The DOI matches its Crossref record; 38 of the 38 references it cites were found in a registry or an index.
RNA sequence‐ and shape‐dependent recognition by proteins in the ribonucleoprotein particle
Open accessAbstract
At all stages of its life (from transcription to translation), an RNA transcript interacts with many different RNA-binding proteins. The composition of this supramolecular assembly, known as a ribonucleoprotein particle, is diverse and highly dynamic. RNA-binding proteins control the generation, maturation and lifespan of the RNA transcript and thus regulate and influence the cellular function of the encoded gene. Here, we review our current understanding of protein-RNA recognition mediated by the two most abundant RNA-binding domains (the RNA-recognition motif and the double-stranded RNA-binding motif) plus the zinc-finger motif, the most abundant nucleic-acid-binding domain. In addition, we discuss how not only the sequence but also the shape of the RNA are recognized by these three classes of RNA-binding protein.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“family members from fungi, protists and algae have all maintained the presumed ancestral CAC core-recognition specificity17, but differ in their preference for flanking nucleotides”
From A compendium of RNA-binding motifs for decoding gene regulation (2013) · cites this paper as [17]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
The sequence of the human genome
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909
Repetitive zinc‐binding domains in the protein transcription factor IIIA from Xenopus oocytes.
Miller, J., McLachlan, A., & Klug, A. (1985) · The EMBO Journal · doi:10.1002/j.1460-2075.1985.tb03825.x · Cited by 2,476
Zinc Finger-DNA Recognition: Crystal Structure of a Zif268-DNA Complex at 2.1 Å
Pavletich, N. P., & Pabo, C. O. (1991) · Science · doi:10.1126/science.2028256 · Cited by 2,081
Messenger-RNA-binding proteins and the messages they carry
Dreyfuss, G., Kim, V. N., & Kataoka, N. (2002) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm760 · Cited by 1,457
DNA Recognition by Cys2His2 Zinc Finger Proteins
Wolfe, S. A., Nekludova, L., & Pabo, C. O. (2000) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.29.1.183 · Cited by 1,053
SMART 4.0: towards genomic data integration
Letunić, I. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh088 · Cited by 997
Oubridge, C., Ito, N., Evans, P. R., Teo, C.-H., & Nagai, K. (1994) · Nature · doi:10.1038/372432a0 · Cited by 832
A conserved double-stranded RNA-binding domain.
Johnston, D. S., Brown, N. H., Gall, J. G., & Jantsch, M. F. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.22.10979 · Cited by 537
Recognition of Polyadenylate RNA by the Poly(A)-Binding Protein
Deo, R. C., Bonanno, J. B., Sonenberg, N., & Burley, S. K. (1999) · Cell · doi:10.1016/s0092-8674(00)81517-2 · Cited by 525
Ryter, J. M., & Schultz, S. C. (1998) · The EMBO Journal · doi:10.1093/emboj/17.24.7505 · Cited by 479
Flagged first, then by citations
Cited by
Sorted by citations
Items 101–175 of 175
Functions of the Muscleblind-like protein family and their role in disease
Zhou, H., Xu, J., & Pan, L. (2025) · Cell Communication and Signaling · doi:10.1186/s12964-025-02102-5 · Cited by 14
Kloetgen, A., Münch, P. C., Borkhardt, A., Hoell, J. I., & McHardy, A. C. (2014) · Briefings in Functional Genomics · doi:10.1093/bfgp/elu020 · Cited by 14
Kailasam, S., Bhattacharyya, D., & Bansal, M. (2014) · BMC Research Notes · doi:10.1186/1756-0500-7-83 · Cited by 14
Haroon, M., Afzal, R., Zafar, M. M., Zhang, H., & Li, L. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23115923 · Cited by 13
Codutti, L., Leppek, K., Zálešák, J., Windeisen, V., Masiewicz, P., Stoecklin, G., & Carlomagno, T. (2015) · Structure · doi:10.1016/j.str.2015.06.001 · Cited by 13
Louis, J. M., Agarwal, A., Aduri, R., & Talukdar, I. (2021) · FEBS Letters · doi:10.1002/1873-3468.14029 · Cited by 13
Noncoding RNAs orchestrating the central dogma
Lozano‐Villada, S., & Puthanveettil, S. V. (2025) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2025.110933 · Cited by 13
Katsantoni, M., van Nimwegen, E., & Zavolan, M. (2023) · Genome biology · doi:10.1186/s13059-023-02913-0 · Cited by 11
Freudenberger, N., Meyer, T., Groitl, P., Dobner, T., & Schreiner, S. (2017) · Journal of Virology · doi:10.1128/jvi.01451-17 · Cited by 12
Zebrafish embryogenesis – A framework to study regulatory RNA elements in development and disease
Zaucker, A., Kumari, P., & Sampath, K. (2019) · Developmental Biology · doi:10.1016/j.ydbio.2019.01.008 · Cited by 13
Bouvrette, L. P. B., Wang, X., Boulais, J., Kong, J., Syed, E. U., Blue, S. M., Zhan, L., Olson, S., Stanton, R., Wei, X., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac971 · Cited by 11
RNA-Binding Proteins: A Role in Neurotoxicity?
