Bas van Steensel group

Chromatin inside a cell nucleus

Our current research project

These are the current project in our lab. If you have any questions about the projects, do not hesitate to contact us.

Last update - 2021.06.03

What makes a LAD border?

The insulator CTCF is enriched at LAD borders, and could help establish such borders. To test this hypothesis, together with the lab of Elzo de Wit we rapidly deplete CTCF and cohesin in mouse embryonic stem cells, and then use our newly developed pA-DamID to map interactions with the NL. Initial results suggest that CTCF is not required for LAD border positioning, but CTCF and cohesin are involved in local escaping from the NL.

Contributors : Tom van Schaik in collaboration with Elzo de Wit's lab

Links between LADs, transcription and DNA supercoiling

The molecular factors and biological processes that play a role in establishing and regulating DNA-NL contacts are basically unknown. By using pA-DamID we aim to understand how transcription affects DNA-NL interactions, and how DNA-NL contacts are controlled by DNA supercoiling and topoisomerases.

Contributor : Stefano Manzo

Decoding the sequence determinants of LADs

LADs are large repressive chromatin domains anchored to the nuclear lamina (NL). To ensure accurate gene expression, LAD recognition and anchoring to the NL have to be tightly regulated. However, little is known about these two mechanisms. My project aims at identifying LAD sequence determinants. For that, I am developing a novel genome-scrambling tool which relies on the recombination between nearby loxP sites randomly integrated by transposable element mobilization. I will determine the effects of the rearrangements on NL association and expression of the surrounding genes and identify sequences that drive LAD formation.

Contributor: Lise Dauban

Identification of factors that mediate transcriptional repression in LADs

LADs are a repressive environment for transcription. Although repressive chromatin marks can partially explain why LADs are not a permissive environment for transcription, the key regulators of LADs repression are unknown.

In collaboration with Brummelkamp Lab at the NKI we are conducting haploid genetic screens in human cells to identify new regulators of lamina-associated repression.

Contributors: Stefano Manzo

Developing a chromatin "unlooper"

This project attempts to physically separate two target loci. We aim to harness the properties of the parMRC segrosome, a complex to push plasmids apart, endogenous to prokaryotes . DNA contacts are strongly correlated with a variety of genomic regulation mechanisms such as gene activation, repression, insulation, DNA repair, etc. Currently, tools to investigate such contacts are invasive, such as deletions which may inadvertently perturb the epigenetic environment. Here we hope to interfere only with spatial contacts, independent of the epigenome, allowing us to literally pick apart the relationship between structure and function of gene regulations in 3D space.

Contributors: Ezequiel Miron & Marcel de Haas

What is the impact of chromatin on DNA double strand break repair?

We aim to understand how the balance between DNA repair pathways is affected by chromatin. To answer this, we combine two technologies: CRISPR/Cas9 & TRIP, that can probe the relative activity of three repair pathways simultaneously in > 1000 genomic locations. This provides detailed insights into the effects of various chromatin environments on DNA repair.

This has been recently published in Molecular Cell.

Contributors : Ruben Schep, Christ Leemans & Xabier Vergara

In this project we aim to profile the role of proteins on DNA repair pathway balance at specific chromatin environments. In close collaboration with the Medema lab we use our DSB TRIP pathway reporter in combination with genetic screens and small molecule screens to identify proteins that play a role in DNA repair in certain chromatin types.

Contributors: Xabier Vergara, Ruben Schep & Max Trauernicht

DNA repair rates of different pathways in the context of chromatin

In this project we make use of the multiplexed reporter assay combined with robotics to measure DSB repair across different loci over many time-points. Using a biophysical model, this allows us to model kinetic rates of individual repair pathways for the different loci. Based on these results we can discover valuable aspects of the relationship between DNA repair and chromatin biology.

Contributors: Christ Leemans & Ruben Schep

Dissecting enhancer-promoter biochemical compatibility

How compatibility between enhancers and promoters works and how it effects gene expression is still largely unknown. We are using variants of our SuRE technology to test thousands of mammalian enhancer-promoter combinations. This approach has showed us that there are different degrees of compatibility between enhancers and promoters. By using computational methods and other technologies from the lab like TRIP we can dissect the underlying mechanisms and how compatibility works in the genome to confer specificity to enhancer - promoter interactions.

Contributor: Miguel Martinez Ara

Dissecting somatic mutations in the non-coding cancer genome

Cancer initiation, progression and metastasis is driven by mutations in the genome. While the impact of mutations in coding regions is well understood, much less is known about the effects of mutations in non-coding regions, which span 97% of the genome. We are using our SuRE technology to systematically identify non-coding mutations that alter the activity of enhancers and promoters in cancer genomes. We study this in colon cancer in collaboration with the Emiel Voest lab and in paediatric leukaemia in collaboration with the Ruben van Boxtel lab.

Contributor: Noud Klaassen

Defining the contribution of sequence content to gene regulation

In this project we use the SuRE technology to measure genome wide autonomous promoter activity. This gives us a rich data-set which we use to computationally model the fine scale individual sequence contribution to this reporter activity. Using this model for every individual promoter in the genome, we aim to predict exactly which sequences in a promoter are responsible for driving its activity. This contributes to a better understanding of gene regulation.

Contributor: Christ Leemans in collaboration with Harmen Bussemaker's lab

Local relocation of regulatory elements in the genome

In order to understand the interplay between regulatory elements in the genome, it will be extremely useful to be able to move such elements to different positions around a gene of interest. We are developing a general strategy to locally "hop around" elements of interest in a highly efficient and scalable manner, and study how this affects the activity of nearby genes. We currently apply this method to study how CTCF can modify the interaction between enhancers and promoters. We anticipate many other applications of this approach.

Contributor: Mathias Eder

Dissection of regulatory sequences

Predicting gene expression from mammalian DNA sequence is a major challenge. As a first step towards this goal, we aim to develop algorithms that predict promoter activity in the absence of distal regulatory elements. We explore both mechanism-based and deep learning algorithms, in collaboration with the lab of Jeroen de Ridder. For this we use data obtained with our SuRE technology. We hope that the extremely high throughput of this technology enables us to unravel the sequence-based rules of promoter activity, to better understand this crucial part of gene regulation.

Contributor: Jérémie Breda

Multiplexed detection of transcription factor activity

Transcription factors (TFs) respond to extra- and intracellular signaling cascades to collectively control the expression of the genome. To better understand how TFs mediate gene regulation, we aim in this project to directly measure the activity of many TFs in parallel using massively parallel reporter assays (MPRAs). Eventually, we also aim to integrate multiple TF reporters into the genome of cells in order to track the activity of multiple TFs in single cells in combination with single-cell mRNA sequencing. This technology platform of multiplexed TF reporters may be broadly used to study how cellular signaling events are transduced to the genome by TFs.

Contributors: Max Trauernicht & Tea Filipovska

Bas van Steensel group

Our current research project

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