Publications
2025
The specificity of CTBP dehydrogenase inhibitors MTOB and 4-Cl-HIPP
C-terminal binding proteins (CTBPs) are conserved transcriptional repressors important in cancer and inflammation. Uniquely amongst transcriptional co-regulators, CTBPs possess a functional dehydrogenase domain. Since multiple malignancies display elevated CTBP levels, CTBP inhibitors targeting this dehydrogenase domain have been developed. While the importance of CTBPs dehydrogenase function for transcriptional regulation remains unclear, several studies have relied on CTBP inhibitors. In vitro experiments have confirmed binding of these compounds to CTBP’s active site, however evidence for specificity is lacking. To address this, we treated wildtype and Ctbp1, 2 double knockout J774.1 cells with MTOB or 4-Cl-HIPP and performed RNA-seq. We observed that both inhibitors elicit distinct transcriptional changes indicating non-overlapping modes of action. Moreover, the majority of changes induced by either inhibitor are observed in Ctbp1/2 double knockout cells suggesting off-target effects. We hypothesize that those CTBP dehydrogenase inhibitors lack specificity to CTBPs and emphasise careful revaluation of findings inferred from studies using those inhibitors.
The human proteome with direct physical access to DNA
In a human cell, DNA is packed with histones, RNA, and chromatin-associated proteins, forming a cohesive gel. At any given moment, only a subset of the proteome has physical access to the DNA and organizes its structure, transcription, replication, repair, and other essential molecular functions. We have developed a “zero-distance” photo-crosslinking approach to quantify proteins in direct contact with DNA in living cells. Collecting DNA interactomes from human breast cancer cells, we present an atlas of over one thousand proteins with physical access to DNA and hundreds of peptide-nucleotide crosslinks pinpointing protein-DNA interfaces with single-amino-acid resolution. Quantitative comparisons of DNA interactomes from differentially treated cells recapitulate the recruitment of key transcription factors as well as DNA repair proteins and uncover fast-acting restrictors of chromatin accessibility on a timescale of minutes. This opens a direct way to explore genomic regulation in a hypothesis-free manner, applicable to many organisms and systems.
C-terminal binding protein 2 interacts with JUNB to control macrophage inflammation
Here, we investigate the role of the transcriptional co-repressors C-terminal binding protein (CTBP) 1 and 2 in murine and human macrophage activation using loss-of-function models to show that CTBP2 but not CTBP1 controls inflammatory gene expression. We find that CTBP2 occupies cis-regulatory elements of inflammatory genes together with the transcription factors NF-κB and AP-1 and forms a co-repressor complex. Rescue of Ctbp1/2 double knockout cells with WT, oligomeric CTBP2 attenuates inflammatory responses, whereas a monomeric mutant does not. Differential profiling of CTBP2’s WT and monomeric interactome confirms oligomer-specific interactions with multiple repressors. Conversely, monomers retain the ability to interact with AP-1 and RNA polymerase II, boosting gene expression. Our findings point to an important function for CTBP2 in fine-tuning inflammatory gene expression, potentially unveiling novel therapeutic targets for the treatment of inflammatory diseases.
2024
Cleavage Under Targets and Release Using Nuclease (CUT&RUN) in Macrophages
Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is a method to detect specific interactions between DNA and DNA-associated proteins. It is valuable for the characterization of the binding of transcription factors or co-regulators genome wide. Furthermore, it can be used for epigenetic profiling, chromatin accessibility assessment, and identification of regulatory elements. Compared to the more commonly used chromatin immunoprecipitation (ChIP), CUT&RUN has several advantages including an in situ approach as well as no need for sonication. However, the biggest advantage is the reduced cell amounts that are required for CUT&RUN, which makes it more attractive for experiments with limited cell numbers. In this chapter, we describe a reliable CUT&RUN protocol for macrophages that can be performed within 2 days and includes a library preparation so that the sample can be directly sequenced
A new book on Chromatin profiling techniques.
The genome stands as the master regulator of our body, encoding all essential information in
its DNA. It plays a pivotal role in orchestrating tissue- and stimulus-specific gene regulatory
networks. These networks, in turn, govern both our fundamental cellular processes and our
intricate responses to environmental challenges. It is hardly surprising, then, that both
scientists and the general public are captivated by the way a fixed DNA sequence can direct
the vast array of functional behaviors within our bodies, and how these encoded instructions
are executed at the cellular level. Central to these regulatory mechanisms are DNA-binding
factors, which serve two main functions: translating the DNA sequence into specific
biological actions or recording the cellular history of an individual cell through various
means, such as histone marks, DNA compaction, and spatial positioning of nucleosomes.
