Sequence-specific binding of single-stranded RNA: is there a code for recognition?
Open accessAbstract
A code predicting the RNA sequence that will be bound by a certain protein based on its amino acid sequence or its structure would provide a useful tool for the design of RNA binders with desired sequence-specificity. Such de novo designed RNA binders could be of extraordinary use in both medical and basic research applications. Furthermore, a code could help to predict the cellular functions of RNA-binding proteins that have not yet been extensively studied. A comparative analysis of Pumilio homology domains, zinc-containing RNA binders, hnRNP K homology domains and RNA recognition motifs is performed in this review. Based on this, a set of binding rules is proposed that hints towards a code for RNA recognition by these domains. Furthermore, we discuss the intermolecular interactions that are important for RNA binding and summarize their importance in providing affinity and specificity.
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
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?
Proteins with a single RNA binding domain (RBD) are believed to interact with three to five contiguous RNA bases, whereas proteins with multiple RBDs can interact with bipartite motifs separated by one or more bases, where the two cores in bipartite motifs are bound by distinct RBDs within the same protein.
“Proteins with a single RNA binding domain (RBD) are believed to interact with three to five contiguous RNA bases, whereas proteins with multiple RBDs can interact with bipartite motifs separated by one or more bases, where the two cores in bipartite motifs are bound by distinct RBDs within the same protein (Auweter et al. 2006; Afroz et al. 2015).”
From ESRP2–microRNA-122 axis promotes the postnatal onset of liver polyploidization and maturation (2025) · cites this paper as Auweter et al. 2006
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measuredCanonical RBDs typically bind short single-stranded RNA sequences, but some also recognize structured RNAs.
“Canonical RBDs typically bind short, single-stranded (ss)RNA sequences3,4, but some also recognize structured RNAs5.”
From A compendium of RNA-binding motifs for decoding gene regulation (2013) · cites this paper as [5]
Inference by simple protein identity is particularly valuable for RBPs for which it may not be possible to derive recognition codes.
“Nonetheless, inference by simple protein identity is particularly valuable for those RBPs for which it may not be possible to derive recognition codes5.”
From A compendium of RNA-binding motifs for decoding gene regulation (2013) · cites this paper as [5]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
MOLMOL: A program for display and analysis of macromolecular structures
Koradi, R., Billeter, M., & Kurt Wüthrich, A. (1996) · Journal of Molecular Graphics · doi:10.1016/0263-7855(96)00009-4 · Cited by 7,163 · see citing works
Electrostatics of nanosystems: Application to microtubules and the ribosome
Baker, N., Sept, D., Joseph, S., Holst, M., & McCammon, J. A. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.181342398 · Cited by 7,125 · see citing works
Cation-π interactions in structural biology
Gallivan, J. P., & Dougherty, D. A. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.17.9459 · Cited by 2,005 · see citing works
Maris, C., Dominguez, C., & Allain, F. H. ‐. (2005) · FEBS Journal · doi:10.1111/j.1742-4658.2005.04653.x · Cited by 1,135 · see citing works
Self-citationHydrogen bonding and biological specificity analysed by protein engineering
Fersht, A. R., Shi, J., Knill-Jones, J. W., Lowe, D. M., Wilkinson, A. J., Blow, D. M., Brick, P., Carter, P. M., Waye, M. M. Y., & Winter, G. P. (1985) · Nature · doi:10.1038/314235a0 · Cited by 1,056 · see citing works
Oubridge, C., Ito, N., Evans, P. R., Teo, C.-H., & Nagai, K. (1994) · Nature · doi:10.1038/372432a0 · Cited by 832 · see citing works
Diffusion-Controlled Macromolecular Interactions
Berg, O. G., & von Hippel, P. H. (1985) · Annual Review of Biophysics and Biophysical Chemistry · doi:10.1146/annurev.bb.14.060185.001023 · Cited by 730 · see citing works
Nucleic Acids: Structures, Properties and Functions
Demidov, V. V. (2001) · Drug Discovery Today · doi:10.1016/s1359-6446(00)01635-4 · Cited by 719 · see citing works
Nucleic Acids: Structures, Properties, and Functions
Bloomfield, V. A., Crothers, D. M., & Tinoco, I. (2000) · Medical Entomology and Zoology · Cited by 674 · see citing works
Structure of the HIV-1 Nucleocapsid Protein Bound to the SL3 Ψ-RNA Recognition Element
De Guzman, R. N., Wu, Z. R., Stalling, C. C., Pappalardo, L., Borer, P. N., & Summers, M. F. (1998) · Science · doi:10.1126/science.279.5349.384 · Cited by 659 · see citing works
Crystal structure of the RNA-binding domain of the U1 small nuclear ribonucleoprotein A
Nagai, K., Oubridge, C., Jessen, T., Li, J., & Evans, P. R. (1990) · Nature · doi:10.1038/348515a0 · Cited by 620 · see citing works
Structural Basis for RNA Unwinding by the DEAD-Box Protein Drosophila Vasa
Sengoku, T., Nureki, O., Nakamura, A., Kobayashi, S., & Yokoyama, S. (2006) · Cell · doi:10.1016/j.cell.2006.01.054 · Cited by 575 · see citing works
Kinetics of protein-protein association explained by Brownian dynamics computer simulation.
