Arjun Udupa
@udupaarjun.bsky.social
PhD Student with @marcbuhler.bsky.social at @fmiscience.bsky.social
Master's in Heidelberg, thesis with @karsten-rippe.bsky.social
Editorial assistant at the @nightsciencepod.bsky.social
gene regulation, chromatin, nuclear organisation, synthetic biology
Master's in Heidelberg, thesis with @karsten-rippe.bsky.social
Editorial assistant at the @nightsciencepod.bsky.social
gene regulation, chromatin, nuclear organisation, synthetic biology
Pinned
Arjun Udupa
@udupaarjun.bsky.social
· Dec 13
🧬 1/ Heterochromatin protein 1 (HP1) still surprises us after all these years: It simply sticks to chromatin when pericentric heterochromatin domains – the chromocenters – are activated in mouse fibroblasts and acts as a local rather than global repressor. New preprint: doi.org/10.1101/2024...
It was an absolute pleasure working on this in the group of @karsten-rippe.bsky.social, joining forces with Robin and @janfabio.bsky.social to understand the repressive role of HP1α in transcription. Glad to see this project come to fruition 🥳
Reposted by Arjun Udupa
This is a such an inspiring book about the art of improvisation and how it applies to our lives in general. I think it’s also very relevant also for what it’s like to do science. It was a pleasure to talk with Stephen about it on the Night Science podcast! open.spotify.com/episode/165i...
November 12, 2025 at 4:47 PM
This is a such an inspiring book about the art of improvisation and how it applies to our lives in general. I think it’s also very relevant also for what it’s like to do science. It was a pleasure to talk with Stephen about it on the Night Science podcast! open.spotify.com/episode/165i...
Reposted by Arjun Udupa
Here is the schedule for the next TriRhena Gene Regulation Club at the FMI @fmiscience.bsky.social in Basel 🇨🇭 next week (5 Nov 2025; 14:00-18:45).
Exciting topics ahead & we are looking forward to the #newPI talks by @julianeg.bsky.social (MPI) & Anupama Hemalatha (FMI).
www.ie-freiburg.mpg.de/grc
Exciting topics ahead & we are looking forward to the #newPI talks by @julianeg.bsky.social (MPI) & Anupama Hemalatha (FMI).
www.ie-freiburg.mpg.de/grc
October 30, 2025 at 9:17 AM
Here is the schedule for the next TriRhena Gene Regulation Club at the FMI @fmiscience.bsky.social in Basel 🇨🇭 next week (5 Nov 2025; 14:00-18:45).
Exciting topics ahead & we are looking forward to the #newPI talks by @julianeg.bsky.social (MPI) & Anupama Hemalatha (FMI).
www.ie-freiburg.mpg.de/grc
Exciting topics ahead & we are looking forward to the #newPI talks by @julianeg.bsky.social (MPI) & Anupama Hemalatha (FMI).
www.ie-freiburg.mpg.de/grc
Reposted by Arjun Udupa
AF-CALVADOS: AlphaFold-guided simulations of multi-domain proteins at the proteome level https://www.biorxiv.org/content/10.1101/2025.10.19.683306v1
October 20, 2025 at 1:47 AM
AF-CALVADOS: AlphaFold-guided simulations of multi-domain proteins at the proteome level https://www.biorxiv.org/content/10.1101/2025.10.19.683306v1
Reposted by Arjun Udupa
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
Reposted by Arjun Udupa
What is a promoter? And how does it work?
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
Enhancer-promoter compatibility is mediated by the promoter-proximal region
Gene promoters induce transcription in response to distal enhancers. How enhancers specifically activate their target promoter while bypassing other promoters remains unclear. Here, we find that the p...
www.biorxiv.org
October 16, 2025 at 3:06 PM
What is a promoter? And how does it work?
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters
www.biorxiv.org/content/10.1...
