Cited by 175RNA Research and SplicingRNA and protein synthesis mechanismsRNA regulation and disease

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 access

Stefl, Richard, Skrisovska, Lenka, Allain, Frédéric H.‐T.·2005·The EMBO Reports

DOI 10.1038/sj.embor.7400325PMC PMC1299235

Open this paper in CoChat — free account

Abstract

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.

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

Crossref · 10.1038/sj.embor.7400325

Cites

38 of 38 references verified0 citation errors · 0 not checkable

Statistics

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?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

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
Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin
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
Molecular basis of double‐stranded RNA‐protein interactions: structure of a dsRNA‐binding domain complexed with dsRNA
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

Show all 38 references

Sorted by citations

A compendium of RNA-binding motifs for decoding gene regulation
Ray, D., Kazan, H., Cook, K. B., Weirauch, M. T., Najafabadi, H. S., Li, X., Gueroussov, S., Albu, M., Zheng, H., Yang, A., et al. (2013) · Nature · doi:10.1038/nature12311 · Cited by 1,480
From Birth to Death: The Complex Lives of Eukaryotic mRNAs
Moore, M. J. (2005) · Science · doi:10.1126/science.1111443 · Cited by 1,035
Structure and function of KH domains
Valverde, R., Edwards, L., & Regan, L. (2008) · FEBS Journal · doi:10.1111/j.1742-4658.2008.06411.x · Cited by 508
RNA Bind-n-Seq: Quantitative Assessment of the Sequence and Structural Binding Specificity of RNA Binding Proteins
Lambert, N. J., Robertson, A. D., Jangi, M., McGeary, S. E., Sharp, P. A., & Burge, C. B. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.04.016 · Cited by 407
Prp8 protein: At the heart of the spliceosome
Grainger, R. J. R., & Beggs, J. D. (2005) · RNA · doi:10.1261/rna.2220705 · Cited by 374
Sequence-specific binding of single-stranded RNA: is there a code for recognition?
Auweter, S. D., Oberstrass, F. C., & Allain, F. H.-T. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl620 · Cited by 314
Self-citation
Mechanisms of dendritic mRNA transport and its role in synaptic tagging
Doyle, M., & Kiebler, M. A. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.278 · Cited by 288
RNA recognition by double-stranded RNA binding domains: a matter of shape and sequence
Masliah, G., Barraud, P., & Allain, F. H. ‐. (2012) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-012-1119-x · Cited by 259
Self-citation
Functional classification of long non-coding RNAs by k-mer content
Kirk, J. M., Kim, S. O., Inoue, K., Smola, M. J., Lee, D. M., Schertzer, M. D., Wooten, J. S., Baker, A. R., Sprague, D., Collins, D. W., et al. (2018) · Nature Genetics · doi:10.1038/s41588-018-0207-8 · Cited by 261
The Solution Structure of the ADAR2 dsRBM-RNA Complex Reveals a Sequence-Specific Readout of the Minor Groove
Štefl, R., Oberstrass, F. C., Hood, J. L., Jourdan, M., Zimmermann, M., Skříšovská, L., Maris, C., Peng, L., Hofr, C., Emeson, R. B., et al. (2010) · Cell · doi:10.1016/j.cell.2010.09.026 · Cited by 240
Self-citation
Roquin binds inducible costimulator mRNA and effectors of mRNA decay to induce microRNA-independent post-transcriptional repression
Glasmacher, E., Hoefig, K. P., Vogel, K. U., Rath, N., Du, L., Wolf, C., Kremmer, E., Wang, X., & Heissmeyer, V. (2010) · Nature Immunology · doi:10.1038/ni.1902 · Cited by 184
