Biology subjects

Zaehringer, J.

Publications and source records attributed to Zaehringer, J..

3 recordsLinked to original sources

bioRxiv2026

FACT frees Ubp10 from nucleosome sequestration after rapid H2B deubiquitination

Chromatin-modifying enzymes must engage their substrate, act on it and release it, but which step limits their turnover is unclear. Using three-color single-molecule fluorescence, we directly visualized the yeast deubiquitinase Ubp10 removing ubiquitin from H2B on individual nucleosomes. Ubp10 cleaved the mark within seconds of binding, without detectable DNA unwrapping, yet it did not let go: ~80% of nucleosomes remained bound after 45 minutes, and unmodified nucleosomes formed similarly long-lived complexes. Ubp10 turnover is therefore limited by release rather than catalysis. The histone chaperone FACT relieved this bottleneck by accelerating Ubp10-nucleosome dissociation. In living yeast, nuclear depletion of the FACT subunit Spt16 increased the slowly diffusing, chromatin-bound fraction of nucleoplasmic Ubp10. These findings identify FACT-dependent release as a likely mechanism for recycling Ubp10 on chromatin. More broadly, a nucleosome can sequester the enzyme acting on it, making enzyme release a step at which chromatin modification can be controlled.

biophysics↗

bioRxiv2025

The elusive neural signature of emotion regulation capabilities: evidence from a large-scale consortium

Cognitive reappraisal is a fundamental emotion regulation strategy for mental and physical well-being, but how its neural mechanisms relate to individual differences remains poorly understood. In a consortium effort analyzing 40 fMRI datasets (N=2,175), we examined the relationship between neural activation during reappraisal tasks and three core individual difference indices of reappraisal capabilities: (1) trait questionnaires, (2) task-based affective ratings, and (3) amygdala down-regulation. Strikingly, there was no shared overlap across these three common indices. Only a very weak correlation emerged between amygdala down-regulation and task-based affective ratings. Whole-brain analyses revealed no reliable neural associations with trait questionnaires, and associations with task-based affective ratings fell outside canonical emotion regulation networks (e.g., prefrontal circuitry). Moreover, amygdala down-regulation, often interpreted as a stable individual marker, was confounded by person-specific whole-brain responses -- a limitation extending to fMRI research beyond the emotion regulation domain. These findings challenge the assumption that an individuals prefrontal activity is a valid indicator of their reappraisal capabilities and suggest that common trait, behavioral, and neural measures might capture distinct facets of emotion regulation. More broadly, our results highlight concrete methodological challenges for fMRI research on individual differences, with implications extending beyond emotion regulation to the neuroscience of personality, psychopathology, and general well-being.

neuroscience↗

bioRxiv2023

Super-Resolved FRET and Co-Tracking in pMINFLUX

Single-molecule FRET (smFRET) is widely used to investigate dynamic (bio) molecular interactions taking place over distances of up to 10 nm. With the advent of recent super-resolution methods such as MINFLUX, MINSTED or RASTMIN, the spatiotemporal resolution of these techniques advanced towards the smFRET regime. While these methods do not suffer from the spatial restriction of FRET, they only visualize one emitter at a time, thus rendering fast dynamics of interactions out of reach. Here, we describe two approaches to overcome this limitation in pMINFLUX using its intrinsic fluorescence lifetime information. First, we combined pMINFLUX with smFRET. This enabled us to track a FRET donor fluorophore and simultaneously colocalize its FRET acceptor with nanometer precision. To extend co-localized tracking beyond the FRET range, we developed pMINFLUX lifetime multiplexing, a method to simultaneously track two fluorophores with similar spectral properties but distinct fluorescence lifetimes. We demonstrated its application on both static and dynamic DNA origami systems with a precision better than 2 nm. Within the FRET range, pMINFLUX lifetime multiplexing additionally uses a novel combined phasor-microtimegating approach. This paves the way for nanometer precise co-localized tracking for inter-dye distances between 4 nm and 100 nm, closing the resolution gap between smFRET and co-tracking. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/534096v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@11459forg.highwire.dtl.DTLVardef@1f1cee2org.highwire.dtl.DTLVardef@4592e6org.highwire.dtl.DTLVardef@1af3e48_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