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Anders Sejr Hansen

@andersshansen.bsky.social
2.7K followers 1.4K following 172 posts

Associate Professor at MIT BE : ashansenlab.com Interested in understanding the relationship between 3D genome structure and function

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Reposted by Anders Sejr Hansen
Anna-Karin Gustavsson @gustavssonlab.bsky.social · 02/10/2026
Excited that our work on Microfluidics-Enhanced 3D DNA-Based Points Accumulation for Imaging in Nanoscale Topography has been published in ACS Applied Materials & Interfaces. doi.org/10.1021/acsa... @pubs.acs.org #microscopy #nanoscale
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Wendy Bickmore @wbickmor.bsky.social · 29/09/2026
Very interesting paper. These <10kb "protrusions" remind me, albeit at a different length scale, of the "looping out" of active regions from chromosome territories. www.sciencedirect.com/science/arti...
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Peter Sarkies @psarkies.bsky.social · 28/09/2026
CpG islands are fascinating both from molecular mechanism point of view and in terms of evolutionary conservation in the context of elevated mutation rate of CpG dinucleotides in mammalian genomes. Lots of new insights from cool technical and theoretical advances from @robklose.bsky.social + lab.
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Anders Sejr Hansen @andersshansen.bsky.social · 28/09/2026
Very nice new paper from Paggi, Long, Zhang using physical modeling of RCMC data to reconstruct physical structures of euchromatin at the nucleosome scale: Euchromatin forms condensed domains and E-P interactions largely occur on the surface! www.nature.com/articles/s41...
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Ed Maibach @maibached.bsky.social · 25/09/2026
Happy Stanislav Petrov Day He passed in 2017. As Encyclopedia Britannica puts it, “He is survived by his two children, two grandchildren, and the entire human race.” If you don't know his story, please take 3 minutes now to learn it. @gchalliance.bsky.social @docsforclimate.bsky.social
sammatey.substack.com
Happy Stanislav Petrov Day
Take five minutes to not destroy civilization
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Nezar Abdennur @nvictus.bsky.social · 19/09/2026
The 4DN Center for 3D Structure and Physics of the Genome proudly presents: "Stepwise reorganization of chromosome conformation and nuclear organization during stem cell differentiation". www.biorxiv.org/content/10.6...
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Anders Sejr Hansen @andersshansen.bsky.social · 16/09/2026
. @matteomazzocca.bsky.social and I were fortunate to contribute single molecule imaging of chromatin dynamics to this beautiful study from K Alimenti and M Blower on SAF-A/HNRNPU:
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Anders Sejr Hansen @andersshansen.bsky.social · 07/09/2026
Enhancer–promoter proximity predicts transcriptional competence but not transcriptional output in the Drosophila brain arxiv.org/pdf/2609.03058
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Anders Sejr Hansen @andersshansen.bsky.social · 03/09/2026
"we found that human sister chromatids are consistently misaligned in the 5′→3′ direction of inherited DNA strands." www.science.org/doi/epdf/10....
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Anders Sejr Hansen @andersshansen.bsky.social · 02/09/2026
Very thankful to the @valleefoundation.bsky.social for supporting our work with a 2026 Vallee Scholar Award: thevalleefoundation.org/news/vallee-...
thevalleefoundation.org
The Vallee Foundation Announces 2026 Vallee Scholars | The Vallee Foundation
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Rada-Iglesias Lab @radaiglesiaslab.bsky.social · 01/09/2026
Have you ever wondered why developmental genes are often regulated by enhancers located at long distances? In this @natgenet.nature.com perspective, we speculate that long-range enhancer positioning may provide regulatory properties essential for proper gene expression www.nature.com/articles/s41...
nature.com
Mechanisms and functional implications of long-range enhancer-dependent gene regulation - Nature Genetics
Development depends on gene regulation by enhancers across long genomic distances. This Perspective discusses mechanisms enabling long-range enhancer–promoter communication and the potential advantage...