Properties and biological impact of RNA G-quadruplexes: from order to turmoil and back
Kharel, P., Becker, G., Цветков, В. Б., & Ivanov, P. V. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa1126 · Cited by 152
RNA–Protein Interactions: An Overview
Re, A., Joshi, T., Kulberkytė, E., Morris, Q., & Workman, C. T. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-709-9_23 · Cited by 144
Widespread uncoupling between transcriptome and translatome variations after a stimulus in mammalian cells
Tebaldi, T., Re, A., Viero, G., Pegoretti, I., Passerini, A., Blanzieri, E., & Quattrone, A. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-220 · Cited by 134
Discovery of Key Physicochemical, Structural, and Spatial Properties of RNA‐Targeted Bioactive Ligands
Morgan, B. S., Forte, J. E., Culver, R. N., Zhang, Y., & Hargrove, A. E. (2017) · Angewandte Chemie International Edition · doi:10.1002/anie.201707641 · Cited by 130
Structure and Specific RNA Binding of ADAR2 Double-Stranded RNA Binding Motifs
Štefl, R., Xu, M. Q., Skříšovská, L., Emeson, R. B., & Allain, F. H. ‐. (2006) · Structure · doi:10.1016/j.str.2005.11.013 · Cited by 122
Self-citation
The human RBPome: From genes and proteins to human disease
Neelamraju, Y., Hashemikhabir, S., & Janga, S. C. (2015) · Journal of Proteomics · doi:10.1016/j.jprot.2015.04.031 · Cited by 119
Shape-specific recognition in the structure of the Vts1p SAM domain with RNA
Oberstrass, F. C., Lee, A., Štefl, R., Janis, M., Chanfreau, G., & Allain, F. H. ‐. (2006) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1038 · Cited by 117
Self-citation
Comprehensive Alanine-scanning Mutagenesis of Escherichia coli CsrA Defines Two Subdomains of Critical Functional Importance
Mercante, J. W., Suzuki, K., Cheng, X., Babitzke, P., & Romeo, T. (2006) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)84098-x · Cited by 113
Ro60 and Y RNAs: structure, functions, and roles in autoimmunity
Boccitto, M., & Wolin, S. L. (2019) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2019.1608902 · Cited by 101
RNA localization: Making its way to the center stage
Chin, A., & Lécuyer, É. (2017) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2017.06.011 · Cited by 109
Global Loss of Set1-mediated H3 Lys4 Trimethylation Is Associated with Silencing Defects in Saccharomyces cerevisiae
Fingerman, I. M., Wu, C., Wilson, B. D., & Briggs, S. D. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.c500097200 · Cited by 108
Progress and challenges for chemical probing of RNA structure inside living cells
Kubota, M., Tran, C., & Spitale, R. C. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1958 · Cited by 106
Structure determination and dynamics of protein–RNA complexes by NMR spectroscopy
Dominguez, C., Schubert, M., Duss, O., Ravindranathan, S., & Allain, F. H. ‐. (2010) · Progress in Nuclear Magnetic Resonance Spectroscopy · doi:10.1016/j.pnmrs.2010.10.001 · Cited by 101
Self-citation
Roles of intrinsic disorder in protein–nucleic acid interactions
Dyson, H. J. (2011) · Molecular BioSystems · doi:10.1039/c1mb05258f · Cited by 97
The role of disorder in RNA binding affinity and specificity
Ottoz, D. S. M., & Berchowitz, L. E. (2020) · Open Biology · doi:10.1098/rsob.200328 · Cited by 91
The testis‐specific human protein RBMY recognizes RNA through a novel mode of interaction
