Sergei Pirogov
@biologsp.bsky.social
PhD student | Mannervik lab | Stockholm University | developmental epigenetics and chromatin of Drosophila| histone acetylation and methylation
Pinned
Sergei Pirogov
@biologsp.bsky.social
· Jun 18
The amazing projects wait for curious minds! From fly genetics to transcriptional kinetics, from whole-embryo single-cell atlases to the charming chromatin microscopy!
Welcoming at @stockholm-uni.bsky.social
#epigenetics #chromatin #DevBio
Welcoming at @stockholm-uni.bsky.social
#epigenetics #chromatin #DevBio
Reposted by Sergei Pirogov
Thrilled to share that I’ll be joining @imbmainz.bsky.social in February 2026 to start my own group!
We will explore new mechanisms in eukaryotic gene expression, leveraging ‘evolutionary play’ to uncover how regulation, repurposing, and hijacking shape RNA biology.
PhD positions available!
We will explore new mechanisms in eukaryotic gene expression, leveraging ‘evolutionary play’ to uncover how regulation, repurposing, and hijacking shape RNA biology.
PhD positions available!
October 12, 2025 at 8:19 PM
Thrilled to share that I’ll be joining @imbmainz.bsky.social in February 2026 to start my own group!
We will explore new mechanisms in eukaryotic gene expression, leveraging ‘evolutionary play’ to uncover how regulation, repurposing, and hijacking shape RNA biology.
PhD positions available!
We will explore new mechanisms in eukaryotic gene expression, leveraging ‘evolutionary play’ to uncover how regulation, repurposing, and hijacking shape RNA biology.
PhD positions available!
Reposted by Sergei Pirogov
Kicked off a series on #Drosophila TE discovery and naming. The first post covers elements that predate the term "mobile element", and more. artemilin.dev/posts/te_nam...
Drosophila TE name origins, Part 1 – Postdoc Postpunk
artemilin.dev
September 21, 2025 at 7:49 PM
Kicked off a series on #Drosophila TE discovery and naming. The first post covers elements that predate the term "mobile element", and more. artemilin.dev/posts/te_nam...
Reposted by Sergei Pirogov
🧬Postdoc position alert! 🚨 We're hiring a postoc in Computational Modeling of Epigenetic Inheritance at the Hubrecht Institute (Alexander van Oudenaarden, Utrecht 🇳🇱) & Danish Cancer Institute (Anja Groth, Copenhagen 🇩🇰).
Come work in our collaberative team of top scientists
shorturl.at/avBBy
Come work in our collaberative team of top scientists
shorturl.at/avBBy
Postdoctoral Researcher - Computational modeling of Epigenetic Inheritance - 38 hours p/w - Hubrecht Institute
About the Project Faithful inheritance of the epigenome in proliferating cells critically underpins human development and health. While DNA replication fidelity and DNA mutation rates are well underst...
shorturl.at
May 16, 2025 at 7:45 AM
🧬Postdoc position alert! 🚨 We're hiring a postoc in Computational Modeling of Epigenetic Inheritance at the Hubrecht Institute (Alexander van Oudenaarden, Utrecht 🇳🇱) & Danish Cancer Institute (Anja Groth, Copenhagen 🇩🇰).
Come work in our collaberative team of top scientists
shorturl.at/avBBy
Come work in our collaberative team of top scientists
shorturl.at/avBBy
Reposted by Sergei Pirogov
We are looking for a student to continue our work on chromatin evolution:
www.nature.com/articles/s41...
www.biorxiv.org/content/10.1...
The project with @seanamontgomery.bsky.social will focus on chromatin state readers across eukaryotes.
More info: recruitment.crg.eu/content/jobs...
www.nature.com/articles/s41...
www.biorxiv.org/content/10.1...
The project with @seanamontgomery.bsky.social will focus on chromatin state readers across eukaryotes.
More info: recruitment.crg.eu/content/jobs...
July 15, 2025 at 11:30 AM
We are looking for a student to continue our work on chromatin evolution:
www.nature.com/articles/s41...
www.biorxiv.org/content/10.1...
The project with @seanamontgomery.bsky.social will focus on chromatin state readers across eukaryotes.
More info: recruitment.crg.eu/content/jobs...
www.nature.com/articles/s41...
www.biorxiv.org/content/10.1...
The project with @seanamontgomery.bsky.social will focus on chromatin state readers across eukaryotes.
More info: recruitment.crg.eu/content/jobs...