Ocharán-Mercado, A., Loaeza-Loaeza, J., Castro-Coronel, Y., Acosta-Saavedra, L. C., Hernández-Kelly, L. C., Hernández-Sotelo, D., & Ortega, A. (2023) · Neurotoxicity research · doi:10.1007/s12640-023-00669-w · Cited by 9
Z-Form Adoption of Nucleic Acid is a Multi-Step Process Which Proceeds through a Melted Intermediate
Nichols, P. J., Krall, J. B., Henen, M. A., Welty, R. S., MacFadden, A., Vicens, Q., & Vögeli, B. (2023) · Journal of the American Chemical Society · doi:10.1021/jacs.3c10406 · Cited by 10
Individualised cancer therapeutics: dream or reality?
Senzer, N. N., Shen, Y., Hill, C., & Nemunaitis, J. J. (2005) · Expert Opinion on Therapeutic Targets · doi:10.1517/14728222.9.6.1189 · Cited by 10
Hasan, M. K., & Brady, L. J. (2024) · Journal of Structural Biology X · doi:10.1016/j.yjsbx.2024.100106 · Cited by 8
Cheng, T., Zimmerman, J. J., & Gimenez-Lirola, L. G. (2022) · Animal Health Research Reviews · doi:10.1017/s1466252322000044 · Cited by 8
Cassola, A., Romaniuk, M. A., Primrose, D. M., Cervini, G., D’Orso, I., & Frasch, A. C. C. (2015) · Molecular Microbiology · doi:10.1111/mmi.13090 · Cited by 8
Solution structures of the double‐stranded RNA‐binding domains from rna helicase A
Nagata, T., Tsuda, K., Kobayashi, N., Shirouzu, M., Kigawa, T., Güntert, P., Yokoyama, S., & Muto, Y. (2012) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24059 · Cited by 8
Functional characterization of
Baethge, D.-B. K., Olbertz, J.-H., der Mathematisch-Naturwissenschaftlichen, D., & Hecht, S. (2014) · Cited by 9
Cifuentes‐Rojas, C., Pavia, P. X., Hernandez, A. J., Osterwisch, D. R., Puerta, C. J., & Cruz‐Reyes, J. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m605554200 · Cited by 7
Tan, C., Li, W., & Wang, W. (2013) · The Journal of Physical Chemistry B · doi:10.1021/jp4052165 · Cited by 7
Azizi, H., Romão, T. P., Charret, K. S., Padmanabhan, P. K., Neto, O. P. D. M., Müller-McNicoll, M., & Papadopoulou, B. (2017) · PLoS ONE · doi:10.1371/journal.pone.0180678 · Cited by 7
Wacquiez, A., Coste, F., Kut, E., Gaudon, V., Trapp, S., Castaing, B., & Marc, D. (2020) · Viruses · doi:10.3390/v12090947 · Cited by 10
RNA aptamers for AMPA receptors
Huang, Z., & Niu, L. (2021) · Neuropharmacology · doi:10.1016/j.neuropharm.2021.108761 · Cited by 6
Efficient Design of Compact Unstructured RNA Libraries Covering All k -mers
Orenstein, Y., & Berger, B. (2015) · Journal of Computational Biology · doi:10.1089/cmb.2015.0179 · Cited by 7
Genome-engineering technologies for modeling and treatment of cystic fibrosis
Dębczyński, M., Mojsak, D., Minarowski, Ł., Maciejewska, M., Lisowski, P., & Mróz, R. M. (2023) · Advances in Medical Sciences · doi:10.1016/j.advms.2023.02.003 · Cited by 5
Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins
Weirick, T., Militello, G., Hosen, M. R., John, D., Moore, J. B., & Uchida, S. (2019) · Microarrays · doi:10.3390/ht8040019 · Cited by 5