Skříšovská, L., Bourgeois, C. F., Štefl, R., Grellscheid, S., Kister, L., Wenter, P., Elliott, D. J., Stévenin, J., & Allain, F. H. ‐. (2007) · EMBO Reports · doi:10.1038/sj.embor.7400910 · Cited by 94
Self-citation
Sequence composition changes in short tandem repeats: heterogeneity, detection, mechanisms and clinical implications
Rajan‐Babu, I., Dolzhenko, E., Eberle, M. A., & Friedman, J. M. (2024) · Nature Reviews Genetics · doi:10.1038/s41576-024-00696-z · Cited by 97
ADAR Proteins: Double-stranded RNA and Z-DNA Binding Domains
Barraud, P., & Allain, F. H. ‐. (2011) · Current topics in microbiology and immunology · doi:10.1007/82_2011_145 · Cited by 92
Self-citation
Structure and Function of the Pre-mRNA Splicing Machine
Sperling, J. M., Azubel, M., & Sperling, R. (2008) · Structure · doi:10.1016/j.str.2008.08.011 · Cited by 88
Structural mechanism for HIV-1 TAR loop recognition by Tat and the super elongation complex
Schulze‐Gahmen, U., & Hurley, J. H. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1806438115 · Cited by 86
A structural perspective of RNA recognition by intrinsically disordered proteins
Basu, S., & Bahadur, R. P. (2016) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-016-2283-1 · Cited by 82
A Non-amyloid Prion Particle that Activates a Heritable Gene Expression Program
Chakravarty, A. K., Smejkal, T., Itakura, A. K., Garcia, D. M., & Jarosz, D. F. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.10.028 · Cited by 77
Controlling activation of the RNA-dependent protein kinase by siRNAs using site-specific chemical modification
Puthenveetil, S., Whitby, L. R., Ren, J., Kelnar, K., Krebs, J., & Beal, P. A. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl464 · Cited by 80
Fungal Virulence and Development Is Regulated by Alternative Pre-mRNA 3′End Processing in Magnaporthe oryzae
Franceschetti, M., Bueno, E., Wilson, R. A., Tucker, S. L., Gómez‐Mena, C., Calder, G., & Sesma, A. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1002441 · Cited by 80
Structural and functional basis of mammalian microRNA biogenesis by Dicer
Zapletal, D., Táborská, E., Pasulka, J., Malı́k, R., Kubíček, K., Zanova, M., Much, C., Šebesta, M., Buccheri, V., Horvat, F., et al. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.10.010 · Cited by 80
Aprataxin Forms a Discrete Branch in the HIT (Histidine Triad) Superfamily of Proteins with Both DNA/RNA Binding and Nucleotide Hydrolase Activities
Kijas, A. W., Harris, J. L., Harris, J. M., & Lavin, M. F. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m507946200 · Cited by 72
Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein–RNA Complexes?
Krepl, M., Havrila, M., Stadlbauer, P., Banas, P., Otyepka, M., Pasulka, J., Štefl, R., & Šponer, J. (2015) · Journal of Chemical Theory and Computation · doi:10.1021/ct5008108 · Cited by 69
RNAEditor: easy detection of RNA editing events and the introduction of editing islands
John, D., Weirick, T., Dimmeler, S., & Uchida, S. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbw087 · Cited by 67
Comprehensive analysis of CCCH-type zinc finger family genes facilitates functional gene discovery and reflects recent allopolyploidization event in tetraploid switchgrass
Yuan, S., Xu, B., Zhang, J., Xie, Z., Cheng, Q., Yang, Z., Cai, Q., & Huang, B. (2015) · BMC Genomics · doi:10.1186/s12864-015-1328-4 · Cited by 64
RBM7 subunit of the NEXT complex binds U-rich sequences and targets 3′-end extended forms of snRNAs
Hroššová, D., Šikorský, T., Potěšil, D., Bartošovič, M., Pasulka, J., Zdráhal, Z., Štefl, R., & Vaňáčová, Š. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv240 · Cited by 68