Our comprehension of the functional genome has been profoundly advanced by the
development of Chromatin Immunoprecipitation (ChIP), as well as next-generation
sequencing (NGS) techniques. These technologies form the cornerstone of the meth-
odologies detailed in this volume. ChIP, a method for identifying the interactions between
proteins and DNA within living cells or tissues, becomes exponentially more powerful when
combined with next-generation sequencing. This combination, known as ChIP-seq, facil-
itates the genome-wide mapping of transcription factors, co-regulators, histone modifica-
tions, and nucleosomes
2023
Machine learning reveals STAT motifs as predictors for GR-mediated gene repression
Glucocorticoids are potent immunosuppressive drugs, but long-term treatment leads to severe side-effects. While there is a commonly accepted model for GR-mediated gene activation, the mechanism behind repression remains elusive. Understanding the molecular action of the glucocorticoid receptor (GR) mediated gene repression is the first step towards developing novel therapies. We devised an approach that combines multiple epigenetic assays with 3D chromatin data to find sequence patterns predicting gene expression change. We systematically tested> 100 models to evaluate the best way to integrate the data types and found that GR-bound regions hold most of the information needed to predict the polarity of Dex-induced transcriptional changes. We confirmed NF-κB motif family members as predictors for gene repression and identified STAT motifs as additional negative predictors.
2022
ATGL-dependent white adipose tissue lipolysis controls hepatocyte PPARα activity.
In hepatocytes, peroxisome proliferator-activated receptor α (PPARα) orchestrates a genomic and metabolic response required for homeostasis during fasting. This includes the biosynthesis of ketone bodies and of fibroblast growth factor 21 (FGF21). Here we show that in the absence of adipose triglyceride lipase (ATGL) in adipocytes, ketone body and FGF21 production is impaired upon fasting. Liver gene expression analysis highlights a set of fasting-induced genes sensitive to both ATGL deletion in adipocytes and PPARα deletion in hepatocytes. Adipose tissue lipolysis induced by activation of the β3-adrenergic receptor also triggers such PPARα-dependent responses not only in the liver but also in brown adipose tissue (BAT). Intact PPARα activity in hepatocytes is required for the cross-talk between adipose tissues and the liver during fat mobilization
In cooperation with Hervé Guillou.
2021
Protocol for using heterologous spike-ins to normalize for technical variation in chromatin immunoprecipitation
Glucocorticoids (GCs) are effective anti-inflammatory drugs; yet, their mechanisms of action are poorly understood. GCs bind to the glucocorticoid receptor (GR), a ligand-gated transcription factor controlling gene expression in numerous cell types. Here, we characterize GR’s protein interactome and find the SETD1A (SET domain containing 1A)/COMPASS (complex of proteins associated with Set1) histone H3 lysine 4 (H3K4) methyltransferase complex highly enriched in activated mouse macrophages. We show that SETD1A/COMPASS is recruited by GR to specific cis-regulatory elements, coinciding with H3K4 methylation dynamics at subsets of sites, upon treatment with lipopolysaccharide (LPS) and GCs. By chromatin immunoprecipitation sequencing (ChIP-seq) and RNA-seq, we identify subsets of GR target loci that display SETD1A occupancy, H3K4 mono-, di-, or tri-methylation patterns, and transcriptional changes. However, our data on methylation status and COMPASS recruitment suggest that SETD1A has additional transcriptional functions. Setd1a loss-of-function studies reveal that SETD1A/COMPASS is required for GR-controlled transcription of subsets of macrophage target genes. We demonstrate that the SETD1A/COMPASS complex cooperates with GR to mediate anti-inflammatory effects.
Enhancer RNA Expression in Response to Glucocorticoid Treatment in Murine Macrophages
Glucocorticoids are potent anti-inflammatory drugs; however, their molecular mode of action remains complex and elusive. They bind to the glucocorticoid receptor (GR), a nuclear receptor that controls gene expression in almost all tissues in a cell type-specific manner. While GR’s transcriptional targets mediate beneficial reactions in immune cells, they also harbor the potential of adverse metabolic effects in other cell types such as hepatocytes. Here, we have profiled nascent transcription upon glucocorticoid stimulation in LPS-activated primary murine macrophages using 4sU-seq. We compared our results to publicly available nascent transcriptomics data from murine liver and bioinformatically identified non-coding RNAs transcribed from intergenic GR binding sites in a tissue-specific fashion. These tissue-specific enhancer RNAs (eRNAs) correlate with target gene expression, reflecting cell type-specific glucocorticoid responses. We further associate GR-mediated eRNA expression with changes in H3K27 acetylation and BRD4 recruitment in inflammatory macrophages upon glucocorticoid treatment. In summary, we propose a common mechanism by which GR-bound enhancers regulate target gene expression by changes in histone acetylation, BRD4 recruitment and eRNA expression. We argue that local eRNAs are potential therapeutic targets downstream of GR signaling which may modulate glucocorticoid response in a cell type-specific way.
