Biology subjects

Burger, L.

Publications and source records attributed to Burger, L..

10 recordsLinked to original sources

bioRxiv2026

Modular control of CpG islands by chromatin-opening transcription factors specifies transcription start sites

CpG islands (CGIs) constitute the dominant class of promoters in vertebrate genomes, yet the mechanisms underlying their transcription initiation remain unclear. Using deep learning and acute perturbation of twelve transcription factors (TFs), we show that chromatin-opening TFs are the primary determinants of initiation site selection, thereby governing promoter output. The dominant TF defines a nucleosome-free region and specifies where transcription begins by binding closest to the transcription start site. Loss of this TF redirects transcription initiation to an adjacent secondary TF position, partially buffering gene expression. Promoter variant analyses validate that this modular control of initiation is encoded in cis and programmable. This principle extends to initiation at enhancers and TATA-box promoters, where chromatin-opening TFs unmask the TATA box for focused initiation. These findings point to a common sequence grammar for transcription across promoters and enhancers, supporting a minimalist and evolvable architecture of cis-regulatory regions.

molecular biology↗

bioRxiv2025

A novel deep learning-based framework reveals a continuum of chromatinsensitivities across transcription factors

The genome-wide binding of many transcription factors (TFs) depends not only on the presence of their recognition motifs, but also on the surrounding chromatin context. This raises the question of how binding specificity is achieved, which is essential for the proper activation of regulatory regions during developmental and differentiation processes. Two competing hypotheses have been proposed: either opening is a hierarchical process, whereby chromatin-insensitive TFs bind initially and make the DNA accessible for other TFs; or multiple chromatin-sensitive TFs bind cooperatively, enabling them to overcome the chromatin barrier. Here, using complementary genomic- and deep-learning-based techniques, we provide a quantitative framework to assess chromatin sensitivity of individual TFs, and hone in on the definitions and implications of such sensitivity. Our findings demonstrate that the degree of chromatin sensitivity is a continuum across TFs, showing that regulatory regions are activated neither by a purely hierarchical nor purely cooperative mechanism, but by a mixture of both mechanisms. The presented framework allows for a locus-specific as well as global, quantitative assessment of chromatin sensitivity and should help in understanding the binding behaviour of individual TFs as well as their potential contribution to gene regulation.

genomics↗

bioRxiv2025

An Fc-SPINK1 fusion protein inhibits pancreatic inflammation in a mouse model

Pancreatitis results from premature activation and impaired inactivation of pancreatic proteases, primarily trypsin, leading to self-digestion, tissue necrosis, fibrosis, and inflammation. SPINK1 is a pancreas-specific inhibitor of trypsin that prevents premature trypsin activation, and could be a candidate therapeutic. However, because of its small size, SPINK1 would be subject to rapid renal clearance, making it ineffective. To construct a long half-life therapeutic inhibitor of trypsin for pancreatitis treatment we fused this protein to the C-terminus of an IgG1 antibody Fc element, increasing the size to [~]78 kDa, thereby exceeding the renal clearance threshold and providing for FcRn-mediated recycling out of cells. A non-glycosylated form of Fc-SPINK1 was expressed in the yeast Pichia pastoris. Fc-SPINK1 inhibits trypsin enzyme activity in vitro. The blood pharmacokinetics in mice are consistent with a three-compartment distribution model and a terminal half-life of [~]3 days. In a caerulein-induced mouse model of pancreatitis, Fc-SPINK1 significantly ameliorated cell death and immune cell infiltration. We developed an automated image analysis technique to quantify pancreatitis-associated loss of tissue cohesion, and found that Fc-SPINK1 also reduced this effect. This study demonstrates the potential of Fc-SPINK1 as a rationally designed therapy for pancreatitis.

pharmacology and toxicology↗

bioRxiv2025

Force Generation by Enhanced Diffusion in Enzyme-Loaded Vesicles

Recent experiments have shown that the diffusion coefficient of some metabolic enzymes increases with the concentration of their cognate substrate, a phenomenon known as enhanced diffusion. In the presence of substrate gradients, enhanced diffusion induces enzymatic drift, resulting in a non-homogeneous enzyme distribution. Here, we study the effects of enhanced diffusion on enzyme-loaded vesicles placed in external substrate gradients using a combination of computer simulations and analytical modeling. We observe that the spatially inhomogeneous enzyme profiles generated by enhanced diffusion result in a pressure gradient across the vesicle, which leads to macroscopically observable effects, such as deformation and self-propulsion of the vesicle. Our analytical model allows us to characterize dependence of the velocity of propulsion on experimentally tunable parameters. The effects predicted by our work provide an avenue for further validation of enhanced diffusion, and might be leveraged for the design of novel synthetic cargo transporters, such as targeted drug delivery systems.

biophysics↗

bioRxiv2024

Sequence motif dynamics in RNA pools

In RNA world scenarios, pools of RNA oligomers form strongly interacting, dynamic systems, which enable molecular evolution. In such pools, RNA oligomers hybridize and dehybridize, ligate and break, ultimately generating longer RNA molecules, which may fold into catalytically active ribozymes. A key process for the elongation of RNA oligomers is templated ligation, which can occur when two RNA strands are adjacently hybridized onto a template strand. Detailed simulations of the dynamics in RNA pools involve a large variety of possible sequences and reactions. Here, we develop a reduced description of these complex dynamics within the space of sequence motifs. We then explore to what extent our reduced description can capture the behavior of detailed simulations that account for the full dynamics in the space of RNA strands. Towards this end, we project the dynamics into a motif space, which accounts only for the abundance of all possible four-nucleotide motifs. A system of ordinary differential equations describes the dynamics of those motifs. Its control parameters are effective rate constants for reactions in motif space, which we obtain from the rate constants for the processes underlying the full dynamics in the space of RNA strands. We find that these reduced motif space dynamics indeed capture important aspects of the informational dynamics of RNA pools in sequence space. This approach could also provide a framework to rationalize and interpret features of the sequence dynamics observed in experimental systems.

biophysics↗

bioRxiv2024

Chromatin-dependent motif syntax defines differentiation trajectories

Transcription factors recognizing short DNA sequences within gene regulatory regions are crucial drivers of cell identity. Despite recent advances, their specificity remains incompletely understood. Here, we address this by contrasting two TFs, NGN2 and MyoD1, which recognize ubiquitous E-box motifs yet instigate distinct cell fates--neurons and muscles, respectively. Following controlled induction in embryonic stem cells, we monitor binding across differentiation trajectories, employing an interpretable machine-learning approach integrating pre-existing DNA accessibility data. This reveals a chromatin-dependent motif syntax, delineating both common and factor-specific binding and predicting genome engagement with high precision. Shared binding sites reside in open chromatin, locally influenced by nucleosomes. In contrast, factor-specific binding in closed chromatin involves NGN2 and MyoD1 acting as pioneer-factors, influenced by multi-motifs, rotational spacing, flanking sequences, and specific interaction partners, accounting for subsequent lineage divergence. Extending our methodology to other models demonstrates how such combination of opportunistic-binding and context-specific chromatin opening underpin transcription factor specificity driving differentiation trajectories.

genomics↗

bioRxiv2024

Theoretical Analysis of Nonenzymatic RNA Replication within the Virtual Circular Genome Scenario

