14. 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
15. Moffitt JR, Hao J, Bambah-Mukku D, Lu T,
Dulac C, Zhuang X (2016) High-performance
multiplexed fluorescence in situ hybridization
in culture and tissue with matrix imprinting
and clearing. Proc Natl Acad Sci U S A 113
(50):14456–14461.
https://doi.org/10.
1073/pnas.1617699113
16. Long X, Colonell J, Wong AM, Singer RH,
Lionnet T (2017) Quantitative mRNA imaging throughout the entire Drosophila brain.
Nat Methods 14(7):703–706. https://doi.
org/10.1038/nmeth.4309
17. Battich N, Stoeger T, Pelkmans L (2013)
Image-based transcriptomics in thousands of
single human cells at single-molecule resolution. Nat Methods 10(11):1127–1133.
https://doi.org/10.1038/nmeth.2657
18. Choi HM, Chang JY, Trinh le A, Padilla JE,
Fraser SE, Pierce NA (2010) Programmable in
situ amplification for multiplexed imaging of
mRNA expression. Nat Biotechnol 28
(11):1208–1212. https://doi.org/10.1038/
nbt.1692
19. Tsanov N, Samacoits A, Chouaib R, Traboulsi
AM, Gostan T, Weber C, Zimmer C, Zibara K,
Walter T, Peter M, Bertrand E, Mueller F
(2016) smiFISH and FISH-quant - a flexible
single RNA detection approach with superresolution capability. Nucleic Acids Res 44
(22):e165.
https://doi.org/10.1093/nar/
gkw784
20. Moffitt JR, Hao J, Wang G, Chen KH, Babcock HP, Zhuang X (2016) High-throughput
single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization. Proc Natl Acad Sci U S A 113
(39):11046–11051.
https://doi.org/10.
1073/pnas.1612826113
21. 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
22. Shah S, Lubeck E, Zhou W, Cai L (2017) seqFISH accurately detects transcripts in single
cells and reveals robust spatial organization in
the hippocampus. Neuron 94(4):752–758.
https://doi.org/10.1016/j.neuron.2017.05.
008
23. Eng CL, Lawson M, Zhu Q, Dries R,
Koulena N, Takei Y, Yun J, Cronin C,
Karp C, Yuan GC, Cai L (2019)
Transcriptome-scale super-resolved imaging in
tissues
by
RNA
seqFISH.
Nature
568:235–239.
https://doi.org/10.1038/
s41586-019-1049-y
24. Shah S, Takei Y, Zhou W, Lubeck E, Yun J, Eng
CL, Koulena N, Cronin C, Karp C, Liaw EJ,
Amin M, Cai L (2018) Dynamics and spatial
genomics of the nascent transcriptome by
intron seqFISH. Cell 174(2):363–376.
https://doi.org/10.1016/j.cell.2018.05.035
25. 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
26. 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
27. Buxbaum AR, Haimovich G, Singer RH
(2015) In the right place at the right time:
visualizing and understanding mRNA localization. Nat Rev Mol Cell Biol 16(2):95–109.
https://doi.org/10.1038/nrm3918
28. Weil TT, Parton RM, Davis I (2010) Making
the message clear: visualizing mRNA localization. Trends Cell Biol 20(7):380–390. https://
doi.org/10.1016/j.tcb.2010.03.006
29. Martin KC, Ephrussi A (2009) mRNA localization: gene expression in the spatial dimension. Cell 136(4):719–730. https://doi.org/
10.1016/j.cell.2009.01.044
30. Lecuyer E, Yoshida H, Parthasarathy N,
Alm C, Babak T, Cerovina T, Hughes TR,
Tomancak P, Krause HM (2007) Global analysis of mRNA localization reveals a prominent
role in organizing cellular architecture and
function. Cell 131(1):174–187. https://doi.
org/10.1016/j.cell.2007.08.003
31. Samacoits A, Chouaib R, Safieddine A, Traboulsi AM, Ouyang W, Zimmer C, Peter M,
Bertrand E, Walter T, Mueller F (2018) A
computational
framework
to
study
sub-cellular RNA localization. Nat Commun
9(1):4584.
https://doi.org/10.1038/
s41467-018-06868-w
32. Das S, Singer RH, Yoon YJ (2019) The travels
of mRNAs in neurons: do they know where
they are going? Curr Opin Neurobiol
57:110–116.
https://doi.org/10.1016/j.
conb.2019.01.016
Imaging Single mRNAs in Living Eukaryotic Cells
141
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
15. Moffitt JR, Hao J, Bambah-Mukku D, Lu T,
Dulac C, Zhuang X (2016) High-performance
multiplexed fluorescence in situ hybridization
in culture and tissue with matrix imprinting
and clearing. Proc Natl Acad Sci U S A 113
(50):14456–14461.
https://doi.org/10.