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Maxim Greenberg @maxvcg.bsky.social · 26/08/2026
We always knew you couldn't trust these antibody data sheets, but the extent to which it is essentially industry practice to manipulate data is truly shocking
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Feiya Ou @feiyaou.bsky.social · 25/08/2026
Glad to share that my preprint "ID2 secures cDC1 specification by antagonizing E proteins at a pleiotropic Zeb2 enhancer" is out today in Nature Immunology. This represents another major piece of my PhD work. www.nature.com/articles/s41... Original preprint thread: bsky.app/profile/feiy...
nature.com
ID2 secures cDC1 specification by antagonizing E proteins at a pleiotropic Zeb2 enhancer - Nature Immunology
Murphy and colleagues report that the transcriptional regulator ID2 promotes cDC1 fate specification by antagonizing E protein activity at E-boxes within the Zeb2 enhancer and establish the Zeb2 −165-...
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Tobias Warnecke @tobiaswarnecke.bsky.social · 22/08/2026
Who needs chromatin anyway...? NOT THIS GUY! www.biorxiv.org/content/10.6... 1/n
biorxiv.org
Chromatin is dispensable for bacterial life
Inside cells, DNA is intimately associated with proteins, forming chromatin. The protein constituents of chromatin vary across the tree of life: histones are the principal building blocks of chromatin...
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The Groth lab @grothlab.bsky.social · 21/08/2026
‼️🚨Out now in Molecular Cell - Our latest study 𝐫𝐞𝐯𝐞𝐚𝐥𝐢𝐧𝐠 𝐧𝐞𝐰 𝐢𝐧𝐬𝐢𝐠𝐡𝐭𝐬 𝐢𝐧𝐭𝐨 𝐅𝐀𝐂𝐓 𝐟𝐮𝐧𝐜𝐭𝐢𝐨𝐧 𝐚𝐧𝐝 𝐭𝐡𝐞 𝐢𝐦𝐩𝐨𝐫𝐭𝐚𝐧𝐜𝐞 𝐨𝐟 𝐧𝐮𝐜𝐥𝐞𝐨𝐬𝐨𝐦𝐞 𝐨𝐫𝐠𝐚𝐧𝐢𝐬𝐚𝐭𝐢𝐨𝐧 𝐟𝐨𝐫 𝟑𝐝 𝐠𝐞𝐧𝐨𝐦𝐞 𝐦𝐚𝐢𝐧𝐭𝐞𝐧𝐚𝐧𝐜𝐞: tinyurl.com/2xctvx38. It was a pleasure to lead this collaborative effort alongside @nilskrietenstein.bsky.social More in🧵below 🪡
tinyurl.com
Maintenance of nucleosome organization through replication and transcription counteracts aberrant coalescence of active chromatin
Nucleosomes with their associated modifications organize and regulate the genome. It is unclear how this is integrated with the requirement of replica…
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Edward Marcotte @edwardmarcotte.bsky.social · 19/08/2026
Exciting news for personalized mRNA cancer vaccines, especially if the phase 3 effect size matches the phase 2 trial (49% reduced death or recurrence), although we have to wait for the official numbers arstechnica.com/health/2026/...
arstechnica.com
mRNA cancer vaccine succeeded in Phase 3 melanoma trial, Moderna and Merck say
The vaccine reportedly thwarted the cancer's return and spread.
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Anders Sejr Hansen @andersshansen.bsky.social · 19/08/2026
we sometimes do bootcamps or workshops over the summer as a lab. Last week we did our microscopy bootcamp: everyone in the lab built a fluorescence microscope :)
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Anders Sejr Hansen @andersshansen.bsky.social · 18/08/2026
Really interesting new paper from Krietenstein and Groth labs showing that FACT depletion has a dramatic effect on microcompartments leading to aberrant microcompartment (AMC) formation through loss of ordered nucleosomes: www.cell.com/molecular-ce...