Reposted by Sergei Pirogov
The "reproducibility crisis" in science constantly makes headlines. Repro efforts are often limited. What if you could assess reproducibility of an entire field?
That's what @brunolemaitre.bsky.social et al. have done. Fly immunity is highly replicable & offers lessons for #metascience
A 🧵 1/n
That's what @brunolemaitre.bsky.social et al. have done. Fly immunity is highly replicable & offers lessons for #metascience
A 🧵 1/n
July 10, 2025 at 8:23 AM
The "reproducibility crisis" in science constantly makes headlines. Repro efforts are often limited. What if you could assess reproducibility of an entire field?
That's what @brunolemaitre.bsky.social et al. have done. Fly immunity is highly replicable & offers lessons for #metascience
A 🧵 1/n
That's what @brunolemaitre.bsky.social et al. have done. Fly immunity is highly replicable & offers lessons for #metascience
A 🧵 1/n
Reposted by Sergei Pirogov
To be or not to be 🤴💀: read how hamlet orchestrates the assembly of adult male reproductive system in #Drosophila in a new paper from our colleagues! Led by Huazhen Wang, a PhD student in Qi Dai group, the study explores how this protein mediates the fusion of testis and supportive gonadal tissue
Drosophila hamlet mediates epithelial tissue assembly of the reproductive system
Hamlet regulates heterotypic epithelial fusion by controlling spatial and temporal expression of known and novel epithelial regulators like Wnt and Tl pathway components, a mechanism potentially conse...
doi.org
July 5, 2025 at 1:02 PM
To be or not to be 🤴💀: read how hamlet orchestrates the assembly of adult male reproductive system in #Drosophila in a new paper from our colleagues! Led by Huazhen Wang, a PhD student in Qi Dai group, the study explores how this protein mediates the fusion of testis and supportive gonadal tissue
Reposted by Sergei Pirogov
Happy to announce a new preprint from my lab looking in to the establishment of polycomb domains in early fly development and contributions from pioneer factors Zelda and GAGA-factor.
Nucleation-dependent propagation of Polycomb modifications emerges during the Drosophila maternal to zygotic transition https://www.biorxiv.org/content/10.1101/2025.07.02.662854v1
July 3, 2025 at 9:44 PM
Happy to announce a new preprint from my lab looking in to the establishment of polycomb domains in early fly development and contributions from pioneer factors Zelda and GAGA-factor.
Reposted by Sergei Pirogov
How did life begin & why does it matter? A new ASM report, supported by the Gordon and Betty Moore Foundation, explores the origins of microbial life & how understanding it can help tackle some of humanity’s biggest questions around climate, biotech & more. Press release➡️ asm.org/press-releas...
June 16, 2025 at 4:27 PM
How did life begin & why does it matter? A new ASM report, supported by the Gordon and Betty Moore Foundation, explores the origins of microbial life & how understanding it can help tackle some of humanity’s biggest questions around climate, biotech & more. Press release➡️ asm.org/press-releas...
Reposted by Sergei Pirogov
Textbooks: “Enhancers are just a bunch of TFBSs”
But how do they REALLY work?
New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social
A 🧵 (1/n)
Free access link: rdcu.be/erD22
But how do they REALLY work?
New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social
A 🧵 (1/n)
Free access link: rdcu.be/erD22
June 18, 2025 at 5:56 PM
Textbooks: “Enhancers are just a bunch of TFBSs”
But how do they REALLY work?
New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social
A 🧵 (1/n)
Free access link: rdcu.be/erD22
But how do they REALLY work?
New paper with many contributors here @berkeleylab.lbl.gov, @anshulkundaje.bsky.social, @anusri.bsky.social
A 🧵 (1/n)
Free access link: rdcu.be/erD22
The amazing projects wait for curious minds! From fly genetics to transcriptional kinetics, from whole-embryo single-cell atlases to the charming chromatin microscopy!
Welcoming at @stockholm-uni.bsky.social
#epigenetics #chromatin #DevBio
Welcoming at @stockholm-uni.bsky.social
#epigenetics #chromatin #DevBio
June 18, 2025 at 2:47 PM
The amazing projects wait for curious minds! From fly genetics to transcriptional kinetics, from whole-embryo single-cell atlases to the charming chromatin microscopy!
Welcoming at @stockholm-uni.bsky.social
#epigenetics #chromatin #DevBio
Welcoming at @stockholm-uni.bsky.social
#epigenetics #chromatin #DevBio
Reposted by Sergei Pirogov
We currently have a call for support that has gone out to European labs, to support FlyBase-UK. We are asking our colleagues from labs in the US and other countries to wait for a similar call to them that will go out in the near future, to support the US sites. We thank you for your patience.