AlphaScreen Identifies MSUT2 Inhibitors for Tauopathy-Targeting Therapeutic Discovery
Baker, J. D., Uhrich, R. L., Strovas, T. J., Saxton, A. D., & Kraemer, B. C. (2020) · SLAS DISCOVERY · doi:10.1177/2472555220958387 · Cited by 6
Noncoding DNA is not "junk" but a necessity for origin and evolution of biological complexity
Mallik, M., & Lakhotia, S. C. (2007) · Cited by 5
RNA-Binding Proteins in Fungi and Their Role in mRNA Localization
Lorkovic, Z. (2012) · CRC Press eBooks · doi:10.1201/9781498713368-11 · Cited by 4
Parvez, F., Amin, Z., Sangpal, D., & Chugh, J. (2024) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.4c04299 · Cited by 3
Inhibition of Pre-mRNA Splicing by a Synthetic Blom7α-Interacting Small RNA
Löscher, M., Schosserer, M., Dausse, E., Lee, K., Ajuh, P., Grillari‐Voglauer, R., Lamond, A. I., Toulmé, J., & Grillari, J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0047497 · Cited by 3
Liao, G., Tseng, Y., Tseng, C., Huang, Y., Tsai, C., Liu, H., & Hsu, W. (2021) · FEBS Letters · doi:10.1002/1873-3468.14099 · Cited by 3
Lim, D., Baek, C., & Blanchette, M. (2024) · iScience · doi:10.1016/j.isci.2024.109002 · Cited by 3
Ewing Sarcoma Related protein 1 recognizes R‐loops by binding DNA forks
Lay, M. A., Thompson, V. F., Adelakun, A. D., & Schwartz, J. C. (2024) · Biopolymers · doi:10.1002/bip.23576 · Cited by 3
Structural requirements for photo-induced RNA-protein cross-linkingPreprint
Knörlein, A., Sarnowski, C. P., de Vries, T., Stoltz, M., Götze, M., Aebersold, R. H., Allain, F. H. ‐., Leitner, A., & Hall, J. (2021) · doi:10.33774/chemrxiv-2021-05zhj · Cited by 3
Self-citationKrepl, M., Pokorná, P., Mlýnský, V., Stadlbauer, P., & Šponer, J. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.22.501120 · Cited by 3
RNA –Protein Interactions: A New Approach for Drugging RNA Biology
Soueid, D. M., & Garner, A. L. (2024) · Methods and principles in medicinal chemistry · doi:10.1002/9783527840458.ch11 · Cited by 3
Mizrahi, O., Corley, M., Feldman, O., Fröhlking, T., Sun, L., Ziesel, A., Antczak, M., Bernetti, M., Elhajjajy, S. I., Huang, W., et al. (2025) · RNA · doi:10.1261/rna.080215.124 · Cited by 2
PhyloPGM: boosting regulatory function prediction accuracy using evolutionary information
Ahsan, F., Yan, Z., Precup, D., & Blanchette, M. (2022) · Bioinformatics · doi:10.1093/bioinformatics/btac259 · Cited by 4
RNA nucleoprotein complexes in biological systems
Mishra, P., Sankar, S. H. H., Gosavi, N., & Bharathavikru, R. S. (2022) · Proceedings of the Indian National Science Academy · doi:10.1007/s43538-022-00087-0 · Cited by 2
Protein Interactions with Double-Stranded RNA in Eukaryotic Cells
Hammann, C. (2006) · Springer eBooks · doi:10.1007/978-3-540-28130-6_5 · Cited by 2
At the heart of the spliceosome.
