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Chapal M, Szlak L, Hutzler A, Nizhberg A,
Itzkovitz S (2015) Bursty gene expression in
the intact mammalian liver. Mol Cell 58
(1):147–156.
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molcel.2015.01.027
34. Raj A, Peskin CS, Tranchina D, Vargas DY,
Tyagi S (2006) Stochastic mRNA synthesis in
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0040309
35. Paul B, Montpetit B (2016) Altered RNA processing and export lead to retention of mRNAs
near transcription sites and nuclear pore complexes or within the nucleolus. Mol Biol Cell
27(17):2742–2756.
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1091/mbc.E16-04-0244
36. Bahar Halpern K, Caspi I, Lemze D, Levy M,
Landen S, Elinav E, Ulitsky I, Itzkovitz S
(2015) Nuclear retention of mRNA in mammalian tissues. Cell Rep 13(12):2653–2662.
https://doi.org/10.1016/j.celrep.2015.11.
036
37. Trcek T, Larson DR, Moldon A, Query CC,
Singer RH (2011) Single-molecule mRNA
decay
measurements
reveal
promoterregulated mRNA stability in yeast. Cell 147
(7):1484–1497. https://doi.org/10.1016/j.
cell.2011.11.051
38. Trcek T, Sato H, Singer RH, Maquat LE
(2013) Temporal and spatial characterization
of nonsense-mediated mRNA decay. Genes
Dev 27(5):541–551. https://doi.org/10.
1101/gad.209635.112
39. Pichon X, Lagha M, Mueller F, Bertrand E
(2018) A growing toolbox to image gene
expression in single cells: sensitive approaches
for demanding challenges. Mol Cell 71
(3):468–480.
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molcel.2018.07.022
40. Bertrand E, Chartrand P, Schaefer M, Shenoy
SM, Singer RH, Long RM (1998) Localization
of ASH1 mRNA particles in living yeast. Mol
Cell 2(4):437–445
41. Peabody DS (1993) The RNA binding site of
bacteriophage MS2 coat protein. EMBO J 12
(2):595–600
42. Fusco D, Bertrand E, Singer RH (2004) Imaging of single mRNAs in the cytoplasm of living
cells. Prog Mol Subcell Biol 35:135–150
43. Tutucci E, Vera M, Singer RH (2018) SinglemRNA detection in living S. cerevisiae using a
re-engineered MS2 system. Nat Protoc 13
(10):2268–2296. https://doi.org/10.1038/
s41596-018-0037-2
44. Brody Y, Neufeld N, Bieberstein N, Causse SZ,
Bohnlein EM, Neugebauer KM, Darzacq X,
Shav-Tal Y (2011) The in vivo kinetics of
RNA polymerase II elongation during
co-transcriptional splicing. PLoS Biol 9(1):
e1000573. https://doi.org/10.1371/journal.
pbio.1000573
45. Darzacq X, Shav-Tal Y, de Turris V, Brody Y,
Shenoy SM, Phair RD, Singer RH (2007) In
vivo dynamics of RNA polymerase II transcription. Nat Struct Mol Biol 14(9):796–806.
https://doi.org/10.1038/nsmb1280
46. Schmidt U, Basyuk E, Robert MC, Yoshida M,
Villemin JP, Auboeuf D, Aitken S, Bertrand E
(2011) Real-time imaging of cotranscriptional
splicing reveals a kinetic model that reduces
noise: implications for alternative splicing
regulation. J. Cell Biol 193(5):819–829.
https://doi.org/10.1083/jcb.201009012
47. Grunwald D, Singer RH (2010) In vivo imaging of labelled endogenous beta-actin mRNA
during nucleocytoplasmic transport. Nature
467(7315):604–607.
https://doi.org/10.
