Supplementary information
RNA imaging in living cells – methods and applications
Martyna O. Urbanek, Paulina Galka-Marciniak, Marta Olejniczak and Wlodzimierz J. Krzyzosiak*
Department of Molecular Biomedicine,
Institute of Bioorganic Chemistry,
Polish Academy of Sciences,
ul. Noskowskiego 12/14,
61-704 Poznan, Poland
*e-mail: wlodkrzy@ibch.poznan.pl
List of supplementary information:
Supplementary Table 1 Characteristics of elements from which RNA-protein and RNA-dye systems are composed.
Supplementary Table 2 Applications of live visualization systems separated according to cell line origin.
1
MS2
hairpin
sequence
λN22
BglG
PP7
U1Ap
HTLV-1 Rev
TAT-TAR
REV-RRE
ACAUGAGGAUUA GCCCTGAAAAAG GGAUUGUUACUG UAAGGAGUUUAU GTGCTAGGTTAGA UAGGCGACGGUA GGCCAGAUCUGA GGUGGGCGCAGC
CCCAUGU
GGC
CAUUCGCAGGCA AUGGAAACCCUU AAAGTCCGGAGT CGCAAGUACUCU GCCUGGGGAGCU UUCGGCUGACGG
AAACC
A
GCAATGGACTGCT UGCGCCGGCCUA CUCUGGCC
UACACC
GGTCGACTCTAGA
AAAGTCCGGAGT
GCAATGGACTG
hairpin
structure
peptide
sequence or
chemical
structure
comment
reference
MASNFTQFVLVDN MDAQTRRRERRAE MNMQITKILNNNV MSKTIVLSVGEAT MAVPETRPNHTIYI MPKTRRRPRRSQR ?
GGTGDVTVAPSNF KQAQWKAAN
VVVIDDQQREKVV RTLTEIQSTADRQI NNLNEKIKKDELK KRP
ANGIAEWISSNSRS
MGRGIGFQKRAGE FEEKVGPLVGRLR KSLYAIFSQFGQIL
QAYKVTCSVRQSS
RINSSGIEKEYALS LTASLRQNGAKTA DILVSRSLKMRGQ
AQNRKYTIKVEVP
SHELN
YRVNLKLDQADV AFVIFKEVSSATNA
KGAWRSYLNMEL
VDCSTSVCGELPK LRSMQGFPFYDKP
TIPIFATNSDCELIV
VRYTQVWSHDVTI MRIQYAKTDSDII
KAMQGLLKDGNPI
VANSTEASRKSLY
PSAIAANSGIY
DLTKSLVATSQVE
DLVVNLVPLGR
C terminus linker
Four peptides spaced Sequence introduced (AD/GCGGATCC) by 21 amino acid
to transcript with two
linkers; four hairpins
hairpins
spaced by four
nucleotides
[1]
[2]
[5] /NCBI Database [3]/NCBI Database [4] /NCBI Database [6]
[7]
?
-
[7]
Supplementary Table 1 (Part 1) Characteristics of elements from which RNA-protein and RNA-dye systems are composed. Folding was performed with sfold [8] or mfold
[9] software. The information are not always obtained from original inventory paper, because of lack of specific sequences provided in them.
2
eiF4A
hairpin
sequence
Spinach
Spinach2
Malachite Green
SRB-2
ACACUCGGAGGACAGCUU GACGCAACUGAAUGAAAUGGUGA GAUGUAACUGAAUGAAAUGG GGAUCCCGACUGGCG GGAACCUCGCUUCGGCGAUGAU
AGAUGCAAAGCCGGAGUG AGGACGGGUCCAGGUGUGGCUGC UGAAGGACGGGUCCAGUAGGC AGAGCCAGGUAACGA GGAGAGGCGCAAGGUUAACCGC
AGUGUACACCCCGCGCCAG UUCGGCAGUGCAGCUUGUUGAGU UGCUUCGGCAGCCUACUUGUU AUGGAUCC
CUCAGGUUCC
GGGAA
AGAGUGUGAGCUCCGUAACUAGU GAGUAGAGUGUGAGCUCCGU
CGCGUC
AACUAGUUACAUC
hairpin
structure
peptide
?*
sequence or
chemical
structure
+
N
O
N
O
O
-
S
O
O
S
O
NH
O
-
+
N
O
O
O
comment
reference
[10]
[11]
Stabilized by the tRNA sequence
[12]
[13]
Supplementary Table 1 (Part 2) * Primers used for the amplification of gene fragments are available within [10].
