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Article
Open AccesspyHiM: a new open-source, multi-platform software package for spatial genomics based on multiplexed DNA-FISH imaging
Genome-wide ensemble sequencing methods improved our understanding of chromatin organization in eukaryotes but lack the ability to capture single-cell heterogeneity and spatial organization. To overcome these ...
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Protocol
Hi-M: A Multiplex Oligopaint FISH Method to Capture Chromatin Conformations In Situ and Accompanying Open-Source Acquisition Software
The simultaneous observation of three-dimensional (3D) chromatin structure and transcription in single cells is critical to understand how DNA is organized inside cells and how this organization influences or ...
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Article
Open Access3D chromatin interactions involving Drosophila insulators are infrequent but preferential and arise before TADs and transcription
In mammals, insulators contribute to the regulation of loop extrusion to organize chromatin into topologically associating domains. In Drosophila the role of insulators in 3D genome organization is, however, unde...
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Article
Open AccessMulti-scale dynamic imaging reveals that cooperative motility behaviors promote efficient predation in bacteria
Many species, such as fish schools or bird flocks, rely on collective motion to forage, prey, or escape predators. Likewise, Myxococcus xanthus forages and moves collectively to prey and feed on other bacterial s...
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Article
Open AccessMultiple parameters shape the 3D chromatin structure of single nuclei at the doc locus in Drosophila
The spatial organization of chromatin at the scale of topologically associating domains (TADs) and below displays large cell-to-cell variations. Up until now, how this heterogeneity in chromatin conformation i...
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Article
Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development
Acquisition of cell fate is thought to rely on the specific interaction of remote cis-regulatory modules (CRMs), for example, enhancers and target promoters. However, the precise interplay between chromatin struc...
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Article
Single-particle tracking photoactivated localization microscopy of membrane proteins in living plant tissues
Super-resolution microscopy techniques have pushed the limit of optical imaging to unprecedented spatial resolutions. However, one of the frontiers in nanoscopy is its application to intact living organisms. H...
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Article
Direct and simultaneous observation of transcription and chromosome architecture in single cells with Hi-M
Simultaneous observation of 3D chromatin organization and transcription at the single-cell level and with high spatial resolution may hold the key to unveiling the mechanisms regulating embryonic development, ...
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Protocol
DNA Organization and Superesolved Segregation
With single-molecule localization microscopy (SMLM) it is possible to reveal the internal composition, architecture, and dynamics of molecular machines and large cellular complexes. SMLM remains technically ch...
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Article
Open AccessSingle-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions
At the kilo- to megabase pair scales, eukaryotic genomes are partitioned into self-interacting modules or topologically associated domains (TADs) that associate to form nuclear compartments. Here, we combine h...
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Article
Open AccessHighly efficient multicolor multifocus microscopy by optimal design of diffraction binary gratings
Multifocus microscopy (MFM) allows sensitive and fast three-dimensional imaging. It relies on the efficient design of diffraction phase gratings yielding homogeneous intensities in desired diffraction orders. ...
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Article
The mechanism of force transmission at bacterial focal adhesion complexes
Various rod-shaped bacteria mysteriously glide on surfaces in the absence of appendages such as flagella or pili. In the deltaproteobacterium Myxococcus xanthus, a putative gliding motility machinery (the Agl–Glt...
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Article
Open AccessBacterial partition complexes segregate within the volume of the nucleoid
Precise and rapid DNA segregation is required for proper inheritance of genetic material. In most bacteria and archaea, this process is assured by a broadly conserved mitotic-like apparatus in which a NTPase (...