Luehrmann, R. (2008) · Max Planck Institute for Plasma Physics · Cited by 2
Study of RNA–Protein Interactions and RNA Structure in Ribonucleoprotein Particles (RNPs)
Marchand, V., Mougin, A., Méreau, A., Behm‐Ansmant, I., Motorin, Y., & Branlant, C. (2014) · Wiley eBooks · doi:10.1002/9783527647064.ch44 · Cited by 2
1H, 13C, and 15N chemical shift assignments for the RNA recognition motif of Nab3
Pergoli, R., Kubíček, K., Hóbor, F., Pasulka, J., & Štefl, R. (2010) · Biomolecular NMR Assignments · doi:10.1007/s12104-010-9221-1 · Cited by 2
Identification of RNA-binding protein residues using machine learning approaches
Huang, H. (2005) · Emerging Information Technology Conference (EITC) · doi:10.1109/eitc.2005.1544341 · Cited by 1
Mapping allosteric rewiring in viral RNA: Sequence-encoded control of protein binding mechanisms
Samant, D., Chakraborty, A., Sinha, A., Sarkar, R., & Roy, S. (2026) · Biophysical Journal · doi:10.1016/j.bpj.2026.03.017 · Cited by 1
A birth‐to‐death view of mRNA from the RNA recognition motif perspective
Kinzy, T. G., Stefano, L. A. D., Esposito, A. M., Hurley, J., Roy, R., Valentín-Acevedo, A., Chang, K., Davila, J., Defren, J., Donovan, J., et al. (2008) · Biochemistry and Molecular Biology Education · doi:10.1002/bmb.20149 · Cited by 1
Neural representation and generation for RNA secondary structuresPreprint
Yan, Z., Hamilton, W. L., & Blanchette, M. (2021) · arXiv (Cornell University) · doi:10.48550/arxiv.2102.00925 · Cited by 3
Molecular basis of indispensable accuracy of mammalian miRNA biogenesisPreprint
Zapletal, D., Táborská, E., Pasulka, J., Malı́k, R., Kubíček, K., Zanova, M., Much, C., Šebesta, M., Buccheri, V., Horvat, F., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.04.13.488181 · Cited by 1
Statistical Analysis of PAR-CLIP data
Golumbeanu, M. (2013) · KTH Publication Database DiVA (KTH Royal Institute of Technology)
Molecular background of three lethal fetal syndromes
Nousiainen, H. O. (2011) · STM:n Hallinnonalan avoin julkaisuarkisto (Julkari)
Barbe, J. H., O’Hayer, K., & Brody, J. R. (2017) · Springer eBooks · doi:10.1007/978-1-4419-0717-2_107
RNA Binding Proteins and its Regulation of Gene Expression
Roh, K. H., Kang, H., Kim, J., Kim, H. U., Lee, K.-R., & Kim, S. H. (2015) · Journal of Applied Biological Chemistry · doi:10.3839/jabc.2015.032
Efficient Design of Compact Unstructured RNA Libraries Covering All k-mers
Orenstein, Y., & Berger, B. (2015) · Lecture notes in computer science · doi:10.1007/978-3-662-48221-6_23 · Cited by 1
Molecular mechanisms of ADAR2 localization and substrate specificity.