3
O
+
N
O
-
NH
Stabilized by the tRNA sequence
[14]
system
organism/
cell line
research purpose
RNA
VIRUSES
MS2
Arabidopsis
Whole-plant virus
spread
TCV
MS2
Fly-E, 3T3,
HEK 293
Transport and export of
MLV RNA
MLV
MS2
MS2
Fly-E, 3T3,
HT1080
Yeast
Endosomal transport of Ψ (MLV)
MLV (structural signal)
Role of p33 and p92 in D-72 (CNV)
CNV replication
MS2
Yeast
Site of DI RNA
replication
MS2
U2OS
HIV-1 transcription
cycle
MS2
U2OS
DI-3
(CymRSV)
HIV-1,
non-coding
RNA U3
HIV-1 transcription site HIV-1
localization
4
hairpin(hp)
location and
number
fluorescent
protein
additional
techniques
reference
in the 3'UTR (5bp
downstream of the
stop codon), 1hp
between the
puromycin gene
and the 3'LTR,
24hp
in the 3'UTR, 24hp
GFP
-
[15]
GFP, YFP
-
[16]
YFP, GFP
-
[17]
BamHI site in
pYC/DI-72bam,
6hp
between blocks II
and III of DI-3
RNA, 6hp in the
positive and
negative
orientation
in the 3'UTR, 24hp
(HIV-1), 1hp (U3,
in apical loop)
between ClaI and
XhoI sites, 24hp
GFP, YFP
-
[18]
GFP
-
[19]
GFP,
mCherry
FRAP
[20]
YFP,
Cherry
FRAP
[21]
MS2
Yeast
BMV and cytoplasmic
bodies interactions
RNA2, RNA3
(BMV)
MS2
N. benthamiana
MS2
BHK, HOS
Function of TMV MP
MP (TMV),
in RNA transport
mRFP
Spatial flavivirus
TBEV
replication organization
MS2
HeLa
MS2
HeLa
MS2
Drosophila
MS2, BglG
MS2, BglG
HIV-1 and Gag
interaction
HIV-1 co-localization
with Ago2 and
RCK/p54 (miRNA
influence on HIV-1)
Sequence-dependent
recruitment of FHV to
the mitochondrial site
of replication
HIV-1
HEK 293
Different transport of
virions, co-packaging
HIV-1
HEK 293
Packaging efficiency of HIV-1
HIV-1, application of
two systems
HIV-1
FHV
5
in the 3'UTR or
second ORF (coat
protein), 2hp, 6hp,
24hp
downstream of the
ORF, 12hp
in the 3'NCR,
12hp, 24hp, 24hp
in opposite
direction
3'end of the gag
gene, 24hp
data not available,
24hp
GFP
-
[22]
GFP
-
[23]
EYFP
-
[24]
GFP
-
[25]
GFP
-
[26]
in the RNA1,
downstream of the
RNA1 region 1 or
upstream of RNA1
regions 4 and 5,
6hp
upstream of the pol
gene, 24hp (MS2),
18hp (BglG)
upstream of the pol
gene, 24hp (MS2),
18hp (BglG)
EGFP
-
[27]
mCherry,
YFP
-
[28]
mCherry,
YFP
-
[5]
MS2
HeLa
Interaction between
vRNA, Gag and
Staufen
Co-imaging of HIV-1
and FIV with gag
proteins
HIV-1,
β-Actin
in proximity to psi
domain, 1hp
Venus
TriFC
[29]
MS2
HeLa,
COS-7,
HEK 293
HIV-1, FIV
YFP, GFP,
mCherry
-
[30]
HEK 293
HIV-1 and HIV-2 copackaging
HIV-1, HIV-2
mCherry,
YFP
-
[31]
MS2, BglG
HEK 293
HIV-2
mCherry,
YFP
-
[32]
MS2
N. benthamiana
GFP
-
[33]
MS2
U2OS
Cherry,
EYFP
-
[34]
MS2
BHK
TBEV
data not available,
24hp
EYFP,
mCherry
FRAP, FLIP
[35]
MS2
N. benthamiana
cis packaging,
localization of vRNA
dimerization
Nuclear localization of
Q-satRNA
Proteins co-localization
with unspliced virus
and release of HIV-1
from transcription site
Virus mobility and
association with
membranes
Localization of BaMV
in chloroplasts
between the
encapsidation
signal and RRE in
HIV, AvrII site of
pCT26 in FIV,
24hp
upstream of the pol
gene, 24hp (MS2),
18hp (BglG)
upstream of the pol
gene, 24hp (MS2),
18hp (BglG)
data not available,
1hp
data not available,
24hp
MS2, BglG
BaMV
downstream of the
stop codon of
ORF1, 8hp
GFP
-
[36]
Q-satRNA,
CMV RNA5
HIV-1
6
MS2
U2OS
MS2
N.bethamiana
MS2
HeLa
MS2
E. coli
MS2
E. coli
eiF4A
E. coli
MS2
C. crescentus
HTLV-1,
λN22
MS2
E. coli
MS2
E. coli
E. coli
Assembly of HIV-1
complexes
BRP1 role in nuclear
importation
of Q-satRNA
HERC5 role in nuclear
export of viral RNA
RNA dynamics in
