Lab News & Events

We find that two anti-parallel transcripts can create gene expression memory when they overlap with each others promoter.

• Antisense transcription can induce expression memory via stable promoter repression. V Mutzel, T Schwämmle, S Oeverdieck, L Librenjak, B Boesen, M Bothe, RAF Gjaltema, I Dunkel, G Noviello, EG Schulz. Genome Biology 2025

We went to a team retreat! And it was the 10 year anniversary of the group! We had a fantastic time together with many of the alumni, with discussions on science and career, workshops on night science and unconscious biases; canoeing and playing pictionary.

Elodie won the best poster award at the #CRISPR25 conference. Congratulations!!!
The conference “CRISPR and Beyond: Perturbations at Scale to Understand Genomes”, hosted at the Wellcome Sanger Institute, UK, covered high-throughput screening and gene editing, exploring emerging technologies and models.

Yay, the lab moved to newly renovated spaces, all brand new and shiny! Nice spacious cell culture as well :)

Ingrid Pelaez Conde won a poster prize at the 2024 EMBL Conference “Quantitative biology to molecular mechanisms”. Congratulations!!!

Our work to study gene-regulatory principles during early embryonic development at the Xist gene is published as a preprint! Our results suggest an earlier binary gene activation, followed by enhancement of expression, each regulated by a different set of transcription factors and cis-regulatory elements.
Congrats to first author Till who drove this epic work!

• Find it here: “Reporter CRISPR screens decipher cis- and trans-regulatory principles at the Xist locus”. Till Schwaemmle, Gemma Noviello, Eleni Kanata, Jonathan J. Froehlich, Melissa Bothe, Aybuge Altay, Jade Scouarnec, Vivi-Yun Feng, Martin Vingron, Edda G Schulz. BioRxiv 2024

Till defended his thesis! Congratulations for this great defense! He will soon start a postdoc with Arnaud Krebs, EMBL Heidelberg DE & Anshul Kundaje Stanford
US.

Youri Han has joined us for an undergraduate project, welcome!

Lena Milanowski has joined us for an undergraduate project, welcome!

Nelly and Edda wrote a review about regulatory principles in random monoallelic expression.

• Read the article here: "Establishment and maintenance of random monoallelic expression". Eleni Kanata, Rachel Duffié, Edda G. Schulz, Development, 30 May 2024

Alex and Edda wrote a review about genome architecture changes during X-chromosome inactivation.

• Read the article here: "Spatial orchestration of the genome: topological reorganisation during X-chromosome inactivation". Alexandra Martitz, Edda G. Schulz, Current Opinion in Genetics & Development, 24 April 2024

Lena Bocian and Emilia Rezzolla join us for undergratuate projects! Welcome to the team!

We find that two anti-parallel transcripts can create gene expression memory when they overlap with each others promoter.

• Antisense transcription can induce expression memory via stable promoter repression. V Mutzel, T Schwämmle, S Oeverdieck, L Librenjak, B Boesen, M Bothe, RAF Gjaltema, I Dunkel, G Noviello, EG Schulz. BioRxiv 2024

Elodie & Jonathan attended a workshop on massively parallel reporter assays and machine learning. Edda improved her skills in supervising creative problem solving sessions. Ingrid & Vivi went to a PhD kick-off retreat by the Berlin University Alliance, and Nelly is at the week-long PhD course of the EMBO Young Investigator Network, both involve broad training for example developing ideas, grant writing, paper reading, research presentations, and more.

Edda wrote a spotlight article about recent work from the Cremins lab. They found that DNA repeat expansions in Fragile X syndrome result in large heterochromatin domains that interact in trans.

• Read the article here: "BREACHing new grounds in fragile X syndrome: Trinucleotide expansion linked to genome-wide heterochromatin domains and genome misfolding". Edda G. Schulz, Molecular Cell 2024

Vivi Feng joins our team as a PhD candidate. Welcome Vivi!

Congratulations to Edda, who got elected into the review board of the main German research funding agency, Deutsche Forschungsgemeinschaft (DFG), or in English: German Research Foundation.
The review board helps to assess research proposals and shape funding policies in the subject “General Genetics and Functional Genomics”.

