Elias Friman
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eliasfriman.bsky.social
Elias Friman
@eliasfriman.bsky.social
460 followers 400 following 65 posts
Chromatin and transcription aficionado. Postdoc in Bickmore lab.
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Elias Friman @eliasfriman.bsky.social · May 11
Is distal gene activation by enhancers inherently different from promoter-proximal activation? We propose not. But both cohesin and cooperativity are important aspects of how transcription is affected. Happy to share our recent preprint (thread below) 1/

www.biorxiv.org/content/10.6...
www.biorxiv.org
Reposted by Elias Friman
sproullab.bsky.social
🚨 #Postdoc position open.

Want to understand non-canonical #epigenetic regulation of mammalian transcription? Come work @uoe-igc.bsky.social in Edinburgh!

We’re looking for a motivated & collaborative colleague with a strong track record.

📅 14 October 2026
📢 Please share

Apply here 👇
Post-Doctoral Research Associate
An exciting postdoctoral position is available to research the role of epigenetic marks in gene regulation.
elxw.fa.em3.oraclecloud.com
September 14, 2026 at 1:51 PM
Reposted by Elias Friman
wbickmor.bsky.social
It was great working with students Kun and Ryan and
@hannahlong.bsky.social, combing the literature to try and find examples of bona fide disease-causing variants in non-coding elements - promoters, enhancers and silencers.
www.nature.com/articles/s41...
Mechanisms underlying disease-causing variants in promoters and enhancers - Nature Genetics
This Review discusses how rare-disease-causing variants in the noncoding genome impact gene regulation, why these examples are so few and how new approaches could accelerate discovery of noncoding var...
www.nature.com
September 8, 2026 at 10:06 AM
Reposted by Elias Friman
radaiglesiaslab.bsky.social
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...
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...
www.nature.com
September 1, 2026 at 11:05 AM
Reposted by Elias Friman
teiflab.bsky.social
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.
August 30, 2026 at 10:52 AM
Reposted by Elias Friman
ceesdekker.bsky.social
Come join our #CDlab!

We have various open positions for PhD students or postdocs, see ceesdekkerlab.nl/come-join-us/

Particularly, I search a PhD student for protein sequencing with nanopores (keywords: nanopores, DNA origami, peptide/protein sequencing)

Apply!

RT=👍
Come join us - Cees Dekker Lab
Cees Dekker Lab
ceesdekkerlab.nl
August 24, 2026 at 8:59 AM
Reposted by Elias Friman
wbickmor.bsky.social
Great to see this lovely functional genomics work from @gweykopf.bsky.social @jmarshlab.bsky.social @kennethbaillie.bsky.social @gorrellmsydney.bsky.social @simonbiddie.bsky.social published. What at first sight seemed to be non-coding turns out to be coding.
www.nature.com/articles/s41...
Disease-associated genetic variants can cause missense effects in tissue-specific protein isoforms - Nature Communications
Isoforms are seldom considered in genetic variant interpretation. Here the authors map common and rare variants to alternative isoforms, which can be highly expressed and tissue-specific. A common DPP...
www.nature.com
August 3, 2026 at 10:51 AM
Reposted by Elias Friman
gweykopf.bsky.social
Very happy to see the first story from my PhD now published! Genetic variants causing coding mutations in alternative isoforms are more common than we thought, plus a novel DPP9 isoform 🧬
@wbickmor.bsky.social @eliasfriman.bsky.social @simonbiddie.bsky.social

www.nature.com/articles/s41...
August 4, 2026 at 6:37 AM
Reposted by Elias Friman
simongaudin.bsky.social
Now out from Bintu lab: compaction following transient KRAB recruitment tracks long-term epigenetic memory. But K9me3 decays after KRAB release and is replaced by DNA methylation. Does compaction help maintain K9me3, or slow its loss enough to facilitate the handoff to DNAme? tinyurl.com/ycay4mrh
Single-cell chromatin state transitions during epigenetic memory formation
Large-scale chromatin compaction quantitatively predicts the percentage of cells with durable epigenetic memory of gene silencing.
tinyurl.com
August 2, 2026 at 6:19 PM
eliasfriman.bsky.social
Great to see Giovanna's paper now out in PLoS Genetics!
journals.plos.org/plosgenetics...
@wbickmor.bsky.social @simonbiddie.bsky.social
July 28, 2026 at 7:14 AM
Reposted by Elias Friman
a-radzisheuskaya.bsky.social
Transcription and Chromatin UK is back!
Join us in York 18–20 November for three days of exciting science and networking. We look forward to seeing you there. www.eventsforce.net/biochemsoc/f...
July 23, 2026 at 9:28 AM
Reposted by Elias Friman
dariloops.bsky.social
🚨 Job Alert - Please share 🙏