single bacterial cell
Evaluation of MS2
system in Bacteria,
transcriptional bursts
eiF4A system
evaluation, RNA
visualization in
Bacteria
MS2 and FISH
comparison
HTLV-1 system
evaluation
Translationindependent mRNA
localization
Dynamics of
transcription under the
lar promoter
HIV-1
mCherry,
GFP
GFP
FRAP
[37]
-
[38]
upstream of the pol
gene, 24hp (MS2)
BACTERIA
LacZ
downstream of the
LacZα, 96hp
RFP1
downstream of the
gene, 96hp
GFP
-
[39]
EGFP
-
[40]
GFP
-
[41]
T7, 5S, LacZ
at the 3'end of the
gene, 2hp
EGFP
BiFC
[10]
mCherry
downstream of the
ORF, 48hp
1hp (HTLV-1),
1hp (λN22)
various
localizations, 6hp
GFP
-
[42]
EGFP
BiFC
[6]
GFP
protein product
visualization
[43]
downstream of the
ORF, 96hp
GFP
-
[44]
Q-satRNA
data not available,
24hp
data not available,
1hp
HIV-1
data not
available
cat, lacY, BglF,
BglG, BglB
RFP1
7
MS2, PP7
E. coli
MS2
E. coli
MS2
E. coli
Spinach
E. coli
MS2
E. coli
MS2
E. coli
MS2
E. coli
MS2
E. coli
MS2
E. coli
Spinach
E. coli
MS2
E. coli
BiFC evaluation of the
MS2-PP7 scaffold
Visualization of
transcriptional bursting
in E. coli
Transcriptional activity
of the promoter
Spinach evaluation
scaffold
Localization and
number of mRNA
molecules
Inducers of lar
promoter
Disposal of non-native
protein aggregates
Dynamics of
transcription under the
tetA promoter
Time-lapse microscopy
improvement
Spinach system
evaluation
RFP1
Activity of the
arabinose promoter
RFP1
RFP1
RFP1
5S RNA
RFP1
RFP1
RFP1
RFP1
RFP1
8
1hp (MS2), 1hp
(PP7)
downstream of the
gene, 96hp
GFP
BiFC
[45]
GFP
-
[46]
downstream of the
gene, 96hp
data not available,
1 aptamer
downstream of the
ORF, 96hp
GFP
-
[47]
-
-
[11]
GFP
-
[48]
downstream of the
ORF, 96hp
downstream of the
ORF, 96hp
downstream of the
gene, 96hp
GFP
-
[49]
GFP
-
[50]
GFP
-
[51]
downstream of the
gene, 96hp
separated from
mRNA with a
spacer, 1 aptamer
downstream of the
gene, 96hp
GFP
-
[52]
-
-
[53]
GFP
-
[54]
MS2
E. coli
SRB-2
E. coli
Spinach
E. coli
MS2
Influence of
temperature on
transcription
SRB-2 system
evaluation
Fluorescence dynamics
of Spinach
S. Typhimurium Salmonella infection
/HeLa
MS2
Yeast
MS2
Yeast
U1Ap
Yeast
MS2
Yeast
MS2 evaluation,
localization of ASH1
mRNA in budding
yeast
Localization of
mRNAs in budding
yeast
She3p as an adapter
protein between Ash1
and myosin motor
CAP role in cell
polarity
Repressor
protein CI
replaced rexAB
region, 48hp
GFP
-
[55]
data not
available
downstream of the
3' end of the RNA,
1 aptamer
data not available,
1 aptamer
Data not available,
24hp
-
-
[14]
data not
available
Data not
available (S.
Typhimurium
RNA)
FUNGI
ASH1
immediately
downstream of the
stop codon, 6hp
-
-
[56]
GFP
-
[57]
GFP
-
[58]
ASH1, NUC,
non-coding
upstream of the
3'UTR or between
the RNAseP leader
and terminator,
2hp
downstream of the
start codon, 4hp
GFP
-
[59]
GFP
-
[60]
immediately
downstream of the
stop codon, 6hp
GFP
-
[61]
ADH2, ASH1
ASH1
9
U1Ap
Yeast
pre-mRNA processing
in nuclear export,
U1Ap system
evaluation
MS2
Yeast
MS2
Yeast
ASH1 localization in
budding yeast
Decapping of mRNA
MS2
Yeast
MS2
Yeast
U1Ap
Yeast
MS2
Yeast
MS2
Yeast
MS2
Yeast
Function of the Puf6p
protein in Ash1
transport
Involvement of the late
secretory pathway in
mRNA transport
mRNA presence in Pbodies
Rbp1p influence on the
recruitment of Por1
mRNA into P bodies
Occurrence of the
retrotransposon Ty3 in
P-body components
Evaluation of the mTAG system
PGK1, RPL25,
SSA4 ORFs
with ASH1,
PGK1 or SSA4
3'UTR
ASH1
MFA2, PGK1
