Nuclear accessibility of β-actin mRNA is measured by 3D single-molecule real-time tracking

Multifocus microscopy combined with precise registration between fluorescently labeled mRNA, nuclear pore complexes, and chromatin reveals that β-actin mRNAs freely access the entire nucleus and most are within 0.5 µm of a nuclear pore.

[1]  Hye Yoon Park,et al.  A transgenic mouse for in vivo detection of endogenous labeled mRNA , 2010, Nature Methods.

[2]  S. Ram,et al.  High accuracy 3D quantum dot tracking with multifocal plane microscopy for the study of fast intracellular dynamics in live cells. , 2008, Biophysical journal.

[3]  Alexander Y Katsov,et al.  fast multicolor 3 d imaging using aberration-corrected multifocus microscopy , 2012 .

[4]  C. Langford,et al.  Selective nuclear export of specific classes of mRNA from mammalian nuclei is promoted by GANP , 2014, Nucleic acids research.

[5]  T. Kues,et al.  Visualization of nuclear pore complex and its distribution by confocal laser scanning microscopy. , 1999, Methods in enzymology.

[6]  R. Singer,et al.  In Vivo Imaging of Labelled Endogenous β-actin mRNA During Nucleocytoplasmic Transport , 2010, Nature.

[7]  L. Trinkle-Mulcahy,et al.  Nuclear bodies: new insights into assembly/dynamics and disease relevance. , 2014, Current opinion in cell biology.

[8]  Davide Marenduzzo,et al.  Entropic organization of interphase chromosomes , 2009, The Journal of cell biology.

[9]  G. Blobel,et al.  Gene gating: a hypothesis. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Mark Bates,et al.  Three-Dimensional Super-Resolution Imaging by Stochastic Optical Reconstruction Microscopy , 2008, Science.

[11]  Tobias Pietzsch,et al.  ImgLib2 - generic image processing in Java , 2012, Bioinform..

[12]  R. Singer,et al.  Movement of nuclear poly(A) RNA throughout the interchromatin space in living cells , 1999, Current Biology.

[13]  E. Hurt,et al.  Functional and structural characterization of the mammalian TREX-2 complex that links transcription with nuclear messenger RNA export , 2012, Nucleic acids research.

[14]  A. Lamond,et al.  Toward a High-Resolution View of Nuclear Dynamics , 2007, Science.

[15]  Tom Misteli,et al.  Dynamic binding of histone H1 to chromatin in living cells , 2000, Nature.

[16]  Jan Padeken,et al.  Nucleolus and nuclear periphery: velcro for heterochromatin. , 2014, Current opinion in cell biology.

[17]  V. Buschmann,et al.  Intranuclear binding kinetics and mobility of single native U1 snRNP particles in living cells. , 2006, Molecular biology of the cell.

[18]  P. Bingham,et al.  Evidence for channeled diffusion of pre-mRNAs during nuclear RNA transport in metazoans , 1993, The Journal of cell biology.

[19]  Joseph N. Mait,et al.  Understanding diffractive optical design in the scalar domain , 1995, OSA Annual Meeting.

[20]  F S Fay,et al.  Visualization of single RNA transcripts in situ. , 1998, Science.

[21]  T. Misteli,et al.  High mobility of proteins in the mammalian cell nucleus , 2000, Nature.

[22]  Stephan Saalfeld,et al.  As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets , 2010, Bioinform..

[23]  Suliana Manley,et al.  Single-particle tracking photoactivated localization microscopy for mapping single-molecule dynamics. , 2010, Methods in Enzymology.

[24]  Thomas Cremer,et al.  The architecture of chicken chromosome territories changes during differentiation , 2004, BMC Cell Biology.

[25]  J. Dobrucki,et al.  Scattering of exciting light by live cells in fluorescence confocal imaging: phototoxic effects and relevance for FRAP studies. , 2007, Biophysical journal.

[26]  S. Stallinga.  Compact description of substrate-related aberrations in high numerical-aperture optical disk readout. , 2005, Applied optics.

[27]  Matthew D Lew,et al.  Simultaneous, accurate measurement of the 3D position and orientation of single molecules , 2012, Proceedings of the National Academy of Sciences.

[28]  Charles Kervrann,et al.  Fast live simultaneous multiwavelength four-dimensional optical microscopy , 2010, Proceedings of the National Academy of Sciences.