Northrup, S. H., & Erickson, H. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.8.3338 · Cited by 572 · see citing works
Rapid, electrostatically assisted association of proteins
Schreiber, G., & Fersht, A. R. (1996) · Nature Structural Biology · doi:10.1038/nsb0596-427 · Cited by 560 · see citing works
The pre-mRNA binding K protein contains a novel evolutionary conserved motif
Siomi, H., Matunis, M. J., Michael, W. M., & Dreyfuss, G. (1993) · Nucleic Acids Research · doi:10.1093/nar/21.5.1193 · Cited by 533 · see citing works
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 513 · see citing works
Modular Recognition of RNA by a Human Pumilio-Homology Domain
Wang, X., McLachlan, J., Zamore, P. D., & Hall, T. M. T. (2002) · Cell · doi:10.1016/s0092-8674(02)00873-5 · Cited by 498 · see citing works
The hydrogen bond in molecular recognition
Fersht, A. R. (1987) · Trends in Biochemical Sciences · doi:10.1016/0968-0004(87)90146-0 · Cited by 474 · see citing works
Structure of PTB Bound to RNA: Specific Binding and Implications for Splicing Regulation
Oberstrass, F. C., Auweter, S., Erat, M. C., Hargous, Y., Henning, A., Wenter, P., Reymond, L., Amir-Ahmady, B., Pitsch, S., Black, D. L., et al. (2005) · Science · doi:10.1126/science.1114066 · Cited by 464 · see citing works
Self-citationStructural basis for recognition of the tra mRNA precursor by the Sex-lethal protein
Handa, N., Nureki, O., Kurimoto, K., Kim, I., Sakamoto, H., Shimura, Y., Muto, Y., & Yokoyama, S. (1999) · Nature · doi:10.1038/19242 · Cited by 372 · see citing works
Recognition of the mRNA AU-rich element by the zinc finger domain of TIS11d
Hudson, B. P., Martinez‐Yamout, M. A., Dyson, H. J., & Wright, P. E. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb738 · Cited by 367 · see citing works
Price, S. R., Evans, P. R., & Nagai, K. (1998) · Nature · doi:10.1038/29234 · Cited by 356 · see citing works
Structural Basis for the Transition from Initiation to Elongation Transcription in T7 RNA Polymerase
Yin, Y. W., & Steitz, T. A. (2002) · Science · doi:10.1126/science.1077464 · Cited by 352 · see citing works
Amarasinghe, G., Guzman, R. D. D., Turner, R. B., Chancellor, K. J., Wu, Z.-R., & Summers, M. F. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3979 · Cited by 337 · see citing works
Crystal Structure of the Rabies Virus Nucleoprotein-RNA Complex
Albertini, A., Wernimont, A. K., Muzioł, T. M., Ravelli, R. B. G., Clapier, C. R., Schoehn, G., Weissenhorn, W., & Ruigrok, R. W. H. (2006) · Science · doi:10.1126/science.1125280 · Cited by 331 · see citing works
Structure of the Vesicular Stomatitis Virus Nucleoprotein-RNA Complex
Green, T. J., Zhang, X., Wertz, G. W., & Luo, M. (2006) · Science · doi:10.1126/science.1126953 · Cited by 329 · see citing works
C_H…O hydrogen bonding in biology
Wahl, M. C. (1997) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(97)01004-9 · Cited by 323 · see citing works
Ding, J., Hayashi, M. K., Zhang, Y., Manche, L., Krainer, A. R., & Xu, R.-M. (1999) · Genes & Development · doi:10.1101/gad.13.9.1102 · Cited by 322 · see citing works
Sequence-Specific RNA Binding by a Nova KH Domain
Lewis, H. A., Musunuru, K., Jensen, K. B., Edo, C., Chen, H., Darnell, R. B., & Burley, S. K. (2000) · Cell · doi:10.1016/s0092-8674(00)80668-6 · Cited by 319 · see citing works
KH domain: one motif, two folds
Grishin, N. V. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.3.638 · Cited by 318 · see citing works
Mechanisms of translational control by the 3′ UTR in development and differentiation
de Moor, C. H., Meijer, H. A., & Lissenden, S. (2005) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2004.11.007 · Cited by 310 · see citing works
Amino/Aromatic Interactions in Proteins: Is the Evidence Stacked Against Hydrogen Bonding?
Mitchell, J. B. O., Nandi, C. L., McDonald, I. K., Thornton, J. M., & Price, S. L. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1370 · Cited by 303 · see citing works
The C–H… O Hydrogen Bond in Crystals
Sutor, D. J. (1962) · Nature · doi:10.1038/195068a0 · Cited by 283 · see citing works
Interaction of barnase with its polypeptide inhibitor barstar studied by protein engineering
Schreiber, G., & Fersht, A. R. (1993) · Biochemistry · doi:10.1021/bi00070a025 · Cited by 280 · see citing works
Context-dependent contributions of backbone hydrogen bonding to β-sheet folding energetics
Deechongkit, S., Nguyen, H., Powers, E. T., Dawson, P. E., Gruebele, M., & Kelly, J. W. (2004) · Nature · doi:10.1038/nature02611 · Cited by 278 · see citing works
Molecular basis of RNA recognition by the human alternative splicing factor Fox-1
Auweter, S. D., Fasan, R., Reymond, L., Underwood, J. G., Black, D. L., Pitsch, S., & Allain, F. H. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7600918 · Cited by 264 · see citing works
Self-citationStructural Basis of Transcription: Separation of RNA from DNA by RNA Polymerase II
Westover, K. D., Bushnell, D. A., & Kornberg, R. D. (2004) · Science · doi:10.1126/science.1090839 · Cited by 256 · see citing works
Specificity of ribonucleoprotein interaction determined by RNA folding during complex formation
Allain, F. H. ‐., Gubser, C. C., Howe, P. W. A., Nagai, K., Neuhaus, D., & Varani, G. (1996) · Nature · doi:10.1038/380646a0 · Cited by 249 · see citing works
Self-citationCrystal Structure of a Pumilio Homology Domain
Wang, X., Zamore, P. D., & Hall, T. M. T. (2001) · Molecular Cell · doi:10.1016/s1097-2765(01)00229-5 · Cited by 248 · see citing works
Structural Basis for Recognition of the Intron Branch Site RNA by Splicing Factor 1
Liu, Z., Luyten, I., Bottomley, M. J., Messias, A. C., Houngninou-Molango, S., Sprangers, R., Zanier, K., Krämer, A., & Sattler, M. (2001) · Science · doi:10.1126/science.1064719 · Cited by 244 · see citing works
Structure-based analysis of protein-RNA interactions using the program ENTANGLE
Allers, J., & Shamoo, Y. E. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4857 · Cited by 242 · see citing works
Structural basis for recognition of AU-rich element RNA by the HuD protein.