Altered RNA Binding Activity Underlies Abnormal Thyroid Hormone Metabolism Linked to a Mutation in Selenocysteine Insertion Sequence-binding Protein 2
Bubenik, J. L., & Driscoll, D. M. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m707059200 · Cited by 64
Dicer structure and function: conserved and evolving features
Zapletal, D., Kubíček, K., Svoboda, P., & Štefl, R. (2023) · EMBO Reports · doi:10.15252/embr.202357215 · Cited by 62
Towards understanding pre-mRNA splicing mechanisms and the role of SR proteins
Sahebi, M., Hanafi, M. M., van Wijnen, A. J., Azizi, P., Abiri, R., Ashkani, S., & Taheri, S. (2016) · Gene · doi:10.1016/j.gene.2016.04.057 · Cited by 64
Graph neural representational learning of RNA secondary structures for predicting RNA-protein interactions
Yan, Z., Hamilton, W. L., & Blanchette, M. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa456 · Cited by 53
Tertiary structural elements determine the extent and specificity of messenger RNA editing
Rieder, L. E., Staber, C. J., Hoopengardner, B., & Reenan, R. A. (2013) · Nature Communications · doi:10.1038/ncomms3232 · Cited by 51
Recognition of Transcription Termination Signal by the Nuclear Polyadenylated RNA-binding (NAB) 3 Protein
Hóbor, F., Pergoli, R., Kubíček, K., Hroššová, D., Bačíková, V., Zimmermann, M., Pasulka, J., Hofr, C., Vaňáčová, Š., & Štefl, R. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.158774 · Cited by 50
Association of a genetic polymorphism (-44 C/G SNP) in the human DEFB1 gene with expression and inducibility of multiple β-defensins in gingival keratinocytes
Kalus, A., Fredericks, L. P., Hacker, B. M., Dommisch, H., Presland, R. B., Kimball, J. R., & Dale, B. A. (2009) · BMC Oral Health · doi:10.1186/1472-6831-9-21 · Cited by 50
A knowledge‐based potential function predicts the specificity and relative binding energy of RNA‐binding proteins
Zheng, S., Robertson, T. A., & Varani, G. (2007) · FEBS Journal · doi:10.1111/j.1742-4658.2007.06155.x · Cited by 47
Development of Resistance to RNAi in Mammalian Cells
Zheng, Z., Tang, S., & Tao, M. (2005) · Annals of the New York Academy of Sciences · doi:10.1196/annals.1359.019 · Cited by 47
Integrative Structural Biology of Protein-RNA Complexes
Dimitrova-Paternoga, L., Jagtap, P. K. A., Chen, P., & Hennig, J. (2019) · Structure · doi:10.1016/j.str.2019.11.017 · Cited by 44
The undertranslated transcriptome reveals widespread translational silencing by alternative 5' transcript leaders
Law, G. L., Bickel, K. S., MacKay, V. L., & Morris, D. (2006) · Genome biology · doi:10.1186/gb-2005-6-13-r111 · Cited by 46
Indirect Readout of tRNA for Aminoacylation
Perona, J. J., & Hou, Y. (2007) · Biochemistry · doi:10.1021/bi7014647 · Cited by 44
Adenosine Triphosphate (ATP) Reduces Amyloid-β Protein Misfolding in vitro
Coskuner‐Weber, O., & Murray, I. V. J. (2014) · Journal of Alzheimer s Disease · doi:10.3233/jad-132300 · Cited by 44
Identification and functional characterization of three TLR signaling pathway genes in Cyclina sinensis
Ren, Y., Pan, H., Pan, B., & Bu, W. (2016) · Fish & Shellfish Immunology · doi:10.1016/j.fsi.2016.01.025 · Cited by 43
Functions of double-stranded RNA-binding domains in nucleocytoplasmic transport
Banerjee, S., & Barraud, P. (2014) · RNA Biology · doi:10.4161/15476286.2014.972856 · Cited by 41
The mRNA-binding Site of Annexin A2 Resides in Helices C–D of its Domain IV
