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Literature DB >> 32176523

Imaging of DNA and RNA in Living Eukaryotic Cells to Reveal Spatiotemporal Dynamics of Gene Expression.

Hanae Sato¹, Sulagna Das¹, Robert H Singer^1,2, Maria Vera^1,3.

Abstract

This review focuses on imaging DNA and single RNA molecules in living cells to define eukaryotic functional organization and dynamic processes. The latest advances in technologies to visualize individual DNA loci and RNAs in real time are discussed. Single-molecule fluorescence microscopy provides the spatial and temporal resolution to reveal mechanisms regulating fundamental cell functions. Novel insights into the regulation of nuclear architecture, transcription, posttranscriptional RNA processing, and RNA localization provided by multicolor fluorescence microscopy are reviewed. A perspective on the future use of live imaging technologies and overcoming their current limitations is provided.

Entities: CellLine Chemical Disease Gene Species

Keywords: fluorescence microscopy; nuclear organization; posttranscriptional regulation; single-molecule techniques; transcription

Mesh：

Substances：

Year: 2020 PMID： 32176523 PMCID： PMC7608990 DOI： 10.1146/annurev-biochem-011520-104955

Source DB: PubMed Journal: Annu Rev Biochem ISSN： 0066-4154 Impact factor: 23.643

160 in total

1. Dynamics of single mRNP nucleocytoplasmic transport and export through the nuclear pore in living cells.

Authors: Amir Mor; Shimrit Suliman; Rakefet Ben-Yishay; Sharon Yunger; Yehuda Brody; Yaron Shav-Tal
Journal: Nat Cell Biol Date: 2010-05-09 Impact factor: 28.824

2. Telomeric noncoding RNA TERRA is induced by telomere shortening to nucleate telomerase molecules at short telomeres.

Authors: Emilio Cusanelli; Carmina Angelica Perez Romero; Pascal Chartrand
Journal: Mol Cell Date: 2013-09-26 Impact factor: 17.970

3. Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos.

Authors: Mustafa Mir; Michael R Stadler; Stephan A Ortiz; Colleen E Hannon; Melissa M Harrison; Xavier Darzacq; Michael B Eisen
Journal: Elife Date: 2018-12-27 Impact factor: 8.140

4. Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing.

Authors: Chun-Kan Chen; Mario Blanco; Constanza Jackson; Erik Aznauryan; Noah Ollikainen; Christine Surka; Amy Chow; Andrea Cerase; Patrick McDonel; Mitchell Guttman
Journal: Science Date: 2016-08-04 Impact factor: 47.728

5. Live cell imaging of telomerase RNA dynamics reveals cell cycle-dependent clustering of telomerase at elongating telomeres.

Authors: Franck Gallardo; Nancy Laterreur; Emilio Cusanelli; Faissal Ouenzar; Emmanuelle Querido; Raymund J Wellinger; Pascal Chartrand
Journal: Mol Cell Date: 2011-12-09 Impact factor: 17.970

6. Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Authors: Erez Lieberman-Aiden; Nynke L van Berkum; Louise Williams; Maxim Imakaev; Tobias Ragoczy; Agnes Telling; Ido Amit; Bryan R Lajoie; Peter J Sabo; Michael O Dorschner; Richard Sandstrom; Bradley Bernstein; M A Bender; Mark Groudine; Andreas Gnirke; John Stamatoyannopoulos; Leonid A Mirny; Eric S Lander; Job Dekker
Journal: Science Date: 2009-10-09 Impact factor: 47.728

7. MS2 coat proteins bound to yeast mRNAs block 5' to 3' degradation and trap mRNA decay products: implications for the localization of mRNAs by MS2-MCP system.

Authors: Jennifer F Garcia; Roy Parker
Journal: RNA Date: 2015-06-19 Impact factor: 4.942

8. 3D imaging of Sox2 enhancer clusters in embryonic stem cells.

Authors: Zhe Liu; Wesley R Legant; Bi-Chang Chen; Li Li; Jonathan B Grimm; Luke D Lavis; Eric Betzig; Robert Tjian
Journal: Elife Date: 2014-12-24 Impact factor: 8.140

9. ECHO-liveFISH: in vivo RNA labeling reveals dynamic regulation of nuclear RNA foci in living tissues.

Authors: Ikumi Oomoto; Asuka Suzuki-Hirano; Hiroki Umeshima; Yong-Woon Han; Hiroyuki Yanagisawa; Peter Carlton; Yoshie Harada; Mineko Kengaku; Akimitsu Okamoto; Tomomi Shimogori; Dan Ohtan Wang
Journal: Nucleic Acids Res Date: 2015-06-22 Impact factor: 16.971

Review 9. Role of Nuclear Non-Canonical Nucleic Acid Structures in Organismal Development and Adaptation to Stress Conditions.

Authors: Célia Alecki; Maria Vera
Journal: Front Genet Date: 2022-02-23 Impact factor: 4.599

Review 10. Spatiotemporal Insights Into RNA-Organelle Interactions in Neurons.

Authors: Shivani C Kharod; Dong-Woo Hwang; Sulagna Das; Young J Yoon
Journal: Front Cell Dev Biol Date: 2021-06-10

Imaging of DNA and RNA in Living Eukaryotic Cells to Reveal Spatiotemporal Dynamics of Gene Expression.

1. Dynamics of single mRNP nucleocytoplasmic transport and export through the nuclear pore in living cells.

2. Telomeric noncoding RNA TERRA is induced by telomere shortening to nucleate telomerase molecules at short telomeres.

3. Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos.

4. Xist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing.

5. Live cell imaging of telomerase RNA dynamics reveals cell cycle-dependent clustering of telomerase at elongating telomeres.

6. Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

7. MS2 coat proteins bound to yeast mRNAs block 5' to 3' degradation and trap mRNA decay products: implications for the localization of mRNAs by MS2-MCP system.

8. 3D imaging of Sox2 enhancer clusters in embryonic stem cells.

9. ECHO-liveFISH: in vivo RNA labeling reveals dynamic regulation of nuclear RNA foci in living tissues.

10. Fluorogenic RNA Mango aptamers for imaging small non-coding RNAs in mammalian cells.

1. A repackaged CRISPR platform increases homology-directed repair for yeast engineering.

2. Real-time imaging of Arc/Arg3.1 transcription ex vivo reveals input-specific immediate early gene dynamics.

3. Long-term imaging of individual mRNA molecules in living cells.

Review 4. RNA transport from transcription to localized translation: a single molecule perspective.

Review 5. The Regulation of RNA Modification Systems: The Next Frontier in Epitranscriptomics?

Review 6. Intracellular mRNA transport and localized translation.

7. Current progress and potential opportunities to infer single-cell developmental trajectory and cell fate.

Review 8. Capturing and Understanding the Dynamics and Heterogeneity of Gene Expression in the Living Cell.

Review 9. Role of Nuclear Non-Canonical Nucleic Acid Structures in Organismal Development and Adaptation to Stress Conditions.

Review 10. Spatiotemporal Insights Into RNA-Organelle Interactions in Neurons.