Xu, M. Q. (2006) · Europe PMC (PubMed Central)
Structural and functional characterization of proteins involved in RNA-mediated gene silencing
Lingel, A. (2006) · Repository for Publications and Research Data (ETH Zurich) · doi:10.3929/ethz-a-005164730
Grechishnikova, D., & Poptsova, M. S. (2017) · BIOPHYSICS · doi:10.1134/s0006350917060070
Patel, D. J., & Westhof, É. (2018) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2018.11.009
Barbe, J. H., O’Hayer, K., & Brody, J. R. (2016) · Springer eBooks · doi:10.1007/978-1-4614-6613-0_107-1
A função de proteínas associadas à Esclerose Lateral Amiotrófica em diferentes contextos celulares
Assoni, A. F. (2022) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/t.41.2022.tde-02082022-190632
G-quadruplexes as key motifs in transcriptomics
Sánchez-Martín, V. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-91810-7.00003-0
Prime-Bspre: A Genome-Wide Protein-Rna Binding Sites Prediction Method Based on TemplatesPreprint
Wei, X., Duan, Y., Li, D., Liu, X., Xie, J., & Liu, S. (2024) · SSRN Electronic Journal · doi:10.2139/ssrn.4889490
Taghavi, A., Chen, J. L., Wang, Z., Sinnadurai, K., Salthouse, D. G., Ozon, M., Feri, A., Fountain, M. A., Choudhary, S., Childs‐Disney, J. L., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.20.608150
Elucidating the Effects of Aromatic Mutations on the RNA Binding Efficacy of CELF2 Protein
Kumari, N., Bhavesh, N. S., & Hasija, Y. (2024) · Molecular Biology · doi:10.1134/s0026893324060062
Katsantoni, M., van Nimwegen, E., & Zavolan, M. (2023) · Figshare · doi:10.6084/m9.figshare.22649185
Katsantoni, M., van Nimwegen, E., & Zavolan, M. (2023) · Figshare · doi:10.6084/m9.figshare.22649161
PRIME-BSPre: a genome-wide protein-RNA binding sites prediction method based on templates
Wei, X., Duan, Y., Li, D., Liu, X., Xie, J., & Liu, S. (2026) · BMC Genomics · doi:10.1186/s12864-026-12657-3
Ribeiro, D. M. (2018) · theses.fr (ABES) · doi:10.70675/7fc623a8z4c1dz4aefz8460zf6be1886d753
Role of Ro60/RNYs complex in lipid-laden macrophages
Fazio, S. (2020) · theses.fr (ABES) · doi:10.70675/cbb164cfz48acz4848zbf5bzed9d16dc6f7a
Wacquiez, A. (2020) · theses.fr (ABES) · doi:10.70675/8b88f11ez1daaz4387z9531z0dbc55b3ec14
RNA Modifications Modulate Biomolecular Condensates in Stress and Disease
Sprecher, Y., Sevilla-Sharon, M., & Moshitch-Moshkovitz, S. (2026) · Genes · doi:10.3390/genes17080973
Deciphering the Molecular Basis of Poly(A)-Binding Protein Selectivity for Homopolymeric RNAs
Chakrabortty, A., & Bandyopadhyay, S. (2026) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.6c02480
Metadata
- Authors
- Stefl, R., Skrisovska, L., & Allain, F. H. ‐.
- Affiliations
- ETH Zurich (CH)
- Venue
- The EMBO Reports
- Published
- 2005-01-01
- Volume
- 6
- Issue
- 1
- Pages
- 33-38
- ISSN
- 1469-221X (ISSN-L)
- 1469-3178
- PMC
- PMC1299235
- OpenAlex
- W2115539119
- Cited by
- 175
- References
- 38
- Citations by year
- 2026: 4 · 2025: 4 · 2024: 9 · 2023: 7 · 2022: 17 · 2021: 5 · 2020: 12 · 2019: 9 · 2018: 5 · 2017: 9 · 2016: 8 · 2015: 13 · 2014: 10 · 2013: 5 · 2012: 7
- FWCI
- 0.94
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- EMBO Reports (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
- Keywords
- ribonucleoprotein particles, RNA-binding proteins, protein-RNA recognition, RNA recognition motif, zinc finger, RNA processing, RNA turnover
- MeSH terms
- Animals, Base Sequence, Humans, Nucleic Acid Conformation, Ribonucleoproteins, RNA, Substrate Specificity, Zinc Fingers
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review