Aukrust, I., Hollås, H., Strand, E., Evensen, L., Travé, G., Flatmark, T., & Vedeler, A. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.02.094 · Cited by 41
RNA-dependent Folding and Stabilization of C5 Protein During Assembly of the E. coli RNase P Holoenzyme
Guo, X., Campbell, F. E., Sun, L., Christian, E. L., Anderson, V. E., & Harris, M. E. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.05.001 · Cited by 41
DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions
Kuang, X., Dhroso, A., Han, J. G., Shyu, C., & Korkin, D. (2016) · Database · doi:10.1093/database/bav114 · Cited by 40
RNA-binding proteins in pluripotency, differentiation, and reprogramming
Guallar, D., & Wang, J. (2014) · Frontiers in Biology · doi:10.1007/s11515-014-1326-y · Cited by 39
Nucleotide-amino acid π-stacking interactions initiate photo cross-linking in RNA-protein complexes
Knörlein, A., Sarnowski, C. P., de Vries, T., Stoltz, M., Götze, M., Aebersold, R. H., Allain, F. H. ‐., Leitner, A., & Hall, J. (2022) · Nature Communications · doi:10.1038/s41467-022-30284-w · Cited by 41
Self-citation
From Structure to Function of RNA Binding Domains
Lorkovic, Z. (2012) · CRC Press eBooks · doi:10.1201/9781498713368-15 · Cited by 38
Amyotrophic Lateral Sclerosis, FUS and Protein Synthesis Defects
Assoni, A. F., Foijer, F., & Zatz, M. (2022) · Stem Cell Reviews and Reports · doi:10.1007/s12015-022-10489-8 · Cited by 37
Solution Structure of the U11-48K CHHC Zinc-Finger Domain that Specifically Binds the 5′ Splice Site of U12-Type Introns
Tidow, H., Andreeva, A. E., Rutherford, T. J., & Fersht, A. R. (2009) · Structure · doi:10.1016/j.str.2008.11.013 · Cited by 34
The role of RNA conformation in RNA-protein recognition
Kligun, E., & Mandel‐Gutfreund, Y. (2015) · RNA Biology · doi:10.1080/15476286.2015.1040977 · Cited by 33
RNA-Centric Methods: Toward the Interactome of Specific RNA Transcripts
Gräwe, C., Stelloo, S., van Hout, F. A. H., & Vermeulen, M. (2020) · Trends in biotechnology · doi:10.1016/j.tibtech.2020.11.011 · Cited by 36
A novel RNA pentaloop fold involved in targeting ADAR2
Štefl, R., & Allain, F. H. ‐. (2005) · RNA · doi:10.1261/rna.7276805 · Cited by 32
Self-citation
The KREPA3 Zinc Finger Motifs and OB-Fold Domain Are Essential for RNA Editing and Survival of Trypanosoma brucei
Guo, X., Ernst, N. L., & Stuart, K. D. (2008) · Molecular and Cellular Biology · doi:10.1128/mcb.01115-08 · Cited by 31
Genome-wide analysis of the C3H zinc finger family reveals its functions in salt stress responses of Pyrus betulaefolia
Liu, C., Xu, X., Kan, J., Cheng, Z. M., YouHong, C., Lin, J., & Li, H. (2020) · PeerJ · doi:10.7717/peerj.9328 · Cited by 30
Conformational Analysis of Misfolded Protein Aggregation by FRET and Live-Cell Imaging Techniques
Kitamura, A., Nagata, K., & Kinjo, M. (2015) · International Journal of Molecular Sciences · doi:10.3390/ijms16036076 · Cited by 28
Differential Impacts of Alternative Splicing Networks on Apoptosis
Lin, J.-C., Tsao, M.-F., & Lin, Y. (2016) · International Journal of Molecular Sciences · doi:10.3390/ijms17122097 · Cited by 36
Identification of new high affinity targets for Roquin based on structural conservation
Braun, J., Fischer, S. E., Xu, Z. Z., Sun, H., Ghoneim, D. H., Gimbel, A. T., Plessmann, U., Urlaub, H., Mathews, D. H., & Weigand, J. E. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky908 · Cited by 28
A zipcode unzipped: Figure 1.Preprint
Doyle, M., & Kiebler, M. A. (2012) · Genes & Development · doi:10.1101/gad.184945.111 · Cited by 26
