Konrad Chudzik
@konrad-chudzik.bsky.social
PhD Candidate in Regulatory Genome program (IRTG2403) |
Robson lab - Berlin Institute for Medical Systems Biology (MDC-BIMSB) & Mundlos Lab - Max Planck Institute for Molecular Genetics |
Genome Regulation, Nuclear Envelope, LADs
Robson lab - Berlin Institute for Medical Systems Biology (MDC-BIMSB) & Mundlos Lab - Max Planck Institute for Molecular Genetics |
Genome Regulation, Nuclear Envelope, LADs
Reposted by Konrad Chudzik
Pretty surreal to see my artwork on the cover of Nature Genetics! Big congrats to @julianeg.bsky.social, @stemundi.bsky.social and the others, and thank you Juliane for letting me help bring your research to life visually.
www.nature.com/ng/volumes/5...
www.nature.com/ng/volumes/5...
July 23, 2025 at 8:06 AM
Pretty surreal to see my artwork on the cover of Nature Genetics! Big congrats to @julianeg.bsky.social, @stemundi.bsky.social and the others, and thank you Juliane for letting me help bring your research to life visually.
www.nature.com/ng/volumes/5...
www.nature.com/ng/volumes/5...
Reposted by Konrad Chudzik
Another paper bluetorial! Today: how does the spatial location of genes influence their function? (1/n) www.nature.com/articles/s41...
The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fate - Nature Cell Biology
Marin et al. report the role of lamin proteins and the lamin B receptor (LBR) in chromatin positioning at the nuclear periphery. Knockout of all lamins and LBR in mouse embryonic stem cells leads to h...
www.nature.com
July 22, 2025 at 5:10 PM
Another paper bluetorial! Today: how does the spatial location of genes influence their function? (1/n) www.nature.com/articles/s41...
Reposted by Konrad Chudzik
I am very excited to share our latest work where we describe a new method to profile genome-wide chromatin transitions over time in single cells. Great collaborative effort with the van Oudenaarden group @hubrechtinstitute.bsky.social @oncodeinstitute.bsky.social www.nature.com/articles/s41....
Retrospective and multifactorial single-cell profiling reveals sequential chromatin reorganization during X inactivation - Nature Cell Biology
Kefalopoulou, Rullens et al. develop Dam&ChIC to assay chromatin state at two different time points in the same cell. The method was used to study the reorganization of LADs during cell division a...
www.nature.com
July 10, 2025 at 2:36 PM
I am very excited to share our latest work where we describe a new method to profile genome-wide chromatin transitions over time in single cells. Great collaborative effort with the van Oudenaarden group @hubrechtinstitute.bsky.social @oncodeinstitute.bsky.social www.nature.com/articles/s41....
Reposted by Konrad Chudzik
Finally out! 🥳 Our paper showing how a transposable element (TE) insertion can cause developmental phenotypes is now published @natgenet.nature.com 🧬🦠🐁
Below is a brief description of the major findings. Check the full version of the paper for more details: www.nature.com/articles/s41588-025-02248-5
Below is a brief description of the major findings. Check the full version of the paper for more details: www.nature.com/articles/s41588-025-02248-5
Enhancer adoption by an LTR retrotransposon generates viral-like particles, causing developmental limb phenotypes - Nature Genetics
Activation of an LTR retrotransposon inserted upstream of the Fgf8 gene produces viral-like particles in the mouse developing limb, triggering apoptosis and causing limb malformation. This phenotype c...
www.nature.com
July 9, 2025 at 10:05 AM
Finally out! 🥳 Our paper showing how a transposable element (TE) insertion can cause developmental phenotypes is now published @natgenet.nature.com 🧬🦠🐁
Below is a brief description of the major findings. Check the full version of the paper for more details: www.nature.com/articles/s41588-025-02248-5
Below is a brief description of the major findings. Check the full version of the paper for more details: www.nature.com/articles/s41588-025-02248-5
Reposted by Konrad Chudzik
Calling all aspiring Postdocs! One extra week to apply to join our exciting HFSP-funded project to uncover how chromatin moves to function.
