11. 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
12. Vera M, Biswas J, Senecal A, Singer RH, Park
HY (2016) Single-cell and single-molecule
analysis of gene expression regulation. Annu
Rev Genet 50:267–291. https://doi.org/10.
1146/annurev-genet-120215-034854
13. 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
14. Long RM, Singer RH, Meng X, Gonzalez I,
Nasmyth K, Jansen RP (1997) Mating type
switching in yeast controlled by asymmetric
localization of ASH1 mRNA. Science 277
(5324):383–387
15. Moor AE, Golan M, Massasa EE, Lemze D,
Weizman T, Shenhav R, Baydatch S,
Mizrahi O, Winkler R, Golani O, SternGinossar N, Itzkovitz S (2017) Global mRNA
polarization regulates translation efficiency in
the
intestinal
epithelium.
Science
357:1299–1303. https://doi.org/10.1126/
science.aan2399
16. Buxbaum AR, Wu B, Singer RH (2014) Single
beta-actin mRNA detection in neurons reveals
a mechanism for regulating its translatability.
Science 343(6169):419–422. https://doi.
org/10.1126/science.1242939
17. Levsky JM, Shenoy SM, Pezo RC, Singer RH
(2002) Single-cell gene expression profiling.
Science 297(5582):836–840. https://doi.
org/10.1126/science.1072241
18. Chen KH, Boettiger AN, Moffitt JR, Wang S,
Zhuang X (2015) RNA imaging. Spatially
resolved, highly multiplexed RNA profiling in
single cells. Science 348(6233):aaa6090.
https://doi.org/10.1126/science.aaa6090
19. Lubeck E, Cai L (2012) Single-cell systems
biology by super-resolution imaging and combinatorial
labeling.
Nat
Methods
9
(7):743–748.
https://doi.org/10.1038/
nmeth.2069
20. Lubeck E, Coskun AF, Zhiyentayev T,
Ahmad M, Cai L (2014) Single-cell in situ
RNA profiling by sequential hybridization.
Nat Methods 11(4):360–361. https://doi.
org/10.1038/nmeth.2892
21. Moffitt JR, Zhuang X (2016) RNA imaging
with multiplexed error-robust fluorescence in
situ hybridization (MERFISH). Methods
Enzymol 572:1–49. https://doi.org/10.
1016/bs.mie.2016.03.020
22. Wittenberg C, Sugimoto K, Reed SI (1990)
G1-specific cyclins of S. cerevisiae: cell cycle
periodicity, regulation by mating pheromone,
and association with the p34CDC28 protein
kinase. Cell 62(2):225–237
23. 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
24. Jansen RP, Dowzer C, Michaelis C, Galova M,
Nasmyth K (1996) Mother cell-specific HO
expression in budding yeast depends on the
unconventional myosin myo4p and other cytoplasmic proteins. Cell 84(5):687–697
25. Long RM, Chartrand P, Gu W, Meng XH,
Schaefer MR, Singer RH (1997) Characterization of transport and localization of ASH1
mRNA in yeast. Mol Biol Cell 8:2060–2060
26. Tutucci E, Vera M, Biswas J, Garcia J, Parker R,
Singer RH (2018) An improved MS2 system
for accurate reporting of the mRNA life cycle.
Nat Methods 15(1):81–89. https://doi.org/
10.1038/nmeth.4502
27. Cosma MP (2004) Daughter-specific repression of Saccharomyces cerevisiae HO: Ash1 is
the commander. EMBO Rep 5(10):953–957.
https://doi.org/10.1038/sj.embor.7400251
28. Pereira G, Schiebel E (2001) The role of the
yeast spindle pole body and the mammalian
centrosome in regulating late mitotic events.
Curr Opin Cell Biol 13(6):762–769
29. Bayer LV, Batish M, Formel SK, Bratu DP
(2015) Single-molecule RNA in situ hybridization (smFISH) and Immunofluorescence
(IF) in the Drosophila egg chamber. Methods
Mol Biol 1328:125–136. https://doi.org/10.
1007/978-1-4939-2851-4_9
30. Eliscovich C, Shenoy SM, Singer RH (2017)
Imaging mRNA and protein interactions
within neurons. Proc Natl Acad Sci U S A
114(10):E1875–E1884. https://doi.org/10.
1073/pnas.1621440114
31. Mueller F, Senecal A, Tantale K, Marie-NellyH, Ly N, Collin O, Basyuk E, Bertrand E,
Darzacq X, Zimmer C (2013) FISH-quant:
automatic counting of transcripts in 3D FISH
images. Nat Methods 10(4):277–278. https://
doi.org/10.1038/nmeth.2406
32. Schindelin J, Arganda-Carreras I, Frise E,
Kaynig V, Longair M, Pietzsch T, Preibisch S,
Rueden C, Saalfeld S, Schmid B, Tinevez JY,
White DJ, Hartenstein V, Eliceiri K,
Tomancak P, Cardona A (2012) Fiji: an opensource platform for biological-image analysis.
