Pradeepa Madapura
@pradeepmadapura.bsky.social
Scientist/Professor of Chromatin&Genome regulation, Blizard Institute, QMUL
@QMULepigenetics, views are my own.
@QMULepigenetics, views are my own.
Pinned
Check out our preprint "De-repression of Transposable Elements by Histone Hyperacetylation Leads to Sterile Inflammation in Preeclampsia" www.researchsquare.com/article/rs-6...
Reposted by Pradeepa Madapura
The TArgeted Cohesin Loader (TACL) paper was just published. Happy that we were able to contribute to this really exciting project!
If you want to learn how targeting cohesin to defined loci in the genome affects the local chromatin environment and transcription, look no further!
rdcu.be/eLiT5
If you want to learn how targeting cohesin to defined loci in the genome affects the local chromatin environment and transcription, look no further!
rdcu.be/eLiT5
Characterization of induced cohesin loop extrusion trajectories in living cells
Nature Genetics - This study introduces a system called TArgeted Cohesin Loader (TACL) that recruits cohesin complexes at defined genomic regions and induces loop extrusion events in living cells,...
rdcu.be
October 16, 2025 at 8:17 PM
The TArgeted Cohesin Loader (TACL) paper was just published. Happy that we were able to contribute to this really exciting project!
If you want to learn how targeting cohesin to defined loci in the genome affects the local chromatin environment and transcription, look no further!
rdcu.be/eLiT5
If you want to learn how targeting cohesin to defined loci in the genome affects the local chromatin environment and transcription, look no further!
rdcu.be/eLiT5
Just back to work after a brief subbatical
October 24, 2025 at 4:43 PM
Just back to work after a brief subbatical
Reposted by Pradeepa Madapura
If you are the market for this, I can highly recommend!
We are recuiting two new Associate Professors here in Oxford Biochemistry. Come join us! Reach out to me if you have any questions. Please repost! tinyurl.com/mr3m7bd3
October 17, 2025 at 4:11 PM
If you are the market for this, I can highly recommend!
Reposted by Pradeepa Madapura
We have added additional functionalities including a collapsible protein pane and zoom scrolling. domaindesigner.farnunglab.com
New week, new tool: Find our Protein Domain Designer tool to generate publication-ready protein domain diagrams here: domaindesigner.farnunglab.com
October 4, 2025 at 7:19 PM
We have added additional functionalities including a collapsible protein pane and zoom scrolling. domaindesigner.farnunglab.com
Reposted by Pradeepa Madapura
Many enhancers that drive tissue-specific gene expression are already connected to gene promoters in human pluripotent cells.
In a new preprint, we share some clues about when, how, and why this happens!
www.biorxiv.org/content/10.1...
In a new preprint, we share some clues about when, how, and why this happens!
www.biorxiv.org/content/10.1...
Poising and connectivity of emergent human developmental enhancers in the transition from naive to primed pluripotency
In primed human pluripotent stem cells (hPSCs) resembling post-implantation epiblast, numerous lineage-specific enhancers assume the poised chromatin state, co-marked by H3K4me1 and Polycomb-associate...
www.biorxiv.org
October 3, 2025 at 3:09 PM
Many enhancers that drive tissue-specific gene expression are already connected to gene promoters in human pluripotent cells.
In a new preprint, we share some clues about when, how, and why this happens!
www.biorxiv.org/content/10.1...
In a new preprint, we share some clues about when, how, and why this happens!
www.biorxiv.org/content/10.1...
Reposted by Pradeepa Madapura
Histone acetylation - not always about transcriptional activation: H4K16ac safeguards the genome replication program by repressing premature replication of heterochromatin. Well done Marta Milan! tinyurl.com/yuy9m8t3
September 30, 2025 at 12:14 PM
Histone acetylation - not always about transcriptional activation: H4K16ac safeguards the genome replication program by repressing premature replication of heterochromatin. Well done Marta Milan! tinyurl.com/yuy9m8t3
Another interesting link between H4K16ac & transposons, genome stability. Congratulations to the Scaffidi lab; we are pleased to contribute to this work.
