Literature DB >> 29956254

Single Molecule Imaging in Live Embryos Using Lattice Light-Sheet Microscopy.

Mustafa Mir1, Armando Reimer2, Michael Stadler1, Astou Tangara1, Anders S Hansen1, Dirk Hockemeyer1, Michael B Eisen1,2,3,4, Hernan Garcia1,2,5, Xavier Darzacq6.   

Abstract

In the past decade, live-cell single molecule imaging studies have provided unique insights on how DNA-binding molecules such as transcription factors explore the nuclear environment to search for and bind to their targets. However, due to technological limitations, single molecule experiments in living specimens have largely been limited to monolayer cell cultures. Lattice light-sheet microscopy overcomes these limitations and has now enabled single molecule imaging within thicker specimens such as embryos. Here we describe a general procedure to perform single molecule imaging in living Drosophila melanogaster embryos using lattice light-sheet microscopy. This protocol allows direct observation of both transcription factor diffusion and binding dynamics. Finally, we illustrate how this Drosophila protocol can be extended to other thick samples using single molecule imaging in live mouse embryos as an example.

Entities:  

Keywords:  Drosophila melanogaster; Lattice light-sheet microscopy; Live embryo imaging; Selective plane illumination microscopy; Single molecule fluorescence; Single molecule imaging; Single molecule kinetics; Single particle tracking; Transcription factor dynamics

Mesh:

Year:  2018        PMID: 29956254      PMCID: PMC6225527          DOI: 10.1007/978-1-4939-8591-3_32

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  14 in total

1.  Real-time dynamics of RNA polymerase II clustering in live human cells.

Authors:  Ibrahim I Cisse; Ignacio Izeddin; Sebastien Z Causse; Lydia Boudarene; Adrien Senecal; Leila Muresan; Claire Dugast-Darzacq; Bassam Hajj; Maxime Dahan; Xavier Darzacq
Journal:  Science       Date:  2013-07-04       Impact factor: 47.728

2.  CTCF and cohesin regulate chromatin loop stability with distinct dynamics.

Authors:  Anders S Hansen; Iryna Pustova; Claudia Cattoglio; Robert Tjian; Xavier Darzacq
Journal:  Elife       Date:  2017-05-03       Impact factor: 8.140

3.  Extracting intracellular diffusive states and transition rates from single-molecule tracking data.

Authors:  Fredrik Persson; Martin Lindén; Cecilia Unoson; Johan Elf
Journal:  Nat Methods       Date:  2013-02-10       Impact factor: 28.547

4.  Single-molecule tracking in live cells reveals distinct target-search strategies of transcription factors in the nucleus.

Authors:  Ignacio Izeddin; Vincent Récamier; Lana Bosanac; Ibrahim I Cissé; Lydia Boudarene; Claire Dugast-Darzacq; Florence Proux; Olivier Bénichou; Raphaël Voituriez; Olivier Bensaude; Maxime Dahan; Xavier Darzacq
Journal:  Elife       Date:  2014-06-12       Impact factor: 8.140

5.  RNA Polymerase II cluster dynamics predict mRNA output in living cells.

Authors:  Won-Ki Cho; Namrata Jayanth; Brian P English; Takuma Inoue; J Owen Andrews; William Conway; Jonathan B Grimm; Jan-Hendrik Spille; Luke D Lavis; Timothée Lionnet; Ibrahim I Cisse
Journal:  Elife       Date:  2016-05-03       Impact factor: 8.140

6.  Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes.

Authors:  Arnauld Sergé; Nicolas Bertaux; Hervé Rigneault; Didier Marguet
Journal:  Nat Methods       Date:  2008-07-06       Impact factor: 28.547

7.  Single-molecule dynamics of enhanceosome assembly in embryonic stem cells.

Authors:  Jiji Chen; Zhengjian Zhang; Li Li; Bi-Chang Chen; Andrey Revyakin; Bassam Hajj; Wesley Legant; Maxime Dahan; Timothée Lionnet; Eric Betzig; Robert Tjian; Zhe Liu
Journal:  Cell       Date:  2014-03-13       Impact factor: 41.582

8.  Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution.