1038/nature09438
48. Smith C, Lari A, Derrer CP, Ouwehand A,
Rossouw A, Huisman M, Dange T,
Hopman M, Joseph A, Zenklusen D, Weis K,
Grunwald D, Montpetit B (2015) In vivo
single-particle imaging of nuclear mRNA
export in budding yeast demonstrates an essential role for Mex67p. J Cell Biol 211
(6):1121–1130. https://doi.org/10.1083/
jcb.201503135
49. Lionnet T, Czaplinski K, Darzacq X, ShavTal Y, Wells AL, Chao JA, Park HY, de
Turris V, Lopez-Jones M, Singer RH (2011)
A transgenic mouse for in vivo detection of
endogenous labeled mRNA. Nat Methods 8
(2):165–170.
https://doi.org/10.1038/
nmeth.1551
50. Park HY, Lim H, Yoon YJ, Follenzi A,
Nwokafor C, Lopez-Jones M, Meng X, Singer
RH (2014) Visualization of dynamics of single
endogenous mRNA labeled in live mouse. Science 343(6169):422–424. https://doi.org/
10.1126/science.1239200
51. Halstead JM, Lionnet T, Wilbertz JH,
Wippich F, Ephrussi A, Singer RH, Chao JA
(2015) Translation. An RNA biosensor for
imaging the first round of translation from single cells to living animals. Science 347
(6228):1367–1671.
https://doi.org/10.
1126/science.aaa3380
52. Katz ZB, English BP, Lionnet T, Yoon YJ,
Monnier N, Ovryn B, Bathe M, Singer RH
(2016) Mapping translation ‘hot-spots’ in live
cells by tracking single molecules of mRNA and
ribosomes. elife 5:e10415
53. Morisaki T, Lyon K, DeLuca KF, DeLuca JG,
English BP, Zhang Z, Lavis LD, Grimm JB,
Viswanathan S, Looger LL, Lionnet T, Stasevich TJ (2016) Real-time quantification of
142
Xavier Pichon et al.
Chapal M, Szlak L, Hutzler A, Nizhberg A,
Itzkovitz S (2015) Bursty gene expression in
the intact mammalian liver. Mol Cell 58
(1):147–156.
https://doi.org/10.1016/j.
molcel.2015.01.027
34. Raj A, Peskin CS, Tranchina D, Vargas DY,
Tyagi S (2006) Stochastic mRNA synthesis in
mammalian cells. PLoS Biol 4(10):e309.
https://doi.org/10.1371/journal.pbio.
0040309
35. Paul B, Montpetit B (2016) Altered RNA processing and export lead to retention of mRNAs
near transcription sites and nuclear pore complexes or within the nucleolus. Mol Biol Cell
27(17):2742–2756.
https://doi.org/10.
1091/mbc.E16-04-0244
36. Bahar Halpern K, Caspi I, Lemze D, Levy M,
Landen S, Elinav E, Ulitsky I, Itzkovitz S
(2015) Nuclear retention of mRNA in mammalian tissues. Cell Rep 13(12):2653–2662.
https://doi.org/10.1016/j.celrep.2015.11.
036
37. Trcek T, Larson DR, Moldon A, Query CC,
Singer RH (2011) Single-molecule mRNA
decay
measurements
reveal
promoterregulated mRNA stability in yeast. Cell 147
(7):1484–1497. https://doi.org/10.1016/j.
cell.2011.11.051
38. Trcek T, Sato H, Singer RH, Maquat LE
(2013) Temporal and spatial characterization
of nonsense-mediated mRNA decay. Genes
Dev 27(5):541–551. https://doi.org/10.