September 26, 2025 at 12:21 PM
Another interesting link between H4K16ac & transposons, genome stability. Congratulations to the Scaffidi lab; we are pleased to contribute to this work.
Reposted by Pradeepa Madapura
Looking forward to catching up with everyone at the @biochemsoc.bsky.social #transcription and #chromatin UK #TCUK meeting today in sunny Manchester! #BiochemEvent 🧬🔬☔️ www.eventsforce.net/biochemsoc/f...
www.eventsforce.net
September 17, 2025 at 6:06 AM
Looking forward to catching up with everyone at the @biochemsoc.bsky.social #transcription and #chromatin UK #TCUK meeting today in sunny Manchester! #BiochemEvent 🧬🔬☔️ www.eventsforce.net/biochemsoc/f...
Handsup 🙌, who is coming to @blizardinstitute.bsky.social to attend the @illingworth-lab.bsky.social seminar this Friday on "polycomb repression in development and disease"? Also, who is joining online for this @qmulepigenetics.bsky.social seminar.
Our next guest speaker webinar is happening on Friday, September 12th at 15:30 GMT. Robert Illingworth will give a talk on 'Passive Yet Essential, Polycomb Repression in Development and Disease’.
To join, please follow this link: qmul.ac.uk/epigenetics/...
To join, please follow this link: qmul.ac.uk/epigenetics/...
September 9, 2025 at 9:06 AM
Handsup 🙌, who is coming to @blizardinstitute.bsky.social to attend the @illingworth-lab.bsky.social seminar this Friday on "polycomb repression in development and disease"? Also, who is joining online for this @qmulepigenetics.bsky.social seminar.
Great news, no more grant deadlines 😀 MRC applicant-led funding – UKRI share.google/lP742F01GmuK...
Simplifying access to MRC applicant-led funding
We’re introducing a new flexible research grant and removing closing dates from our board funding opportunities.
share.google
September 8, 2025 at 6:30 PM
Great news, no more grant deadlines 😀 MRC applicant-led funding – UKRI share.google/lP742F01GmuK...
Reposted by Pradeepa Madapura
Our work "Aquarius helicase facilitates HIV-1 integration into R-loop enriched genomic regions" is out @natmicrobiol.nature.com, showing HIV-1 integration into R-loop genomic regions upon their resolution by cellular splicing helicase Aquarius (AQR) of the Intron Binding Complex (IBC)🧵.
August 20, 2025 at 7:42 PM
Our work "Aquarius helicase facilitates HIV-1 integration into R-loop enriched genomic regions" is out @natmicrobiol.nature.com, showing HIV-1 integration into R-loop genomic regions upon their resolution by cellular splicing helicase Aquarius (AQR) of the Intron Binding Complex (IBC)🧵.
Reposted by Pradeepa Madapura
This preprint is now a published peer-reviewed paper! Thanks to all the co-authors involved, to the funders and to @reviewcommons.org and @embopress.org @emboreports.org for a smooth editorial process! Excited to see this in press! www.embopress.org/doi/full/10....
@imperiallifesci.bsky.social
@imperiallifesci.bsky.social
August 20, 2025 at 1:23 PM
This preprint is now a published peer-reviewed paper! Thanks to all the co-authors involved, to the funders and to @reviewcommons.org and @embopress.org @emboreports.org for a smooth editorial process! Excited to see this in press! www.embopress.org/doi/full/10....
@imperiallifesci.bsky.social
@imperiallifesci.bsky.social
Reposted by Pradeepa Madapura
Our next guest speaker webinar is happening on Friday, September 12th at 15:30 GMT. Robert Illingworth will give a talk on 'Passive Yet Essential, Polycomb Repression in Development and Disease’.
To join, please follow this link: qmul.ac.uk/epigenetics/...
To join, please follow this link: qmul.ac.uk/epigenetics/...
August 15, 2025 at 8:24 AM
Our next guest speaker webinar is happening on Friday, September 12th at 15:30 GMT. Robert Illingworth will give a talk on 'Passive Yet Essential, Polycomb Repression in Development and Disease’.