Reposted by Arjun Udupa
Super excited about first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to the brilliant Chase Suiter (not here) & @greenahn.bsky.social on the work! Preprint here:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
October 14, 2025 at 6:45 PM
Super excited about first Shendure/Baker Lab collaboration & preprint on a multiplex sequencing-based strategy for screening de novo proteome editors in mammalian cells. Kudos to the brilliant Chase Suiter (not here) & @greenahn.bsky.social on the work! Preprint here:
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Arjun Udupa
q.e.d Science
Critical Thinking AI for constructive criticism and science evaluation
qedscience.com
October 15, 2025 at 12:22 PM
Reposted by Arjun Udupa
Paper alert! doi.org/10.1038/s443... - "A scheduler for rhythmic gene expression". We show how 9 txn factors suffice for rhythmic gene expression of thousands of genes with any phase or amplitude in #Celegans larvae (and also look at the tissues where oscillations happen) 1/n
October 10, 2025 at 2:17 PM
Paper alert! doi.org/10.1038/s443... - "A scheduler for rhythmic gene expression". We show how 9 txn factors suffice for rhythmic gene expression of thousands of genes with any phase or amplitude in #Celegans larvae (and also look at the tissues where oscillations happen) 1/n
Reposted by Arjun Udupa
Identification of human RNA Polymerase II interactors at early stages of transcription. https://www.biorxiv.org/content/10.1101/2025.10.08.681243v1
October 9, 2025 at 4:20 AM
Identification of human RNA Polymerase II interactors at early stages of transcription. https://www.biorxiv.org/content/10.1101/2025.10.08.681243v1
Reposted by Arjun Udupa
🧵1/ Excited to share our new paper introducing a new #singlecell assay: scTF-seq, a high-throughput single-cell approach to explore how transcription factor (TF) dose shapes cell identity and reprogramming outcomes. 🔗 www.nature.com/articles/s41... Big congrats to the entire team @EPFL & @SIAT_China
Dissecting the impact of transcription factor dose on cell reprogramming heterogeneity using scTF-seq - Nature Genetics
This study introduces single-cell transcription factor (TF) sequencing, a single-cell barcoded and doxycycline-inducible TF overexpression approach that reveals dose-sensitive functional classes of TFs and cellular heterogeneity by mapping TF dose-dependent transcriptomic changes during the reprogramming of mouse embryonic multipotent stromal cells.
www.nature.com
October 6, 2025 at 6:57 AM
🧵1/ Excited to share our new paper introducing a new #singlecell assay: scTF-seq, a high-throughput single-cell approach to explore how transcription factor (TF) dose shapes cell identity and reprogramming outcomes. 🔗 www.nature.com/articles/s41... Big congrats to the entire team @EPFL & @SIAT_China
Reposted by Arjun Udupa
New week, new tool: Find our Protein Domain Designer tool to generate publication-ready protein domain diagrams here: domaindesigner.farnunglab.com
September 29, 2025 at 3:01 PM
New week, new tool: Find our Protein Domain Designer tool to generate publication-ready protein domain diagrams here: domaindesigner.farnunglab.com
Reposted by Arjun Udupa
2nd Meeting on Early Embryogenesis and Epigenetics
16 - 18 Feb 2026 at MPI for Molecular Genetics, Berlin
with support by the Weizmann Institute for Science.
Early bird registration until 30 Sep - register now👇
www.molgen.mpg.de/embryo2026
16 - 18 Feb 2026 at MPI for Molecular Genetics, Berlin
with support by the Weizmann Institute for Science.
Early bird registration until 30 Sep - register now👇
www.molgen.mpg.de/embryo2026
September 26, 2025 at 1:09 PM
2nd Meeting on Early Embryogenesis and Epigenetics
16 - 18 Feb 2026 at MPI for Molecular Genetics, Berlin
with support by the Weizmann Institute for Science.
Early bird registration until 30 Sep - register now👇
www.molgen.mpg.de/embryo2026
16 - 18 Feb 2026 at MPI for Molecular Genetics, Berlin
with support by the Weizmann Institute for Science.
Early bird registration until 30 Sep - register now👇
www.molgen.mpg.de/embryo2026
Reposted by Arjun Udupa
Engineering Inducible Cell Fate Transitions by Harnessing Epigenetic Silencing https://www.biorxiv.org/content/10.1101/2025.09.29.679324v1
September 30, 2025 at 5:04 PM
Engineering Inducible Cell Fate Transitions by Harnessing Epigenetic Silencing https://www.biorxiv.org/content/10.1101/2025.09.29.679324v1
Reposted by Arjun Udupa
We’re excited to host the next TriRhena Gene Regulation Club on November 5!
Attendance is free, but registration (by October 20) is mandatory 👇🏽
Attendance is free, but registration (by October 20) is mandatory 👇🏽
👉 The next TriRhena Gene Regulation Club takes place at the Friedrich Miescher Institute @fmiscience.bsky.social in Basel.
📅 Nov. 5th, 2025 (14:00-20:00)
📌 FMI, Basel
✍️ Registration deadline: Oct. 20th, 2025
Attendance is free 💸 , but registration mandatory:
www.ie-freiburg.mpg.de/gene-regulat...
📅 Nov. 5th, 2025 (14:00-20:00)
📌 FMI, Basel
✍️ Registration deadline: Oct. 20th, 2025
Attendance is free 💸 , but registration mandatory:
www.ie-freiburg.mpg.de/gene-regulat...