Regulation of pluripotency and reprogramming by RNA binding proteins
Li, D., Kishta, M. S., & Wang, J. (2020) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2020.01.003 · Cited by 25
Impact of DEFB1 gene regulatory polymorphisms on hBD-1 salivary concentration
Polesello, V., Zupin, L., Lenarda, R. D., Biasotto, M., Ottaviani, G., Gobbo, M., Cecco, L., Alberi, G., Pozzato, G., Crovella, S., et al. (2015) · Archives of Oral Biology · doi:10.1016/j.archoralbio.2015.03.009 · Cited by 25
A deep learning method for miRNA/isomiR target detection
Talukder, A., Zhang, W. C., Li, X., & Hu, H. (2022) · Scientific Reports · doi:10.1038/s41598-022-14890-8 · Cited by 24
Towards deciphering the principles underlying an mRNA recognition code
Serganov, A., & Patel, D. J. (2008) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2007.12.006 · Cited by 24
Discovery of Key Physicochemical, Structural, and Spatial Properties of RNA‐Targeted Bioactive Ligands
Morgan, B. S., Forte, J. E., Culver, R. N., Zhang, Y., & Hargrove, A. E. (2017) · Angewandte Chemie · doi:10.1002/ange.201707641 · Cited by 23
Spontaneous binding of single-stranded RNAs to RRM proteins visualized by unbiased atomistic simulations with a rescaled RNA force field
Krepl, M., Pokorná, P., Mlýnský, V., Stadlbauer, P., & Šponer, J. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1106 · Cited by 23
MD and QM/MM Study of the Quaternary HutP Homohexamer Complex with mRNA, l -Histidine Ligand, and Mg 2+
Pokorná, P., Krepl, M., Kruse, H., & Šponer, J. (2017) · Journal of Chemical Theory and Computation · doi:10.1021/acs.jctc.7b00598 · Cited by 22
Cardiomyogenic differentiation is fine-tuned by differential mRNA association with polysomes
Pereira, I. T., Spangenberg, L., Robert, A. W., Amorín, R., Stimamiglio, M. A., Naya, H., & Dallagiovanna, B. (2019) · BMC Genomics · doi:10.1186/s12864-019-5550-3 · Cited by 20
Polyadenylation proteins CstF-64 and τCstF-64 exhibit differential binding affinities for RNA polymers
Monarez, R. R., MacDonald, C. C., & Dass, B. (2007) · Biochemical Journal · doi:10.1042/bj20061097 · Cited by 22
Rrp47 and the function of the Sas10/C1D domain
Mitchell, P. (2010) · Biochemical Society Transactions · doi:10.1042/bst0381088 · Cited by 21
Specificity of Phage Display Selected Peptides for Modified Anticodon Stem and Loop Domains of tRNA
Eshete, M., Marchbank, M. T., Deutscher, S. L., Sproat, B. S., Leszczyńska, G., Małkiewicz, A. J., & Agris, P. F. (2007) · The Protein Journal · doi:10.1007/s10930-006-9046-z · Cited by 20
A missense mutation in the CSTF2 gene that impairs the function of the RNA recognition motif and causes defects in 3′ end processing is associated with intellectual disability in humans
Grozdanov, P. N., Masoumzadeh, E., Kalscheuer, V. M., Bienvenu, T., Billuart, P., Delrue, M., Latham, M. P., & MacDonald, C. C. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa689 · Cited by 23
Solution structure of the N-terminal dsRBD of Drosophila ADAR and interaction studies with RNA
Barraud, P., Heale, B. S. E., O’Connell, M. A., & Allain, F. H. ‐. (2011) · Biochimie · doi:10.1016/j.biochi.2011.12.017 · Cited by 20
Self-citation
Archaea Signal Recognition Particle Shows the Way
Zwieb, C. W., & Bhuiyan, S. (2010) · Archaea · doi:10.1155/2010/485051 · Cited by 20
Solution Structure of the N-terminal Zinc Fingers of the Xenopus laevis double-stranded RNA-binding Protein ZFa
Möller, H. M., Martinez‐Yamout, M. A., Dyson, H. J., & Wright, P. E. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.06.032 · Cited by 20