(2001) · Nature Structural Biology · doi:10.1038/84131 · Cited by 234 · see citing works
Cozzi, F., & Siegel, J. S. (1995) · Pure and Applied Chemistry · doi:10.1351/pac199567050683 · Cited by 221 · see citing works
Wintjens, R. T., Liévin, J., Rooman, M. J., & Buisine, E. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4040 · Cited by 217 · see citing works
Molecular basis of sequence‐specific recognition of pre‐ribosomal RNA by nucleolin
Allain, F. H. ‐., Bouvet, P., Dieckmann, T., & Feigon, J. F. (2000) · The EMBO Journal · doi:10.1093/emboj/19.24.6870 · Cited by 214 · see citing works
Self-citationStructural basis for packaging the dimeric genome of Moloney murine leukaemia virus
D'Souza, V., & Summers, M. F. (2004) · Nature · doi:10.1038/nature02944 · Cited by 204 · see citing works
Mazza, C., Segref, A., Mattaj, I. W., & Cusack, S. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf538 · Cited by 193 · see citing works
RNA sequence‐ and shape‐dependent recognition by proteins in the ribonucleoprotein particle
Stefl, R., Skrisovska, L., & Allain, F. H. ‐. (2005) · The EMBO Reports · doi:10.1038/sj.embor.7400325 · Cited by 175 · see citing works
Self-citationStatistical analysis of atomic contacts at RNA–protein interfaces
Treger, M., & Westhof, É. (2001) · Journal of Molecular Recognition · doi:10.1002/jmr.534 · Cited by 170 · see citing works
Structural basis of m7GpppG binding to the nuclear cap-binding protein complex
Calero, G. A., Wilson, K. F., Ly, T. K., Ríos-Steiner, J. L., Clardy, J., & Cerione, R. A. (2002) · Nature Structural Biology · doi:10.1038/nsb874 · Cited by 170 · see citing works
Structure and dynamics of KH domains from FBP bound to single-stranded DNA
Braddock, D. T., Louis, J. M., Baber, J. L., Levens, D., & Clore, G. M. (2002) · Nature · doi:10.1038/4151051a · Cited by 165 · see citing works
Spassov, D. S., & Jurecic, R. (2003) · IUBMB Life · doi:10.1080/15216540310001603093 · Cited by 163 · see citing works
Structural basis of the RNA‐binding specificity of human U1A protein
Allain, F. H. ‐., Howe, P. W. A., Neuhaus, D., & Varani, G. (1997) · The EMBO Journal · doi:10.1093/emboj/16.18.5764 · Cited by 160 · see citing works
Self-citationBraddock, D. T., Baber, J. L., Levens, D., & Clore, G. M. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf352 · Cited by 153 · see citing works
Varani, G., Varani, L., Gunderson, S., Mattaj, I. W., Kay, L. E., & Neuhaus, D. (2000) · Nature Structural Biology · doi:10.1038/74101 · Cited by 135 · see citing works
Structure of a Mycobacterium tuberculosis NusA–RNA complex
Beuth, B., Pennell, S., Arnvig, K. B., Martin, S. R., & Taylor, I. A. (2005) · The EMBO Journal · doi:10.1038/sj.emboj.7600829 · Cited by 120 · see citing works
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 · see citing works
Self-citationRNA Recognition and Cleavage by a Splicing Endonuclease
Xue, S., Calvin, K., & Li, H. (2006) · Science · doi:10.1126/science.1126629 · Cited by 114 · see citing works
Backe, P. H., Messias, A. C., Ravelli, R. B. G., Sattler, M., & Cusack, S. (2005) · Structure · doi:10.1016/j.str.2005.04.008 · Cited by 111 · see citing works
Deardorff, J. A., & Sachs, A. B. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1013 · Cited by 100 · see citing works
Structure of the two most C‐terminal RNA recognition motifs of PTB using segmental isotope labeling
Vitali, F., Henning, A., Oberstrass, F. C., Hargous, Y., Auweter, S., Erat, M. C., & Allain, F. H. ‐. (2005) · The EMBO Journal · doi:10.1038/sj.emboj.7600911 · Cited by 96 · see citing works
Self-citationStructural Basis of Single-Stranded RNA Recognition
Messias, A. C., & Sattler, M. (2004) · Accounts of Chemical Research · doi:10.1021/ar030034m · Cited by 93 · see citing works
On the molecular discrimination between adenine and guanine by proteins
Nobeli, I. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.21.4294 · Cited by 88 · see citing works
Two Functionally Distinct Steps Mediate High Affinity Binding of U1A Protein to U1 Hairpin II RNA
Katsamba, P. S., Myszka, D. G., & Laird‐Offringa, I. A. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m101624200 · Cited by 86 · see citing works
Enokizono, Y., Konishi, Y., Nagata, K., Ouhashi, K., Uesugi, S., Ishikawa, F., & Katahira, M. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m411822200 · Cited by 86 · see citing works
Law, M. J. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj436 · Cited by 80 · see citing works
Molecular Interactions of Nucleic Acid Bases. A Review of Quantum-Chemical Studies
Šponer, J., & Hobza, P. (2003) · Collection of Czechoslovak Chemical Communications · doi:10.1135/cccc20032231 · Cited by 79 · see citing works
Chen, Y. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh785 · Cited by 78 · see citing works
Biot, C., Buisine, E., & Rooman, M. J. (2003) · Journal of the American Chemical Society · doi:10.1021/ja035223e · Cited by 78 · see citing works
Electrostatic Interactions in a Peptide–RNA Complex
Garcı́a-Garcı́a, C., & Draper, D. E. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00615-6 · Cited by 76 · see citing works
Johansson, C. A., Finger, L. D., Trantı́rek, L., Mueller, T. D., Kim, S., Laird‐Offringa, I. A., & Feigon, J. F. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.01.056 · Cited by 76 · see citing works
Nucleotide Analog Interference Mapping
Ryder, S. P., & Strobel, S. A. (1999) · Methods · doi:10.1006/meth.1999.0755 · Cited by 75 · see citing works
Towards therapeutic applications of engineered zinc finger proteins
Klug, A. (2004) · FEBS Letters · doi:10.1016/j.febslet.2004.10.104 · Cited by 74 · see citing works
Hart, D. J. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.4.1063 · Cited by 66 · see citing works
Zuberek, J., Jemielity, J., Jabłonowska, A., Stȩpiński, J., Dadlez, M., Stolarski, R., & Darżynkiewicz, E. (2004) · Biochemistry · doi:10.1021/bi030266t · Cited by 65 · see citing works
Du, Z., Lee, J. K., Tjhen, R., Li, S., Pan, H., Stroud, R. M., & James, T. L. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m508183200 · Cited by 64 · see citing works
Nolan, S., Shiels, J. C., Tuite, J. B., Cecere, K. L., & Baranger, A. M. (1999) · Journal of the American Chemical Society · doi:10.1021/ja991617n · Cited by 64 · see citing works
Mutagenesis of a stacking contact in the MS2 coat protein‐RNA complex.