To join, please follow this link: qmul.ac.uk/epigenetics/...
To join, please follow this link: qmul.ac.uk/epigenetics/...
Multiple TF-coactivators regulate enhancer/promoter activity. Right?
But how can just one histone modification (H3K27ac) distinguish an enhancer from a non-enhancer?
While still a valuable indicator, it is just one component of a complex feature.
But how can just one histone modification (H3K27ac) distinguish an enhancer from a non-enhancer?
While still a valuable indicator, it is just one component of a complex feature.
“Our findings suggest the existence of tens of thousands of enhancers that remain undiscovered by currently available chromatin data, underscoring the continued need for expanding resources for enhancer discovery.”
Great paper and very important finding - many congrats Axel & team! 👏👏
Great paper and very important finding - many congrats Axel & team! 👏👏
August 8, 2025 at 9:50 PM
Multiple TF-coactivators regulate enhancer/promoter activity. Right?
But how can just one histone modification (H3K27ac) distinguish an enhancer from a non-enhancer?
While still a valuable indicator, it is just one component of a complex feature.
But how can just one histone modification (H3K27ac) distinguish an enhancer from a non-enhancer?
While still a valuable indicator, it is just one component of a complex feature.
Reposted by Pradeepa Madapura
🚨 New paper alert 🚨
I am excited to share our new work on epigenetic enhancer priming in early mammalian development
genomebiology.biomedcentral.com/articles/10....
Fantastic collaboration with Wolf Reik’s team, with key contributions from many others, led by the excellent Chris Todd.
Short 🧵
I am excited to share our new work on epigenetic enhancer priming in early mammalian development
genomebiology.biomedcentral.com/articles/10....
Fantastic collaboration with Wolf Reik’s team, with key contributions from many others, led by the excellent Chris Todd.
Short 🧵
Epigenetic priming of mammalian embryonic enhancer elements coordinates developmental gene networks - Genome Biology
Background Embryonic development requires the accurate spatiotemporal execution of cell lineage-specific gene expression programs, which are controlled by transcriptional enhancers. Developmental enha...
genomebiology.biomedcentral.com
July 22, 2025 at 10:26 PM
🚨 New paper alert 🚨
I am excited to share our new work on epigenetic enhancer priming in early mammalian development
genomebiology.biomedcentral.com/articles/10....
Fantastic collaboration with Wolf Reik’s team, with key contributions from many others, led by the excellent Chris Todd.
Short 🧵
I am excited to share our new work on epigenetic enhancer priming in early mammalian development
genomebiology.biomedcentral.com/articles/10....
Fantastic collaboration with Wolf Reik’s team, with key contributions from many others, led by the excellent Chris Todd.
Short 🧵
Reposted by Pradeepa Madapura
Excited to share our hot-off-the-press @biorxivpreprint.bsky.social
that explores how PRC1-mediated H2AK119ub deposition safeguards lineage fidelity during forebrain development. Fantastic work by @lucyadoyle.bsky.social and our colleagues & collaborators. 🥳🧬🧠🔬
www.biorxiv.org/content/10.1...
that explores how PRC1-mediated H2AK119ub deposition safeguards lineage fidelity during forebrain development. Fantastic work by @lucyadoyle.bsky.social and our colleagues & collaborators. 🥳🧬🧠🔬
www.biorxiv.org/content/10.1...
H2AK119ub Safeguards Against Ectopic Transcription Factor Mediated Gene Activation in the Developing Forebrain
The PRC1 complex regulates developmental gene expression in mammals by ubiquitinating histones (H2AK119ub) and nucleating repressive chromatin interactions. Human genetic data and functional experimen...
www.biorxiv.org
July 12, 2025 at 12:50 AM
Excited to share our hot-off-the-press @biorxivpreprint.bsky.social
that explores how PRC1-mediated H2AK119ub deposition safeguards lineage fidelity during forebrain development. Fantastic work by @lucyadoyle.bsky.social and our colleagues & collaborators. 🥳🧬🧠🔬
www.biorxiv.org/content/10.1...
that explores how PRC1-mediated H2AK119ub deposition safeguards lineage fidelity during forebrain development. Fantastic work by @lucyadoyle.bsky.social and our colleagues & collaborators. 🥳🧬🧠🔬
www.biorxiv.org/content/10.1...
