Fluorescence in situ hybridization (FISH): History, limitations and what to expect from micro-scale FISH? DOI Creative Commons

Deborah Huber,

Lena Voith von Voithenberg, Govind V. Kaigala

et al.

Micro and Nano Engineering, Journal Year: 2018, Volume and Issue: 1, P. 15 - 24

Published: Oct. 31, 2018

In this article, we review an important cytogenetic technique - fluorescence in situ hybridization (FISH) which is used for obtaining spatial genomic and transcriptomic information. FISH widely utilized cell biological research as well diagnostic applications preventive reproductive medicine, oncology. It the gold standard detection of chromosomal abnormalities. Despite high specificity possibility direct quantitative imaging, some its key limitations prevent regular use diagnostics. To promote extensive these applications, assay time probe consumption will need to be addressed. Microfluidic technologies hold great promise improving exactly parameters. past two decades, microtechnology has matured enabled a new line analysis tools biomedical chemical sciences. Incidentally, convergence with microfluidics starting have decisive impact field medical By miniaturizing implementations assays, special characteristics fluid flow small volumes can leveraged modify reaction kinetics thus reagent delivery assays. Here highlight selected historical views on FISH, current implementations, provide perspective future developments micro-scale FISH.

Language: Английский

SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues DOI
Jocelyn Y. Kishi,

Sylvain W. Lapan,

Brian J. Beliveau

et al.

Nature Methods, Journal Year: 2019, Volume and Issue: 16(6), P. 533 - 544

Published: May 20, 2019

Language: Английский

Citations

370
Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation DOI Creative Commons

Sharmistha Kundu,

Fei Ji,

Hongjae Sunwoo

et al.

Molecular Cell, Journal Year: 2017, Volume and Issue: 65(3), P. 432 - 446.e5

Published: Feb. 1, 2017

Language: Английский

Citations

319
Switchable Fluorophores for Single-Molecule Localization Microscopy DOI
Honglin Li, Joshua C. Vaughan

Chemical Reviews, Journal Year: 2018, Volume and Issue: 118(18), P. 9412 - 9454

Published: Sept. 17, 2018

The past decade has witnessed an explosion in the use of super-resolution fluorescence microscopy methods biology and other fields. Single-molecule localization (SMLM) is one most widespread these owes its success large part to ability control on–off state fluorophores through various chemical, photochemical, or binding–unbinding mechanisms. We provide here a comprehensive overview switchable SMLM including detailed review all major classes fluorophores, we also address strategies for labeling specimens, considerations multichannel live-cell imaging, potential pitfalls, areas future development.

Language: Английский

Citations

282
TADs are 3D structural units of higher-order chromosome organization in Drosophila DOI Creative Commons
Quentin Szabo, Daniel Jost, Jia‐Ming Chang

et al.

Science Advances, Journal Year: 2018, Volume and Issue: 4(2)

Published: Feb. 2, 2018

Drosophila chromosomes are organized in a series of nanocompartments that correspond to topologically associating domains.

Language: Английский

Citations

272
CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells DOI Open Access
Wulan Deng, Xinghua Shi, Robert Tjian

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2015, Volume and Issue: 112(38), P. 11870 - 11875

Published: Aug. 31, 2015

Significance We have derived a new technology for the detection of genes within undisturbed nuclei fixed cells and tissues. Previous approaches used fluorescent DNA probes to hybridize interest, requiring treatment heat disruptive chemicals that distort natural organization nucleus. Instead, we bacterial protein, CRISPR (clustered regularly interspaced short palindromic repeats), combined with an RNA sequence as find interest in intact genome. This approach preserves spatial relationships genetic elements, which are important understanding gene expression, process is remarkably rapid (15 min), convenient, can be directly on tissues diagnosis disease.

Language: Английский

Citations

259
Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling DOI Creative Commons
Guy Nir, Irene Farabella, Cynthia Pérez Estrada

et al.

