References
1. Singh G, Pratt G, Yeo GW et al (2015) The
clothes make the mRNA: past and present
trends in mRNP fashion. Annu Rev Biochem
84:325–354
2. Staiger D (2001) RNA-binding proteins and
circadian rhythms in Arabidopsis thaliana.
Philos Trans R Soc Lond B Biol Sci
356:755–1759
3. Kupsch C, Ruwe H, Gusewski S et al (2012)
Arabidopsis chloroplast RNA binding proteins
CP31A and CP29A associate with large transcript pools and confer cold stress tolerance by
influencing multiple chloroplast RNA processing steps. Plant Cell 24:4266–4280
4. Kang H, Park SJ, Kwak KJ (2013) Plant RNA
chaperones in stress response. Trends Plant Sci
18:100–106
5. Lewinski M, Hallmann A, Staiger D (2016)
Genome-wide identification and phylogenetic
analysis of plant RNA binding proteins comprising both RNA recognition motifs and contiguous glycine residues. Mol Gen Genomics
291:763–773
6. Rataj K, Simpson GG (2014) Message ends:
RNA 3
0 processing and flowering time control.
J Exp Bot 65:353–363
7. Mili S, Steitz JA (2004) Evidence for reassociation of RNA-binding proteins after cell lysis:
implications for the interpretation of immunoprecipitation analyses. RNA 10:1692–1694
8. Xing D, Wang Y, Hamilton M et al (2015)
Transcriptome-wide identification of RNA targets of Arabidopsis SERINE/ARGININERICH45 uncovers the unexpected roles of
this RNA binding protein in RNA processing.
Plant Cell 27:3294–3308
9. Ko ¨ster T, Meyer K (2018) Plant ribonomics:
proteins in search of RNA partners. Trends
Plant Sci 23:352–365
10. Ko ¨ster T, Staiger D (2014) RNA-binding protein immunoprecipitation from whole-cell
extracts. Methods Mol Biol 1062:679–695
11. Ko ¨ster T, Haas M, Staiger D (2014) The RIPper case: identification of RNA-binding protein
targets by RNA immunoprecipitation. Methods Mol Biol 1158:107–121
12. Meyer K, Ko ¨ster T, Nolte C et al (2017) Adaptation of iCLIP to plants determines the
binding landscape of the clock-regulated
RNA-binding protein AtGRP7. Genome Biol
18:204
13. Zhang Y, Gu L, Hou Y et al (2015) Integrative
genome-wide analysis reveals HLP1, a novel
RNA-binding protein, regulates plant flowering by targeting alternative polyadenylation.
Cell Res 25:864–876
14. Marondedze C, Thomas L, Serrano NL et al
(2016) The RNA-binding protein repertoire of
Arabidopsis thaliana. Sci Rep 6:29766
15. Reichel M, Liao Y, Rettel M et al (2016) In
planta determination of the mRNA-binding
proteome of Arabidopsis etiolated seedlings.
Plant Cell 28:2435–2452
16. Zhang Z, Boonen K, Ferrari P et al (2016) UV
crosslinked mRNA-binding proteins captured
from leaf mesophyll protoplasts. Plant Methods 12:42
17. Ko ¨ster T, Marondedze C, Meyer K et al (2017)
RNA-binding proteins revisited – the emerging
Arabidopsis mRNA interactome. Trends Plant
Sci 22:512–526
18. Ko ¨ster T, Reichel M, Staiger D (2019) CLIP
and RNA interactome studies to unravel
genome-wide
RNA-protein
interactions
in vivo in Arabidopsis thaliana. Methods.
https://doi.org/10.1016/j.ymeth.2019.09.
005
19. Sugimoto Y, Konig J, Hussain S et al (2012)
Analysis of CLIP and iCLIP methods for
nucleotide-resolution studies of protein-RNA
interactions. Genome Biol 13:R67
20. Ko ¨nig J, Zarnack K, Rot G et al (2010) iCLIP
reveals the function of hnRNP particles in
splicing at individual nucleotide resolution.
Nat Struct Mol Biol 17:909–915
21. Wang Z, Kayikci M, Briese M et al (2010)
iCLIP predicts the dual splicing effects of
TIA-RNA interactions. PLoS Biol 8:e1000530
22. Zarnack K, Ko ¨nig J, Tajnik M et al (2013)
Direct competition between hnRNP C and
U2AF65 protects the transcriptome from the
exonization of alu elements. Cell 152:453–466
23. Huppertz I, Attig J, D’Ambrogio A et al
(2014) iCLIP: Protein–RNA interactions at
nucleotide resolution. Methods 65:274–287
Plant iCLIP
267
1. Singh G, Pratt G, Yeo GW et al (2015) The
clothes make the mRNA: past and present
trends in mRNP fashion. Annu Rev Biochem
84:325–354
2. Staiger D (2001) RNA-binding proteins and
circadian rhythms in Arabidopsis thaliana.
