- Halstead JM, Lionnet T, Wilbertz JH, Wip-
pich 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. doi:10.1126/science.
aaa3380 - Wu B, Buxbaum AR, Katz ZB, Yoon YJ,
Singer RH (2015) Quantifying protein-
mRNA interactions in single live cells. Cell
162(1):211–220. doi:10.1016/j.cell.2015.
05.054 - Mitchell SF, Parker R (2014) Principles and
properties of eukaryotic mRNPs. Mol Cell 54
(4):547–558. doi:10.1016/j.molcel.2014.
04.033 - McHugh CA, Russell P, Guttman M (2014)
Methods for comprehensive experimental
identification of RNA-protein interactions.
Genome Biol 15(1):203. doi:10.1186/
gb4152 - Courchaine EM, Lu A, Neugebauer KM
(2016) Droplet organelles? EMBO J 35
(15):1603–1612. doi:10.15252/embj.
201593517 - Konig J, Zarnack K, Luscombe NM, Ule J
(2011) Protein-RNA interactions: new geno-
mic technologies and perspectives. Nat Rev
Genet 13(2):77–83. doi:10.1038/nrg3141 - Ule J, Jensen KB, Ruggiu M, Mele A, Ule A,
Darnell RB (2003) CLIP identifies Nova-
regulated RNA networks in the brain. Science
302(5648):1212–1215. doi:10.1126/sci
ence.1090095 - Konig J, Zarnack K, Rot G, Curk T, Kayikci
M, Zupan B, Turner DJ, Luscombe NM, Ule
J (2010) iCLIP reveals the function of
hnRNP particles in splicing at individual
nucleotide resolution. Nat Struct Mol Biol
17(7):909–915. doi:10.1038/nsmb.1838 - Hafner M, Landthaler M, Burger L, Khorshid
M, Hausser J, Berninger P, Rothballer A,
Ascano M, Jungkamp AC, Munschauer M,
Ulrich A, Wardle GS, Dewell S, Zavolan M,
Tuschl T (2010) PAR-CliP—a method to
identify transcriptome-wide the binding sites
of RNA binding proteins. J Vis Exp 41.
doi:10.3791/2034 - Sugimoto Y, Vigilante A, Darbo E, Zirra A,
Militti C, D’Ambrogio A, Luscombe NM,
Ule J (2015) hiCLIP reveals the in vivo atlas
of mRNA secondary structures recognized by
Staufen 1. Nature 519(7544):491–494.
doi:10.1038/nature14280 - McMahon AC, Rahman R, Jin H, Shen JL,
Fieldsend A, Luo W, Rosbash M (2016)
TRIBE: hijacking an RNA-editing enzyme
to identify cell-specific targets of RNA-
binding proteins. Cell 165(3):742–753.
doi:10.1016/j.cell.2016.03.007- Lapointe CP, Wilinski D, Saunders HA, Wick-
ens M (2015) Protein-RNA networks
revealed through covalent RNA marks. Nat
Methods 12(12):1163–1170. doi:10.1038/
nmeth.3651 - Leppek K, Stoecklin G (2014) An optimized
streptavidin-binding RNA aptamer for purifi-
cation of ribonucleoprotein complexes iden-
tifies novel ARE-binding proteins. Nucleic
Acids Res 42(2):e13. doi:10.1093/nar/
gkt956 - Said N, Rieder R, Hurwitz R, Deckert J,
Urlaub H, Vogel J (2009) In vivo expression
and purification of aptamer-tagged small
RNA regulators. Nucleic Acids Res 37(20):
e133. doi:10.1093/nar/gkp719 - Chu C, Zhang QC, da Rocha ST, Flynn RA,
Bharadwaj M, Calabrese JM, Magnuson T,
Heard E, Chang HY (2015) Systematic dis-
covery of Xist RNA binding proteins. Cell
161(2):404–416. doi:10.1016/j.cell.2015.
03.025 - McHugh CA, Chen CK, Chow A, Surka CF,
Tran C, McDonel P, Pandya-Jones A, Blanco
M, Burghard C, Moradian A, Sweredoski MJ,
Shishkin AA, Su J, Lander ES, Hess S, Plath
K, Guttman M (2015) The Xist lncRNA
interacts directly with SHARP to silence tran-
scription through HDAC3. Nature 521
(7551):232–236. doi:10.1038/nature14443 - Minajigi A, Froberg JE, Wei C, Sunwoo H,
Kesner B, Colognori D, Lessing D, Payer B,
Boukhali M, Haas W, Lee JT (2015) Chro-
mosomes. A comprehensive Xist interactome
reveals cohesin repulsion and an RNA-
directed chromosome conformation. Science
349(6245). doi:10.1126/science.aab2276 - Baltz AG, Munschauer M, Schwanhausser B,
Vasile A, Murakawa Y, Schueler M, Youngs N,
Penfold-Brown D, Drew K, Milek M, Wyler
E, Bonneau R, Selbach M, Dieterich C, Land-
thaler M (2012) The mRNA-bound prote-
ome and its global occupancy profile on
protein-coding transcripts. Mol Cell 46
(5):674–690. doi:10.1016/j.molcel.2012.
05.021 - Castello A, Fischer B, Eichelbaum K, Horos
R, Beckmann BM, Strein C, Davey NE,
Humphreys DT, Preiss T, Steinmetz LM,
Krijgsveld J, Hentze MW (2012) Insights
into RNA biology from an atlas of mammalian
mRNA-binding proteins. Cell 149
(6):1393–1406. doi:10.1016/j.cell.2012.
04.031
26 Caroline Medioni and Florence Besse