Visualization of endogenous enhancer-promoter interactions in a single nucleus through chromatin labeling.

Recent studies highlight the critical role of nuclear genome organization in regulating gene expression. Dynamic changes in the hierarchical structure of chromatin modulate transcription by influencing the recruitment of transcription factors and altering the epigenetic landscape. Among these regulatory mechanisms, enhancer-promoter (E-P) interactions are of particular importance.

Correlation functions from tensor network influence functionals: The case of the spin-boson model.

We investigate the application of matrix product state (MPS) representations of the influence functionals (IFs) for the calculation of real-time equilibrium correlation functions in open quantum systems. Focusing specifically on the unbiased spin-boson model, we explore the use of IF-MPSs for complex time propagation, as well as IF-MPSs for constructing correlation functions in the steady state. We examine three different IF approaches: one based on the Kadanoff-Baym contour targeting correlation functions at all times, one based on a complex contour targeting the correlation function at a single time, and a steady state formulation, which avoids imaginary or complex times, while providing access to correlation functions at all times.

Emerging insights into transcriptional condensates.

Eukaryotic transcription, a fundamental process that governs cell-specific gene expression, has long been the subject of extensive investigations in the fields of molecular biology, biochemistry, and structural biology. Recent advances in microscopy techniques have led to a fascinating concept known as "transcriptional condensates." These dynamic assemblies are the result of a phenomenon called liquid‒liquid phase separation, which is driven by multivalent interactions between the constituent proteins in cells.

Ideal refocusing of an optically active spin qubit under strong hyperfine interactions.

Combining highly coherent spin control with efficient light-matter coupling offers great opportunities for quantum communication and computing. Optically active semiconductor quantum dots have unparalleled photonic properties but also modest spin coherence limited by their resident nuclei. The nuclear inhomogeneity has thus far bound all dynamical decoupling measurements to a few microseconds.

Effects of Transcription-Dependent Physical Perturbations on the Chromosome Dynamics in Living Cells.

Recent studies with single-particle tracking in live cells have revealed that chromatin dynamics are directly affected by transcription. However, how transcription alters the chromatin movements followed by changes in the physical properties of chromatin has not been elucidated. Here, we measured diffusion characteristics of chromatin by targeting telomeric DNA repeats with CRISPR-labeling.

CTCF-mediated chromatin looping provides a topological framework for the formation of phase-separated transcriptional condensates.

CTCF is crucial to the organization of mammalian genomes into loop structures. According to recent studies, the transcription apparatus is compartmentalized and concentrated at super-enhancers to form phase-separated condensates and drive the expression of cell-identity genes. However, it remains unclear whether and how transcriptional condensates are coupled to higher-order chromatin organization.