Authors:  Bi-Chang Chen; Wesley R Legant; Kai Wang; Lin Shao; Daniel E Milkie; Michael W Davidson; Chris Janetopoulos; Xufeng S Wu; John A Hammer; Zhe Liu; Brian P English; Yuko Mimori-Kiyosue; Daniel P Romero; Alex T Ritter; Jennifer Lippincott-Schwartz; Lillian Fritz-Laylin; R Dyche Mullins; Diana M Mitchell; Joshua N Bembenek; Anne-Cecile Reymann; Ralph Böhme; Stephan W Grill; Jennifer T Wang; Geraldine Seydoux; U Serdar Tulu; Daniel P Kiehart; Eric Betzig
Journal:  Science       Date:  2014-10-23       Impact factor: 47.728

9.  Objective comparison of particle tracking methods.

Authors:  Nicolas Chenouard; Ihor Smal; Fabrice de Chaumont; Martin Maška; Ivo F Sbalzarini; Yuanhao Gong; Janick Cardinale; Craig Carthel; Stefano Coraluppi; Mark Winter; Andrew R Cohen; William J Godinez; Karl Rohr; Yannis Kalaidzidis; Liang Liang; James Duncan; Hongying Shen; Yingke Xu; Klas E G Magnusson; Joakim Jaldén; Helen M Blau; Perrine Paul-Gilloteaux; Philippe Roudot; Charles Kervrann; François Waharte; Jean-Yves Tinevez; Spencer L Shorte; Joost Willemse; Katherine Celler; Gilles P van Wezel; Han-Wei Dan; Yuh-Show Tsai; Carlos Ortiz de Solórzano; Jean-Christophe Olivo-Marin; Erik Meijering
Journal:  Nat Methods       Date:  2014-01-19       Impact factor: 28.547

10.  Single-molecule analysis of transcription factor binding at transcription sites in live cells.

Authors:  Tatsuya Morisaki; Waltraud G Müller; Nicole Golob; Davide Mazza; James G McNally
Journal:  Nat Commun       Date:  2014-07-18       Impact factor: 14.919

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  6 in total

Review 1.  Mechanisms regulating zygotic genome activation.

Authors:  Katharine N Schulz; Melissa M Harrison
Journal:  Nat Rev Genet       Date:  2019-04       Impact factor: 53.242

2.  A new class of disordered elements controls DNA replication through initiator self-assembly.

Authors:  Matthew W Parker; Maren Bell; Mustafa Mir; Jonchee A Kao; Xavier Darzacq; Michael R Botchan; James M Berger
Journal:  Elife       Date:  2019-09-27       Impact factor: 8.140

3.  Lattice Light-Sheet Microscopy Multi-dimensional Analyses (LaMDA) of T-Cell Receptor Dynamics Predict T-Cell Signaling States.

Authors:  Jillian Rosenberg; Guoshuai Cao; Fernanda Borja-Prieto; Jun Huang
Journal:  Cell Syst       Date:  2020-05-20       Impact factor: 10.304

4.  Radial pair correlation of molecular brightness fluctuations maps protein diffusion as a function of oligomeric state within live-cell nuclear architecture.

Authors:  Ashleigh Solano; Jieqiong Lou; Lorenzo Scipioni; Enrico Gratton; Elizabeth Hinde
Journal:  Biophys J       Date:  2022-04-30       Impact factor: 3.699

Review 5.  Advances in Chromatin and Chromosome Research: Perspectives from Multiple Fields.

Authors:  Andrews Akwasi Agbleke; Assaf Amitai; Jason D Buenrostro; Aditi Chakrabarti; Lingluo Chu; Anders S Hansen; Kristen M Koenig; Ajay S Labade; Sirui Liu; Tadasu Nozaki; Sergey Ovchinnikov; Andrew Seeber; Haitham A Shaban; Jan-Hendrik Spille; Andrew D Stephens; Jun-Han Su; Dushan Wadduwage
Journal:  Mol Cell       Date:  2020-08-07       Impact factor: 17.970

Review 6.  A 50 year history of technologies that drove discovery in eukaryotic transcription regulation.

Authors:  John T Lis
Journal:  Nat Struct Mol Biol       Date:  2019-08-22       Impact factor: 15.369

  6 in total

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