The glucocorticoid receptor recruits the COMPASS complex to regulate inflammatory transcription at macrophage enhancers
Quantifying differential genome occupancy by chromatin immunoprecipitation (ChIP) remains challenging due to variation in chromatin fragmentation, immunoprecipitation efficiencies, and intertube variability. In this protocol, we add heterologous spike-ins from Drosophila chromatin as an internal control to the mice chromatin before immunoprecipitation to normalize for technical variation in ChIP-qPCR or ChIP-seq. The choice of spike-in depends on the evolutionary conservation of the protein of interest and the antibody used.
- "Cardioprotective Effects of Palmitoleic Acid (C16:1n7) in a Mouse Model of Catecholamine-Induced Cardiac Damage Are Mediated by PPAR Activation"
Palmitoleic acid (C16:1n7) has been identified as a regulator of physiological cardiac hypertrophy. In the present study, we aimed to investigate the molecular pathways involved in C16:1n7 responses in primary murine cardiomyocytes (PCM) and a mouse model of isoproterenol (ISO)-induced cardiac damage. PCMs were stimulated with C16:1n7 or a vehicle. Afterwards, RNA sequencing was performed using an Illumina HiSeq sequencer. Confirmatory analysis was performed in PCMs and HL-1 cardiomyocytes. For an in vivo study, 129 sv mice were orally treated with a vehicle or C16:1n7 for 22 days. After 5 days of pre-treatment, the mice were injected with ISO (25 mg/kg/d s. c.) for 4 consecutive days. Cardiac phenotyping was performed using echocardiography. In total, 129 genes were differentially expressed in PCMs stimulated with C16:1n7, including Angiopoietin-like factor 4 (Angptl4) and Pyruvate Dehydrogenase Kinase 4 (Pdk4). Both Angptl4 and Pdk4 are proxisome proliferator-activated receptor α/δ (PPARα/δ) target genes. Our in vivo results indicated cardioprotective and anti-fibrotic effects of C16:1n7 application in mice. This was associated with the C16:1n7-dependent regulation of the cardiac PPAR-specific signaling pathways. In conclusion, our experiments demonstrated that C16:1n7 might have protective effects on cardiac fibrosis and inflammation. Our study may help to develop future lipid-based therapies for catecholamine-induced cardiac damage.
in cooperation with Anna Foryst-Ludwig.
2020
Anti-inflammatory functions of the glucocorticoid receptor require DNA binding
The glucocorticoid receptor is an important immunosuppressive drug target and metabolic regulator that acts as a ligand-gated transcription factor. Generally, GR’s anti-inflammatory effects are attributed to the silencing of inflammatory genes, while its adverse effects are ascribed to the upregulation of metabolic targets. GR binding directly to DNA is proposed to activate, whereas GR tethering to pro-inflammatory transcription factors is thought to repress transcription. Using mice with a point mutation in GR’s zinc finger, that still tether via protein–protein interactions while being unable to recognize DNA, we demonstrate that DNA binding is essential for both transcriptional activation and repression. Performing ChIP-Seq, RNA-Seq and proteomics under inflammatory conditions, we show that DNA recognition is required for the assembly of a functional co-regulator complex to mediate glucocorticoid responses. Our findings may contribute to the development of safer immunomodulators with fewer side effects.
Anti-inflammatory glucocorticoid action: genomic insights and emerging concepts Glucocorticoids (GCs) are widely used immunomodulators. They regulate gene expression by binding and activating the Glucocorticoid Receptor (GR), but underlying transcriptional mechanisms remain enigmatic. This review summarizes recent findings identifyingspecific GR-bound DNA sequences whose configuration may affect transcriptional output. Additional factors affecting GR’s anti-inflammatory actions, including different chromatin states such as DNAse hypersensitive regions and histone marks will be discussed, together with the relevant transcriptional co-regulators and promoter/enhancer features. Furthermore, the involvement of non-coding RNAs such as lncRNAs, miRNAs and eRNAs adds another level of regulation to the GR’s transcriptional activity. Characterizing and understanding these multiple mechanisms will be crucial for developing more targeted immunomodulatory therapies with reduced adverse effects such as obesity, diabetes and osteoporosis.
Exercise-dependent increases in protein synthesis are accompanied by chromatin modifications and increased MRTF-SRF signalling
We identified a new phosphorylation site on Myocardin-Related Transcription Factor B (MRTF-B), a co-activator of serum response factor (SRF). Phosphorylation of MRTF-B is required for its nuclear translocation after exercise and is accompanied by the transcription of the SRF target gene Fos. In addition, high-intensity exercise also remodels chromatin at specific SRF target gene loci through the phosphorylation of histone 3 on serine 10 in myonuclei of both mice and humans. Ablation of the MAP kinase member MSK1/2 is sufficient to prevent this histone phosphorylation, reduce induction of SRF-target genes, and prevent increases in protein synthesis after exercise.
In cooperation with Bert Blauuw