LacZ+ASH1
(different
lengths), ASH1
ASH1
PGK1, MFA
POR1
Ty3
ASH1, SRO7,
PEX3, OXA1
10
between the ORF
and the 3'UTR,
16hp
GFP
-
[4]
upstream of the
RNA, 2hp
downstream of the
poly(G) tract, 2 hp
upstream of the
ORF, 6hp
GFP
-
[62]
GFP
-
[63]
GFP
-
[64]
in the 3'UTR, 2hp
GFP
-
[65]
in the 3'UTR, data GFP
not available
between the stop
GFP, RFP
codon and the
3′UTR, 6hp
downstream of Ty3 GFP
POL3 ORF, 2hp
-
[66]
-
[67]
-
[68]
between the ORF
and the 3'UTR,
12hp
-
[69]
GFP
MS2
Yeast
MS2
MS2
Yeast
Yeast
MS2, λN22
Yeast
MS2
Yeast
MS2
Yeast
MS2
Yeast
MS2
Yeast
MS2
Yeast
U1Ap
Yeast
Polarity of the
localization of selected
mRNAs
RNA decay
Daughter cell-specific
transcription
MS2-λN22 covisualization evaluation
SRO7, CDC42,
SEC4, OXA1,
PEX3,MSO1
MFA2
CTS1
between the ORF
and the 3'UTR,
12hp
in the 3'UTR, 2hp
in the 3'UTR, 12hp
GFP
protein product
visualization
[70]
GFP
GFP, red
-
[71]
[72]
ASH1, IST2,
HOM2, ESC2
GFP, RFP
-
[73]
V Myosin impact on
ASH1 transport in
budding yeast
PTC1 involvement in
ASH1mRNA
localization
Localization of
mRNAs encoding
peroxisomal proteins
(mPPs)
3D microscopy
tracking of single
mRNA evaluation
V Myosin impact on
ASH1 transport in
budding yeast
U3 localization signal
investigation
ASH1
36nt upstream of
the AUG codon,
12hp (boxB), 6hp
(MS2)
upstream of the
3'UTR, 6hp
GFP
-
[74]
ASH1
upstream of the
3'UTR, 2hp
GFP
-
[75]
different mPPs
downstream of the
ORF, 12hp
3xGFP,
4xGFP
m-TAG
[76]
ARG3
between the ORF
and the 3'UTR,
12hp
upstream of the
3'UTR, 6hp
3xEGFP
3D microscopy
[77]
GFP
-
[78]
upstream of the
U3, 4hp
GFP
-
[79]
ASH1
U3, STE2+U3
11
MS2
Yeast
Influence of She2p
protein on the
localization of ASH1
mRNA in budding
yeast
Telomerase RNA
dynamics during the
cell cycle
Evaluation of the mpTAG system in
visualizing transcripts
and their products
ABP140 movement in
yeast
ASH1
immediately
downstream of the
stop codon, 6hp
GFP
-
[80]
MS2
Yeast
TLC1
upstream of the
mature 3'end, 10hp
GFP
-
[81]
MS2
Yeast
ATP2, HHF2,
VPH1, YEF3
between the 3'UTR
and the ORF, 12hp
3xGFP
-
[82]
MS2, U1Ap
Yeast
ABP140
GFP
-
[83]
Yeast
Measurement of the
SIC1 mRNA number
SIC1
3xGFP
-
[84]
PP7
Yeast
GLT1, MDN1
GFP
-
[85]
MS2
Yeast
Transcription kinetics
of genes in yeast
mRNA connections
with the cytoskeleton
3xGFP
-
[86]
MS2, U1Ap
Yeast
in the 3'UTR, 6hp
(MS2), 16hp
(U1Ap)
between the 3'UTR
and the SIC1 gene,
12hp
in the 5'UTR or the
3'UTR, 24hp
between the ORF
and the 3'UTR,
12hp
between the ORF
and the 3'UTR,
16hp (U1ApN),
12hp (MS2)
MS2
mCherry,
GFP
-
[87]
mRNAs in stress
granules
ARG3, ASH1,
BBC1, LAS17,
VRP1
MFA2, UFO1,
HSP12, ASH1,
OXA1
12
MS2
Yeast
ER influence on
mRNA localization
ASH1, WSC2,
IST2, SRL1,
EAR1
Ty3
in the 3'UTR, 12hp
3xGFP
-
[88]
MS2
Yeast
Ty3 retrotransposition
analysis
downstream of the
Ty3 POL3 ORF,
2hp
80nt upstream of
the telomeric
repeats, 12hp
(PP7), 2hp, 6hp
(MS2)
between the ORF
and the 3'UTR,
12hp
upstream of the
3'UTR, 6hp
RFP
-
[89]
MS2, PP7
Yeast
TERRA RNA in
telomere shortening
TERRA from
telomere 1L, 6R
GFP,
Tomato
-
[90]
MS2
Yeast
mSMPs (eg.
SUC2, USE1)
MS2
Yeast
MS2, PP7
Yeast
Translationindependent mRNA
localization
Diverse
small molecule
fluorophores for RNA
visualization
Single-allele gene
expression
3xGFP,
4xGFP
mp-TAG
[91]
eGFP,
eDHFR,
SNAP
-
[92]
MDN1
in the 3'UTR,
24hp (MS2), 24hp
(PP7)
EGFP,
mCherry
-
[93]
MS2
Yeast
Relocalization of
mRNAs to P-bodies
RPS16A,
RPS23B,
PGK1, SPG4,
SUE1, VNX1,
TDP1, RRP43
within 3’UTR,
N.A.