LeCuyer, K. A., Behlen, L. S., & Uhlenbeck, O. C. (1996) · The EMBO Journal · doi:10.1002/j.1460-2075.1996.tb01076.x · Cited by 61 · see citing works
Laird‐Offringa, I. A., & Belasco, J. G. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.25.11859 · Cited by 59 · see citing works
Mao, L., Wang, Y., Liu, Y., & Hu, X. (2003) · Journal of the American Chemical Society · doi:10.1021/ja036096p · Cited by 53 · see citing works
Dey, A., York, D., Smalls-Mantey, A., & Summers, M. F. (2005) · Biochemistry · doi:10.1021/bi047639q · Cited by 46 · see citing works
Myers, J. C., & Shamoo, Y. E. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.07.029 · Cited by 42 · see citing works
A binding mechanism in protein–nucleotide interactions: Implication for U1A RNA binding
Guallar, V., & Borrelli, K. W. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0500888102 · Cited by 40 · see citing works
The role of RNA structure in the interaction of U1A protein with U1 hairpin II RNA
Law, M. J., Rice, A. J., Lin, P., & Laird‐Offringa, I. A. (2006) · RNA · doi:10.1261/rna.75206 · Cited by 40 · see citing works
Kranz, J. K., Lu, J., & Hall, K. B. (1996) · Protein Science · doi:10.1002/pro.5560050812 · Cited by 31 · see citing works
Contributions of basic residues to ribosomal protein L11 recognition of RNA
GuhaThakurta, D., & Draper, D. E. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.3372 · Cited by 27 · see citing works
High-Resolution Structural Validation of the Computational Redesign of Human U1A Protein
Dobson, N., Dantas, G. A., Baker, D. A., & Varani, G. (2006) · Structure · doi:10.1016/j.str.2006.02.011 · Cited by 24 · see citing works
Schüler, W., Dong, C., Wecker, K., & Roques, B. P. (1999) · Biochemistry · doi:10.1021/bi990378d · Cited by 22 · see citing works
Assembly of the U1 snRNP involves interactions with the backbone of the terminal stem of U1 snRNA
McConnell, T., Lokken, R. P., & STEITZ, J. A. (2003) · RNA · doi:10.1261/rna.2136103 · Cited by 21 · see citing works
Protein structures and complexes: what they reveal about the interactions that stabilize them
Thornton, J. M., MacArthur, M. W., McDonald, I. K., Jones, D. T., Mitchell, J. B. O., Nandi, C. L., Price, S. L., & Zvelebil, M. (1993) · Philosophical Transactions of the Royal Society of London Series A Physical and Engineering Sciences · doi:10.1098/rsta.1993.0123 · Cited by 12 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
A census of human RNA-binding proteins
Gerstberger, S., Hafner, M., & Tuschl, T. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3813 · Cited by 2,032 · see citing works
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 · see citing works
RNA-binding proteins: modular design for efficient function
Lunde, B. M., Moore, C. L., & Varani, G. (2007) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2178 · Cited by 1,322 · see citing works
How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms
Corley, M., Burns, M. C., & Yeo, G. W.-M. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.03.011 · Cited by 848 · see citing works
RBPDB: a database of RNA-binding specificities
Cook, K. B., Kazan, H., Zuberi, K., Morris, Q., & Hughes, T. R. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1069 · Cited by 638 · see citing works
RNA recognition motifs: boring? Not quite
Cléry, A., Blatter, M., & Allain, F. H. ‐. (2008) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2008.04.002 · Cited by 637 · see citing works
Self-citationSequence, Structure, and Context Preferences of Human RNA Binding Proteins
Dominguez, D., Freese, P., Alexis, M. S., Su, A., Hochman, M., Palden, T., Bazile, C., Lambert, N. J., Van Nostrand, E. L., Pratt, G. A., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.05.001 · Cited by 562 · see citing works
Hua, Y., Vickers, T. A., Okunola, H. L., Bennett, C. F., & Krainer, A. R. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.01.014 · Cited by 570 · see citing works
Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins
Ray, D., Kazan, H., Chan, E. T., Peña‐Castillo, L., Chaudhry, S., Talukder, S., Blencowe, B. J., Morris, Q., & Hughes, T. R. (2009) · Nature Biotechnology · doi:10.1038/nbt.1550 · Cited by 479 · see citing works
iCLIP: Protein–RNA interactions at nucleotide resolution
Huppertz, I., Attig, J., D’Ambrogio, A., Easton, L. E., Sibley, C. R., Sugimoto, Y., Tajnik, M., König, J., & Ule, J. (2013) · Methods · doi:10.1016/j.ymeth.2013.10.011 · Cited by 430 · see citing works
Wu, B., Su, S., Patil, D. P., Liu, H., Gan, J., Jaffrey, S. R., & Ma, J. (2018) · Nature Communications · doi:10.1038/s41467-017-02770-z · Cited by 389 · see citing works
The YTH Domain Is a Novel RNA Binding Domain
Zhang, Z., Theler, D., Kaminska, K. H., Hiller, M., de la Grange, P., Pudimat, R., Rafalska, I., Heinrich, B., Bujnicki, J. M., Allain, F. H. ‐., et al. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m110.104711 · Cited by 304 · see citing works