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Pablo Navarro @pablonavarrolab.bsky.social · 15/08/2026
Happy to share our last work on mitotic bookmarking where we describe a new role for extensively studied TFs. Heroic effort by first author Inma over many years. genesdev.cshlp.org/content/earl...
genesdev.cshlp.org
Mitotic MAX bookmarking drives MYC-dependent hypertranscription at TBP-bound promoters
A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields
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Craig Kaplan @triggerloop.bsky.social · 14/08/2026
Amazing physical chemical analysis of chromosome condensation and decondensation from Andrew Beel, PJ Mattei, and Roger Kornberg. I was tickled to see some expressions that I am used to from Roger's writing in the paper www.science.org/doi/10.1126/...
science.org
The eukaryote chromosome, a two-state system with interconversion by a volume phase transition
The formation of metaphase chromosomes requires the activity of condensins, DNA translocases that reduce chromosomal length through the process of loop extrusion. Reduction of length, however, does no...
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Anders Sejr Hansen @andersshansen.bsky.social · 14/08/2026
Multi-way Micro-C to go beyond pair-wise interactions:
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Anders Sejr Hansen @andersshansen.bsky.social · 14/08/2026
Nucleosomes and IDRs suppress promiscuous GCN4 binding on minichromosomes www.nature.com/articles/s41...
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Arnaud Krebs @arnaudkr.bsky.social · 12/08/2026
How many TFs to you need to open chromatin at enhancers? Very excited to see this one out! Check out the augmented version with combinatorial motif mutant libraries in Figure 5! Very proud of @guidobarzaghi.bsky.social @valentinabaderna.bsky.social @embl.org
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Steve Ramirez @okaysteve.bsky.social · 11/08/2026
It was an honor to write this remembrance of Susumu Tonegawa (1939–2026) -- a scientist whose discoveries transformed biology and whose lab shaped generations of neuroscientists. I hope this piece captures even a small part of his remarkable legacy. www.nature.com/articles/s41...
nature.com
Susumu Tonegawa (1939–2026) - Nature Neuroscience
On 11 July 2026, neuroscience lost one of its most visionary scientists with the passing of Susumu Tonegawa at the age of 86. Across an extraordinary career spanning more than five decades, Tonegawa p...
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Matt Jones @mattjones.bsky.social · 10/08/2026
New paper from my group at @mitkochinstitute.bsky.social, MIT IMES, and MIT Biology! I am thrilled to share that our paper describing scAmp, a new method for analyzing extrachromosomal DNA amplifications at single-cell resolution, has been published in @natcomms.nature.com. Thread below 👇
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Di Jiang @dijiang319.bsky.social · 08/08/2026
@science.org Generative design of bacteriophages with genome language models | Science www.science.org/doi/10.1126/...
science.org
Generative design of bacteriophages with genome language models
Many important biological functions arise not from single genes but from complex interactions encoded by entire genomes. We report the first generative design of complete bacteriophage genomes using g...
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Stefan Schoenfelder @stefanschoenfelder.bsky.social · 07/08/2026
Very happy to see this story finally out in @natbiotech.nature.com: www.nature.com/articles/s41... Fantastic collaboration with @lancasterlab.bsky.social on how to identify and ‘fix’ differentiation-compromised human pluripotent stem cells. @babrahaminst.bsky.social @mrclmb.ac.uk 🧵 below
nature.com
Reversible epiblast regionalization determines differentiation potential of human pluripotent stem cells - Nature Biotechnology
The differentiation variability of human pluripotent stem cell lines is diagnosed and corrected.
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Vincent Guacci Ph.D. @sciencevinman.bsky.social · 07/08/2026
We just submitted a manuscript to biorxiv. Keep in mind that this hasn't been peer reviewed yet but is submitted to PNAS for peer review. Our lab has closed so it will be the 2nd to last paper we publish. Data for one final paper will be written up in my retirement www.biorxiv.org/content/10.6...
biorxiv.org
Cohesin promotes genomic stability by suppressing unequal sister chromatid exchange
The protein complex cohesin plays critical roles in genomic stability by tethering together sister chromatids at their pericentric regions and along their arms from S phase until anaphase. Cohesin-med...
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varshram.bsky.social @varshram.bsky.social · 07/08/2026
Happy to share my first preprint! We looked at how the 3D genome changes during red blood cell differentiation, especially at erythroid CREs. It was fun to work on this collab with many wonderful people from the @andersshansen.bsky.social and @bloodgenes.bsky.social labs esp. Chun-Jie.
