tissue and cells. Nat Methods 10(9):857–860.
doi:10.1038/nmeth.2563
- Lee JH, Daugharthy ER, Scheiman J, Kalhor
R, Yang JL, Ferrante TC, Terry R, Jeanty SS,
Li C, Amamoto R, Peters DT, Turczyk BM,
Marblestone AH, Inverso SA, Bernard A, Mali
P, Rios X, Aach J, Church GM (2014) Highly
multiplexed subcellular RNA sequencing in
situ. Science 343(6177):1360–1363. doi:10.
1126/science.1250212
- Janiszewska M, Liu L, Almendro V, Kuang Y,
Paweletz C, Sakr RA, Weigelt B, Hanker AB,
Chandarlapaty S, King TA, Reis-Filho JS,
Arteaga CL, Park SY, Michor F, Polyak K
(2015) In situ single-cell analysis identifies
heterogeneity for PIK3CA mutation and
HER2 amplification in HER2-positive breast
cancer. Nat Genet 47(10):1212–1219.
doi:10.1038/ng.3391
- 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 Biotech-
nol 28(11):1208–1212. doi:10.1038/nbt.
1692
- Sylwestrak EL, Rajasethupathy P, Wright MA,
Jaffe A, Deisseroth K (2016) Multiplexed
intact-tissue transcriptional analysis at cellular
resolution. Cell 164(4):792–804. doi:10.
1016/j.cell.2016.01.038
- Battich N, Stoeger T, Pelkmans L (2015)
Control of transcript variability in single
mammalian cells. Cell 163(7):1596–1610.
doi:10.1016/j.cell.2015.11.018
- Bahar Halpern K, Tanami S, Landen S, Cha-
pal M, Szlak L, Hutzler A, Nizhberg A, Itz-
kovitz S (2015) Bursty gene expression in the
intact mammalian liver. Mol Cell 58
(1):147–156. doi:10.1016/j.molcel.2015.
01.027
- Symmons O, Raj A (2016) What’s luck got to
do with it: single cells, multiple fates, and
biological Nondeterminism. Mol Cell 62
(5):788–802. doi:10.1016/j.molcel.2016.
05.023
- Sanchez A, Golding I (2013) Genetic deter-
minants and cellular constraints in noisy gene
expression. Science 342(6163):1188–1193.
doi:10.1126/science.1242975
- Hocine S, Raymond P, Zenklusen D, Chao
JA, Singer RH (2013) Single-molecule analy-
sis of gene expression using two-color RNA
labeling in live yeast. Nat Methods 10
(2):119–121. doi:10.1038/nmeth.2305
- 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. doi:10.1016/j.celrep.
2015.11.036
- Lin Y, Sohn CH, Dalal CK, Cai L, Elowitz
MB (2015) Combinatorial gene regulation by
modulation of relative pulse timing. Nature
527(7576):54–58. doi:10.1038/
nature15710
- Jambor H, Surendranath V, Kalinka AT, Mej-
strik P, Saalfeld S, Tomancak P (2015) Sys-
tematic imaging reveals features and changing
localization of mRNAs in Drosophila devel-
opment. eLife 4. doi:10.7554/eLife.05003
- Lecuyer E, Yoshida H, Parthasarathy N, Alm
C, Babak T, Cerovina T, Hughes TR, Toman-
cak P, Krause HM (2007) Global analysis of
mRNA localization reveals a prominent role in
organizing cellular architecture and function.
Cell 131(1):174–187. doi:10.1016/j.cell.
2007.08.003
- Wilk R, Hu J, Blotsky D, Krause HM (2016)
Diverse and pervasive subcellular distributions
for both coding and long noncoding RNAs.
Genes Dev 30(5):594–609. doi:10.1101/
gad.276931.115
- Buxbaum AR, Haimovich G, Singer RH
(2015) In the right place at the right time:
visualizing and understanding mRNA locali-
zation. Nat Rev Mol Cell Biol 16(2):95–109.
doi:10.1038/nrm3918
- Medioni C, Mowry K, Besse F (2012) Princi-
ples and roles of mRNA localization in animal
development. Development 139
(18):3263–3276. doi:10.1242/dev.078626
- Mardakheh FK, Paul A, Kumper S, Sadok A,
Paterson H, McCarthy A, Yuan Y, Marshall
CJ (2015) Global analysis of mRNA, transla-
tion, and protein localization: local translation
is a key regulator of cell protrusions. Dev Cell
35(3):344–357. doi:10.1016/j.devcel.2015.
10.005
- Li L, Feng J, Liu H, Tong L, Tang B (2016)
Two-color imaging of microRNA with
enzyme-free signal amplification via hybridi-
zation chain reactions in living cells. Chem Sci
7:1940–1945
- Alonas E, Lifland AW, Gudheti M, Vanover
D, Jung J, Zurla C, Kirschman J, Fiore VF,
Douglas A, Barker TH, Yi H, Wright ER,
Crowe JE Jr, Santangelo PJ (2014) Combin-
ing single RNA sensitive probes with
subdiffraction-limited and live-cell imaging
enables the characterization of virus dynamics
in cells. ACS Nano 8(1):302–315. doi:10.
1021/nn405998v
- Jung J, Lifland AW, Zurla C, Alonas EJ, San-
tangelo PJ (2013) Quantifying RNA-protein
The Secret Life of RNA 23