[29]  P. Lichter,et al.  Experimental evidence for the influence of molecular crowding on nuclear architecture , 2007, Journal of Cell Science.

[30]  S. Masich,et al.  The intranuclear movement of Balbiani ring premessenger ribonucleoprotein particles. , 1999, Experimental cell research.

[31]  H. Leonhardt,et al.  Probing Intranuclear Environments at the Single-Molecule Level , 2007, Biophysical journal.

[32]  Johannes E. Schindelin,et al.  Fiji: an open-source platform for biological-image analysis , 2012, Nature Methods.

[33]  Enrico Gratton,et al.  3D Particle Tracking on a Two-Photon Microscope , 2005, Journal of Fluorescence.

[34]  Y. Shav-Tal,et al.  Dynamics of single mRNP nucleocytoplasmic transport and export through the nuclear pore in living cells , 2010, Nature Cell Biology.

[35]  Karsten Rippe,et al.  Nuclear body movement is determined by chromatin accessibility and dynamics. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[36]  V. Buschmann,et al.  Direct observation of single protein molecules in aqueous solution. , 2006, Chemphyschem : a European journal of chemical physics and physical chemistry.

[37]  A H Greenaway,et al.  Simultaneous multiplane imaging with a distorted diffraction grating. , 1999, Applied optics.

[38]  Robert H Singer,et al.  Materials and Methods Som Text Figs. S1 to S8 References and Notes Dynamics of Single Mrnps in Nuclei of Living Cells , 2022 .

[39]  Robert H. Singer,et al.  Highly localized tracks of specific transcripts within interphase nuclei visualized by in situ hybridization , 1989, Cell.

[40]  Job Dekker,et al.  Molecular Cell Review The Hierarchy of the 3 D Genome , 2013 .

[41]  J. Gall,et al.  Cajal bodies, nucleoli, and speckles in the Xenopus oocyte nucleus have a low-density, sponge-like structure. , 2004, Molecular biology of the cell.

[42]  M. Dundr,et al.  Nucleation of nuclear bodies by RNA , 2011, Nature Cell Biology.

[43]  Thomas Cremer,et al.  Chromosome territories--a functional nuclear landscape. , 2006, Current opinion in cell biology.

[44]  D. Ish-Horowicz,et al.  Apical localization of pair-rule transcripts requires 3′ sequences and limits protein diffusion in the Drosophila blastoderm embryo , 1991, Cell.

[45]  B. Edgar,et al.  Repression and turnover pattern fushi tarazu RNA in the early Drosophila embryo , 1986, Cell.

[46]  P. Agutter.  Models for solid‐state transport: messenger RNA movement from nucleus to cytoplasm. , 1994, Cell biology international.

[47]  M. Gustafsson,et al.  Subdiffraction Multicolor Imaging of the Nuclear Periphery with 3D Structured Illumination Microscopy , 2008, Science.

[48]  Stephan Saalfeld,et al.  Software for bead-based registration of selective plane illumination microscopy data , 2010, Nature Methods.

[49]  F. Waharte,et al.  The human TREX-2 complex is stably associated with the nuclear pore basket , 2013, Journal of Cell Science.

[50]  Robert C. Bolles,et al.  Random sample consensus: a paradigm for model fitting with applications to image analysis and automated cartography , 1981, CACM.

[51]  Lawrence M. Lifshitz,et al.  Rapid, diffusional shuttling of poly(A) RNA between nuclear speckles and the nucleoplasm. , 2005, Molecular biology of the cell.

[52]  S. Semrau,et al.  Quantification of biological interactions with particle image cross-correlation spectroscopy (PICCS). , 2011, Biophysical journal.

[53]  J. Dekker,et al.  The hierarchy of the 3D genome. , 2013, Molecular cell.

[54]  J. Braat.  Influence of substrate thickness on optical disk readout. , 1997, Applied optics.

[55]  B. Daneholt.  Pre-mRNP particles: From gene to nuclear pore , 1999, Current Biology.

[56]  Matthew A. Brown,et al.  Invariant Features from Interest Point Groups , 2002, BMVC.

[57]  A. Raap,et al.  RNAs radiate from gene to cytoplasm as revealed by fluorescence in situ hybridization. , 1995, Journal of cell science.