Technological advances in probing 4D genome organization

Soroczynski, Jan; Risca, Viviana I.

doi:10.1016/j.ceb.2023.102211

Cited by 3 publications

(1 citation statement)

References 65 publications

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“…As such, this review will focus on those optical tools that can be readily used in transgenesis and will not cover the tools for interrogating biological processes via fixed samples, nonoptical means, or by using tools that require external biochemical treatments. In the first instance, there are several available extensive reviews covering advances in chromatin architectural characterization techniques [1,2], fluorescent in situ hybridization (FISH)-related methods [3,4], and transcriptomics [5,6] and proteomics [7,8]. Similarly, improvements in multiomics [9], mass spectrometry [10,11], DamID and BioID [12][13][14] have been recently chronicled.…”

Section: Introductionmentioning

confidence: 99%

Opticool: Cutting-edge transgenic optical tools

Fenelon,

Krause,

Koromila

2024

PLoS Genet

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Only a few short decades have passed since the sequencing of GFP, yet the modern repertoire of transgenically encoded optical tools implies an exponential proliferation of ever improving constructions to interrogate the subcellular environment. A myriad of tags for labeling proteins, RNA, or DNA have arisen in the last few decades, facilitating unprecedented visualization of subcellular components and processes. Development of a broad array of modern genetically encoded sensors allows real-time, in vivo detection of molecule levels, pH, forces, enzyme activity, and other subcellular and extracellular phenomena in ever expanding contexts. Optogenetic, genetically encoded optically controlled manipulation systems have gained traction in the biological research community and facilitate single-cell, real-time modulation of protein function in vivo in ever broadening, novel applications. While this field continues to explosively expand, references are needed to assist scientists seeking to use and improve these transgenic devices in new and exciting ways to interrogate development and disease. In this review, we endeavor to highlight the state and trajectory of the field of in vivo transgenic optical tools.

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Section: Introductionmentioning

confidence: 99%

Opticool: Cutting-edge transgenic optical tools

Fenelon,

Krause,

Koromila

2024

PLoS Genet

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Regulation of Gene Expression

Klinge,

Clark

2024

Reference Module in Biomedical Sciences

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Space-time dynamics of genome replication studied with super-resolved microscopy

Gelléri,

Sterr,

Strickfaden

et al. 2024

Preprint

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Genome replication requires duplication of the complete set of DNA sequences together with nucleosomes and epigenetic signatures. Notwithstanding profound knowledge on mechanistic details of DNA replication, major problems of genome replication have remained unresolved. In this perspective article, we consider the accessibility of replication machines to all DNA sequences in due course, the maintenance of functionally important positional and structural features of chromatid domains during replication, and the rapid transition of CTs into prophase chromosomes with two chromatids. We illustrate this problem with EdU pulse-labeling (10 min) and chase experiments (80 min) performed with mouse myeloblast cells. Following light optical serial sectioning of nuclei with 3D structured illumination microscopy (SIM), seven DNA intensity classes were distinguished as proxies for increasing DNA compaction. In nuclei of cells fixed immediately after the pulse-label, we observed a relative under-representation of EdU-labeled DNA in low DNA density classes, representing the active nuclear compartment (ANC), and an over-representation in high density classes representing the inactive nuclear compartment (INC). Cells fixed after the chase revealed an even more pronounced shift to high DNA intensity classes. This finding contrasts with previous studies of the transcriptional topography demonstrating an under-representation of epigenetic signatures for active chromatin and RNAPII in high DNA intensity classes and their over-representation in low density classes. We discuss these findings in the light of current models viewing CDs either as structural chromatin frameworks or as phase-separated droplets, as well as methodological limitations that currently prevent an integration of this contrasting evidence for the spatial nuclear topography of replication and transcription into a common framework of the dynamic nuclear architecture.

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Technological advances in probing 4D genome organization

Cited by 3 publications

References 65 publications

Opticool: Cutting-edge transgenic optical tools

Opticool: Cutting-edge transgenic optical tools

Regulation of Gene Expression

Space-time dynamics of genome replication studied with super-resolved microscopy

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