Biology subjects

Schuebeler, D.

Publications and source records attributed to Schuebeler, D..

4 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↗

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↗

bioRxiv2020

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

Gene activation requires the cooperative activity of multiple transcription factors at cis-regulatory elements. Yet, most transcription factors have short residence time, questioning the requirement of their physical co-occupancy on DNA to achieve cooperativity. Here, we advance Single Molecule Footprinting to detect individual molecular interactions of transcription factors and nucleosomes with DNA at mouse cis-regulatory elements. We apply this strategy to quantify the simultaneous binding of multiple transcription factors on single DNA molecules. Analysis of the binary occupancy patterns at thousands of motif combinations reveals that for most types of transcription factors high DNA co-occupancy can occur in absence of direct physical interaction, at sites of competition with nucleosomes. Perturbation of pairwise interactions demonstrates the function of molecular co-occupancy for binding cooperativity. These findings elucidate the binding cooperativity mechanism used by transcription factors in absence of strict organisation of their binding motifs, a characteristic feature of most of enhancers.

genomics↗

bioRxiv2018

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

Targeting genes to specific neuronal or glial cell types is valuable both for understanding and for repairing brain circuits. Adeno-associated viral vectors (AAVs) are frequently used for gene delivery, but targeting expression to specific cell types is a challenge. We created a library of 230 AAVs, each with a different synthetic promoter designed using four independent strategies. We show that ~11% of these AAVs specifically target expression to neuronal and glial cell types in the mouse retina, mouse brain, non-human primate retina in vivo, and in the human retina in vitro. We demonstrate applications for recording, stimulation, and molecular characterization, as well as the intersectional and combinatorial labeling of cell types. These resources and approaches allow economic, fast, and efficient cell-type targeting in a variety of species, both for fundamental science and for gene therapy.

neuroscience↗