Interested in 3D gene regulation in development & evolution? 🤓🧬

💥 Our lab at @cabd-upo-csic.bsky.social is expanding!

✅ 4 years fully funded PhD position
💻🧪 Experimental or computational backgrounds welcome

👇 Details below

#PhDPosition #PhDOpportunity #AcademicJobs
July 21, 2026 at 10:50 AM
Reposted by Elias Friman
lucagiorgetti.bsky.social
Our preprint is now out in @natgenet.nature.com !
doi.org/10.1038/s415...

We measured Sox2 promoter bursting dynamics with the SCR enhancer positioned at different distances within a genomic locus devoid of confounding effects in mESC:

Main findings in the 🧵 below:
July 15, 2026 at 2:05 PM
Reposted by Elias Friman
andersshansen.bsky.social
Very interesting and comprehensive study using synthetic activation of enhancers to probe the rules of distal vs. proximal gene regulations:
eliasfriman.bsky.social Elias Friman @eliasfriman.bsky.social · May 11
Is distal gene activation by enhancers inherently different from promoter-proximal activation? We propose not. But both cohesin and cooperativity are important aspects of how transcription is affected. Happy to share our recent preprint (thread below) 1/

www.biorxiv.org/content/10.6...
www.biorxiv.org
July 14, 2026 at 12:57 AM
Reposted by Elias Friman
dewitlab.bsky.social
(1/10) The majority of human genetic variation is located in non-coding regions. The great challenge of the post-genomic era is to assign function to these variants. We reasoned that combining haplotyping with allele-specific multiomics can help pinpoint the functional ones: rdcu.be/fgr5W. A thread:
Mapping functional non-coding variation in individual human genomes through haplotyping, multiomics, and deep learning
Nature Communications - How non-coding mutations in DNA contribute to phenotypes is a largely unresolved question. Here the authors integrate personal genomics and machine learning to identify...
rdcu.be
July 6, 2026 at 7:30 AM
Reposted by Elias Friman
yjtan.bsky.social
Does every enhancer work with every promoter?

With @jengreitz.bsky.social and Will Greenleaf, we revisit this long-debated question and resolve an outstanding contradiction in the field.

A tour 🧵👇
www.biorxiv.org/content/10.6...
Intrinsic promoter responsiveness dictates sensitivity to transcriptional activation by enhancers
Enhancers activate specific target promoters, but whether intrinsic enhancer-promoter compatibility contributes to this specificity is debated. Recent studies using different reporter assays have reac...
www.biorxiv.org
June 30, 2026 at 3:07 PM
Reposted by Elias Friman
andersshansen.bsky.social
(1/n) Very excited to share tri-lab collab (Mirny & Zechner) led by Harvey, Henrik & Jack:

Q: How do enhancers & promoters interact in space (contact vs. action-at-a-distance) and time (stable vs. transient)?

A: Transient E-P contact (~25-42 nm lasting ~10-20 sec):
www.biorxiv.org/content/10.6...
June 22, 2026 at 3:32 PM
Reposted by Elias Friman
dansarni.bsky.social
What if DNA methylation changes aren’t just ticking of our biological clock but rather the rust breaking the gears? Very excited to share our work - how DNA methylation contributes to stem cell dysfunction and aging, published in @natgenet.nature.com doi.org/10.1038/s415... #epigenetics #aging 1/11
A progeria syndrome links DNA hypermethylation to age-related pathology - Nature Genetics
This study investigates the consequences of hypermethylation in a progeria syndrome caused by gain-of-function DNMT3A mutations, finding effects on adult stem cell function.
doi.org
June 18, 2026 at 12:34 AM
Reposted by Elias Friman
craigandersn.bsky.social
Please help me find a great student!