3xGFP
m-TAG
[94]
RP51A+lacZ
13
PROTISTA
MS2
Dictyostelium
Transcriptional pulsing
and memory
dscA
at the 5' end of the
gene, 6 bp
downstream of
ATG codon, 24hp
GFP
-
[95]
MS2
Dictyostelium
Transcriptional
memory
act5, scd
in the 5′regions of
genes, 24hp
GFP
-
[96]
MS2
Dictyostelium
Signal-induced
transcription
ecmA
in the 5′regions of
genes, 24hp
GFP
-
[97]
MS2
Dictyostelium
Transcriptional pulse
differences between
housekeeping and
developmental genes,
RNA stability
housekeeping
genes(abpE,
act5, cinD, rpl5,
scd),
developmental
genes (carA,
csaA, cofC,
hspF, zfaA)
in the 5′regions of
genes, 24hp
GFP
FRAP
[98]
MS2
Dictyostelium
Transcription dynamics
csaA
in the 5'UTR, 24hp
GFP
-
[99]
MS2
Dictyostelium
Transcription dynamics
of GtaC-dependent
gene
csaA
in the 5′regions of
genes, 24hp
GFP
-
[100]
14
PLANTS
MS2
Tobacco BY-2,
rice endosperm
cells
MS2
A. cepa
MS2
N. benthamiana
miRNA processing
MS2
Arabidopsis
MS2, λN22
N. benthamiana
Localization of primiRNA with D-bodies
λN system evaluation
(co-visualization with
protein or the MS2
system)
MS2
MS2
Primary
hippocampal
neurons
HeLa
mRNA localization in
the ER in rice
endosperm; movement
dynamics and speed;
transport dependence
on microfilaments
shortORF mRNA
interactions with
MtRBP1
CaMKIIα 3′ UTR
localization
Intranuclear
visualization
GUS+
prolamine
between the
reporter protein
and the prolamine
ORF, 6hp
GFP
-
[101]
enod40
(Medicago
truncatula), delMtapk1,
Mtapk1
pri-miR163
data not available,
2hp
GFP
-
[102]
in the 3'UTR of
pri-miR163, 6hp
downstream of the
pri-miRNA, 24hp
in the 3'UTR or in
the 5'UTR, 6hp
(MS2), 16hp
(boxB)
Venus,
mCherry
YFP
-
[103]
-
[104]
CFP, GFP,
mVenus,
mCherry
-
[105]
pri-miR173
tagRFP and
other not
specified
ANIMALS
CamKIIα
upstream of the
3'UTR, 8hp
GFP
-
[106]
snoRNA
YFP, GFP
-
[107]
between two short
box C/D motifs
inside a β globin
intron, 24hp
15
MS2
DRG, P19
MS2
COS-7
MS2
Drosophila
MS2
Rat
hippocampal
neurons
MS2
U2OS
MS2
U2OS
Differences in motility
between isoforms of
kor mRNAs
Movement of mRNA,
dependence on
cytoskeleton, influence
of zipcode on
movement
Localization of nanos
RNA in oocytes
A, B and C
isoforms of kor
mRNA
SV40, hGH, βactin
upstream of the
3'UTR, 3hp
GFP
-
[108]
between LacZ and
the 3'UTR, 6hp,
12hp, 24hp
EGFP, YFP
-
[109]
nos
EGFP
-
[110]
Investigating
SYNCRIP role in
mRNA granules in
neurons
Gene expression at the
levels of DNA, RNA
and protein in living
cells
IP3R1
in the 3'UTR (500nt
downstream of the
stop codon), 6hp
upstream of the
RNA, 12hp
Venus
-
[111]
-
[112]
FRAP,
photoactivation
[113]
Visualizing mRNPs
movement in nuclei
CFP + SKL + β- between
YFP
globin
peroxisomal
targeting signal SKL
and β-globin
intron/exon module,
24hp
β globin
downstream of the
YFP, GFP
ORF, 24hp
16
MS2
COS-7
MS2
U2OS
MS2
PC12
MS2
Dorsal Root
Ganglia cells
MS2
Drosophila
MS2
Drosophila
neurons
MS2
COS-7
RNA-protein direct and normal and
indirect interactions
mutated
versions of βactin zipcode,
IRE, G quartet
sequence,
FMR1, c-myc
Transcription of
β-globin + CFP
snoRNA
Peripherin mRNA and CFP+peripherin
translation product
localization
3' and 5'UTRs in
kor, SV40
mRNA transport to
axons
Localization of bicoid
bicoid, nos
mRNA in oocytes
CamKII altered
Drosophila
localization in memory CamKII, 3'UTR
process
of Drosophila
CamKII, 3'UTR
of mouse
αCamKII
Cellular function of
3'UTR or
Dazl in the mouse male 5'UTR of Tpx1,
germ cells
Cdc25C,
Cdc25A, Mvh
17
upstream of the
zipcode, 1hp
Venus
TriFC
[114]
in the 3'UTR, 18hp
