Biology subjects

Berger, S. E.

Publications and source records attributed to Berger, S. E..

4 recordsLinked to original sources

bioRxiv2024

Single-Molecule Imaging Reveals the Mechanism of Bidirectional Replication Initiation in Metazoa

Metazoan genomes are copied bidirectionally from thousands of replication origins. Replication initiation entails the assembly and activation of two CMG (Cdc45*Mcm2-7*GINS) helicases at each origin. This requires several firing factors (including TopBP1, RecQL4, DONSON) whose exact roles remain unclear. How two helicases are correctly assembled and activated at every single origin is a long-standing question. By visualizing the recruitment of GINS, Cdc45, TopBP1, RecQL4, and DONSON in real time, we uncovered a surprisingly dynamic picture of initiation. Firing factors transiently bind origins but do not travel with replisomes. Two Cdc45 simultaneously arrive at each origin and two GINS are recruited together, even though neither protein can dimerize. The synchronized delivery of two GINS is mediated by DONSON, which acts as a dimerization scaffold. We show that RecQL4 promotes DONSON dissociation and facilitates helicase activation. The high fidelity of bidirectional origin firing can be explained by a Hopfield-style kinetic proofreading mechanism.

molecular biology↗

bioRxiv2022

Beyond TADs: microscopy reveals 2 axes of chromosome organization by CTCF and cohesin

While population level analyses reveal significant roles for CTCF and cohesin in mammalian genome organization, their contribution to chromatin structure and gene regulation at the single-cell level remain incompletely understood 1-4. Here, we use a super-resolution microscopy approach, Optical Reconstruction of Chromatin Architecture (ORCA) 5 to measure the effects of removal of CTCF or cohesin on genome folding across genomic scales. In untreated embryonic stem cells, we observe intricate, frequently stacked loops of chromatin which are largely dissolved upon cohesin removal. The loops compact chromatin at the < 3 Mb scale, increasing proximity between sequences not only within but also between TADs. We find multi-way contacts among loop anchors, preferentially at TAD borders, and these hubs largely dissolve upon CTCF degradation. CTCF-hubs bridge intervening TAD boundaries while keeping border distal regions from neighboring TADs apart outside the hub. Cohesin dependent loops at the < 3 Mb scale impede mixing at larger chromosomal scales through steric effects of loop stacking, dramatically reducing genomic cross-talk. Disruption of this ordered chromosomal structure led to increased cell-cell variability in gene expression, exceeding changes to average expression. Together our data revise the TAD-centric understanding of CTCF and cohesin, and provide a multi-scale, structural picture of how they organize the genome on the single-cell level through distinct contributions to loop stacking.

biophysics↗

bioRxiv2018

Identification of traits and functional connectivity-based neuropsychotypes of chronic pain

Psychological and personality factors, socioeconomic status, and brain properties all contribute to chronic pain but have essentially been studied independently. Here, we administered a broad battery of questionnaires to patients with chronic back pain (CBP). Clustering and network analyses revealed four orthogonal dimensions accounting for 60% of the variance, and defining chronic pain traits. Two of these traits - Pain-trait and Emote-trait - were related to back pain characteristics and could be predicted from distinct distributed functional networks in a cross-validation procedure, identifying neurotraits. These neurotraits were relatively stable in time and segregated CBP patients into subtypes showing distinct traits, pain affect, pain qualities, and socioeconomic status (neuropsychotypes). The results unravel the trait space of chronic pain leading to reliable categorization of patients into distinct types. The approach provides metrics aiming at unifying the psychology and the neurophysiology of chronic pain across diverse clinical conditions, and promotes prognostics and individualized therapeutics.

neuroscience↗

bioRxiv2017

Brain and psychological determinants of placebo pill response in chronic pain patients

Placebo response is universally observed in randomized controlled trials (RCTs), yet these effects are commonly dismissed as consequences of uncontrollable confounds. In this prospective neuroimaging-based RCT performed in chronic back pain patients, we demonstrate that the intensity, but not quality, of pain is diminished with placebo pill ingestion. The response to placebo pills depended on brain: subcortical limbic volume asymmetry, sensorimotor cortical thickness, and functional coupling of the dorsolateral prefrontal cortex (DLPFC) with the periaqueductal grey (PAG), the rostral anterior cingulate cortex (rACC), and the precentral gyrus (PreCG); and psychological factors. All features were present before exposure to the pill; most remained stable across treatment and washout periods, although specific functional coupling between DLPFC and PAG dissipated with repeated exposure. These brain properties and specific psychological factors, such as interoceptive awareness and openness, were also predictive of the magnitude of response (continuous variable). We used machine learning in a fully cross-validated procedure and demonstrated that psychological factors were sufficient for classifying and predicting response magnitude; and response magnitude could also be predicted from a functional network (nodes mainly located in the limbic community, the DLPFC, the orbitofrontal cortex, and the temporo-parietal junction); the combined model explained 36% of the variance. Together, our results demonstrate that placebo pill analgesia observed in clinical trials depends on a combination of brain properties and specific psychological factors.

neuroscience↗