References
1. van Nues, R. et al. Kinetic CRAC uncovers a role for Nab3 in
determining gene expression profiles during stress. Nat. Commun.8 , 12 (2017).
2. Chu, L. C. et al. The RNA-bound proteome of MRSA reveals
post-transcriptional roles for helix-turn-helix DNA-binding and
Rossmann-fold proteins. Nat. Commun. 2022 131 13 , 1–18
(2022).
3. Urdaneta, E. C. & Beckmann, B. M. Fast and unbiased purification of
RNA-protein complexes after UV cross-linking. Methods178 , 72–82 (2020).
4. Ramanathan, M., Porter, D. F. & Khavari, P. A. Methods to study
RNA–protein interactions. Nat. Methods 16 , 225–234
(2019).
5. Hentze, M. W., Castello, A., Schwarzl, T. & Preiss, T. A brave new
world of RNA-binding proteins. Nat. Rev. Mol. Cell Biol.19 , 327–341 (2018).
6. Huppertz, I. et al. Riboregulation of Enolase 1 activity
controls glycolysis and embryonic stem cell differentiation. Mol.
Cell 82 , 2666-2680.e11 (2022).
7. Castello, A. et al. Insights into RNA Biology from an Atlas of
Mammalian mRNA-Binding Proteins. Cell 149 , 1393–1406
(2012).
8. Bao, X. et al. Capturing the interactome of newly transcribed
RNA. Nat. Methods 15 , 213–220 (2018).
9. Huang, R., Han, M., Meng, L. & Chen, X. Transcriptome-wide discovery
of coding and noncoding RNA-binding proteins. Proc. Natl. Acad.
Sci. U. S. A. 115 , E3879–E3887 (2018).
10. Meng, L. et al. Metabolic RNA labeling for probing RNA
dynamics in bacteria. Nucleic Acids Res. 48 ,
12566–12576 (2020).
11. Smirnov, A. et al. Grad-seq guides the discovery of ProQ as a
major small RNA-binding protein. Proc. Natl. Acad. Sci. U. S. A.113 , 11591–11596 (2016).
12. Voß, B. et al. The World of Stable Ribonucleoproteins and Its
Mapping With Grad-Seq and Related Approaches. Front. Mol. Biosci.8 , :661448 (2021).
13. Chihara, K., Gerovac, M., Hörb, J. & Vogel, J. Global profiling of
the RNA and protein complexes of Escherichia coli by size exclusion
chromatography followed by RNA sequencing and mass spectrometry
(SEC-seq). RNA 29 , 123–139 (2022).
14. Queiroz, R. M. L. et al. Comprehensive identification of
RNA–protein interactions in any organism using orthogonal organic phase
separation (OOPS). Nat. Biotechnol. 37 , 169–178 (2019).
15. Urdaneta, E. C. et al. Purification of cross-linked
RNA-protein complexes by phenol-toluol extraction. Nat. Commun.
2019 101 10 , 1–17 (2019).
16. Trendel, J. et al. The Human RNA-Binding Proteome and Its
Dynamics during Translational Arrest. Cell 176 , 391–403
(2019).
17. Smith, T. et al. Organic phase separation opens up new
opportunities to interrogate the RNA-binding proteome. Curr. Opin.
Chem. Biol. 54 , 70–75 (2020).
18. Asencio, C., Chatterjee, A. & Hentze, M. W. Silica-based
solid-phase extraction of cross-linked nucleic acid–bound proteins.Life Sci. Alliance 1 , (2018).
19. Shchepachev, V. et al. Defining the RNA interactome by total
RNA-associated protein purification. Mol. Syst. Biol.15 , e8689 (2019).
20. Stützer, A. et al. Analysis of protein-DNA interactions in
chromatin by UV induced cross-linking and mass spectrometry. Nat.
Commun. 11 , 5250 (2020).
21. McKellar, S. W. et al. Monitoring Protein-RNA Interaction
Dynamics in vivo at High Temporal Resolution using χCRAC. J. Vis.
Exp 61027 (2020).
22. Ule, J. et al. CLIP Identifies Nova-Regulated RNA Networks in
the Brain. Science (80-. ). 302 , 1212–1215 (2003).
23. Granneman, S., Kudla, G., Petfalski, E. & Tollervey, D.
Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV
cross-linking and high-throughput analysis of cDNAs. Proc. Natl.
Acad. Sci. 106 , 9613 LP – 9618 (2009).
24. Van Nostrand, E. L. et al. Robust transcriptome-wide
discovery of RNA-binding protein binding sites with enhanced CLIP
(eCLIP). Nat. Methods 2016 136 13 , 508–514 (2016).
25. Hafner, M. et al. Transcriptome-wide Identification of
RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP. Cell141 , 129–141 (2010).
26. Huppertz, I. et al. iCLIP: Protein-RNA interactions at
nucleotide resolution. Methods 65 , 274–287 (2014).
27. Lee, F. C. Y. & Ule, J. Advances in CLIP Technologies for Studies
of Protein-RNA Interactions. Mol. Cell 69 , 354–369
(2018).
28. Darnell, R. B. HITS-CLIP: panoramic views of protein–RNA regulation
in living cells. WIREs RNA 1 , 266–286 (2010).
29. Sharma, D. et al. The kinetic landscape of an RNA-binding
protein in cells. Nat. 2021 5917848 591 , 152–156
(2021).
30. Bresson, S. et al. Stress-Induced Translation Inhibition
through Rapid Displacement of Scanning Initiation Factors. Mol.
Cell 80 , 470-484.e8 (2020).
31. Tawk, C., Sharan, M., Eulalio, A. & Vogel, J. A systematic analysis
of the RNA-targeting potential of secreted bacterial effector proteins.Sci. Rep. 7 , 9328 (2017).