I hope to see many chromatin and transcription enthusiasts at this annual event, this time in Manchester.
Please register as soon as possible and submit abstracts for oral presentations and posters.
Please register as soon as possible and submit abstracts for oral presentations and posters.
Taking place on 17-19 September 2025, Transcription and Chromatin UK will showcase cutting-edge research and is a ‘mustattend’ for anyone within the transcription and epigenetics community🧪. Register now: www.eventsforce.net/biochemsoc/2...
July 10, 2025 at 8:56 PM
I hope to see many chromatin and transcription enthusiasts at this annual event, this time in Manchester.
Please register as soon as possible and submit abstracts for oral presentations and posters.
Please register as soon as possible and submit abstracts for oral presentations and posters.
Registration for Transcription and Chromatin UK is OPEN! Taking place from September 17 to 19, 2025, this conference will showcase cutting-edge research and is a ‘must-attend’ event for the UK transcription and chromatin community & both at home and abroad.
Pl register ow.ly/7QQb50W9Alo & share
Pl register ow.ly/7QQb50W9Alo & share
June 26, 2025 at 4:59 PM
Registration for Transcription and Chromatin UK is OPEN! Taking place from September 17 to 19, 2025, this conference will showcase cutting-edge research and is a ‘must-attend’ event for the UK transcription and chromatin community & both at home and abroad.
Pl register ow.ly/7QQb50W9Alo & share
Pl register ow.ly/7QQb50W9Alo & share
Reposted by Pradeepa Madapura
Looking for a Postdoc? A PDRA position is available in the LSI Exeter with Prof Brian Hendrich from September 2025. Do you have experience in mammalian stem cell culture and a solid understanding of molecular & biochemical lab techniques? Apply! Job Ref: Q05546 jobs.exeter.ac.uk/hrpr_webrecr...
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jobs.exeter.ac.uk
June 9, 2025 at 2:01 PM
Looking for a Postdoc? A PDRA position is available in the LSI Exeter with Prof Brian Hendrich from September 2025. Do you have experience in mammalian stem cell culture and a solid understanding of molecular & biochemical lab techniques? Apply! Job Ref: Q05546 jobs.exeter.ac.uk/hrpr_webrecr...
It was great to catch up with many friends and meet new people. Thank you all for participating in this event.
Thank you everyone for participating in the QMUL epigenetics centre launch event. It was a great success. Special thanks to SAB @deborahbourchis.bsky.social @lab-turner.bsky.social
Bas Heijmans and @elisaoricchio.bsky.social for interaction with our centre.
Bas Heijmans and @elisaoricchio.bsky.social for interaction with our centre.
June 5, 2025 at 3:27 PM
It was great to catch up with many friends and meet new people. Thank you all for participating in this event.
Reposted by Pradeepa Madapura
In our last preprint we identify endogenous dsRNAs capable of activating the interferon response. Could these be relevant to our understanding of DiGeorge syndrome (22qDS)?
In collaboration with @herassr.bsky.social and @heick.bsky.social labs
www.biorxiv.org/content/10.1...
In collaboration with @herassr.bsky.social and @heick.bsky.social labs
www.biorxiv.org/content/10.1...
Control of retrotransposon-driven activation of the interferon response by the double-stranded RNA binding protein DGCR8
The type I interferon (IFN) response is the main innate immune pathway against viruses in mammals. This pathway must be tightly regulated to prevent viral spread while avoiding excessive immune respon...
www.biorxiv.org
June 2, 2025 at 12:55 PM
In our last preprint we identify endogenous dsRNAs capable of activating the interferon response. Could these be relevant to our understanding of DiGeorge syndrome (22qDS)?
In collaboration with @herassr.bsky.social and @heick.bsky.social labs
www.biorxiv.org/content/10.1...
