Christopher H. Bohrer
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A methodology to reduce the localization error in multi-loci microscopy provides new insights into enhancer biology Open
Numerous functions hinge on the spatial arrangement of different genomic loci. Hence, microscopy techniques, such as chromatin tracing, have been developed to localize multiple loci in fixed cells. Depending on the throughput and specifics…
Chromosomal Topological Domain Formation Modulates Transcription and the Coupling of Neighboring Genes in <i>Escherichia coli</i> Open
Chromosomal topology and transcription are tightly coupled, yet the quantitative impact of topological constraints on transcription, supercoiling, and the potential coupling between neighboring genes in vivo remains unclear. In this work, …
A methodology to reduce the localization error in multi-loci microscopy provides new insights into enhancer biology Open
Numerous functions hinge on the spatial dynamics of different genomic loci. Hence, microscopy techniques, such as chromatin tracing, have been developed to localize multiple loci in living and fixed cells. Depending on the throughput and s…
View article: Light-dependent modulation of protein localization and function in living bacteria cells
Light-dependent modulation of protein localization and function in living bacteria cells Open
Most bacteria lack membrane-enclosed organelles to compartmentalize cellular processes. In lieu of physical compartments, bacterial proteins are often recruited to macromolecular scaffolds at specific subcellular locations to carry out the…
3D chromatin architecture, BRD4, and Mediator have distinct roles in regulating genome-wide transcriptional bursting and gene network Open
Discontinuous transcription is evolutionarily conserved and a fundamental feature of gene regulation; yet, the exact mechanisms underlying transcriptional bursting are unresolved. Analyses of bursting transcriptome-wide have focused on the…
HiTIPS: High-Throughput Image Processing Software for the Study of Nuclear Architecture and Gene Expression Open
High-throughput imaging (HTI) generates complex imaging datasets from a large number of experimental perturbations. Commercial HTI software for image analysis workflows does not allow full customization and adoption of new image processing…
Synthetic analysis of chromatin tracing and live-cell imaging indicates pervasive spatial coupling between genes Open
The role of the spatial organization of chromosomes in directing transcription remains an outstanding question in gene regulation. Here, we analyze two recent single-cell imaging methodologies applied across hundreds of genes to systematic…
A spatially resolved stochastic model reveals the role of supercoiling in transcription regulation Open
In Escherichia coli , translocation of RNA polymerase (RNAP) during transcription introduces supercoiling to DNA, which influences the initiation and elongation behaviors of RNAP. To quantify the role of supercoiling in transcription regul…
Synthetic analysis of chromatin tracing and live-cell imaging indicates pervasive spatial coupling between genes Open
The role of the spatial organization of chromosomes in directing transcription remains an outstanding question in gene regulation. Here, we analyze two recent single-cell imaging methodologies applied across hundreds of genes to systematic…
View article: Light-dependent modulation of protein localization and function in living bacteria cells
Light-dependent modulation of protein localization and function in living bacteria cells Open
Most bacteria lack membrane-enclosed organelles to compartmentalize cellular processes. In lieu of physical compartments, bacterial proteins are often recruited to macromolecular scaffolds at specific subcellular locations to carry out the…
A spatially resolved stochastic model reveals the role of supercoiling in transcription regulation Open
In Escherichia coli , translocation of RNA polymerase (RNAP) during transcription introduces supercoiling to DNA, which influences the initiation and elongation behaviors of RNAP. To quantify the role of supercoiling in transcription regul…
Tau forms oligomeric complexes on microtubules that are distinct from tau aggregates Open
Significance Tau is a neuronal protein whose aggregation is a hallmark of several neurodegenerative diseases collectively known as tauopathies. Due to a lack of suitable tools, discriminating small, pathological tau aggregates from physiol…
Tau forms oligomeric complexes on microtubules that are distinct from tau aggregates Open
Tau is a microtubule-associated protein, which promotes neuronal microtubule assembly and stability. Accumulation of tau into insoluble aggregates known as neurofibrillary tangles (NFTs) is a pathological hallmark of several neurodegenerat…
Tau forms oligomeric complexes on microtubules that are distinct from tau aggregates Open
Tau is a microtubule-associated protein, which promotes neuronal microtubule assembly and stability. Accumulation of tau into insoluble aggregates known as neurofibrillary tangles (NFTs) is a pathological hallmark of several neurodegenerat…
The Stochastic Genome and Its Role in Gene Expression Open
Mammalian genomes have distinct levels of spatial organization and structure that have been hypothesized to play important roles in transcription regulation. Although much has been learned about these architectural features with ensemble t…
Spatially compartmentalized phase regulation of a Ca2+-cAMP-PKA oscillatory circuit Open
Signaling networks are spatiotemporally organized to sense diverse inputs, process information, and carry out specific cellular tasks. In β cells, Ca 2+ , cyclic adenosine monophosphate (cAMP), and Protein Kinase A (PKA) exist in an oscill…
Spatially compartmentalized phase regulation of a Ca <sup>2+</sup> -cAMP-PKA oscillatory circuit Open
Signaling networks are spatiotemporally organized in order to sense diverse inputs, process information, and carry out specific cellular tasks. In pancreatic β cells, Ca 2+ , cyclic adenosine monophosphate (cAMP), and Protein Kinase A (PKA…
Spatial organization of RNA polymerase and its relationship with transcription in <i>Escherichia coli</i> Open
Recent studies have shown that RNA polymerase (RNAP) is organized into distinct clusters in Escherichia coli and Bacillus subtilis cells. Spatially organized molecular components in prokaryotic systems imply compartmentalization without th…
RNA polymerase organizes into distinct spatial clusters independent of ribosomal RNA transcription in <i>E. coli</i> Open
Recent studies have shown that RNA polymerase (RNAP) is spatially organized into distinct clusters in E. coli and B. subtilis cells. Spatially organized molecular components in prokaryotic systems imply compartmentalization without the use…
View article: Improved single-molecule localization precision in astigmatism-based 3D superresolution imaging using weighted likelihood estimation
Improved single-molecule localization precision in astigmatism-based 3D superresolution imaging using weighted likelihood estimation Open
Astigmatism-based superresolution microscopy is widely used to determine the position of individual fluorescent emitters in three-dimensions (3D) with subdiffraction-limited resolutions. This point spread function (PSF) engineering techniq…
New Cell Fate Potentials and Switching Kinetics Uncovered in a Classic Bistable Genetic Switch Open
Bistable switches are common gene regulatory motifs directing two mutually exclusive gene expression states, and consequently distinct cell fates. Theoretical studies suggest that the simple circuitry of bistable switches is sufficient to …