Deadline July 15th.
www.mdc-berlin.de/career/jobs/...
Deadline July 15th.
www.mdc-berlin.de/career/jobs/...
July 8, 2025 at 9:12 AM
Calling all aspiring Postdocs! One extra week to apply to join our exciting HFSP-funded project to uncover how chromatin moves to function.
Deadline July 15th.
www.mdc-berlin.de/career/jobs/...
Deadline July 15th.
www.mdc-berlin.de/career/jobs/...
Reposted by Konrad Chudzik
How do non-coding variants in enhancers lead to disease? Happy to share our recent work, led by @ewholling.bsky.social, in which we discovered that poised chromatin sensitizes enhancers to aberrant activation by non-coding mutations, contributing to disease. www.biorxiv.org/content/10.1... 1/
June 23, 2025 at 12:57 PM
How do non-coding variants in enhancers lead to disease? Happy to share our recent work, led by @ewholling.bsky.social, in which we discovered that poised chromatin sensitizes enhancers to aberrant activation by non-coding mutations, contributing to disease. www.biorxiv.org/content/10.1... 1/
Reposted by Konrad Chudzik
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 2, 2025 at 11:26 PM
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
Reposted by Konrad Chudzik
How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...
Conservation of regulatory elements with highly diverged sequences across large evolutionary distances
Nature Genetics - Combining functional genomic data from mouse and chicken with a synteny-based strategy identifies positionally conserved cis-regulatory elements in the absence of direct sequence...
rdcu.be
May 27, 2025 at 12:19 PM
How to find Evolutionary Conserved Enhancers in 2025? 🐣-🐭
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...
Check out our paper - fresh off the press!!!
We find widespread functional conservation of enhancers in absence of sequence homology
Including: a bioinformatic tool to map sequence-diverged enhancers!
rdcu.be/enVDN
github.com/tobiaszehnde...
Reposted by Konrad Chudzik
We're thrilled to continue our deep dive into how chromatin mechanics govern how our genomes function with our A-team @andersshansen.bsky.social @Davide Michieletto, and @Sandra Tenreiro.
A huge thanks to the @dfg.de and @hfspo.bsky.social for supporting us.
Stay tuned! PhDs/Postdocs coming soon!
A huge thanks to the @dfg.de and @hfspo.bsky.social for supporting us.
Stay tuned! PhDs/Postdocs coming soon!
@drmrobson.bsky.social has won two grants from @dfg.de & @hfspo.bsky.social totaling over €2 million. He and his lab now work to decode the mechanics of #chromatin, hoping to finally define its physical state and better understand how it governs gene regulation
www.mdc-berlin.de/news/news/mi...
www.mdc-berlin.de/news/news/mi...
May 31, 2025 at 12:38 PM
We're thrilled to continue our deep dive into how chromatin mechanics govern how our genomes function with our A-team @andersshansen.bsky.social @Davide Michieletto, and @Sandra Tenreiro.
A huge thanks to the @dfg.de and @hfspo.bsky.social for supporting us.
Stay tuned! PhDs/Postdocs coming soon!
A huge thanks to the @dfg.de and @hfspo.bsky.social for supporting us.
Stay tuned! PhDs/Postdocs coming soon!
Reposted by Konrad Chudzik
@drmrobson.bsky.social has won two grants from @dfg.de & @hfspo.bsky.social totaling over €2 million. He and his lab now work to decode the mechanics of #chromatin, hoping to finally define its physical state and better understand how it governs gene regulation
www.mdc-berlin.de/news/news/mi...
www.mdc-berlin.de/news/news/mi...