• Election results (.pdf).
• Press release of the DFG about election.

 

Read our fresh work: GATA transcription factors are tissue-specific activators of Xist in early embryos, and required for initiation of X inactivation!

• Press release: Equality in gene expression. <<<---
• Publication: GATA transcription factors drive initial Xist upregulation after fertilization through direct activation of long-range enhancers. Liat Ravid Lustig, Abhishek Sampath Kumar, Till Schwämmle, Ilona Dunkel, Gemma Noviello, Elodie Limberg, Raha Weigert, Guido Pacini, René Buschow, Afrah Ghauri, Maximilian Stötzel, Lars Wittler, Alexander Meissner & Edda G. Schulz  Nature Cell Biology 2023
• Edda's tweetorial.

Edda will participate at two upcoming conferences and speak about our work. Please reach out when you are there!

• "Epigenetics and condensates in lineage decisions” (EMBO Workshop) 28–30 Sep 2023 in Dresden, Germany.
• "The Non-coding Genome” (EMBO/EMBL Symposium) 11–14 Oct 2023 in Heidelberg, Germany.

Diana Mojica and Ingrid Pelaez Conde are starting their PhD project and Heleen Mallie joins us for an internship. Welcome to the team!

Read our work: we used serial perturbations with quantitative mathematical modelling to discover the signaling pathways that regulate differences between stem cells with two (female) and one X-chromosome.

• Publication: Modeling unveils sex differences of signaling networks in mouse embryonic stem cells. Zeba Sultana, Mathurin Dorel, Bertram Klinger, Anja Sieber, Ilona Dunkel, Nils Blüthgen, Edda G Schulz. Molecular Systems Biology 2023

Till presents his work on how two different developmental signals are integrated by TFs and cis-regulatory DNA, at the Xist locus. Meet Till here:

• “16th Berlin Summer Meeting of the Berlin Institute for Medical Systems Biology (BIMSB)”, 6 Sep– 7 Sep 2023 in Berlin, Germany.
• “11th Conference of the German Stem Cell Network (GSCN)”, 13 Sep– 15 Sep 2023 in Ulm, Germany.

The lab is excited about the X-chromosome inactivation meeting, 19-22 June 2023, in Berlin. Edda is co-organizer; the whole lab is assisting, and we are all looking forward to meeting the community!

• Meeting website
• Gemma speaks on Tuesday, Edda on Wednesday, and we present posters: Alex (II-62), Elodie (II-46), Nelly (I-39), and Till (II-70)

CasTuner - our tool to tune endogenous gene expression:
Out in a peer-reviewed version, tested on additional targets, in human cells and on physiological phenotypes.

• Publication: CasTuner is a degron and CRISPR/Cas-based toolkit for analog tuning of endogenous gene expression. Noviello G, Gjaltema R, Schulz EG. Nature Communications 2023
• Blog post “behind the paper”: here.

Reach out to Gemma Noviello at the
“EMBO workshop: Systems biology: Linking chromatin and epigenetics to disease and development”, 25 May– 28 May 2023 in Alexandroupoli, Greece.
Gemma will present her work on CasTuner and non-linear dose-responses in X-inactivation.
 

Edda presents our work on how signals are decoded at the Xist locus:

• May 16th, 10:05 am EMBL conference "Chromatin and epigenetics", #EMBLChromatin.

Gemma presents CasTuner, the CRISPR/Cas-based toolkit for analog tuning of gene expression:

• May 10th, 5.30 pm RNA club Berlin.
• May 16th, 6 pm, Bionnale Berlin "Speed Lecture Awards", register and come to vote.

We went on a two-day retreat with the group of Luca Giorgetti!
It started with icebreakers and brief project presentations. For most of the time we brainstormed on our shared research interests to develop several exciting ideas for collaboration. In between we found time for a fun hike and escape room challenge. Thanks to the Giorgetti lab and the EMBO YIP for support!