GFP, RFP
-
[115]
between the ORF
YFP
and the 3'UTR, 24hp
-
[116]
upstream of the
3'UTR, 3hp
EGFP
-
[117]
in the 3'UTR, 6hp
RFP, GFP
FRAP, FLIP
[118]
upstream of the
3'UTR, 8hp
GFP
-
[119]
data not available,
6hp, 12hp
GFP
-
[120]
MS2
Dorsal root
ganglia cells
U2OS
λN22
NRK
MS2
HeLa, E18 rat
cortical neurons
NIH3T3
Localization of Arc
mRNA in neurons
RNA localization
mediated through
microtubules
Drosophila
neurons
Cortical neurons
of wild-type and
FMR1 KO mice
HeLa
nanos targeting signals
MS2
MS2
MS2
MS2
MS2
Function of Copb1 in
neurons
Dynamics of RNA
polymerase II
transcription
λN system evaluation
kor, SV40
DsRed+Arc
CFP+β-globin
RFP+β-actin
zipcode, Srprb,
SRP
β-globin with
rab13, pkp4,
rhoA, rac1
3'UTR or
without 3’UTR
nos
Role of FMRP in
mRNA transport
CaMKIIα
Mobility of mRNA
between stress
granules and cytoplasm
β-Gal reporter
18
upstream of the
3'UTR, 3hp
downstream of the
ORF, 24hp
EGFP
-
[121]
GFP
FRAP,
photoactivation
[122]
downstream of the
mEGFP
mRFP or before βactin zipcode, 4hp,
16hp
between the ORF
GFP
and the 3'UTR, 6hp
between the ORF
GFP
and the 3'UTR, 24hp
FRAP
[2]
-
[123]
FRAP
[124]
data not available,
18hp
upstream of the
3'UTR, 8hp
RFP
-
[125]
GFP
-
[126]
data not available,
6hp, 24hp
GFP
FRAP
[127]
MS2
Xenopus
CPE-regulation of
maternal mRNAs
MS2
Drosophila
MS2
C2C12
oscar mRNA in
Drosophila oocytes
MS2 protocol
MS2
Drosophila
MS2
COS-7
MS2
Drosophila
MS2
Drosophila
MS2
MS2
Role of FMRP in
mRNA transport
RARα role in the
inhibition of translation
Difference in motility
of grk mRNA between
stages of oogenesis
miRNA role in
Drosophila oogenesis
Chicken embryo Dependency of
fibroblasts
localization on
molecular mass
Chicken embryo β-Actin transcript and
fibroblasts
protein product
localization in chicken
embryos
luciferase ORF
with 3'UTR
from Xkid,
wild-typeTPX2
or TPX2 with
CPEs
inactivated
osk
between the ORF
GFP
and the 3'UTR, 12hp
downstream of the
stop codon, 10hp
DMPK
upstream of the
3'UTR, 24hp
CG9293, chic
downstream of the
mRNA, 12hp
firefly luciferase in the 3'UTR, 12hp
-
[128]
GFP
-
[129]
GFP
-
[1]
GFP
FRAP
[130]
EGFP
-
[131]
gurken
in the 3'UTR, 343
GFP, RFP
bp downstream of
the stop codon, 12hp
FRAP
[132]
osk
added to the 3'UTR,
16hp
downstream of the
3'UTR, 4hp
GFP
-
[133]
EGFP
-
[134]
downstream of the
3'UTR, 4hp
EGFP
protein product
visualization
[135]
different length
of β-Actin
β-Actin
19
MS2
C. elegans
DLK-1 function in
neurons, increasing
stability of mRNA by
protein
UV Inhibits the Pol II
Elongation Rate
RNG105 colocalization with NKA
mRNAs
CEBP-1, UNC54
in the 3'UTR, 6hp
GFP
-
[136]
MS2
U2OS
HIV-1
data not available,
24hp
data not available,
24hp
GFP
FRAP
[137]
MS2
MS2
Primary
cultured
neurons from
E17.5 mouse
cerebral cortex
NIH3T3
GFP
-
[138]
Evaluation of isolation
MS2-streptavidin
method, RBPs search
mRNP transport in
nucleus and export
mRFP+OXA1,
β-actin,
GAPDH
dystrophin
(different
lengths),
β-globin
minigene
CFP + SKL + βglobin
upstream of the
3'UTR, 24hp
GFP
streptavidin
purification
[139]
MS2
U2OS
in the 3'UTR, 24hp
YFP
FRAP
[140]
MS2
U2OS
Transcription
activation by VP16and p53-activator
-
[141]
MS2
Rat
hippocampal
neurons
ApoE mRNA region
responsible for
dendritic transport
-
[142]
Na+/K+
ATPase Subunit
Isoforms
ApoE (different
lengths)
20
between
YFP
peroxisomal
targeting signal SKL
and β-globin
intron/exon module,
24hp
upstream of the
GFP
ORF, 8hp
MS2
HEK 293
MS2
Rat cortical
neurons
MS2
Primary
hippocampal
neurons of wildtype or FMR1
