changes. 10/n
Using RNA FISH at the c-MYC locus, we found they are — local RNA compartments stay compromised even after repair, mirroring structural chromatin changes. 10/n
☕Li, Burgos-Bravo et al. report that NDF #PhaseSeparation regulates FACT condensation, which enhances transcription by generating a localized biochemical environment that promotes nucleosome disassembly while preserving #chromatin integrity by retaining histones.
bit.ly/3JwVetO
bit.ly/3JwVetO
Phase-separated NDF−FACT condensates facilitate transcription elongation on chromatin - Nature Cell Biology
Li, Burgos-Bravo and colleagues report that NDF phase separation regulates FACT condensation, which enhances transcription by generating a localized biochemical environment that promotes nucleosome di...
bit.ly
November 4, 2025 at 6:22 PM
☕Li, Burgos-Bravo et al. report that NDF #PhaseSeparation regulates FACT condensation, which enhances transcription by generating a localized biochemical environment that promotes nucleosome disassembly while preserving #chromatin integrity by retaining histones.
bit.ly/3JwVetO
bit.ly/3JwVetO
Check out the perspective my lab wrote with @freudlab.bsky.social. We provide our perspective on recent work describing the structural basis of chromatin-based base excision repair!
🎉 Joint paper from the Freudenthal and @tmweaver.bsky.social Labs!
Abbey Vito’s first publication discusses a tug-of-war between BER enzymes and chromatin for access to damaged DNA, a battle central to genome stability.
Built on Tyler's foundational work! tinyurl.com/ywkt2bt5
Abbey Vito’s first publication discusses a tug-of-war between BER enzymes and chromatin for access to damaged DNA, a battle central to genome stability.
Built on Tyler's foundational work! tinyurl.com/ywkt2bt5
Base excision repair in chromatin: A tug-of-war for DNA damage
Base excision repair (BER) is a genome surveillance pathway responsible for repairing DNA base lesions distributed throughout the chromatinized eukary…
tinyurl.com
November 4, 2025 at 11:10 AM
Check out the perspective my lab wrote with @freudlab.bsky.social. We provide our perspective on recent work describing the structural basis of chromatin-based base excision repair!
Issue 21 highlights:
Paxilin’s nuclear switch in the brain
RING E3s reading & extending ADPr-ubiquitin
Review: Decoding immunometabolism
Nuclear actin limits chromatin leakage upon migratory squeeze
Cover by @syncellbiolab.bsky.social: unlike Odin-archael FtsZ twins
www.embopress.org/toc/14602075...
Paxilin’s nuclear switch in the brain
RING E3s reading & extending ADPr-ubiquitin
Review: Decoding immunometabolism
Nuclear actin limits chromatin leakage upon migratory squeeze
Cover by @syncellbiolab.bsky.social: unlike Odin-archael FtsZ twins
www.embopress.org/toc/14602075...
November 3, 2025 at 11:23 AM
Issue 21 highlights:
Paxilin’s nuclear switch in the brain
RING E3s reading & extending ADPr-ubiquitin
Review: Decoding immunometabolism
Nuclear actin limits chromatin leakage upon migratory squeeze
Cover by @syncellbiolab.bsky.social: unlike Odin-archael FtsZ twins
www.embopress.org/toc/14602075...
Paxilin’s nuclear switch in the brain
RING E3s reading & extending ADPr-ubiquitin
Review: Decoding immunometabolism
Nuclear actin limits chromatin leakage upon migratory squeeze
Cover by @syncellbiolab.bsky.social: unlike Odin-archael FtsZ twins
www.embopress.org/toc/14602075...
🎉 Joint paper from the Freudenthal and @tmweaver.bsky.social Labs!
Abbey Vito’s first publication discusses a tug-of-war between BER enzymes and chromatin for access to damaged DNA, a battle central to genome stability.
Built on Tyler's foundational work! tinyurl.com/ywkt2bt5
Abbey Vito’s first publication discusses a tug-of-war between BER enzymes and chromatin for access to damaged DNA, a battle central to genome stability.
Built on Tyler's foundational work! tinyurl.com/ywkt2bt5
Base excision repair in chromatin: A tug-of-war for DNA damage
Base excision repair (BER) is a genome surveillance pathway responsible for repairing DNA base lesions distributed throughout the chromatinized eukary…
tinyurl.com
November 3, 2025 at 3:47 PM
🎉 Joint paper from the Freudenthal and @tmweaver.bsky.social Labs!
Abbey Vito’s first publication discusses a tug-of-war between BER enzymes and chromatin for access to damaged DNA, a battle central to genome stability.
Built on Tyler's foundational work! tinyurl.com/ywkt2bt5
Abbey Vito’s first publication discusses a tug-of-war between BER enzymes and chromatin for access to damaged DNA, a battle central to genome stability.
Built on Tyler's foundational work! tinyurl.com/ywkt2bt5
H3K4me3 is one of the most highly conserved and well-studied chromatin marks. Yet, its function remains debated. Spoiler alert – our work provides more pieces of evidence to stack on the pile in favour of it having a direct instructive effect on transcription.
November 5, 2025 at 9:30 PM
H3K4me3 is one of the most highly conserved and well-studied chromatin marks. Yet, its function remains debated. Spoiler alert – our work provides more pieces of evidence to stack on the pile in favour of it having a direct instructive effect on transcription.
To overcome this, we turned to the mammalian H3K4 methyltransferase, PRDM9. Not only does PRDM9 function brilliantly to activate gene expression, it also results in less off-target. Perhaps the orthogonality of PRDM9 means nothing to recruit /stabilise at non-targeted plant chromatin..?
November 5, 2025 at 9:30 PM
To overcome this, we turned to the mammalian H3K4 methyltransferase, PRDM9. Not only does PRDM9 function brilliantly to activate gene expression, it also results in less off-target. Perhaps the orthogonality of PRDM9 means nothing to recruit /stabilise at non-targeted plant chromatin..?
☕Li, He, Liu et al characterize the dynamic bivalent #chromatin landscape during mouse peri- #implantation development. They find that factor ZBTB17 works with KDM6A/B to resolve transiently maintained bivalent domains and prime gene activation.
👉https://rdcu.be/eOgUb
bit.ly/4nBjnNC
👉https://rdcu.be/eOgUb
bit.ly/4nBjnNC
Remodelling bivalent chromatin is essential for mouse peri-implantation embryogenesis - Nature Cell Biology
Li, He, Liu and colleagues characterize the dynamic bivalent chromatin landscape during mouse peri-implantation development. They find that factor ZBTB17 works with KDM6A/B to resolve transiently main...
bit.ly
November 4, 2025 at 6:32 PM
☕Li, He, Liu et al characterize the dynamic bivalent #chromatin landscape during mouse peri- #implantation development. They find that factor ZBTB17 works with KDM6A/B to resolve transiently maintained bivalent domains and prime gene activation.
👉https://rdcu.be/eOgUb
bit.ly/4nBjnNC
👉https://rdcu.be/eOgUb
bit.ly/4nBjnNC