In collaboration with @herassr.bsky.social and @heick.bsky.social labs
www.biorxiv.org/content/10.1...
Reposted by Pradeepa Madapura
Using Promoter Capture Hi-C, we linked STARR-seq enhancers to their putative target genes. This revealed that genes interacting with active enhancers had the highest expression levels, followed by genes interacting with primed enhancers, followed by genes interacting with poised enhancers.
June 2, 2025 at 11:32 PM
Using Promoter Capture Hi-C, we linked STARR-seq enhancers to their putative target genes. This revealed that genes interacting with active enhancers had the highest expression levels, followed by genes interacting with primed enhancers, followed by genes interacting with poised enhancers.
Reposted by Pradeepa Madapura
Generating the first STARR-seq map in a non-cancer human cell line, we classified the identified STARR-seq+ enhancers into:
- Active (ATAC-seq+; H3K4me1+; H3K27ac+)
- Primed/Inactive (ATAC-seq+; H3K4me1+; H3K27ac-)
- Poised (ATAC-seq+; H3K27me3+)
- Chromatin repressed (ATAC-seq-)
- Active (ATAC-seq+; H3K4me1+; H3K27ac+)
- Primed/Inactive (ATAC-seq+; H3K4me1+; H3K27ac-)
- Poised (ATAC-seq+; H3K27me3+)
- Chromatin repressed (ATAC-seq-)
June 2, 2025 at 11:31 PM
Generating the first STARR-seq map in a non-cancer human cell line, we classified the identified STARR-seq+ enhancers into:
- Active (ATAC-seq+; H3K4me1+; H3K27ac+)
- Primed/Inactive (ATAC-seq+; H3K4me1+; H3K27ac-)
- Poised (ATAC-seq+; H3K27me3+)
- Chromatin repressed (ATAC-seq-)
- Active (ATAC-seq+; H3K4me1+; H3K27ac+)
- Primed/Inactive (ATAC-seq+; H3K4me1+; H3K27ac-)
- Poised (ATAC-seq+; H3K27me3+)
- Chromatin repressed (ATAC-seq-)
Happy to be part of this exciting work. A must-read for enhancer aficionados: A massive effort has gone into generating genome-wide STARRseq in hPSCs and conducting functional validation assays. Congratulations to all authors, Stefan and Ufuk, for leading this project 🎉.
Delighted & excited to share our latest preprint on non-canonical enhancers in human pluripotent stem cells, the result of a fantastic and fun collaboration with @guenesdoganlab.bsky.social:
www.biorxiv.org/content/10.1...
🧵 below
www.biorxiv.org/content/10.1...
🧵 below
Non-canonical enhancers control gene expression and cell fate in human pluripotent stem cells
Enhancers are key gene regulatory elements that ensure the precise spatiotemporal execution of developmental gene expression programmes. However recent findings indicate that approaches to identify en...
www.biorxiv.org
June 3, 2025 at 6:06 AM
Happy to be part of this exciting work. A must-read for enhancer aficionados: A massive effort has gone into generating genome-wide STARRseq in hPSCs and conducting functional validation assays. Congratulations to all authors, Stefan and Ufuk, for leading this project 🎉.
Reposted by Pradeepa Madapura
Oh wow. Starting grant 0-10 years post PhD from 2027, Consolidator 5-15
Planning to apply for #research #funding from the ERC?
From the next application rounds, expect changes to the:
• proposal structure
• evaluation process
• extra funding you can request
• eligibility for Starting & Consolidator #Grants (from 2027)
More 👇 europa.eu/!RPHWvv
From the next application rounds, expect changes to the:
• proposal structure
• evaluation process
• extra funding you can request
• eligibility for Starting & Consolidator #Grants (from 2027)
More 👇 europa.eu/!RPHWvv
Changes to the 2026 and 2027 Work Programmes
With the launch of the competitions for grants under ERC Work Programme 2026 in July of this year, several changes to the submission of applications and the evaluation of proposals will apply. The mai...
europa.eu
June 2, 2025 at 12:17 PM
Oh wow. Starting grant 0-10 years post PhD from 2027, Consolidator 5-15