1073/pnas.1617699113
16. Long X, Colonell J, Wong AM, Singer RH,
Lionnet T (2017) Quantitative mRNA imaging throughout the entire Drosophila brain.
Nat Methods 14(7):703–706. https://doi.
org/10.1038/nmeth.4309
17. Battich N, Stoeger T, Pelkmans L (2013)
Image-based transcriptomics in thousands of
single human cells at single-molecule resolution. Nat Methods 10(11):1127–1133.
https://doi.org/10.1038/nmeth.2657
18. Choi HM, Chang JY, Trinh le A, Padilla JE,
Fraser SE, Pierce NA (2010) Programmable in
situ amplification for multiplexed imaging of
mRNA expression. Nat Biotechnol 28
(11):1208–1212. https://doi.org/10.1038/
nbt.1692
19. Tsanov N, Samacoits A, Chouaib R, Traboulsi
AM, Gostan T, Weber C, Zimmer C, Zibara K,
Walter T, Peter M, Bertrand E, Mueller F
(2016) smiFISH and FISH-quant - a flexible
single RNA detection approach with superresolution capability. Nucleic Acids Res 44
(22):e165.
https://doi.org/10.1093/nar/
gkw784
20. Moffitt JR, Hao J, Wang G, Chen KH, Babcock HP, Zhuang X (2016) High-throughput
single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization. Proc Natl Acad Sci U S A 113
(39):11046–11051.
https://doi.org/10.
1073/pnas.1612826113
21. 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
22. Shah S, Lubeck E, Zhou W, Cai L (2017) seqFISH accurately detects transcripts in single
cells and reveals robust spatial organization in
the hippocampus. Neuron 94(4):752–758.
https://doi.org/10.1016/j.neuron.2017.05.
008
23. Eng CL, Lawson M, Zhu Q, Dries R,
Koulena N, Takei Y, Yun J, Cronin C,
Karp C, Yuan GC, Cai L (2019)
Transcriptome-scale super-resolved imaging in
tissues
by
RNA
seqFISH.
Nature
568:235–239.
https://doi.org/10.1038/
s41586-019-1049-y
24. Shah S, Takei Y, Zhou W, Lubeck E, Yun J, Eng
CL, Koulena N, Cronin C, Karp C, Liaw EJ,
Amin M, Cai L (2018) Dynamics and spatial
genomics of the nascent transcriptome by
intron seqFISH. Cell 174(2):363–376.
https://doi.org/10.1016/j.cell.2018.05.035
25. 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
26. 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
27. Buxbaum AR, Haimovich G, Singer RH
(2015) In the right place at the right time:
visualizing and understanding mRNA localization. Nat Rev Mol Cell Biol 16(2):95–109.
https://doi.org/10.1038/nrm3918
28. Weil TT, Parton RM, Davis I (2010) Making
the message clear: visualizing mRNA localization. Trends Cell Biol 20(7):380–390. https://
doi.org/10.1016/j.tcb.2010.03.006
29. Martin KC, Ephrussi A (2009) mRNA localization: gene expression in the spatial dimension. Cell 136(4):719–730. https://doi.org/
10.1016/j.cell.2009.01.044
30. Lecuyer E, Yoshida H, Parthasarathy N,
Alm C, Babak T, Cerovina T, Hughes TR,
Tomancak P, Krause HM (2007) Global analysis of mRNA localization reveals a prominent
role in organizing cellular architecture and
function. Cell 131(1):174–187. https://doi.
org/10.1016/j.cell.2007.08.003
31. Samacoits A, Chouaib R, Safieddine A, Traboulsi AM, Ouyang W, Zimmer C, Peter M,
Bertrand E, Walter T, Mueller F (2018) A
computational
framework
to
study
sub-cellular RNA localization. Nat Commun
9(1):4584.
https://doi.org/10.1038/
s41467-018-06868-w
32. Das S, Singer RH, Yoon YJ (2019) The travels
of mRNAs in neurons: do they know where
they are going? Curr Opin Neurobiol
57:110–116.
https://doi.org/10.1016/j.
conb.2019.01.016
Imaging Single mRNAs in Living Eukaryotic Cells
141