TriRhena Gene Regulation Club
The TriRhena Gene Regulation Club is a one-day symposium that brings together researchers from France (IGBMC), Germany (MPI-IE) and Switzerland (FMI) who share a common interest in gene regulation.
www.ie-freiburg.mpg.de
September 26, 2025 at 8:25 AM
We’re excited to host the next TriRhena Gene Regulation Club on November 5!
Attendance is free, but registration (by October 20) is mandatory 👇🏽
Attendance is free, but registration (by October 20) is mandatory 👇🏽
Reposted by Arjun Udupa
Really excited to share our latest work led by @mattiaubertini.bsky.social and @nesslfy.bsky.social: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication.
www.biorxiv.org/content/10.1...
A🧵👇
www.biorxiv.org/content/10.1...
A🧵👇
September 24, 2025 at 9:45 PM
Really excited to share our latest work led by @mattiaubertini.bsky.social and @nesslfy.bsky.social: we report that cohesin loop extrusion creates rare but long-lived encounters between genomic sequences which underlie efficient enhancer-promoter communication.
www.biorxiv.org/content/10.1...
A🧵👇
www.biorxiv.org/content/10.1...
A🧵👇
Reposted by Arjun Udupa
Cecilia Payne-Gaposchkin ✨ figured out what stars are made of ✨ when she was just 25. 🔭🧪
Her PhD thesis basically established the Harvard astro department — at a time when Harvard didn't officially allow woman students.
I wrote this little profile to mark the 100th anniversary of her thesis:
Her PhD thesis basically established the Harvard astro department — at a time when Harvard didn't officially allow woman students.
I wrote this little profile to mark the 100th anniversary of her thesis:
September 24, 2025 at 9:14 AM
Cecilia Payne-Gaposchkin ✨ figured out what stars are made of ✨ when she was just 25. 🔭🧪
Her PhD thesis basically established the Harvard astro department — at a time when Harvard didn't officially allow woman students.
I wrote this little profile to mark the 100th anniversary of her thesis:
Her PhD thesis basically established the Harvard astro department — at a time when Harvard didn't officially allow woman students.
I wrote this little profile to mark the 100th anniversary of her thesis:
Reposted by Arjun Udupa
🔥 New episode of the Night Science Podcast with Akiko Iwasaki @virusesimmunity.bsky.social Yale & HHMI professor, and one of Time Magazine’s 100 most influential people in 2024! Akiko explains how leading large collaborations requires managing expectations, not micromanaging the research.
September 22, 2025 at 7:32 PM
🔥 New episode of the Night Science Podcast with Akiko Iwasaki @virusesimmunity.bsky.social Yale & HHMI professor, and one of Time Magazine’s 100 most influential people in 2024! Akiko explains how leading large collaborations requires managing expectations, not micromanaging the research.
Reposted by Arjun Udupa
🔥A really interesting new episode of the Night Science Podcast came out today! Akiko Iwasaki talks about the art of creativity management & how a discovery is like a gem hidden inside a hairball. nightscience.buzzsprout.com/1744020/epis... @virusesimmunity.bsky.social @nightsciencepod.bsky.social
77 | Akiko Iwasaki and the art of creativity maintenance - Night Science
Akiko Iwasaki, a Yale professor and Howard Hughes Investigator, was named one of Time Magazine’s 100 most influential people in 2024. Together, we reflect on how diverse backgrounds enrich research, a...
nightscience.buzzsprout.com
September 23, 2025 at 3:23 AM
🔥A really interesting new episode of the Night Science Podcast came out today! Akiko Iwasaki talks about the art of creativity management & how a discovery is like a gem hidden inside a hairball. nightscience.buzzsprout.com/1744020/epis... @virusesimmunity.bsky.social @nightsciencepod.bsky.social
Reposted by Arjun Udupa
Check out @cassyni.bsky.social seminar Mechanisms of cellular plasticity presented by @itaiyanai.bsky.social
Great talk about how cells evade chemo with stepwise reprogramming of their transcriptional repertoire -fascinating, and profound implications for therapy!
cassyni.com/events/ApfsK...
Great talk about how cells evade chemo with stepwise reprogramming of their transcriptional repertoire -fascinating, and profound implications for therapy!
cassyni.com/events/ApfsK...
Cassyni | Science starts with a seminar
Seamlessly organise, run and publish academic research seminars. Get started in minutes.
cassyni.com
September 22, 2025 at 9:05 PM
Check out @cassyni.bsky.social seminar Mechanisms of cellular plasticity presented by @itaiyanai.bsky.social
Great talk about how cells evade chemo with stepwise reprogramming of their transcriptional repertoire -fascinating, and profound implications for therapy!
cassyni.com/events/ApfsK...
