Literature DB >> 27893965

Single-Cell and Single-Molecule Analysis of Gene Expression Regulation.

Maria Vera1, Jeetayu Biswas1, Adrien Senecal1, Robert H Singer1,2, Hye Yoon Park3,4.   

Abstract

Recent advancements in single-cell and single-molecule imaging technologies have resolved biological processes in time and space that are fundamental to understanding the regulation of gene expression. Observations of single-molecule events in their cellular context have revealed highly dynamic aspects of transcriptional and post-transcriptional control in eukaryotic cells. This approach can relate transcription with mRNA abundance and lifetimes. Another key aspect of single-cell analysis is the cell-to-cell variability among populations of cells. Definition of heterogeneity has revealed stochastic processes, determined characteristics of under-represented cell types or transitional states, and integrated cellular behaviors in the context of multicellular organisms. In this review, we discuss novel aspects of gene expression of eukaryotic cells and multicellular organisms revealed by the latest advances in single-cell and single-molecule imaging technology.

Entities:  

Keywords:  gene expression; mRNA localization; single cell; single-molecule imaging; transcription; translation

Mesh:

Substances:

Year:  2016        PMID: 27893965      PMCID: PMC5149423          DOI: 10.1146/annurev-genet-120215-034854

Source DB:  PubMed          Journal:  Annu Rev Genet        ISSN: 0066-4197            Impact factor:   16.830


  160 in total

Review 1.  P-bodies and stress granules: possible roles in the control of translation and mRNA degradation.

Authors:  Carolyn J Decker; Roy Parker
Journal:  Cold Spring Harb Perspect Biol       Date:  2012-09-01       Impact factor: 10.005

2.  Visualization of dynamics of single endogenous mRNA labeled in live mouse.

Authors:  Hye Yoon Park; Hyungsik Lim; Young J Yoon; Antonia Follenzi; Chiso Nwokafor; Melissa Lopez-Jones; Xiuhua Meng; Robert H Singer
Journal:  Science       Date:  2014-01-24       Impact factor: 47.728

3.  Real-time quantification of single RNA translation dynamics in living cells.

Authors:  Tatsuya Morisaki; Kenneth Lyon; Keith F DeLuca; Jennifer G DeLuca; Brian P English; Zhengjian Zhang; Luke D Lavis; Jonathan B Grimm; Sarada Viswanathan; Loren L Looger; Timothee Lionnet; Timothy J Stasevich
Journal:  Science       Date:  2016-05-05       Impact factor: 47.728

Review 4.  High-throughput functional genomics using CRISPR-Cas9.

Authors:  Ophir Shalem; Neville E Sanjana; Feng Zhang
Journal:  Nat Rev Genet       Date:  2015-04-09       Impact factor: 53.242

5.  Programmable RNA Tracking in Live Cells with CRISPR/Cas9.

Authors:  David A Nelles; Mark Y Fang; Mitchell R O'Connell; Jia L Xu; Sebastian J Markmiller; Jennifer A Doudna; Gene W Yeo
Journal:  Cell       Date:  2016-03-17       Impact factor: 41.582

Review 6.  Tracing epithelial stem cells during development, homeostasis, and repair.

Authors:  Alexandra Van Keymeulen; Cédric Blanpain
Journal:  J Cell Biol       Date:  2012-05-28       Impact factor: 10.539

7.  Frequency-modulated nuclear localization bursts coordinate gene regulation.

Authors:  Long Cai; Chiraj K Dalal; Michael B Elowitz
Journal:  Nature       Date:  2008-09-25       Impact factor: 49.962

8.  Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system.