• Photo impressions
• Giorgetti group

Till went to the week-long PhD course of the EMBO Young Investigator Network in Heidelberg. Daniela & Jade participated in a course at the Institut Curie in Paris. Gemma was at the meeting of her PhD training network Pep-NET in Naples. The programs included presenting the own work and workshops on soft skills, grant writing, paper reviewing, research presentations, and more. Elodie joined a course on deep reading of publications.

Our own Daniela Cecalev won a prize for best presentation & participation at the Curie institutes “18th Course on Epigenetics 2023”. Congratulations Daniela !
 

5^th X-inactivation meeting (EMBO)
19-22 June 2023, in Berlin

Registration deadline: 01 April 2023.
25 talks selected from abstracts.

• Meeting website

Some time back, a german film team visited us for a documentary on gender medicine. It's now online, we are in the first part :

• Link to video (in German)

Ilona celebrates her 40-year anniversary of working at this institute! We are very grateful to have her on our team, managing the lab and doing the most challenging experiments!

Rafael Galupa will stay with us for two months to do several CRISPR screens. Welcome!
 

Jonathan Froehlich joins the team as a Postdoc. Welcome!
 

Our Nelly Kanata won a poster prize at the 2022 Max Planck Freiburg Epigenetics Meeting. Congratulations @nellykanata !
 

The new round of PhD program recruitment is open, deadline is January 6^th, 2023.

• IMPRS PhD program

Our lab proposes two potential projects. One to study how different levels in gene regulatory factors affect cellular decision. The second to study how gene regulatory DNA affects cell-to-cell heterogeneity in transcriptional responses. Both projects will be relevant to better understand gene regulation and cell fate; using CRISPR tools, genomic profiling techniques, and relevant computational analysis.

• Project sketches

We present CasTuner, a CRISPR-based toolkit that allows analog tuning of endogenous gene expression.

• CasTuner: a degron and CRISPR/Cas-based toolkit for analog tuning of endogenous gene expression. Noviello G, Rutger RAF, and Schulz EG. BioRxiv 2022
• Edda & Gemma's tweetorial

Nelly will attend the “Max Planck Freiburg 6th Epigenetics Meeting”
30 Nov – 02 Dec 2022
Reach out to Nelly Kanata!
https://events.ie-freiburg.mpg.de/3161/1About_the_conference

 

Till will attend “EMBO - From functional genomics to systems biology”
15 - 18 Nov 2022
Reach out to Till Schwämmle!
https://www.embl.org/about/info/course-and-conference-office/events/omx22-01/
 

We scanned the regulatory landscape of Xist and found several proximal and distal enhancers, as well as a new ncRNA Xert, that all control X-inactivation.

• Distal and proximal cis-regulatory elements sense X-chromosomal dosage and developmental state at the Xist locus. Gjaltema RAF*, Schwämmle T*, Kautz P, Robson M, Schöpflin R, Lustig LR, Brandenburg L, Dunkel I, Vechiatto C, Ntini E, Mutzel V, Schmiedel V, Marsico A, Mundlos S, Schulz EG. Molecular Cell 2021
• Preview by Elphège Nora here.
• Institute’s press release here.

Edda has been accepted by the European Molecular Biology Organization (EMBO) into its Young Investigators Programme. Every year, the organization honors the most promising young researchers in Europe.

• Institute’s press release here.

Our work together with the Marsico lab, where we use machine learning to identify the rules of Xist-mediated gene silencing was published:

• Kinetics of Xist-induced gene silencing can be predicted from combinations of epigenetic and genomic features. Barros de Andrade E Sousa L, Jonkers I, Syx L, Dunkel I, Chaumeil J, Picard C, Foret B, Chen CJ, Lis JT, Heard E, Schulz EG, Marsico A. Genome Res. 2019

First mathematical model of Xist regulatory network published. See press release

• A symmetric toggle switch explains the onset of random X inactivation in different mammals. Mutzel V, Okamoto I, Dunkel I, Saitou M, Giorgetti L, Heard E, Schulz EG. Nature Structural and Molecular Biology 2019

As part of the "Max Planck Day" we got a visit from the Youtuber Dr Watson to explain our work on X inactivation.

• Link to the video "Welche Geheimnisse haben X-Chromosomen?" (in German).
• Information about the Max Planck Day (in German).