URGENT: FlyBase has lost practically all its funding overnight; even user fees are tied up in denied grant funding. 🤬🤯
Any lab using @flybase.bsky.social please donate using the link in post below.
This incredible community, on whose backs our #Drosophila labs depend, can't be left out to dry.
Any lab using @flybase.bsky.social please donate using the link in post below.
This incredible community, on whose backs our #Drosophila labs depend, can't be left out to dry.
My lab studies bacterial infections. We spend a lot of time looking at (or for) species-specific genetic and genomic databases for hosts and microbes. FlyBase is the best of all—there is literally no comparison. Its existence is under threat. Please donate.
www.philanthropy.cam.ac.uk/give-to-camb...
www.philanthropy.cam.ac.uk/give-to-camb...
June 3, 2025 at 9:17 PM
We currently have a call for support that has gone out to European labs, to support FlyBase-UK. We are asking our colleagues from labs in the US and other countries to wait for a similar call to them that will go out in the near future, to support the US sites. We thank you for your patience.
Very interesting! I liked James's comment "We should probably think of decision making as a dynamical process rather than an event. And relate to this to dev bio concepts such as competence, specification and commitment."
I wonder how it would look like if applied to scATAC/scCUT&Tag data. Fuzzier?
I wonder how it would look like if applied to scATAC/scCUT&Tag data. Fuzzier?
Surprising Finding: Studying neural tube differentiation, we discovered an unexpected circular topology
Cells that initially diverge into different lineages can converge through multiple routes to the same fate
This challenges the traditional "branching tree" view of development
Cells that initially diverge into different lineages can converge through multiple routes to the same fate
This challenges the traditional "branching tree" view of development
May 30, 2025 at 1:42 PM
Very interesting! I liked James's comment "We should probably think of decision making as a dynamical process rather than an event. And relate to this to dev bio concepts such as competence, specification and commitment."
I wonder how it would look like if applied to scATAC/scCUT&Tag data. Fuzzier?
I wonder how it would look like if applied to scATAC/scCUT&Tag data. Fuzzier?
Excited to share our new paper in @cp-molcell.bsky.social Molecular Cell: "Catalytic-dependent and independent functions of the histone acetyltransferase CBP promote pioneer-factor-mediated zygotic genome activation" — the big part of my PhD! www.cell.com/molecular-ce...
Catalytic-dependent and independent functions of the histone acetyltransferase CBP promote pioneer-factor-mediated zygotic genome activation
Marsh, Pirogov, et al. use the early Drosophila embryo to demonstrate that the conserved
histone acetyltransferase CBP is required for pioneer-factor-mediated transcriptional
activation of the zygotic...
www.cell.com
May 30, 2025 at 12:52 PM
Excited to share our new paper in @cp-molcell.bsky.social Molecular Cell: "Catalytic-dependent and independent functions of the histone acetyltransferase CBP promote pioneer-factor-mediated zygotic genome activation" — the big part of my PhD! www.cell.com/molecular-ce...
The superb conference in EMBL Epigenetics&Chromatin is over. Fantastic talks, a lot of incredible research in the poster section. I was glad to present two of my PhD projects: catalytic and non-catalytic function of CBP/p300 in development, and single-cell epigenetic landscapes of Drosophila embryo.
May 16, 2025 at 4:28 PM
The superb conference in EMBL Epigenetics&Chromatin is over. Fantastic talks, a lot of incredible research in the poster section. I was glad to present two of my PhD projects: catalytic and non-catalytic function of CBP/p300 in development, and single-cell epigenetic landscapes of Drosophila embryo.
Reposted by Sergei Pirogov
Attending the EMBL conference on Chromatin and epigenetics www.embl.org/about/info/c... ?? Check out posters 184 and 185 by SCENTINEL partners Mattias Mannervik and Sergei Pirogov, cbp/p300 unexpected function! Just accepted! doi.org/10.1101/2024...
Catalytic-dependent and independent functions of the histone acetyltransferase CBP promote pioneer factor-mediated zygotic genome activation
Immediately after fertilization the genome is transcriptionally quiescent. Maternally encoded pioneer transcription factors reprogram the chromatin state and facilitate the transcription of the zygoti...
doi.org
May 12, 2025 at 7:12 PM
Attending the EMBL conference on Chromatin and epigenetics www.embl.org/about/info/c... ?? Check out posters 184 and 185 by SCENTINEL partners Mattias Mannervik and Sergei Pirogov, cbp/p300 unexpected function! Just accepted! doi.org/10.1101/2024...