32. Urlaub, H., Hartmuth, K. & Lührmann, R. A two-tracked approach to
analyze RNA–protein crosslinking sites in native, nonlabeled small
nuclear ribonucleoprotein particles. Methods 26 ,
170–181 (2002).
33. Van Nostrand, E. L., Shishkin, A. A., Pratt, G. A., Nguyen, T. B. &
Yeo, G. W. Variation in single-nucleotide sensitivity of eCLIP derived
from reverse transcription conditions. Methods 126 ,
29–37 (2017).
34. Schaughency, P., Merran, J. & Corden, J. L. Genome-Wide Mapping of
Yeast RNA Polymerase II Termination. PLOS Genet. 10 ,
e1004632 (2014).
35. Wittmann, S. et al. The conserved protein Seb1 drives
transcription termination by binding RNA polymerase II and nascent RNA.Nat. Commun. 8 , 14861 (2017).
36. Ojha, S. & Jain, C. Development of PAR-CLIP to analyze RNA-protein
interactions in prokaryotes. bioRxiv (2023) doi:10.1101/855189.
37. König, J. et al. iCLIP reveals the function of hnRNP
particles in splicing at individual nucleotide resolution. Nat.
Struct. Mol. Biol. 17 , 909–915 (2010).
38. Friedersdorf, M. B. & Keene, J. D. Advancing the functional utility
of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs.Genome Biol. 15 , R2 (2014).
39. Maticzka, D., Ilik, I. A., Aktas, T., Backofen, R. & Akhtar, A.
uvCLAP is a fast and non-radioactive method to identify in vivo targets
of RNA-binding proteins. Nat. Commun. 9 , 1142 (2018).
40. Rosenberg, M. et al. Denaturing CLIP, dCLIP, Pipeline
Identifies Discrete RNA Footprints on Chromatin-Associated Proteins and
Reveals that CBX7 Targets 3′ UTRs to Regulate mRNA Expression.Cell Syst. 5 , 368-385.e15 (2017).
41. McMahon, A. C. et al. TRIBE: Hijacking an RNA-Editing Enzyme
to Identify Cell-Specific Targets of RNA-Binding Proteins In Brief
TRIBE: Hijacking an RNA-Editing Enzyme to Identify Cell-Specific Targets
of RNA-Binding Proteins. Cell 165 , 742–53 (2016).
42. Brannan, K. W. et al. Robust single-cell discovery of RNA
targets of RNA-binding proteins and ribosomes. Nat. Methods18 , 507–519 (2021).
43. Patton, R. D. et al. Chemical crosslinking enhances RNA
immunoprecipitation for efficient identification of binding sites of
proteins that photo-crosslink poorly with RNA. RNA 26 ,
1216–1233 (2020).
44. Weidmann, C. A., Mustoe, A. M., Jariwala, P. B., Calabrese, J. M. &
Weeks, K. M. Analysis of RNA-protein networks with RNP-MaP defines
functional hubs on RNA. Nat. Biotechnol. 39 , 347–356
(2021).
45. Han, Y., Guo, X., Zhang, T., Wang, J. & Ye, K. Development of an
RNA-protein crosslinker to capture protein interactions with diverse RNA
structures in cells. RNA 28 , 390–399 (2022).
46. Kudla, G., Granneman, S., Hahn, D., Beggs, J. D. & Tollervey, D.
Cross-linking, ligation, and sequencing of hybrids reveals RNA-RNA
interactions in yeast. Proc. Natl. Acad. Sci. 108 ,
10010–10015 (2011).
47. Sugimoto, Y. et al. hiCLIP reveals the in vivo atlas of mRNA
secondary structures recognized by Staufen 1. Nature519 , 491–494 (2015).
48. Melamed, S. et al. Global Mapping of Small RNA-Target
Interactions in Bacteria. Mol. Cell 63 , 884–897 (2016).
49. Helwak, A., Kudla, G., Dudnakova, T. & Tollervey, D. Mapping the
Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding.Cell 153 , 654–665 (2013).
50. McKellar, S. W. et al. RNase III CLASH in MRSA uncovers sRNA
regulatory networks coupling metabolism to toxin expression. Nat.
Commun. 13 , 3560 (2022).
51. Mediati, D. G. et al. RNase III-CLASH of multi-drug resistant
Staphylococcus aureus reveals a regulatory mRNA 3′UTR required for
intermediate vancomycin resistance. Nat. Commun. 13 ,
3558 (2022).
52. Waters, S. A. et al. Small RNA interactome of pathogenic
E. coli revealed through crosslinking of RN ase E . EMBO J.36 , 374–387 (2017).
53. Melamed, S., Adams, P. P., Zhang, A., Zhang, H. & Storz, G. RNA-RNA
Interactomes of ProQ and Hfq Reveal Overlapping and Competing Roles.Mol. Cell 77 , 411-425.e7 (2020).
54. Matera, G. et al. Global RNA interactome of Salmonella
discovers a 5′ UTR sponge for the MicF small RNA that connects
membrane permeability to transport capacity. Mol. Cell82 , 629-644.e4 (2022).
55. Mizrahi, S. P. et al. The impact of Hfq-mediated sRNA-mRNA
interactome on the virulence of enteropathogenic Escherichia coli.Sci. Adv. 7 , (2021).
56. Hussain, S. et al. NSun2-mediated cytosine-5 methylation of
vault noncoding RNA determines its processing into regulatory small
RNAs. Cell Rep. 4 , 255–261 (2013).
57. Schwartz, S. et al. High-resolution mapping reveals a
conserved, widespread, dynamic mRNA methylation program in yeast
meiosis. Cell 155 , (2013).