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

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 · see citing works

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 · see citing works

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 · see citing works

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 1,469 · see citing works

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 · see citing works

SMART 4.0: towards genomic data integration

Letunić, I. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh088 · Cited by 997 · see citing works

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 · see citing works

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 · 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

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 · see citing works

Structural 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

RNA recognition by a Staufen double‐stranded RNA‐binding domain

Ramos, A., Grünert, S., Adams, J., Micklem, D., Proctor, M. R., Freund, S. M. V., Bycroft, M., Johnston, D. S., & Varani, G. (2000) · The EMBO Journal · doi:10.1093/emboj/19.5.997 · Cited by 366 · see citing works

Crystal structure of the spliceosomal U2B″–U2A′ protein complex bound to a fragment of U2 small nuclear RNA

Price, S. R., Evans, P. R., & Nagai, K. (1998) · Nature · doi:10.1038/29234 · Cited by 356 · see citing works

The dsRNA binding protein family: critical roles, diverse cellular functions

Saunders, L. R., & Barber, G. N. (2003) · The FASEB Journal · doi:10.1096/fj.02-0958rev · Cited by 338 · see citing works

Crystal structure of the two-RRM domain of hnRNP A1 (UP1) complexed with single-stranded telomeric DNAPreprint

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

RNA recognition: A family matter?

Mattaj, I. W. (1993) · Cell · doi:10.1016/0092-8674(93)90265-r · Cited by 252 · see citing works

Isolation of a 7S particle from Xenopus laevis oocytes: a 5S RNA-protein complex.

Picard, B., & Wegnez, M. R. (1979) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.76.1.241 · Cited by 246 · see citing works

Proteins binding to duplexed RNA: one motif, multiple functions

Fierro-Monti, I., & Mathews, M. B. (2000) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)01580-2 · Cited by 243 · 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

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

Crystal structure of a zinc-finger–RNA complex reveals two modes of molecular recognition

Lü, D., Searles, M. A., & Klug, A. (2003) · Nature · doi:10.1038/nature02088 · Cited by 203 · see citing works

Large‐scale induced fit recognition of an m7GpppG cap analogue by the human nuclear cap‐binding complex

Mazza, C., Segref, A., Mattaj, I. W., & Cusack, S. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf538 · Cited by 193 · see citing works

A novel mode of RBD-protein recognition in the Y14–Mago complex

Fribourg, S., Gatfield, D., Izaurralde, E., & Conti, E. (2003) · Nature Structural & Molecular Biology · doi:10.1038/nsb926 · Cited by 170 · see citing works

RNA and DNA binding zinc fingers in Xenopus TFIIIA

Theunissen, O., Rudt, F., Guddat, U., Mentzel, H., & Pieler, T. (1992) · Cell · doi:10.1016/0092-8674(92)90601-8 · Cited by 169 · 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

RNA Chaperones Exist and DEAD Box Proteins Get a Life

Lorsch, J. R. (2002) · Cell · doi:10.1016/s0092-8674(02)00804-8 · Cited by 158 · see citing works

Structural basis for recognition of the AGNN tetraloop RNA fold by the double-stranded RNA-binding domain of Rnt1p RNase III

Wu, H., Henras, A. K., Chanfreau, G., & Feigon, J. F. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0402627101 · Cited by 155 · see citing works

The NMR structure of the 38 kDa U1A protein - PIE RNA complex reveals the basis of cooperativity in regulation of polyadenylation by human U1A protein.

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

Zinc-finger proteins

Berg, J. M. (1993) · Current Opinion in Structural Biology · doi:10.1016/0959-440x(93)90195-q · Cited by 133 · see citing works

Structural 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

New and old roles of the double-stranded RNA-binding domain

Doyle, M. (2002) · Journal of Structural Biology · doi:10.1016/s1047-8477(02)00544-0 · Cited by 78 · see citing works

Solution Structure of the Complex Formed by the Two N-terminal RNA-binding Domains of Nucleolin and a Pre-rRNA Target

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

In vitro analysis of the binding of ADAR2 to the pre-mRNA encoding the GluR-B R/G site

Öhman, M., KÄLLMAN, A. M., & Bass, B. (2000) · RNA · doi:10.1017/s1355838200000200 · Cited by 76 · see citing works

The Binding Selectivity of ADAR2's dsRBMs Contributes to RNA-Editing Selectivity

Stephens, O. M., Haudenschild, B. L., & Beal, P. A. (2004) · Chemistry & Biology · doi:10.1016/j.chembiol.2004.06.009 · Cited by 75 · see citing works