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Anders Sejr Hansen @andersshansen.bsky.social · 06/08/2026
(12/12) This has been a wonderful and close collab with @bloodgenes.bsky.social & lab. All credit to Varshini who led all computational work and put it all together and to Chun-Jie who led many experiments with important contributions from all the authors. We'd love feedback and discussion!
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Anders Sejr Hansen @andersshansen.bsky.social · 06/08/2026
(11/n) Other "3D CREs" have been described incl. beautiful work on Facilitators (Kassouf/Higgs) & Range Extenders (Kvon). A key distinction, Matchmakers promote looping indirectly: Matchmakers mostly don't themselves form loops. Instead they promote crosser loops through targeted cohesin loading.
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Anders Sejr Hansen @andersshansen.bsky.social · 06/08/2026
(10/n) Due to key role of cohesin in E-P regulation www.biorxiv.org/content/10.6... , it may be very important to allocate extrusion near key genes in erythropoiesis, where most of the genome is compacted and silenced and an increasingly specialized gene expression program is adopted.
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Anders Sejr Hansen @andersshansen.bsky.social · 06/08/2026
(9/n) Working in primary human donor-derived cells prevents degron tagging of cohesin. But we perturbed STAG1/2&NIPBL in primary cells and STAG2 in myeloid cells and re-analyzed Blobel lab NIPBL&SMC3 erythroblast data. All perturbations consistent with Matchmaker cohesin-dependence.
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Anders Sejr Hansen @andersshansen.bsky.social · 06/08/2026
(8/n) Matchmakers strengthen during erythropoiesis and correlate with stronger expression of key erythroid genes. KO of key matchmaker-binding TF NFE2 leads to modest reduction in matchmaking and nearby gene expression.
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Anders Sejr Hansen @andersshansen.bsky.social · 06/08/2026
(7/n) Inspired by fountain work, we tested if moderate targeted cohesin loading can explain Matchmakers: stronger crosser loops without visible fountains. Varshini confirmed this w polymer sims. Interestingly, erythropoiesis lead to chromatin compaction, and compaction hides fountains in 3D maps.
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Anders Sejr Hansen @andersshansen.bsky.social · 06/08/2026
(6/n) In contrast to fountains, Matchmakers do not show "fountain pattern" at single loci. Instead, Matchmakers are composed of “crosser loops”. Matchmakers are "altruistic": they help nearby elements form loops largely without themselves engaging as a loop anchor.
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Anders Sejr Hansen @andersshansen.bsky.social · 06/08/2026
(5/n) Prev work identified “orthogonal extrusion stripes” in 3D maps named “plumes” (de Wit), “jets” (Merkenschlager), “fountains” (Mirny, Meister, Ercan et al) and similar aggregate patterns (Vahedi, Xue, et al) Key distinction: Fountains are extrusion stripes at single loci, but not Matchmakers.
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Anders Sejr Hansen @andersshansen.bsky.social · 06/08/2026
(4/n) As expected, pile-up analysis on CTCF sites and promoters show clear insulation. Varshini clustered eryTFs into 4 clusters and saw strong “anti-insulation” at clusters 3+4. We call cluster 3+4 eryTF "MatchMakers" because they match make loops across themselves, without forming loops directly
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Anders Sejr Hansen @andersshansen.bsky.social · 06/08/2026
(3/n) Recently @bloodgenes.bsky.social lab ID’d key ‘eryTF’ CREs www.science.org/doi/full/10.... When Varshini examined 3D structure around these CREs she discovered “anti-insulation” pattern: Loops that cross these CREs are stronger than loops that don't --> This is opposite of insulation.
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Anders Sejr Hansen @andersshansen.bsky.social · 06/08/2026
(2/n) Collab with @bloodgenes.bsky.social began with genetic variation: We mapped ultra-high-res 3D genome structure across erythropoiesis using primary human donor derived cells. We can see the E-P loop that FDA-approved cure for Sickle cell disease targets (Fig 1D), but we also see new loops!