68
Evelina Tutucci and Robert H. Singer
(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
12. Vera M, Biswas J, Senecal A, Singer RH, Park
HY (2016) Single-cell and single-molecule
analysis of gene expression regulation. Annu
Rev Genet 50:267–291. https://doi.org/10.
1146/annurev-genet-120215-034854
13. 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
14. Long RM, Singer RH, Meng X, Gonzalez I,
Nasmyth K, Jansen RP (1997) Mating type
switching in yeast controlled by asymmetric
localization of ASH1 mRNA. Science 277
(5324):383–387
15. Moor AE, Golan M, Massasa EE, Lemze D,
Weizman T, Shenhav R, Baydatch S,
Mizrahi O, Winkler R, Golani O, SternGinossar N, Itzkovitz S (2017) Global mRNA
polarization regulates translation efficiency in
the
intestinal
epithelium.
Science
357:1299–1303. https://doi.org/10.1126/
science.aan2399
16. Buxbaum AR, Wu B, Singer RH (2014) Single
beta-actin mRNA detection in neurons reveals
a mechanism for regulating its translatability.
Science 343(6169):419–422. https://doi.
org/10.1126/science.1242939
17. Levsky JM, Shenoy SM, Pezo RC, Singer RH
(2002) Single-cell gene expression profiling.
Science 297(5582):836–840. https://doi.
org/10.1126/science.1072241
18. Chen KH, Boettiger AN, Moffitt JR, Wang S,
Zhuang X (2015) RNA imaging. Spatially
resolved, highly multiplexed RNA profiling in
single cells. Science 348(6233):aaa6090.
https://doi.org/10.1126/science.aaa6090
19. Lubeck E, Cai L (2012) Single-cell systems
biology by super-resolution imaging and combinatorial
labeling.
Nat
Methods
9
(7):743–748.
https://doi.org/10.1038/
nmeth.2069
20. Lubeck E, Coskun AF, Zhiyentayev T,
Ahmad M, Cai L (2014) Single-cell in situ
RNA profiling by sequential hybridization.
Nat Methods 11(4):360–361. https://doi.
org/10.1038/nmeth.2892
21. Moffitt JR, Zhuang X (2016) RNA imaging
with multiplexed error-robust fluorescence in
situ hybridization (MERFISH). Methods
Enzymol 572:1–49. https://doi.org/10.
1016/bs.mie.2016.03.020
22. Wittenberg C, Sugimoto K, Reed SI (1990)
G1-specific cyclins of S. cerevisiae: cell cycle
periodicity, regulation by mating pheromone,
and association with the p34CDC28 protein
kinase. Cell 62(2):225–237
23. 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
24. Jansen RP, Dowzer C, Michaelis C, Galova M,
Nasmyth K (1996) Mother cell-specific HO
expression in budding yeast depends on the
unconventional myosin myo4p and other cytoplasmic proteins. Cell 84(5):687–697
25. Long RM, Chartrand P, Gu W, Meng XH,
Schaefer MR, Singer RH (1997) Characterization of transport and localization of ASH1
mRNA in yeast. Mol Biol Cell 8:2060–2060
26. Tutucci E, Vera M, Biswas J, Garcia J, Parker R,
Singer RH (2018) An improved MS2 system
for accurate reporting of the mRNA life cycle.
Nat Methods 15(1):81–89. https://doi.org/
10.1038/nmeth.4502
27. Cosma MP (2004) Daughter-specific repression of Saccharomyces cerevisiae HO: Ash1 is
the commander. EMBO Rep 5(10):953–957.
https://doi.org/10.1038/sj.embor.7400251
28. Pereira G, Schiebel E (2001) The role of the
yeast spindle pole body and the mammalian
centrosome in regulating late mitotic events.
Curr Opin Cell Biol 13(6):762–769
29. Bayer LV, Batish M, Formel SK, Bratu DP
(2015) Single-molecule RNA in situ hybridization (smFISH) and Immunofluorescence
(IF) in the Drosophila egg chamber. Methods
Mol Biol 1328:125–136. https://doi.org/10.
1007/978-1-4939-2851-4_9
30. Eliscovich C, Shenoy SM, Singer RH (2017)
Imaging mRNA and protein interactions
within neurons. Proc Natl Acad Sci U S A
114(10):E1875–E1884. https://doi.org/10.
1073/pnas.1621440114
31. Mueller F, Senecal A, Tantale K, Marie-NellyH, Ly N, Collin O, Basyuk E, Bertrand E,
Darzacq X, Zimmer C (2013) FISH-quant:
automatic counting of transcripts in 3D FISH
images. Nat Methods 10(4):277–278. https://
doi.org/10.1038/nmeth.2406
32. Schindelin J, Arganda-Carreras I, Frise E,
Kaynig V, Longair M, Pietzsch T, Preibisch S,
Rueden C, Saalfeld S, Schmid B, Tinevez JY,
White DJ, Hartenstein V, Eliceiri K,
Tomancak P, Cardona A (2012) Fiji: an opensource platform for biological-image analysis.
68
Evelina Tutucci and Robert H. Singer