I have a PhD position in my lab in Munich, looking at the dynamics of DNA damage and repair from chemotherapy: jobs.dkfz.de/en/jobs/1686...

The application deadline is 02.07.26

@dkfz.bsky.social @lmu-klinikum.bsky.social
PhD Student in Mutagenic Chemotherapy Driving Treatment Resistance
jobs.dkfz.de
June 11, 2026 at 6:06 AM
Reposted by Elias Friman
elphegenoralab.bsky.social
Why can't we explain enhancer action despite 2 decades of chromosome conformation technologies? 😬

Our new study spearheaded by Leonid Mirny's group points to a flaw in our assumptions, and to a solution from physical principles

By @timothyfoldes.bsky.social 💻& @karissalhansen.bsky.social 🧪

🧵👇
May 12, 2026 at 11:01 PM
Reposted by Elias Friman
gweykopf.bsky.social
Distal and proximal transcriptional activation may not be so different - check out the latest pre-print from @eliasfriman.bsky.social
Very happy to have contributed a small part and seen this story develop!
eliasfriman.bsky.social Elias Friman @eliasfriman.bsky.social · May 11
Is distal gene activation by enhancers inherently different from promoter-proximal activation? We propose not. But both cohesin and cooperativity are important aspects of how transcription is affected. Happy to share our recent preprint (thread below) 1/

www.biorxiv.org/content/10.6...
www.biorxiv.org
May 11, 2026 at 3:43 PM
Reposted by Elias Friman
hannahjuellig.bsky.social
Check out the🧵below on the latest pre-print from @eliasfriman.bsky.social

I am really glad to have had the opportunity to contribute to this exciting project! ✨
eliasfriman.bsky.social Elias Friman @eliasfriman.bsky.social · May 11
Is distal gene activation by enhancers inherently different from promoter-proximal activation? We propose not. But both cohesin and cooperativity are important aspects of how transcription is affected. Happy to share our recent preprint (thread below) 1/

www.biorxiv.org/content/10.6...
www.biorxiv.org
May 11, 2026 at 5:38 PM
Reposted by Elias Friman
dornan.bsky.social
A fascinating thread highlighting compelling investigations of the effects (or lack thereof) of distal vs proximal enhancer activation of promoters.
The ability for elements to promote transcription from megabases away has always astounded me. Excellent work - with clearly more to do!
eliasfriman.bsky.social Elias Friman @eliasfriman.bsky.social · May 11
Is distal gene activation by enhancers inherently different from promoter-proximal activation? We propose not. But both cohesin and cooperativity are important aspects of how transcription is affected. Happy to share our recent preprint (thread below) 1/

www.biorxiv.org/content/10.6...
www.biorxiv.org
May 11, 2026 at 6:30 PM
eliasfriman.bsky.social
Is distal gene activation by enhancers inherently different from promoter-proximal activation? We propose not. But both cohesin and cooperativity are important aspects of how transcription is affected. Happy to share our recent preprint (thread below) 1/

www.biorxiv.org/content/10.6...
www.biorxiv.org
May 11, 2026 at 3:30 PM
Reposted by Elias Friman
wbickmor.bsky.social
Although cohesin-sensitive, long-range enhancer activation is equivalent in nature to proximal activation. Cooperativity can arise from different levels of activation inputs operating on a non-linear response function. @eliasfriman.bsky.social @uoe-igc.bsky.social

www.biorxiv.org/content/10.6...
May 8, 2026 at 9:10 AM
Reposted by Elias Friman
dewitlab.bsky.social
New paper in Genes & Dev: we dissected how Sox2 — a key pluripotency TF — is regulated by a distal enhancer cluster (SCR) 100 kb away. The results challenge simple models of cohesin-mediated loop extrusion of gene regulation. genesdev.cshlp.org/content/earl... 🧵
Cohesin-mediated loop extrusion and enhancer-associated factors additively contribute to Sox2 looping with its distal enhancer
A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields
genesdev.cshlp.org
April 15, 2026 at 9:40 AM