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Krzysztof Herka @kherka.bsky.social · 28/01/2026

Come and talk 3D #genome, #epigenetics, #enhancers and #G4s at #FOG2026 at London ExCeL today and tomorrow! festivalofgenomics.com/london/poste... and some fresh stuff in there too!

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Krzysztof Herka @kherka.bsky.social · 02/09/2025

Brilliant #PhD opportunities for anyone interested in #chromatin, #genetics or #epigenetics!

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Krzysztof Herka @kherka.bsky.social · 27/08/2025

Lots of exciting chromatin biology - and great recaps!

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Reposted by Krzysztof Herka

Cancer Research UK Cambridge Institute @cruk-ci.bsky.social · 21/07/2025

Beyond carrying out vital research, our staff are involved in lots of science outreach activities every year. Recently, we hosted pupils for our annual Careers Lab. This programme is designed to inspire the next generation of STEM scientists & supporters. More: www.cruk.cam.ac.uk/students/car...

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Krzysztof Herka @kherka.bsky.social · 04/06/2025

Many thanks especially to Colm Doyle (now at @embl.org), who began this work with his beta globin locus study and @seanflynn.bsky.social (now of sites.google.com/view/flynnlab/ at @exeter.ac.uk - great things to come) for an incredible journey, as well as all authors at @cruk-ci.bsky.social! 9/9

sites.google.com

Flynn Lab

FLYNNLAB Chromatin biology

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Krzysztof Herka @kherka.bsky.social · 04/06/2025

....then edited them out to show how the regulation of genes in 3D contact was affected. 8/9

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Krzysztof Herka @kherka.bsky.social · 04/06/2025

How do G4s function at enhancers? In our #proteomics pulldowns, RNA polymerase II subunits were enriched, together with known G4 binding proteins - but not some common architectural factors (e.g. YY1, CTCF) - we confirmed that some RNAPII subunits specifically bind G4s (Fig. 4A, F). 6/9

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Krzysztof Herka @kherka.bsky.social · 04/06/2025

Inserting an unrelated G4 structure (Pu27 from the #Myc promoter - as featured in @isabelesain.bsky.social's brilliant work www.pnas.org/doi/abs/10.1...) recovers original globin expression and enhancer function (Figure 3D) 5/9

pnas.org

PNAS

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

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Krzysztof Herka @kherka.bsky.social · 04/06/2025

For the beta HS2 enhancer, this effect is masked by hyper activation of the neighbouring enhancer, HS3 - removing HS3 unveils a similar effect (Figure 3A-D for alpha, Figure 3E-H for beta). 4/9

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Krzysztof Herka @kherka.bsky.social · 04/06/2025

What happened? In the alpha HS-40 enhancer, such a mutation (seven G-to-T mutations) was sufficient to reduce globin gene expression to levels observed when the whole enhancer region (of around 350 bases) is deleted. Enhancer-promoter contacts and local #chromatin accessibility is also reduced. 3/9

We found a G4 in HS-40, the dominant enhancer of the alpha-globin locus regulatory region, replaced it with a sequence that can no longer form a G4; cognate gene expression, chromatin accessibility, and enhancer-promoter contacts were reduced. We then introduced a different G4-forming sequence - enhancer activity was restored.

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Krzysztof Herka @kherka.bsky.social · 04/06/2025

Using the classic #globin #superenhancer systems, we discovered two G4 structures in dominant enhancers in both the alpha globin and beta globin locus control systems - and replaced them with non-G4-forming sequences using CRISPR. 2/9

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Krzysztof Herka @kherka.bsky.social · 04/06/2025

How does (local #DNA) structure affect (3D #genome) structure? Can mutating G4s abolish #enhancers key for #blood function? In the second part of our explorations of #G4s in gene regulation, we show how abolishing G-quadruplex structures in the genome disrupts enhancers. 1/9 doi.org/10.1186/s130...

doi.org

DNA G-quadruplex structures act as functional elements in α- and β-globin enhancers - Genome Biology

Background Enhancer elements interact with target genes at a distance to modulate their expression, but the molecular details of enhancer–promoter interaction are incompletely understood. G-quadruplex...

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Reposted by Krzysztof Herka

Genetics Society UK @gensocuk.bsky.social · 23/04/2025

We heard about "Alternative DNA structures in enhancer-promoter communication" from @seanflynn.bsky.social from @uniofexeter.bsky.social #Epigenetics2025 @uniofexeternews.bsky.social

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Reposted by Krzysztof Herka

Cancer Research UK Cambridge Institute @cruk-ci.bsky.social · 19/03/2025

🚨 We’re Hiring!🚨 Passionate about cancer research? Join Madzia Crossley's team to investigate how R-loop dysregulation contributes to cancer. We have two exciting opportunities: Research Associate: jobs.cam.ac.uk/job/50675/ Senior Scientific Associate: jobs.cam.ac.uk/job/50689/

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Reposted by Krzysztof Herka

Cancer Research UK Cambridge Institute @cruk-ci.bsky.social · 05/03/2025

🚨 Fully funded #PhD opportunity! 🚨 Passionate about cancer research? Join Dr Madzia Crossley's team to investigate how R-loop dysregulation contributes to cancer. 📍 Cambridge, UK 💰 Fully funded 📅 Apply by 24 March 2025 www.cruk.cam.ac.uk/vacancies/ph...

cruk.cam.ac.uk

PhD Studentship: Investigating the causes and consequences of R-loop dysregulation in cancer - Cancer Research UK Cambridge Institute

Supervisor: Dr Magdalena Crossley Department/location: Cancer Research UK Cambridge Institute (CRUK CI) Course start date: 1st October 2025 Overview Dr Magdalena Crossley wishes to recruit a PhD stude...

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Krzysztof Herka @kherka.bsky.social · 03/03/2025

A great opportunity to work on #epigenetics, #genetics and gene regulation in #neuroscience with an inspirational young PI - please share and apply!

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Reposted by Krzysztof Herka

Cancer Research UK Cambridge Institute @cruk-ci.bsky.social · 03/12/2024

Congratulations to @isabelesain.bsky.social, who is awarded the 2024 CRUK Cambridge Institute PhD Thesis Prize. In her doctoral research, Bel discovered a new molecular mechanism in cancer gene regulation opening up a new therapeutic window for cancer treatments. www.cruk.cam.ac.uk/news/bel-esa...

Dr Isabel Esain Garcia receives Cancer Research UK Cambridge Institute 2024 PhD Thesis Prize

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Krzysztof Herka @kherka.bsky.social · 22/11/2024

A great #PhD opportunity for anyone interested in #epigenetics in #neurons and the broader context of #neuroscience - having worked with @seanflynn.bsky.social and Jack, they are brilliant choices for mentors!

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Krzysztof Herka @kherka.bsky.social · 15/11/2024

Thank you @seanflynn.bsky.social - looking forward to sharing science (mostly #epigenetics, #G4, gene regulation and #chromatin) with everyone, especially great work from the Flynn Lab!

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