Neuronal temporal identity in post-embryonic Drosophila brain
Yu, H., & Lee, T. (2007) · Trends in Neurosciences · doi:10.1016/j.tins.2007.07.003 · Cited by 20
Inherent conformational plasticity in dsRBDs enables interaction with topologically distinct RNAs
Paithankar, H., Tarang, G. S., Parvez, F., Marathe, A., Joshi, M., & Chugh, J. (2022) · Biophysical Journal · doi:10.1016/j.bpj.2022.02.005 · Cited by 19
Role of Bmznf-2, a Bombyx mori CCCH zinc finger gene, in masculinisation and differential splicing of Bmtra-2
Gopinath, G., Arunkumar, K. P., Mita, K., & Nagaraju, J. (2016) · Insect Biochemistry and Molecular Biology · doi:10.1016/j.ibmb.2016.05.008 · Cited by 19
RNA binding proteins (RBPs) on genetic stability and diseases
Aborode, A. T., Ohilebo, A. A., Nasiru, S., Eigbobo, M. U., Nefishatu, S., Idowu, A., Tiamiyu, Z. A., Awaji, A. A., Idowu, N. J., Babawale, R. B., et al. (2025) · Global Medical Genetics · doi:10.1016/j.gmg.2024.100032 · Cited by 20
Integrating transcription and splicing into cell fate: Transcription factors on the block
Boumpas, P., Merabet, S., & Carnesecchi, J. (2022) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1752 · Cited by 23
Conservation of tRNA mimicry in the 5′-untranslated region of distinct HIV-1 subtypes
Comandur, R., Olson, E. D., & Musier-Forsyth, K. (2017) · RNA · doi:10.1261/rna.062182.117 · Cited by 17
Genomic Screening of Wistar and Wistar-Kyoto Rats Exposed to Chronic Mild Stress and Deep Brain Stimulation of Prefrontal Cortex
Papp, M., Gruca, P., Faron‐Górecka, A., Kuśmider, M., & Willner, P. (2019) · Neuroscience · doi:10.1016/j.neuroscience.2019.10.015 · Cited by 17
Emergence of Compensatory Mutations Reveals the Importance of Electrostatic Interactions between HIV-1 Integrase and Genomic RNA
Mugisha, C. S., Dinh, T., Kumar, A., Tenneti, K., Eschbach, J. E., Davis, K., Gifford, R. J., Kvaratskhelia, M., & Kutluay, S. B. (2022) · mBio · doi:10.1128/mbio.00431-22 · Cited by 17
Isolation of Chromatoid Bodies from Mouse Testis as a Rich Source of Short RNAs
Meikar, O., & Kotaja, N. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-0931-5_2 · Cited by 20
Rbm14 maintains the integrity of genomic DNA during early mouse embryogenesis via mediating alternative splicing
Li, J., Wang, C., Feng, G., Zhang, L., Chen, G., Sun, H., Wang, J., Zhang, Y., Zhou, Q., & Li, W. (2019) · Cell Proliferation · doi:10.1111/cpr.12724 · Cited by 16
Structure and semi-sequence-specific RNA binding of Nrd1
Bačíková, V., Pasulka, J., Kubíček, K., & Štefl, R. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku446 · Cited by 15
Localization elements and zip codes in the intracellular transport and localization of messenger RNAs in Saccharomyces cerevisiae
Chaudhuri, A., Das, S., & Das, B. (2020) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1591 · Cited by 16

Authors: Stefl, R., Skrisovska, L., & Allain, F. H. ‐.
Affiliations: ETH Zurich (CH)
ORCID: Allain, Frédéric H.‐T.
Venue: The EMBO Reports
Publisher: Springer Science and Business Media LLC
Published: 2005-01-01
Volume: 6
Issue: 1
Pages: 33-38
ISSN: 1469-221X (ISSN-L)
1469-3178
DOI: 10.1038/sj.embor.7400325
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
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
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

RNA sequence‐ and shape‐dependent recognition by proteins in the ribonucleoprotein particle

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks