Dirk Schübeler

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

The paper shows chromatin-opening transcription factors determine transcription start sites by binding near the initiation site, with loss of these factors redirecting initiation to secondary sites.

The genetic architecture of the human bZIP family

The paper systematically mutagenizes human bZIP domains and uses deep mutational scanning to quantify interactions, revealing complex genetic architecture and enabling synthetic bZIP design.

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

This paper introduces a deep learning framework to quantify chromatin sensitivity of transcription factors, revealing a continuum of sensitivity rather than distinct hierarchical or cooperative mechanisms.

Chromatin-dependent motif syntax defines differentiation trajectories

The paper identifies chromatin-dependent motif syntax that distinguishes binding patterns of NGN2 and MyoD1 during differentiation, revealing how context-specific chromatin states influence transcription factor specificity.

Nuclear rerouting of paracrine Fgf3 in source cells represses target genes to pattern morphogen responses

The paper shows that Fgf3 in zebrafish lateral line organogenesis represses target genes through nuclear accumulation, distinct from its extracellular signaling role.

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

The paper shows that NURF subunit BPTF is critical for chromatin accessibility and CTCF function, affecting cohesin positioning and insulation.

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

This study shows that Trim24 restricts p53's ability to open chromatin by binding to closed chromatin regions and interacting with unmethylated histone H3 lysine 4.

monaLisa: an R/Bioconductor package for identifying regulatory motifs

monaLisa identifies transcription factors from experimental data by integrating with Bioconductor packages for motif analysis.

ZFP462 targets heterochromatin to transposon-derived enhancers restricting transcription factor binding and expression of lineage-specifying genes

This study identifies ZFP462's role in restricting endodermal gene expression by targeting transposon-derived enhancers and modulating histone methylation in mouse embryonic stem cells.

Single molecule occupancy patterns of transcription factors reveal determinants of cooperative binding in vivo

The paper uses single molecule footprinting to study transcription factor co-occupancy and cooperativity in mouse cis-regulatory elements, finding that high DNA co-occupancy can occur without direct physical interaction.

Targeting neuronal and glial cell types with synthetic promoter AAVs in mice, non-human primates, and humans

The paper develops synthetic promoter AAVs for cell-type-specific gene delivery in mice, non-human primates, and humans, showing 11% of AAVs target neuronal and glial cell types in multiple species.