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Anders Sejr Hansen @andersshansen.bsky.social · 06/08/2026
(1/n) Excited to share close collab w @bloodgenes.bsky.social led by Varshini & Chun-jie et al How to induce expression of key genes while silencing much of the genome during Erythropoiesis? A: Matchmaker CREs load cohesin near key genes to promote looping & exp: www.biorxiv.org/content/10.6...
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Mikhail Spivakov @mspivakov.bsky.social · 04/08/2026
Very happy to see this story finally out (link in comments)! We used low-input Capture Hi-C to profile promoter-anchored chromosomal interactions in Type 3 innate lymphoid cells (ILC3s) - rare tissue-resident lymphocytes that lack antigen receptors and regulate barrier immunity.
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Jesse Engreitz @jengreitz.bsky.social · 04/08/2026
Update: scE2G is now online at Nature Genetics! Since the preprint, we added a new benchmark on a fully held-out CRISPR dataset. scE2G continues to show state-of-the-art performance, reinforcing that it generalizes well nature.com/articles/s41588-026-02695-8 1/
Held-out CRISPR benchmark: n=189 positives, 4,175 tested pairs from 5 cell types. Weighted AUPRC bar chart with scE2G-Multiome and scE2G-ATAC highest, above Distance to TSS, ABC, and 8 other single-cell methods.
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Kaushik Ragunathan @kaushikr.bsky.social · 03/08/2026
Our new study shows a CHD-family remodeler can nucleate and spread H3K9 methylation de novo, inverting the canonical hierarchy between writers and remodelers. www.biorxiv.org/content/10.6...
biorxiv.org
Nucleosome remodeling by a CHD enzyme promotes H3K9 methylation establishment and spreading via remodeler-writer feedback
In Schizosaccharomyces pombe , the conserved CHD remodeler Mit1 function within the SHREC remodeler-deacetylase complex (a homolog of the metazoan Mi-2/NuRD complex), which is essential for H3K9 methy...
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Elena Torlai Triglia @elett.bsky.social · 29/07/2026
1/ New paper alert! 🎉🧬 Our study on #9p21 gene regulation is out in #CellGenomics: "Chromatin topology and distal elements underlie divergent cell-type-specific regulation of 9p21 locus cell cycle genes" (Torlai Triglia, Miller, et al. www.cell.com/cell-genomic... 🧵
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Jeff Groh @jeffgroh.bsky.social · 28/07/2026
Avocados come in 2 varieties - A-types start each day female and switch to male midday. B-types do the reverse. In work just published from the last chapter of my PhD, we show this system evolved 40+million yrs ago and is regulated by alleles of 1 transcription factor www.pnas.org/doi/10.1073/...
pnas.org
Balanced polymorphism in a floral transcription factor underlies the ancient rhythm of daily sex alternation in avocado | PNAS
In avocado and certain wild relatives in Lauraceae, a highly synchronized daily rhythm of floral sex timing promotes cross-pollination between two ...
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Christophe 🔬 Leterrier @christlet.bsky.social · 27/07/2026
Controlled blinking of upconverting nanoparticles - no bleaching means attractive potential as an SMLM probe! www.nature.com/articles/s41...
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Anders Sejr Hansen @andersshansen.bsky.social · 25/07/2026
We know little about proteins required for long-range compartment 3D interactions, but this @kyleeagen.bsky.social lab preprint shows that NSD3 can make Mb-scale long-range compartment-like interactions: www.biorxiv.org/content/10.6...
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Anders Sejr Hansen @andersshansen.bsky.social · 25/07/2026
Very interesting study showing that active non-equilibrium fluctuations are required to explain chromatin organization at the 10-100kb scale:
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Benoit Bruneau @benoitbruneau.bsky.social · 23/07/2026
our paper starts with an analysis of the dynamics of 3D chromatin in cardiac differentiation, for ventricular and atrial cardiomyocytes. They are different! And by single cell methyl-HiC we can discern subtype differences. www.science.org/doi/10.1126/...
science.org
Dose-dependent sensitivity of human three-dimensional chromatin to a heart disease–linked transcription factor
Dosage-sensitive transcription factors (TFs) underlie altered gene regulation in human developmental disorders, and cell type–specific gene regulation is linked to the reorganization of three-dimensio...
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