Authors:  Baohui Chen; Luke A Gilbert; Beth A Cimini; Joerg Schnitzbauer; Wei Zhang; Gene-Wei Li; Jason Park; Elizabeth H Blackburn; Jonathan S Weissman; Lei S Qi; Bo Huang
Journal:  Cell       Date:  2013-12-19       Impact factor: 41.582

9.  Recruitment to the nuclear periphery can alter expression of genes in human cells.

Authors:  Lee E Finlan; Duncan Sproul; Inga Thomson; Shelagh Boyle; Elizabeth Kerr; Paul Perry; Bauke Ylstra; Jonathan R Chubb; Wendy A Bickmore
Journal:  PLoS Genet       Date:  2008-03-21       Impact factor: 5.917

Review 10.  Contribution of Topological Domains and Loop Formation to 3D Chromatin Organization.

Authors:  Vuthy Ea; Marie-Odile Baudement; Annick Lesne; Thierry Forné
Journal:  Genes (Basel)       Date:  2015-07-27       Impact factor: 4.096

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  45 in total

1.  Robustness, Accuracy, and Cell State Heterogeneity in Biological Systems.

Authors:  Roy Wollman
Journal:  Curr Opin Syst Biol       Date:  2017-12-15

Review 2.  Recent progress in single-molecule studies of mRNA localization in vivo.

Authors:  Songhee H Kim; Melissa Vieira; Jae Youn Shim; Hongyoung Choi; Hye Yoon Park
Journal:  RNA Biol       Date:  2018-11-14       Impact factor: 4.652

3.  IRIS3: integrated cell-type-specific regulon inference server from single-cell RNA-Seq.

Authors:  Anjun Ma; Cankun Wang; Yuzhou Chang; Faith H Brennan; Adam McDermaid; Bingqiang Liu; Chi Zhang; Phillip G Popovich; Qin Ma
Journal:  Nucleic Acids Res       Date:  2020-07-02       Impact factor: 16.971

4.  Quantifying phenotypes in single cells using droplet microfluidics.

Authors:  Fengjiao Lyu; Lucas R Blauch; Sindy K Y Tang
Journal:  Methods Cell Biol       Date:  2018-10-25       Impact factor: 1.441

5.  Single-cell systems biology: probing the basic unit of information flow.

Authors:  Simona Patange; Michelle Girvan; Daniel R Larson
Journal:  Curr Opin Syst Biol       Date:  2017-12-06

Review 6.  Functional roles of microbial cell-to-cell heterogeneity and emerging technologies for analysis and control.

Authors:  Nadia Maria Vieira Sampaio; Mary J Dunlop
Journal:  Curr Opin Microbiol       Date:  2020-09-09       Impact factor: 7.934

Review 7.  Covalent labeling of nucleic acids.

Authors:  Nils Klöcker; Florian P Weissenboeck; Andrea Rentmeister
Journal:  Chem Soc Rev       Date:  2020-10-21       Impact factor: 54.564

Review 8.  Imaging of DNA and RNA in Living Eukaryotic Cells to Reveal Spatiotemporal Dynamics of Gene Expression.

Authors:  Hanae Sato; Sulagna Das; Robert H Singer; Maria Vera
Journal:  Annu Rev Biochem       Date:  2020-03-16       Impact factor: 23.643

Review 9.  Chromatin reprogramming in breast cancer.

Authors:  Erin E Swinstead; Ville Paakinaho; Gordon L Hager
Journal:  Endocr Relat Cancer       Date:  2018-04-24       Impact factor: 5.678

10.  Dual inhibition of MDMX and MDM2 as a therapeutic strategy in leukemia.

Authors:  Luis A Carvajal; Daniela Ben Neriah; Adrien Senecal; Lumie Benard; Victor Thiruthuvanathan; Tatyana Yatsenko; Swathi-Rao Narayanagari; Justin C Wheat; Tihomira I Todorova; Kelly Mitchell; Charles Kenworthy; Vincent Guerlavais; D Allen Annis; Boris Bartholdy; Britta Will; Jesus D Anampa; Ioannis Mantzaris; Manuel Aivado; Robert H Singer; Robert A Coleman; Amit Verma; Ulrich Steidl
Journal:  Sci Transl Med       Date:  2018-04-11       Impact factor: 17.956

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