Philos Trans R Soc Lond B Biol Sci
356:755–1759
3. Kupsch C, Ruwe H, Gusewski S et al (2012)
Arabidopsis chloroplast RNA binding proteins
CP31A and CP29A associate with large transcript pools and confer cold stress tolerance by
influencing multiple chloroplast RNA processing steps. Plant Cell 24:4266–4280
4. Kang H, Park SJ, Kwak KJ (2013) Plant RNA
chaperones in stress response. Trends Plant Sci
18:100–106
5. Lewinski M, Hallmann A, Staiger D (2016)
Genome-wide identification and phylogenetic
analysis of plant RNA binding proteins comprising both RNA recognition motifs and contiguous glycine residues. Mol Gen Genomics
291:763–773
6. Rataj K, Simpson GG (2014) Message ends:
RNA 3
0 processing and flowering time control.
J Exp Bot 65:353–363
7. Mili S, Steitz JA (2004) Evidence for reassociation of RNA-binding proteins after cell lysis:
implications for the interpretation of immunoprecipitation analyses. RNA 10:1692–1694
8. Xing D, Wang Y, Hamilton M et al (2015)
Transcriptome-wide identification of RNA targets of Arabidopsis SERINE/ARGININERICH45 uncovers the unexpected roles of
this RNA binding protein in RNA processing.
Plant Cell 27:3294–3308
9. Ko ¨ster T, Meyer K (2018) Plant ribonomics:
proteins in search of RNA partners. Trends
Plant Sci 23:352–365
10. Ko ¨ster T, Staiger D (2014) RNA-binding protein immunoprecipitation from whole-cell
extracts. Methods Mol Biol 1062:679–695
11. Ko ¨ster T, Haas M, Staiger D (2014) The RIPper case: identification of RNA-binding protein
targets by RNA immunoprecipitation. Methods Mol Biol 1158:107–121
12. Meyer K, Ko ¨ster T, Nolte C et al (2017) Adaptation of iCLIP to plants determines the
binding landscape of the clock-regulated
RNA-binding protein AtGRP7. Genome Biol
18:204
13. Zhang Y, Gu L, Hou Y et al (2015) Integrative
genome-wide analysis reveals HLP1, a novel
RNA-binding protein, regulates plant flowering by targeting alternative polyadenylation.
Cell Res 25:864–876
14. Marondedze C, Thomas L, Serrano NL et al
(2016) The RNA-binding protein repertoire of
Arabidopsis thaliana. Sci Rep 6:29766
15. Reichel M, Liao Y, Rettel M et al (2016) In
planta determination of the mRNA-binding
proteome of Arabidopsis etiolated seedlings.
Plant Cell 28:2435–2452
16. Zhang Z, Boonen K, Ferrari P et al (2016) UV
crosslinked mRNA-binding proteins captured
from leaf mesophyll protoplasts. Plant Methods 12:42
17. Ko ¨ster T, Marondedze C, Meyer K et al (2017)
RNA-binding proteins revisited – the emerging
Arabidopsis mRNA interactome. Trends Plant
Sci 22:512–526
18. Ko ¨ster T, Reichel M, Staiger D (2019) CLIP
and RNA interactome studies to unravel
genome-wide
RNA-protein
interactions
in vivo in Arabidopsis thaliana. Methods.
https://doi.org/10.1016/j.ymeth.2019.09.
005
19. Sugimoto Y, Konig J, Hussain S et al (2012)
Analysis of CLIP and iCLIP methods for
nucleotide-resolution studies of protein-RNA
interactions. Genome Biol 13:R67
20. Ko ¨nig J, Zarnack K, Rot G et al (2010) iCLIP
reveals the function of hnRNP particles in
splicing at individual nucleotide resolution.
Nat Struct Mol Biol 17:909–915
21. Wang Z, Kayikci M, Briese M et al (2010)
iCLIP predicts the dual splicing effects of
TIA-RNA interactions. PLoS Biol 8:e1000530
22. Zarnack K, Ko ¨nig J, Tajnik M et al (2013)
Direct competition between hnRNP C and
U2AF65 protects the transcriptome from the
exonization of alu elements. Cell 152:453–466
23. Huppertz I, Attig J, D’Ambrogio A et al
(2014) iCLIP: Protein–RNA interactions at
nucleotide resolution. Methods 65:274–287
Plant iCLIP
267