Reposted by Sergei Pirogov
I’m very excited to share our work on the early evolution of animal regulatory genome architecture - the main project of my postdoc, carried out across two wonderful and inspirational labs of @arnausebe.bsky.social and @mamartirenom.bsky.social. www.nature.com/articles/s41...
Chromatin loops are an ancestral hallmark of the animal regulatory genome - Nature
The physical organization of the genome in non-bilaterian animals and their closest unicellular relatives is characterized; comparative analysis shows chromatin looping is a conserved feature of ...
www.nature.com
May 7, 2025 at 3:23 PM
I’m very excited to share our work on the early evolution of animal regulatory genome architecture - the main project of my postdoc, carried out across two wonderful and inspirational labs of @arnausebe.bsky.social and @mamartirenom.bsky.social. www.nature.com/articles/s41...
Reposted by Sergei Pirogov
Read the paper here! www.biorxiv.org/content/10.1...
Congrats to Janith and the rest of the lab @petermaccc.bsky.social, and thanks to collaborators Shabih Shakeel @wehi-research.bsky.social, @benparkerlab.bsky.social and @burrlab.bsky.social, and ongoing support from @snowmedical.bsky.social
(6/6)
Congrats to Janith and the rest of the lab @petermaccc.bsky.social, and thanks to collaborators Shabih Shakeel @wehi-research.bsky.social, @benparkerlab.bsky.social and @burrlab.bsky.social, and ongoing support from @snowmedical.bsky.social
(6/6)
Embryonic stem cell factors DPPA2/4 facilitate a unique chromatin state in non-small cell lung cancer
Embryonic regulators are often re-expressed in cancers, however the functional and molecular significance of this is not always understood. The epigenetic priming factors Developmental Pluripotency As...
www.biorxiv.org
April 28, 2025 at 11:07 AM
Read the paper here! www.biorxiv.org/content/10.1...
Congrats to Janith and the rest of the lab @petermaccc.bsky.social, and thanks to collaborators Shabih Shakeel @wehi-research.bsky.social, @benparkerlab.bsky.social and @burrlab.bsky.social, and ongoing support from @snowmedical.bsky.social
(6/6)
Congrats to Janith and the rest of the lab @petermaccc.bsky.social, and thanks to collaborators Shabih Shakeel @wehi-research.bsky.social, @benparkerlab.bsky.social and @burrlab.bsky.social, and ongoing support from @snowmedical.bsky.social
(6/6)
Reposted by Sergei Pirogov
Last day to apply to a PhD position in my lab - comparative epigenomic project focusing on development nad evolution of the human brain. Apply below 👇
PhD Position Available! 🧑🎓🧠🧬
We’re looking for a motivated PhD student to join our team and explore the fascinating world of human brain development and evolution.
su.varbi.com/what:job/job...
We’re looking for a motivated PhD student to join our team and explore the fascinating world of human brain development and evolution.
su.varbi.com/what:job/job...
Doktorand i neurokemi
Institutionen för biokemi och biofysik , institutionens lokaler ligger huvudsakligen i Arrheniuslaboratorierna tillsammans med de andra kemiinstitutionerna och andra institutioner inom Naturvetenskap
su.varbi.com
April 21, 2025 at 9:21 PM
Last day to apply to a PhD position in my lab - comparative epigenomic project focusing on development nad evolution of the human brain. Apply below 👇
Reposted by Sergei Pirogov
Our recent paper reports extremely long-range (up to 5.1 Mb 😲) regulation of certain genes in fly neurons and provides new insights into how they form (see short thread below 👇).
genesdev.cshlp.org/gca?gca=gene...
genesdev.cshlp.org/gca?gca=gene...
Sign In
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genesdev.cshlp.org
April 18, 2025 at 6:50 PM
Our recent paper reports extremely long-range (up to 5.1 Mb 😲) regulation of certain genes in fly neurons and provides new insights into how they form (see short thread below 👇).
genesdev.cshlp.org/gca?gca=gene...
genesdev.cshlp.org/gca?gca=gene...