May 30, 2025 at 12:50 PM
@drmrobson.bsky.social has won two grants from @dfg.de & @hfspo.bsky.social totaling over €2 million. He and his lab now work to decode the mechanics of #chromatin, hoping to finally define its physical state and better understand how it governs gene regulation
www.mdc-berlin.de/news/news/mi...
www.mdc-berlin.de/news/news/mi...
🚨 Preprint 🚨
Ever wondered how cells prepare their genomes to enable new cell-fates? In this team up with the Kind lab, we show that genes are repositioned in the nucleus to get ready for future activation and tissue formation. Read 🧵👇 to find out how and when this happens!
doi.org/10.1101/2025...
Ever wondered how cells prepare their genomes to enable new cell-fates? In this team up with the Kind lab, we show that genes are repositioned in the nucleus to get ready for future activation and tissue formation. Read 🧵👇 to find out how and when this happens!
doi.org/10.1101/2025...
Reconfiguration of genome-lamina interactions marks the commissioning of limb cell-fates
Diverse forms of heterochromatin block inappropriate transcription and safeguard differentiation and cell identity. Yet, how and when heterochromatin is reconfigured to facilitate changes in cell-fate...
www.biorxiv.org
May 8, 2025 at 9:43 AM
🚨 Preprint 🚨
Ever wondered how cells prepare their genomes to enable new cell-fates? In this team up with the Kind lab, we show that genes are repositioned in the nucleus to get ready for future activation and tissue formation. Read 🧵👇 to find out how and when this happens!
doi.org/10.1101/2025...
Ever wondered how cells prepare their genomes to enable new cell-fates? In this team up with the Kind lab, we show that genes are repositioned in the nucleus to get ready for future activation and tissue formation. Read 🧵👇 to find out how and when this happens!
doi.org/10.1101/2025...
Reposted by Konrad Chudzik
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 Konrad Chudzik
I am elated to share that our manuscript describing Variant-EFFECTS, a high-throughput technology we developed to precisely and quantitatively measure the effects of CRISPR-mediated edits on gene expression, is now published at @cellpress.bsky.social: authors.elsevier.com/c/1kxgiL7PXu...
authors.elsevier.com
April 17, 2025 at 6:20 PM
I am elated to share that our manuscript describing Variant-EFFECTS, a high-throughput technology we developed to precisely and quantitatively measure the effects of CRISPR-mediated edits on gene expression, is now published at @cellpress.bsky.social: authors.elsevier.com/c/1kxgiL7PXu...
🚨 Preprint alert 🚨
Excited to share our work on "Ab-trapping," an antibody artifact causing misleading peripheral ("rim") staining in imaging & genomics (IF, CUT&Tag, CUT&RUN). Antibodies fail to penetrate structures, accumulating at the periphery. A 🧵👇
doi.org/10.1101/2025...
Excited to share our work on "Ab-trapping," an antibody artifact causing misleading peripheral ("rim") staining in imaging & genomics (IF, CUT&Tag, CUT&RUN). Antibodies fail to penetrate structures, accumulating at the periphery. A 🧵👇
doi.org/10.1101/2025...
Ab-trapping - a peripheral staining artifact in antibody-based microscopy and genomics
Antibodies (Ab) are essential for detecting specific epitopes in microscopy and genomics, but can produce artifacts leading to erroneous interpretations. Here, we characterize a novel artifact, Ab-tra...
doi.org
April 14, 2025 at 8:08 PM
🚨 Preprint alert 🚨
Excited to share our work on "Ab-trapping," an antibody artifact causing misleading peripheral ("rim") staining in imaging & genomics (IF, CUT&Tag, CUT&RUN). Antibodies fail to penetrate structures, accumulating at the periphery. A 🧵👇
doi.org/10.1101/2025...
Excited to share our work on "Ab-trapping," an antibody artifact causing misleading peripheral ("rim") staining in imaging & genomics (IF, CUT&Tag, CUT&RUN). Antibodies fail to penetrate structures, accumulating at the periphery. A 🧵👇
doi.org/10.1101/2025...