PLoS Genetics, Journal Year: 2018, Volume and Issue: 14(12), P. e1007872 - e1007872

Published: Dec. 26, 2018

Chromosome organization is crucial for genome function. Here, we present a method visualizing chromosomal DNA at super-resolution and then integrating Hi-C data to produce three-dimensional models of chromosome organization. Using the microscopy methods OligoSTORM OligoDNA-PAINT, trace 8 megabases human 19, structures ranging in size from few kilobases over megabase. Focusing on regions that contribute compartments, discover distinct that, spite considerable variability, can predict whether such correspond active (A-type) or inactive (B-type) compartments. Imaging through depths entire nuclei, capture pairs homologous diploid cells, obtaining evidence maternal paternal be differentially organized. Finally, using restraint-based modeling integrate imaging data, implement method–integrative genomic (IMGR)–to increase resolution our traces 10 kb.

Language: Английский

Citations

243
Microscopy-Based Chromosome Conformation Capture Enables Simultaneous Visualization of Genome Organization and Transcription in Intact Organisms DOI Creative Commons
Andrés M. Cardozo Gizzi, Diego I. Cattoni, Jean-Bernard Fiche

et al.

Molecular Cell, Journal Year: 2019, Volume and Issue: 74(1), P. 212 - 222.e5

Published: Feb. 19, 2019

Language: Английский

Citations

223
OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes DOI Creative Commons
Brian J. Beliveau, Jocelyn Y. Kishi, Guy Nir

et al.

Proceedings of the National Academy of Sciences, Journal Year: 2018, Volume and Issue: 115(10)

Published: Feb. 20, 2018

Significance FISH enables researchers to visualize the subcellular distribution of RNA and DNA molecules in individual cells. The recent development methods employing probes composed synthetic oligonucleotides (oligos) allows tightly control aspects probe design such as binding energy genomic specificity. Although oligo are central many recently developed massively multiplexed superresolution imaging methods, no dedicated computational utility exists facilitate on genome-wide scale. Here, we introduce a streamlined pipeline for rapid, genome-scale validate our approach by using conventional imaging. Our method provides framework with which oligo-based hybridization experiments.

Language: Английский

Citations

223
Fluorescence In situ Hybridization: Cell-Based Genetic Diagnostic and Research Applications DOI Creative Commons

Chenghua Cui,

Wei Shu, Peining Li

et al.

Frontiers in Cell and Developmental Biology, Journal Year: 2016, Volume and Issue: 4

Published: Sept. 5, 2016

Fluorescence in situ hybridization (FISH) is a macromolecule recognition technology based on the complementary nature of DNA or DNA/RNA double strands. Selected strands incorporated with fluorophore-coupled nucleotides can be used as probes to hybridize onto sequences tested cells and tissues then visualized through fluorescence microscope an imaging system. This was initially developed physical mapping tool delineate genes within chromosomes. Its high analytical resolution single gene level sensitivity specificity enabled immediate application for genetic diagnosis constitutional common aneuploidies, microdeletion/microduplication syndromes subtelomeric rearrangements. FISH tests using panels gene-specific somatic recurrent losses, gains translocations have been routinely applied hematologic solid tumors are one fastest-growing areas cancer diagnosis. has also detect infectious microbials parasites like malaria human blood cells. Recent advances involve various methods improving probe labeling efficiency use super systems direct visualization intra-nuclear chromosomal organization profiling RNA transcription Cas9-mediated (CASFISH) allowed repetitive single-copy without disruption nuclear genomic fixed living Using oligopaint-FISH super-resolution chromosome haplotypes from differentially specified single-nucleotide polymorphism loci. Single molecule (smRNA-FISH) combinatorial sequential barcoding by multiple round were measure mRNA expression Research applications these techniques structure sub-cellular transcriptional dynamics many revealed their functions biological processes.

Language: Английский

Citations

201
Nuclear compartmentalization as a mechanism of quantitative control of gene expression DOI
Prashant Bhat, Drew D. Honson, Mitchell Guttman

et al.

Nature Reviews Molecular Cell Biology, Journal Year: 2021, Volume and Issue: 22(10), P. 653 - 670

Published: Aug. 2, 2021

Language: Английский

Citations

199