The p53-induced mouse zinc finger protein wig-1 binds double-stranded RNA with high affinity

Méndez‐Vidal, C. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.9.1991 · Cited by 61 · see citing works

A new α‐helical extension promotes RNA binding by the dsRBD of Rnt1p RNAse III

Leulliot, N., Quevillon‐Chéruel, S., Graille, M., TILBEURGH, H. V., Leeper, T. C., Godin, K. S., Edwards, T. E., Sigurdsson, S. T., Rozenkrants, N., Nagel, R. J., et al. (2004) · The EMBO Journal · doi:10.1038/sj.emboj.7600260 · Cited by 58 · see citing works

A Xenopus zinc finger protein that specifically binds dsRNA and RNA-DNA hybrids

Finerty, P. J., & Bass, B. (1997) · Journal of Molecular Biology · doi:10.1006/jmbi.1997.1177 · Cited by 45 · 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

From Birth to Death: The Complex Lives of Eukaryotic mRNAs

Moore, M. J. (2005) · Science · doi:10.1126/science.1111443 · Cited by 1,003 · see citing works

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 · see citing works

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 389 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 250 · see citing works

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 · see citing works

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 · see citing works

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 163 · see citing works

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 134 · see citing works

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 131 · see citing works

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 · see citing works

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 · see citing works

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 · 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

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 · see citing works

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 · 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

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 105 · see citing works

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 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

Roles of intrinsic disorder in protein–nucleic acid interactions

Dyson, H. J. (2011) · Molecular BioSystems · doi:10.1039/c1mb05258f · Cited by 95 · see citing works

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 · see citing works

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 · see citing works

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 93 · see citing works

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 · 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

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 82 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 64 · see citing works

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 · see citing works

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 · 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

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 52 · see citing works

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 · see citing works

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 · see citing works

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 49 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

Indirect Readout of tRNA for Aminoacylation

Perona, J. J., & Hou, Y. (2007) · Biochemistry · doi:10.1021/bi7014647 · Cited by 44 · see citing works

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 43 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 39 · see citing works

From Structure to Function of RNA Binding Domains

Lorkovic, Z. (2012) · CRC Press eBooks · doi:10.1201/9781498713368-15 · Cited by 38 · see citing works

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 35 · see citing works

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 · see citing works

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 · see citing works

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 32 · see citing works

A novel RNA pentaloop fold involved in targeting ADAR2

Štefl, R., & Allain, F. H. ‐. (2005) · RNA · doi:10.1261/rna.7276805 · Cited by 32 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 29 · see citing works

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 · see citing works

A zipcode unzipped: Figure 1.Preprint

Doyle, M., & Kiebler, M. A. (2012) · Genes & Development · doi:10.1101/gad.184945.111 · Cited by 26 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

Rrp47 and the function of the Sas10/C1D domain

Mitchell, P. (2010) · Biochemical Society Transactions · doi:10.1042/bst0381088 · Cited by 21 · see citing works

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 · see citing works

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 20 · see citing works

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 · see citing works

Archaea Signal Recognition Particle Shows the Way

Zwieb, C. W., & Bhuiyan, S. (2010) · Archaea · doi:10.1155/2010/485051 · Cited by 20 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 · see citing works

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 18 · see citing works

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 18 · see citing works

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 · see citing works

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 · see citing works

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 16 · see citing works

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 17 · see citing works

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 · see citing works

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 · see citing works

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 15 · see citing works

How proteins and RNA recognize each other

Varani, G. (2005) · FEBS Journal · doi:10.1111/j.1742-4658.2005.04701.x · Cited by 2 · see citing works

How Proteins Recognize RNA

Lamichhane, R. (2019) · Biological and medical physics, biomedical engineering · doi:10.1007/978-1-4939-9726-8_1

The RNA recognition motif, a plastic RNA‐binding platform to regulate post‐transcriptional gene expression

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

RNA RECOGNITION BY RNP PROTEINS DURING RNA PROCESSING

Varani, G., & Nagai, K. (1998) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.27.1.407 · Cited by 306 · see citing works

Integrated structural biology to unravel molecular mechanisms of protein-RNA recognition

Schlundt, A., Tants, J., & Sattler, M. (2017) · Methods · doi:10.1016/j.ymeth.2017.03.015 · Cited by 58 · see citing works