KO mice
HeLa, U2OS
MS2
Single allele
transcription kinetics
Htt role in BDNF
transport
GFP
FRAP
[143]
3'UTR of
upstream of the
BDNF
3'UTR, 12hp
(different
lengths)
CaMKIIα, Fmr1 upstream of the
3'UTR, 8hp
Venus
-
[144]
GFP
-
[145]
Retrotransposition
efficiency
Dendritic role of
Huntingtin in RNA
transport
retrotransposone
L1
IP3R1, RFP+βactin zipcode
GFP, CFP
-
[146]
EGFP,
Venus
-
[147]
CFP+chicken βactin+β-globin
intron-exonintron
APP, just
hairpins
downstream of the
ORF2 of L1, 24hp
between mRFP and
the β-actin zipcode
or before the 3'UTR,
4hp (boxB) , 12hp
(MS2)
between the ORF
and the 3'UTR, 24hp
YFP
FRAP
[148]
data not available,
24hp
YFP
siRNA
[149]
downstream of the
ORF, 24hp
YFP
-
[150]
Role of FMRP in
mRNA transport under
mGluR5 receptor
stimulation
MS2, λN22
Rat cortical
neurons
MS2
U2OS
β-actin mRNA route
from transcription to
translation point
MS2
BE2-M17
MS2
U2OS
FMRP and hnRNP C
competitive translation
control of APP mRNA
Fokl influence on
transcript accumulation
CCND1
in the 3'UTR, 24hp
CFP-SKL
21
MS2
HOS_A4
MS2
MS2
Hippocampal
neurons
Mouse
hippocampal
neurons
C2C12
MS2
U2OS
MS2
J1 ES
MS2
HeLa
MS2
U2OS
MS2
Dynamics of RNA
Polymerase II (single
and tandem integration)
Kv4.2 mRNA transport
in dendrites
Kv4.2-3′UTR is
Important for Dendritic
Targeting
Influence of CUG
repeats on the
localization of DMPK
transcript
Kinetics of Pol II
elongation in the
context of splicing
Evaluation of a system
to visualize noncoding
RNAs, Xist role in X
chromosome
inactivation
Competitive regulation
of nucleolin expression
by HuR and miR-494
Proteolytic activity at
the induced
transcription site
HIV-1, U3
downstream of the
LTR promoter, 1hp
(U3), 24hp
upstream of the
sequence, 2hp
upstream of the
3'UTR, 6hp
Cherry,
EYFP
FRAP, iFRAP
[151]
GFP
-
[152]
GFP
-
[153]
LacZ + 3'UTR
of DMPK
(5/145CUG)
upstream of the
3'UTR, 24hp
GFP,
mCherry
FRAP, FLIP
[154]
β-globin
(multiplied 2
intron) + CFPSKL
Xist
downstream of the
gene, 18hp
YFP
FRAP
[155]
at the 3'end of Xist,
24hp
GFP
FRAP
[156]
RL+NCL
upstream of the
ORF, 24hp
YFP
siRNA, miRNA
[157]
CFP + β-globin
in the 3'UTR, 18hp
GFP, RFP
-
[158]
Kv4.2,
CaMKIIα
Kv4.2, Arc,
only hairpins
22
MS2
U2OS
Premature termination
codon in nonsensemediated mRNA decay
Splicing kinetics
MS2
U2OS
MS2
Drosophila
Protein starvation in
Drosophila oogenesis
MS2
HeLa
MS2
U2OS
HuR influence on
TOP2A mRNA
movement between
polysomes and PBs
Effects of DRAQ5 on
mRNA accumulation
MS2
MS2
Knock-in mice
(neurons and
fibroblasts)
HepG2
MS2
Drosophila
MS2
Primary
hippocampal
neurons
Evaluation of MS2 in
vivo, β-actin
observations
Insulin influence on
ApoB mRNA
localization
Evaluation of genetic
in vivo system to detect
asymmetrically
distributed RNA
Stau2 involvement in
mRNA movement
mini µ reporter
gene (WT and
PTC+)
MINX intron +
LacZ
oskar
in the 3'UTR, 24hp
YFP,
Dendra2
FRAP,
[159]
photoconversion
in an intron or exon,
4hp
directly downstream
of the stop codon,
10hp
upstream of the
3'UTR, 24hp
GFP
FRAP
[160]
GFP
-
[161]
YFP
siRNA
[162]
unspecified
inducible
transgene
β-actin
in the 3'UTR, 24hp
GFP
-
[163]
in the 3'UTR, 24hp
YFP
-
[164]
apoB, β-globin
downstream of the
3'UTR, 24hp
EGFP
-
[165]
nos, EP vector
induces random
integration into
the genome
Map1b, Map2
between the
transcriptional start
site and the 3′ Pelement, 6hp
upstream of the
3'UTR, 24hp
EGFP, RFP
-
[166]
mCherry
siRNA
[167]
TOP2A
23
MS2
C2C12
MS2, λN22
Rat cortical
neurons
MS2
Hippocampal
neurons
HeLa
MS2
MS2, λN22
Drosophila