1101/gad.209635.112
39. Pichon X, Lagha M, Mueller F, Bertrand E
(2018) A growing toolbox to image gene
expression in single cells: sensitive approaches
for demanding challenges. Mol Cell 71
(3):468–480.
https://doi.org/10.1016/j.
molcel.2018.07.022
40. Bertrand E, Chartrand P, Schaefer M, Shenoy
SM, Singer RH, Long RM (1998) Localization
of ASH1 mRNA particles in living yeast. Mol
Cell 2(4):437–445
41. Peabody DS (1993) The RNA binding site of
bacteriophage MS2 coat protein. EMBO J 12
(2):595–600
42. Fusco D, Bertrand E, Singer RH (2004) Imaging of single mRNAs in the cytoplasm of living
cells. Prog Mol Subcell Biol 35:135–150
43. Tutucci E, Vera M, Singer RH (2018) SinglemRNA detection in living S. cerevisiae using a
re-engineered MS2 system. Nat Protoc 13
(10):2268–2296. https://doi.org/10.1038/
s41596-018-0037-2
44. Brody Y, Neufeld N, Bieberstein N, Causse SZ,
Bohnlein EM, Neugebauer KM, Darzacq X,
Shav-Tal Y (2011) The in vivo kinetics of
RNA polymerase II elongation during
co-transcriptional splicing. PLoS Biol 9(1):
e1000573. https://doi.org/10.1371/journal.
pbio.1000573
45. Darzacq X, Shav-Tal Y, de Turris V, Brody Y,
Shenoy SM, Phair RD, Singer RH (2007) In
vivo dynamics of RNA polymerase II transcription. Nat Struct Mol Biol 14(9):796–806.
https://doi.org/10.1038/nsmb1280
46. Schmidt U, Basyuk E, Robert MC, Yoshida M,
Villemin JP, Auboeuf D, Aitken S, Bertrand E
(2011) Real-time imaging of cotranscriptional
splicing reveals a kinetic model that reduces
noise: implications for alternative splicing
regulation. J. Cell Biol 193(5):819–829.
https://doi.org/10.1083/jcb.201009012
47. Grunwald D, Singer RH (2010) In vivo imaging of labelled endogenous beta-actin mRNA
during nucleocytoplasmic transport. Nature
467(7315):604–607.
https://doi.org/10.
1038/nature09438
48. Smith C, Lari A, Derrer CP, Ouwehand A,
Rossouw A, Huisman M, Dange T,
Hopman M, Joseph A, Zenklusen D, Weis K,
Grunwald D, Montpetit B (2015) In vivo
single-particle imaging of nuclear mRNA
export in budding yeast demonstrates an essential role for Mex67p. J Cell Biol 211
(6):1121–1130. https://doi.org/10.1083/
jcb.201503135
49. Lionnet T, Czaplinski K, Darzacq X, ShavTal Y, Wells AL, Chao JA, Park HY, de
Turris V, Lopez-Jones M, Singer RH (2011)
A transgenic mouse for in vivo detection of
endogenous labeled mRNA. Nat Methods 8
(2):165–170.
https://doi.org/10.1038/
nmeth.1551
50. Park HY, Lim H, Yoon YJ, Follenzi A,
Nwokafor C, Lopez-Jones M, Meng X, Singer
RH (2014) Visualization of dynamics of single
endogenous mRNA labeled in live mouse. Science 343(6169):422–424. https://doi.org/
10.1126/science.1239200
51. Halstead JM, Lionnet T, Wilbertz JH,
Wippich F, Ephrussi A, Singer RH, Chao JA
(2015) Translation. An RNA biosensor for
imaging the first round of translation from single cells to living animals. Science 347
(6228):1367–1671.
https://doi.org/10.
1126/science.aaa3380
52. Katz ZB, English BP, Lionnet T, Yoon YJ,
Monnier N, Ovryn B, Bathe M, Singer RH
(2016) Mapping translation ‘hot-spots’ in live
cells by tracking single molecules of mRNA and
ribosomes. elife 5:e10415
53. Morisaki T, Lyon K, DeLuca KF, DeLuca JG,
English BP, Zhang Z, Lavis LD, Grimm JB,
Viswanathan S, Looger LL, Lionnet T, Stasevich TJ (2016) Real-time quantification of
142
Xavier Pichon et al.