Great talk about how cells evade chemo with stepwise reprogramming of their transcriptional repertoire -fascinating, and profound implications for therapy!
cassyni.com/events/ApfsK...
Reposted by Arjun Udupa
✨Exciting news: the main story of my PhD is out in Science!
Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation.
📖 Read the full story here: www.science.org/doi/10.1126/...
Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation.
📖 Read the full story here: www.science.org/doi/10.1126/...
Functional maps of a genomic locus reveal confinement of an enhancer by its target gene
Genes are often activated by enhancers located at large genomic distances, and the importance of this positioning is poorly understood. By relocating promoter-reporter constructs into thousands of alt...
www.science.org
September 19, 2025 at 2:09 PM
✨Exciting news: the main story of my PhD is out in Science!
Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation.
📖 Read the full story here: www.science.org/doi/10.1126/...
Together with Christine Moene @cmoene.bsky.social, we explored what happens when you scramble the genome—revealing how Sox2’s position shapes enhancer activation.
📖 Read the full story here: www.science.org/doi/10.1126/...
Reposted by Arjun Udupa
New preprint is up, led by former postdoc Braulio Bonilla.
We know these remodelers regulate nucleosome positions and occupancy, but do they have a role in regulating higher order chromatin structure? We take a peek for BAF and INO80C.
www.biorxiv.org/content/10.1...
We know these remodelers regulate nucleosome positions and occupancy, but do they have a role in regulating higher order chromatin structure? We take a peek for BAF and INO80C.
www.biorxiv.org/content/10.1...
esBAF and INO80C fine-tune subcompartments and differentially regulate enhancer-promoter interactions
The genome is compacted in the nucleus through a hierarchical chromatin organization, ranging from chromosome territories to compartments, topologically associating domains (TADs), and individual nucl...
www.biorxiv.org
September 18, 2025 at 3:00 PM
New preprint is up, led by former postdoc Braulio Bonilla.
We know these remodelers regulate nucleosome positions and occupancy, but do they have a role in regulating higher order chromatin structure? We take a peek for BAF and INO80C.
www.biorxiv.org/content/10.1...
We know these remodelers regulate nucleosome positions and occupancy, but do they have a role in regulating higher order chromatin structure? We take a peek for BAF and INO80C.
www.biorxiv.org/content/10.1...
Reposted by Arjun Udupa
When the cell needs to respond to the environment: A chromatin-splicing love affair
When the cell needs to respond to the environment: A chromatin-splicing love affair
Alternative splicing allows rapid phenotypic adaptation, but the underlying mechanisms remain unclear. Moreau et al. highlight new findings on the critical role of chromatin modifications and 3D nuclear organization in regulating splicing dynamics. Understanding these chromatin-mediated processes provides insights into how organisms sustainably adapt to environmental challenges for rapid responses.
dlvr.it
September 15, 2025 at 7:50 PM
When the cell needs to respond to the environment: A chromatin-splicing love affair
Reposted by Arjun Udupa
Interested in cellular plasticity? Come to my live virtual talk at the Night Science Seminar Series! Free register here: cassyni.com/events/ApfsK...
September 12, 2025 at 9:17 PM
Interested in cellular plasticity? Come to my live virtual talk at the Night Science Seminar Series! Free register here: cassyni.com/events/ApfsK...
Reposted by Arjun Udupa
Engineered histones reshape chromatin in human cells https://www.biorxiv.org/content/10.1101/2025.09.10.674980v1
September 11, 2025 at 8:04 PM
Engineered histones reshape chromatin in human cells https://www.biorxiv.org/content/10.1101/2025.09.10.674980v1
Reposted by Arjun Udupa
Our new pre-print from the Greenberg and Churchman labs shows that activity-dependent modulation of RNA stability is a major, and underappreciated, mechanism of gene regulation in neurons. Tutorial below! www.biorxiv.org/content/10.1... (1/11)
HuD controls widespread RNA stability to drive neuronal activity-dependent responses
Neuronal activity shapes brain development and refines synaptic connectivity in part through dynamic changes in gene expression. While activity-regulated transcriptional programs have been extensively...
www.biorxiv.org
September 9, 2025 at 2:41 PM
Our new pre-print from the Greenberg and Churchman labs shows that activity-dependent modulation of RNA stability is a major, and underappreciated, mechanism of gene regulation in neurons. Tutorial below! www.biorxiv.org/content/10.1... (1/11)