Self-citationElectron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems
Tanaka, S., Mochizuki, Y., Komeiji, Y., Okiyama, Y., & Fukuzawa, K. (2014) · Physical Chemistry Chemical Physics · doi:10.1039/c4cp00316k · Cited by 301 · see citing works
The recruitment of chromatin modifiers by long noncoding RNAs: lessons from PRC2
Davidovich, C., & Cech, T. R. (2015) · RNA · doi:10.1261/rna.053918.115 · Cited by 295 · see citing works
Specificity and nonspecificity in RNA–protein interactions
Jankowsky, E., & Harris, M. E. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm4032 · Cited by 277 · see citing works
The multiple roles of TDP-43 in pre-mRNA processing and gene expression regulation
Buratti, E., & Baralle, F. E. (2010) · RNA Biology · doi:10.4161/rna.7.4.12205 · Cited by 284 · see citing works
Delannoy, É., Stanley, W. A., Bond, C. S., & Small, I. (2007) · Biochemical Society Transactions · doi:10.1042/bst0351643 · Cited by 230 · see citing works
RRM–RNA recognition: NMR or crystallography…and new findings
Daubner, G. M., Cléry, A., & Allain, F. H. ‐. (2012) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2012.11.006 · Cited by 219 · see citing works
Self-citationZBP1 recognition of β-actin zipcode induces RNA loopingPreprint
Chao, J. A., Patskovsky, Y., Patel, V., Levy, M., Almo, S. C., & Singer, R. H. (2010) · Genes & Development · doi:10.1101/gad.1862910 · Cited by 205 · see citing works
Genetic variants in mRNA untranslated regions
Steri, M., Idda, M. L., Whalen, M. B., & Orrù, V. (2018) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1474 · Cited by 200 · see citing works
Molecular basis of messenger RNA recognition by the specific bacterial repressing clamp RsmA/CsrA
Schubert, M., Lapouge, K., Duss, O., Oberstrass, F. C., Jelesarov, I., Haas, D., & Allain, F. H. ‐. (2007) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1285 · Cited by 202 · see citing works
Self-citationPre-mRNA Secondary Structures Influence Exon Recognition
Hiller, M., Zhang, Z., Backofen, R., & Stamm, S. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030204 · Cited by 199 · see citing works
Hammani, K., Okuda, K., Tanz, S. K., Chateigner‐Boutin, A., Shikanai, T., & Small, I. (2009) · The Plant Cell · doi:10.1105/tpc.109.071472 · Cited by 191 · see citing works
The selenium to selenoprotein pathway in eukaryotes: More molecular partners than anticipated
Allmang, C., Wurth, L., & Krol, A. (2009) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2009.03.003 · Cited by 189 · see citing works
RNABindR: a server for analyzing and predicting RNA-binding sites in proteins
Terribilini, M., Sander, J. D., Lee, J., Zaback, P., Jernigan, R. L., Honavar, V., & Dobbs, D. L. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm294 · Cited by 186 · see citing works
Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression
Kishore, S., Luber, S., & Zavolan, M. (2010) · Briefings in Functional Genomics · doi:10.1093/bfgp/elq028 · Cited by 178 · see citing works
Warf, M. B., & Berglund, J. A. (2007) · RNA · doi:10.1261/rna.610607 · Cited by 178 · see citing works
Spatial arrangement of an RNA zipcode identifies mRNAs under post-transcriptional controlPreprint
Patel, V., Mitra, S., Harris, R., Buxbaum, A. R., Lionnet, T., Brenowitz, M. D., Girvin, M. E., Levy, M., Almo, S. C., Singer, R. H., et al. (2012) · Genes & Development · doi:10.1101/gad.177428.111 · Cited by 167 · see citing works
A universal code for RNA recognition by PUF proteins
Filipovska, A., Razif, M. F. M., Nygård, K. K. A., & Rackham, O. (2011) · Nature Chemical Biology · doi:10.1038/nchembio.577 · Cited by 164 · see citing works
Yang, Q., Gilmartin, G. M., & Doublié, S. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000848107 · Cited by 154 · see citing works
Mechanism of substrate selection by a highly specific CRISPR endoribonuclease
Sternberg, S. H., Haurwitz, R. E., & Doudna, J. A. (2012) · RNA · doi:10.1261/rna.030882.111 · Cited by 153 · see citing works
Gerstberger, S. C., Hafner, M., Ascano, M., & Tuschl, T. (2014) · Advances in experimental medicine and biology · doi:10.1007/978-1-4939-1221-6_1 · Cited by 145 · see citing works
Grossoehme, N. E., Li, L., Keane, S. C., Liu, P., Dann, C. E., Leibowitz, J. L., & Giedroc, D. P. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.09.040 · Cited by 148 · see citing works
The N-terminus of TDP-43 promotes its oligomerization and enhances DNA binding affinity
Chang, C., Wu, T.-H., Wu, C.-Y., Chiang, M.-H., Toh, E. K.-W., Hsu, Y.-C., Lin, K.-F., Liao, Y.-H., Huang, T.-H., & Huang, J. J. (2012) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2012.07.071 · Cited by 142 · see citing works
Advances in CRISPR-Cas systems for RNA targeting, tracking and editing
Wang, F., Wang, L., Zou, X., Duan, S., Li, Z., Deng, Z., Luo, J., Lee, S. Y., & Chen, S. (2019) · Biotechnology Advances · doi:10.1016/j.biotechadv.2019.03.016 · Cited by 128 · see citing works