oocytes
MS2
MS2
Primary
hippocampal
neurons
Rat cortical
neurons
J1 ES
MS2, PP7
MEF
MS2
Paraspecles creation
and dynamics,
noncoding RNAs
visualization
β-actin transport in
dendrites dependence
on Htt and other
proteins
Co-localization of two
mRNAs
Splicing regulation
Menε/β
upstream of the
Menε/β, 24hp
EYFP
FRAP
[168]
β-actin
upstream of the βactin zipcode, 12hp
(MS2), 4hp (boxB)
Venus,
RFP, EGFP
-
[169]
CaMKIIα
YFP
ISH
[170]
EGFP
-
[171]
Localization of
transcript with mutated
SOLE structure and
sequence
Movement of MMP-9
mRNA
different osk
upstream of the
3'UTR, 24hp
downstream of the
5'ss D1, 2hp
data not available
GFP
-
[172]
EGFP
-
[173]
mRNA localization in
dendrites
Transcriptional pulsing
dynamics of high
expressing retroviral
transgenes in
embryonic Stem Cells
PP7 and MS2 systems
comparison
Arc, Dendrin
upstream of the
coding sequence,
24hp
upstream of the
3'UTR, 6hp
downstream of the
ORF, 16hp, 24hp
EGFP
-
[174]
EGFP
-
[175]
in the 3'UTR, 24hp
(PP7), 24hp (MS2)
EGFP
-
[176]
D1
MMP-9
mRFP
CFP+β-actin
24
MS2
Neurons
MMP-9 mRNA
HEK 293
FMRP interaction with
MMP-9 mRNA
Dynamics of proteinRNA interactions
Splicing visualization
MS2
U2OS
MS2, λN22
MS2
Neurons
Transport of nos RNPs
nos, osk
MS2
Drosophila
Transcription activity
CFP-SKL
MS2
CNS1
CPE
TAT-TAR,
REV-RRE,
MS2
MS2
MDCK
MS2
Spinach2
HEK 293
COS-7
MS2
INHS
MS2
IEC-6
CPEB1 role in
shuttling mRNA
between nucleus and
cytoplasm
Evaluation of TATTAR and REV-RRE
systems
mRNA
localization
polarity
Transcription kinetics
Spinach2 system
evaluation, CGG RNA
nuclear aggregation
NF1 interactions with
mRNAs
miR-195 influence on
strim1 mRNA decay
Xenopus
data not
available
β-globin, IgM
influenza viral
mRNAs NS, M,
and NP.
VLE, β-globin
GOI
(CGG)60 RNA
CamKIIα
stim1, only
hairpins
25
data not available,
24hp
data not available,
24hp
inside introns, 24hp
(MS2), 25hp (λN22)
data not available,
6hp, 18hp
downstream of the
ORF, 24hp
in the 3'UTR, 12hp
GFP
-
[177]
mCherry
FRAP,
photoactivation
-
[178]
-
[180]
GFP
-
[181]
GFP
-
[182]
upstream of the
investigated signal
sequence, 1hp
downstream of the
RNA, 24hp
in the 3'UTR, 24hp
downstream of the
ORF, 1 aptamer
GFP, ECFP
TriFC
[183]
mCherry
[184]
GFP
-
FRAP,
Photoactivation
FRAP
-
upstream of the
3'UTR, 8hp
upstream of the
RNA, 24hp
GFP
-
[186]
YFP
-
[187]
GFP,
mCherry
RFP
[179]
[185]
[12]
MS2
U2OS-2-6-3
MS2
RIE-1
MS2
Hippocampal
neurons
U2OS
MS2, PP7
Condensin II
recruitment to genes
TGF-β induces mRNA
transport to P-bodies
Local translation in
synaptic stimulation
BiFC evaluation with
MS2 and PP7 systems
CFP-SKL
in the ORF, 96hp
YFP
-
[188]
COX
upstream of the
3'UTR, 12hp
in the 3'UTR, 24hp
YFP
-
[189]
GFP
-
[190]
in the 3'UTR, 12hp
(MS2+PP7), 24hp
(MS2)
in the 3'UTR, 24hp
Venus
BiFC
[191]
β-globin
data not
available
mRNA visualization in β-globin
GFP
[192]
tissues
U2OS
Better dyes for
(CGG)60 RNA downstream of the
[193]
Spinach2
Spinach2
ORF, 1 aptamer
HeLa
Tudor protein coAGTR1
Downstream of the
GFP
[194]
MS2
localization with
3’UTR, 24hp
AGTR1 transcript
Supplementary Table 2 Applications of live visualization systems separated according to cell line origin. Experiments were annotated with
the name of the system, the cell line or organism in which visualization was performed, the research purpose, the labeled RNA, the number and
localization of hairpins, the fluorescent protein (if applicable), additional techniques and references.
MS2
MCP mice
26
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