The transition from prebiotic chemistry to living systems requires the emergence of a scheme for enzyme-free genetic replication. Here, we analyze a recently proposed prebiotic replication scenario, the so-called Virtual Circular Genome (VCG) [Zhou et al., RNA 27, 1-11 (2021)]: Replication takes place in a pool of oligomers, where each oligomer contains a subsequence of a circular genome, such that the oligomers encode the full genome collectively. While the sequence of the circular genome may be reconstructed based on long oligomers, monomers and short oligomers merely act as replication feedstock. We observe a competition between the predominantly error-free ligation of a feedstock molecule to a long oligomer and the predominantly erroneous ligation of two long oligomers. Increasing the length of long oligomers and reducing their concentration decreases the fraction of erroneous ligations, enabling high-fidelity replication in the VCG. Alternatively, the formation of erroneous products can be suppressed if each ligation involves at least one monomer, while ligations between two long oligomers are effectively prevented. This kinetic discrimination (favoring monomer incorporation over oligomer-oligomer ligation) may be an intrinsic property of the activation chemistry, or can be externally imposed by selectively activating only monomers in the pool. Surprisingly, under these conditions, shorter oligomers are extended by monomers more quickly than long oligomers, a phenomenon which has already been observed experimentally [Ding et al., JACS 145, 7504-7515 (2023)]. Our work provides a theoretical explanation for this behavior, and predicts its dependence on system parameters such as the concentration of long oligomers. Taken together, the VCG constitutes a promising scenario of prebiotic information replication: It could mitigate challenges of in non-enzymatic copying via template-directed polymerization, such as short lengths of copied products and high error rates.

biophysics↗

bioRxiv2023

Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for proper CTCF function

Catalytic activity of the ISWI family of remodelers is critical for nucleosomal organization and DNA binding of transcription factors, including the insulator protein CTCF. To define which subcomplex mediates these diverse functions, we derived a panel of isogenic mouse stem cell lines each lacking one of six ISWI accessory subunits. Individual deletions of subunits of either CERF, RSF, ACF, WICH or NoRC subcomplexes only moderately affect the chromatin landscape, while removal of the NURF-specific subunit BPTF leads to drastic reduction in chromatin accessibility and SNF2H ATPase localization around CTCF sites. While this affects adjacent nucleosome occupancy, it only modestly impacts CTCF binding itself. In the absence of accessibility, the structural function of CTCF is nevertheless impaired resulting in lower occupancy of cohesin and cohesin release factor, and reduced physical insulation at these sites, highlighting the need of NURF-mediated remodeling for open chromatin and proper CTCF function. These results separate local CTCF binding from insulator function in nuclear organization and reveal a specific role for NURF in mediating SNF2H localization and chromatin opening at bound CTCF sites. They designate local accessibility as critical for cohesin positioning and establishment of physical insulation.

molecular biology↗

bioRxiv2022

Readout of histone methylation by Trim24 locally restricts chromatin opening by p53

The genomic binding sites of the transcription factor (TF) and tumour suppressor p53 are unusually diverse in regards to their chromatin features, including histone modifications, opening the possibility that chromatin provides context-dependence for p53 regulation. Here, we show that the ability of p53 to open chromatin and activate its target genes is indeed locally restricted by its cofactor Trim24. Trim24 binds to both p53 and unmethylated lysine 4 of histone H3, thereby preferentially locating to those p53 sites that reside in closed chromatin, while it is deterred from accessible chromatin by lysine 4 methylation. The presence of Trim24 increases cell viability upon stress and enables p53 to impact gene expression as a function of the local chromatin state. These findings link histone methylation to p53 function and illustrate how specificity in chromatin can be achieved, not by TF-intrinsic sensitivity to histone modifications, but by employing chromatin-sensitive cofactors which locally modulate TF function.

genomics↗

bioRxiv2021

monaLisa: an R/Bioconductor package for identifying regulatory motifs

Proteins binding to specific nucleotide sequences, such as transcription factors, play key roles in the regulation of gene expression. Their binding can be indirectly observed via associated changes in transcription, chromatin accessibility, DNA methylation and histone modifications. Identifying candidate factors that are responsible for these observed experimental changes is critical to understand the underlying biological processes. Here we present monaLisa, an R/Bioconductor package that implements approaches to identify relevant transcription factors from experimental data. The package can be easily integrated with other Bioconductor packages and enables seamless motif analyses without any software dependencies outside of R. AvailabilitymonaLisa is implemented in R and available on Bioconductor at https://bioconductor.org/packages/monaLisa with the development version hosted on GitHub at https://github.com/fmicompbio/monaLisa. Contactmichael.stadler@fmi.ch

bioinformatics↗