A syn–anti conformational difference allows SRSF2 to recognize guanines and cytosines equally well
Daubner, G. M., Cléry, A., Jayne, S., Stévenin, J., & Allain, F. H. ‐. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.367 · Cited by 133 · see citing works
Self-citationSpliceAid: a database of experimental RNA target motifs bound by splicing proteins in humans
Piva, F., Giulietti, M., Nocchi, L., & Principato, G. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp124 · Cited by 127 · see citing works
Khorshid, M., Rodak, C., & Zavolan, M. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq940 · Cited by 128 · see citing works
Inhibition of RNA-binding proteins with small molecules
Wu, P. (2020) · Nature Reviews Chemistry · doi:10.1038/s41570-020-0201-4 · Cited by 129 · see citing works
Harnessing CRISPR/Cas systems for programmable transcriptional and post-transcriptional regulation
Mahas, A., Stewart, C. N., & Mahfouz, M. M. (2017) · Biotechnology Advances · doi:10.1016/j.biotechadv.2017.11.008 · Cited by 121 · see citing works
Molecular basis for AU-rich element recognition and dimerization by the HuR C-terminal RRM
Ripin, N., Boudet, J., Duszczyk, M., Hinniger, A., Faller, M., Krepl, M., Gadi, A., Schneider, R. J., Šponer, J., Meisner-Kober, N. C., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1808696116 · Cited by 114 · see citing works
Self-citationWilliams-Carrier, R. E., Kroeger, T. S., & Barkan, A. (2008) · RNA · doi:10.1261/rna.1077708 · Cited by 112 · see citing works
Molecular basis of purine-rich RNA recognition by the human SR-like protein Tra2-β1
Cléry, A., Jayne, S., Benderska, N., Dominguez, C., Stamm, S., & Allain, F. H. ‐. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2001 · Cited by 111 · see citing works
Self-citationCharacterization of a Family of RanBP2-Type Zinc Fingers that Can Recognize Single-Stranded RNA
Nguyen, C. D., Mansfield, R. E., Leung, W., Vaz, P. M., Loughlin, F. E., Grant, R. P., & Mackay, J. P. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2010.12.041 · Cited by 111 · see citing works
HuR biological function involves RRM3-mediated dimerization and RNA binding by all three RRMs
Pabiś, M., Popowicz, G. M., Stehle, R., Fernández‐Ramos, D., Asami, S., Warner, L., García‐Mauriño, S. M., Schlundt, A., Martínez‐Chantar, M. L., Díaz‐Moreno, I., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1138 · Cited by 107 · see citing works
Specific and Modular Binding Code for Cytosine Recognition in Pumilio/FBF (PUF) RNA-binding Domains
Dong, S., Wang, Y., Cassidy-Amstutz, C., Lu, G., Bigler, R. L., Jezyk, M. R., Li, C., Hall, T. M. T., & Wang, Z. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.244889 · Cited by 106 · see citing works
Engineering RNA ‐binding proteins for biology
Chen, Y., & Varani, G. (2013) · FEBS Journal · doi:10.1111/febs.12375 · Cited by 106 · see citing works
Engineering RNA endonucleases with customized sequence specificities
Choudhury, R., Tsai, Y., Dominguez, D., Wang, Y., & Wang, Z. (2012) · Nature Communications · doi:10.1038/ncomms2154 · Cited by 106 · see citing works
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 103 · see citing works
Trans‐acting translational regulatory RNA binding proteins
Harvey, R. F., Smith, T. S., Mulroney, T. E., Queiroz, R. M. L., Pizzinga, M., Dezi, V., Villanueva, E., Ramakrishna, M., Lilley, K. S., & Willis, A. E. (2018) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1465 · Cited by 104 · see citing works
Molecular Basis of RNA Recognition by the Embryonic Polarity Determinant MEX-5
Pagano, J. M., Farley, B. M., McCoig, L. M., & Ryder, S. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m700079200 · Cited by 104 · see citing works
Beckmann, B. M., Castelló, A., & Medenbach, J. (2016) · Pflügers Archiv - European Journal of Physiology · doi:10.1007/s00424-016-1819-4 · Cited by 103 · see citing works
Synthetic oligonucleotides recruit ILF2/3 to RNA transcripts to modulate splicing
Rigo, F., Hua, Y., Chun, S. J., Prakash, T. P., Krainer, A. R., & Bennett, C. F. (2012) · Nature Chemical Biology · doi:10.1038/nchembio.939 · Cited by 102 · see citing works
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 · see citing works
Self-citationDe novo prediction of RNA–protein interactions from sequence information
Wang, Y., Chen, X., Liu, Z., Huang, Q., Wang, Y., Xu, D., Zhang, X.-S., Chen, R., & Chen, L. (2012) · Molecular BioSystems · doi:10.1039/c2mb25292a · Cited by 99 · see citing works
One, Two, Three, Four! How Multiple RRMs Read the Genome Sequence
Afroz, T., Cienikova, Z., Cléry, A., & Allain, F. H. T. (2015) · Methods in Enzymology · doi:10.1016/bs.mie.2015.01.015 · Cited by 104 · see citing works
Self-citationFinding the target sites of RNA ‐binding proteins
Li, X., Kazan, H., Lipshitz, H. D., & Morris, Q. (2013) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1201 · Cited by 91 · see citing works
The ins and outs of lncRNA structure: How, why and what comes next?