Reposted by Sergei Pirogov
Thrilled to see my postdoc work at Adelman Lab @hms-bcmp.bsky.social on Integrator(INT) now out @cp-cell.bsky.social. We found that INT deficiency allows immature+unlicensed RNAPII to precociously enter genes. This immature RNAPII can transcribe short genes but terminates prematurely in long genes:
April 14, 2025 at 4:56 PM
Thrilled to see my postdoc work at Adelman Lab @hms-bcmp.bsky.social on Integrator(INT) now out @cp-cell.bsky.social. We found that INT deficiency allows immature+unlicensed RNAPII to precociously enter genes. This immature RNAPII can transcribe short genes but terminates prematurely in long genes:
Reposted by Sergei Pirogov
Earnshaw, Goloborodko, Dekker & Mirny labs are excited to present our latest work, "Rules of engagement for condensins and cohesins guide mitotic chromosome formation" - now accepted!!
www.science.org/doi/10.1126/...
A short clip describing the key results:
www.youtube.com/watch?v=pmvO...
www.science.org/doi/10.1126/...
A short clip describing the key results:
www.youtube.com/watch?v=pmvO...
Rules of Engagement
YouTube video by Johan Gibcus
www.youtube.com
April 11, 2025 at 7:45 AM
Earnshaw, Goloborodko, Dekker & Mirny labs are excited to present our latest work, "Rules of engagement for condensins and cohesins guide mitotic chromosome formation" - now accepted!!
www.science.org/doi/10.1126/...
A short clip describing the key results:
www.youtube.com/watch?v=pmvO...
www.science.org/doi/10.1126/...
A short clip describing the key results:
www.youtube.com/watch?v=pmvO...
Reposted by Sergei Pirogov
The importance of moving away from bulk! Occupancy of Pol II at promoters is dramatically different between fly and mouse cells! When looking single molecule! Proud of the team! @kasitc.bsky.social @molinalab.bsky.social doi.org/10.1038/s443...
April 2, 2025 at 8:47 AM
The importance of moving away from bulk! Occupancy of Pol II at promoters is dramatically different between fly and mouse cells! When looking single molecule! Proud of the team! @kasitc.bsky.social @molinalab.bsky.social doi.org/10.1038/s443...
Reposted by Sergei Pirogov
I could not be more excited to have our lab's first story online where we report our discovery that HDACs ~reverse~ their activity to ADD acyl groups to lysine! We found this for our favorite ketone body, BHB, but this pathway controls other lysine modifications too!🧵
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reversible histone deacetylase activity catalyzes lysine acylation - Nature Chemical Biology
Tsusaka et al. discover that histone deacetylases, which are well known to remove protein modifications, such as lysine acetylation and β-hydroxybutyrylation, can also reverse their chemical activity ...
www.nature.com
March 26, 2025 at 2:02 PM
I could not be more excited to have our lab's first story online where we report our discovery that HDACs ~reverse~ their activity to ADD acyl groups to lysine! We found this for our favorite ketone body, BHB, but this pathway controls other lysine modifications too!🧵
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Sergei Pirogov
Kseniia Petrova, a Russian scientist at Harvard Medical School, was detained at Logan Airport after returning from France and sent to an ICE detention in Louisiana, The Insider reports.
A big critic of Putin and the war in Ukraine, she may now be deported to Russia.
A big critic of Putin and the war in Ukraine, she may now be deported to Russia.
March 27, 2025 at 8:53 PM
Kseniia Petrova, a Russian scientist at Harvard Medical School, was detained at Logan Airport after returning from France and sent to an ICE detention in Louisiana, The Insider reports.
A big critic of Putin and the war in Ukraine, she may now be deported to Russia.
A big critic of Putin and the war in Ukraine, she may now be deported to Russia.
Reposted by Sergei Pirogov
So, is it compaction or decompaction? Here is a notable alternative hypothesis: "Our data suggest that the process of..loop extrusion per se is not required for enhancer function..Rather, it is the chromatin compaction brought about by loop extrusion that may be the important factor to consider."
Plenty of work required to rigorously test the proposed hypothesis but my initial thoughts are this perspective by Adrian Bird in @cp-molcell.bsky.social may well be the most significant conceptual advance in the 3D genome organisation field in years:
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Cohesin as an essential disruptor of chromosome organization
Cohesin is a multi-subunit molecular machine that is able to create lateral chromatin loops within a linear chromosome fiber. Despite intense study, a…
www.sciencedirect.com
March 26, 2025 at 4:01 PM
So, is it compaction or decompaction? Here is a notable alternative hypothesis: "Our data suggest that the process of..loop extrusion per se is not required for enhancer function..Rather, it is the chromatin compaction brought about by loop extrusion that may be the important factor to consider."