Blythe, A. J., Fox, A. H., & Bond, C. S. (2015) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2015.08.009 · Cited by 94 · see citing works
Moreno, R., & Rojo, F. (2007) · Journal of Bacteriology · doi:10.1128/jb.01604-07 · Cited by 92 · see citing works
Loedige, I., Jakob, L., Treiber, T., Ray, D., Stotz, M., Treiber, N., Hennig, J., Cook, K. B., Morris, Q., Hughes, T. R., et al. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.09.068 · Cited by 91 · see citing works
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 · see citing works
Structure-function relationships of the polypyrimidine tract binding protein
Auweter, S., & Allain, F. H. ‐. (2007) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-007-7378-2 · Cited by 87 · see citing works
Self-citationDifferential protein occupancy profiling of the mRNA transcriptome
Schueler, M., Munschauer, M., Gregersen, L. H., Finzel, A., Loewer, A., Chen, W., Landthaler, M., & Dieterich, C. (2014) · Genome biology · doi:10.1186/gb-2014-15-1-r15 · Cited by 81 · see citing works
High-throughput characterization of protein-RNA interactions
Cook, K. B., Hughes, T., & Morris, Q. (2014) · Briefings in Functional Genomics · doi:10.1093/bfgp/elu047 · Cited by 82 · see citing works
Structural basis for the sequence-specific RNA-recognition mechanism of human CUG-BP1 RRM3
Tsuda, K., Kuwasako, K., Takahashi, M., Someya, T., Inoue, M., Terada, T., Kobayashi, N., Shirouzu, M., Kigawa, T., Tanaka, A., et al. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp546 · Cited by 79 · see citing works
Han, A., Stoilov, P., Linares, A. J., Zhou, Y., Fu, X., & Black, D. L. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003442 · Cited by 78 · see citing works
Modulation of miRNA function by natural and synthetic RNA-binding proteins in cancer
Vos, P. D., Leedman, P. J., Filipovska, A., & Rackham, O. (2019) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-019-03163-9 · Cited by 74 · see citing works
Structural Insights into RNA Recognition by the Alternate-Splicing Regulator CUG-Binding Protein 1
Teplova, M., Song, J., Gaw, H. Y., Теплов, А. А., & Patel, D. J. (2010) · Structure · doi:10.1016/j.str.2010.06.018 · Cited by 75 · see citing works
RNA Recognition and Stress Granule Formation by TIA Proteins
Waris, S., Wilce, M. C. J., & Wilce, J. (2014) · International Journal of Molecular Sciences · doi:10.3390/ijms151223377 · Cited by 73 · see citing works
CircRNA—Protein Interactions in Muscle Development and Diseases
Zheng, S., Zhang, X., Odame, E., Xu, X., Chen, Y., Ye, J., Zhou, H., Dai, D., Kyei, B., Zhan, S., et al. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22063262 · Cited by 72 · see citing works
Structural basis for the dual RNA-recognition modes of human Tra2-β RRM
Tsuda, K., Someya, T., Kuwasako, K., Takahashi, M., He, F., Unzai, S., Inoue, M., Harada, T., Watanabe, S., Terada, T., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq854 · Cited by 73 · see citing works
Different modes of interaction by TIAR and HuR with target RNA and DNA
Kim, H. S., Wilce, M. C. J., Yoga, Y. M. K., Pendini, N. R., Gunzburg, M. J., Cowieson, N. P., Wilson, G. M., Williams, B. R. G., Gorospe, M., & Wilce, J. A. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq837 · Cited by 73 · see citing works
Gene and genon concept: coding versus regulation
Scherrer, K., & Jost, J. (2007) · Theory in Biosciences · doi:10.1007/s12064-007-0012-x · Cited by 72 · see citing works
Ray, D., Ha, K., Nie, K., Zheng, H., Hughes, T. R., & Morris, Q. (2016) · Methods · doi:10.1016/j.ymeth.2016.12.003 · Cited by 68 · see citing works
Zacco, E., Martin, S. R., Thorogate, R., & Pastore, A. (2018) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2018.00372 · Cited by 72 · see citing works
Modular recognition of nucleic acids by PUF, TALE and PPRproteins
Filipovska, A., & Rackham, O. (2012) · Molecular BioSystems · doi:10.1039/c2mb05392f · Cited by 69 · see citing works
Gherghe, C., Lombo, T., Leonard, C. W., Datta, S. A. K., Bess, J. W., Gorelick, R. J., Rein, A., & Weeks, K. M. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1006897107 · Cited by 69 · see citing works
A Fast and Robust Poisson–Boltzmann Solver Based on Adaptive Cartesian Grids
Boschitsch, A. H., & Fenley, M. O. (2011) · Journal of Chemical Theory and Computation · doi:10.1021/ct1006983 · Cited by 66 · see citing works
Splicing Factor Mutations in Myelodysplasias: Insights from Spliceosome Structures
Jenkins, J. L., & Kielkopf, C. L. (2017) · Trends in Genetics · doi:10.1016/j.tig.2017.03.001 · Cited by 66 · see citing works
Dimerization of FIR upon FUSE DNA binding suggests a mechanism of c‐myc inhibition
Crichlow, G. V., Zhou, H., Hsiao, H.-H. T., Frederick, K. B., Debrosse, M., Yang, Y., Folta‐Stogniew, E. J., Chung, H., Fan, C., Cruz, E. M. D. L., et al. (2007) · The EMBO Journal · doi:10.1038/sj.emboj.7601936 · Cited by 66 · see citing works
In silico characterization and prediction of global protein–mRNA interactions in yeast
Pancaldi, V., & Bähler, J. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr160 · Cited by 65 · see citing works
The sequence selectivity of KSRP explains its flexibility in the recognition of the RNA targets
García‐Mayoral, M. F., Díaz‐Moreno, I., Hollingworth, D., & Ramos, A. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn509 · Cited by 65 · see citing works
Muto, Y., & Yokoyama, S. (2012) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1107 · Cited by 64 · see citing works
Molecular basis for AU-rich element recognition and dimerization by the HuR C-terminal RRM
Ripin, N., & Allain, F. H. ‐. (2018) · Worldwide Protein Data Bank · doi:10.2210/pdb6gc5/pdb · Cited by 64 · see citing works
Self-citationRNA ‐protein interactions in an unstructured context
Žagrović, B., Bartonek, L., & Polyansky, A. A. (2018) · FEBS Letters · doi:10.1002/1873-3468.13116 · Cited by 61 · see citing works
Varjak, M., Saul, S., Arike, L., Lulla, A., Peil, L., & Merits, A. (2013) · Journal of Virology · doi:10.1128/jvi.01105-13 · Cited by 62 · see citing works
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 62 · see citing works
Structures and target RNA preferences of the RNA-binding protein family of IGF2BPs: An overview
Korn, S. M., Ulshöfer, C. J., Schneider, T. P., & Schlundt, A. (2021) · Structure · doi:10.1016/j.str.2021.05.001 · Cited by 61 · see citing works
Functional Interactions Between microRNAs and RNA Binding Proteins
Jiang, P., & Coller, H. (2012) · MicroRNA e · doi:10.2174/2211536611201010070 · Cited by 62 · see citing works
Rethinking RNA-binding proteins: Riboregulation challenges prevailing views
Hentze, M. W., Sommerkamp, P., Ravi, V., & Gebauer, F. (2025) · Cell · doi:10.1016/j.cell.2025.06.021 · Cited by 61 · see citing works
Kinked β-strands mediate high-affinity recognition of mRNA targets by the germ-cell regulator DAZL
Jenkins, H. T., Malkova, B., & Edwards, T. A. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1105211108 · Cited by 60 · see citing works
RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing
Cereda, M., Pozzoli, U., Rot, G., Juvan, P., Schweitzer, A. C., Clark, T. A., & Ule, J. (2014) · Genome biology · doi:10.1186/gb-2014-15-1-r20 · Cited by 58 · see citing works
PTBP1 Is Required for Embryonic Development before Gastrulation
Suckale, J., Wendling, O., Masjkur, J., Jäger, M., Münster, C., Anastassiadis, K., Stewart, A. F., & Solimena, M. (2011) · PLoS ONE · doi:10.1371/journal.pone.0016992 · Cited by 55 · see citing works
“RRMs of different proteins bind 2–8 nucleotides with the RRMs of PTBP1 binding 3–5 with slightly different sequence preference [35].”
BackgroundThe RNA Binding Specificity of Human APOBEC3 Proteins Resembles That of HIV-1 Nucleocapsid
York, A., Kutluay, S. B., Errando, M., & Bieniasz, P. D. (2016) · PLoS Pathogens · doi:10.1371/journal.ppat.1005833 · Cited by 58 · see citing works
The prospects for designer single-stranded RNA-binding proteins
Mackay, J. P., Font, J. S., & Segal, D. J. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2005 · Cited by 56 · see citing works
White, M. R., & Garcin, E. D. (2015) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1315 · Cited by 56 · see citing works
Rbfox2 function in RNA metabolism is impaired in hypoplastic left heart syndrome patient hearts
Verma, S. K., Deshmukh, V., Nutter, C. A., Jaworski, E. A., Jin, W., Wadhwa, L., Abata, J., Ricci, M., Lincoln, J., Martin, J. F., et al. (2016) · Scientific Reports · doi:10.1038/srep30896 · Cited by 56 · see citing works
RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific
Ray, D., Laverty, K. U., Jolma, A., Nie, K., Samson, R., Pour, S. E., Tam, C. L., von Krosigk, N., Nabeel‐Shah, S., Albu, M., et al. (2023) · Scientific Reports · doi:10.1038/s41598-023-32245-9 · Cited by 53 · see citing works
Stacking interactions in PUF–RNA complexes
Koh, Y. Y., Wang, Y., Qiu, C., Opperman, L., Gross, L., Hall, T. M. T., & Wickens, M. (2011) · RNA · doi:10.1261/rna.2540311 · Cited by 54 · see citing works
Principles of mRNA transport in yeast
Heym, R. G., & Niessing, D. (2011) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-011-0902-4 · Cited by 53 · see citing works
- Authors
- Auweter, S. D., Oberstrass, F. C., & Allain, F. H.-T.
- Affiliations
- ETH Zurich (CH)
- Corresponding author
- Allain, Frédéric H.-T.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-09-18
- Volume
- 34
- Issue
- 17
- Pages
- 4943-4959
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC1635273
- OpenAlex
- W2020433571
- Cited by
- 314
- References
- 90
- Citations by year
- 2026: 7 · 2025: 11 · 2024: 16 · 2023: 15 · 2022: 7 · 2021: 11 · 2020: 11 · 2019: 10 · 2018: 17 · 2017: 14 · 2016: 11 · 2015: 16 · 2014: 26 · 2013: 15 · 2012: 29
- FWCI
- 1.30
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by-nc
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed (publishedVersion)
- Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by-nc)
- ETH Zürich Research Collection
- Funders
- National Science Foundation
- University of Southern California
- Florida State University
- University of Oxford
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
- Eidgenössische Technische Hochschule Zürich
- 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
- RNA-binding proteins, sequence-specific RNA binding, RNA recognition motif, binding specificity, binding affinity, intermolecular interactions
- MeSH terms
- Base Sequence, Binding Sites, Models, Molecular, Protein Binding, RNA, Protein Engineering, RNA-Binding Proteins, Protein Structure, Tertiary
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