RNA‐binding proteins and post‐transcriptional gene regulation

Systematic Evolution of Ligands by Exponential Enrichment: RNA Ligands to Bacteriophage T4 DNA Polymerase

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Conserved Structures and Diversity of Functions of RNA-Binding Proteins

Burd, C. G., & Dreyfuss, G. (1994) · Science · doi:10.1126/science.8036511 · Cited by 1,878 · see citing works

Genome-Wide Survey of Human Alternative Pre-mRNA Splicing with Exon Junction Microarrays

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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

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

Demonstration That CFTR Is a Chloride Channel by Alteration of Its Anion Selectivity

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HuR and mRNA stability

Brennan, C. M., & Steitz*, J. A. (2001) · Cellular and Molecular Life Sciences · doi:10.1007/pl00000854 · Cited by 1,095 · see citing works

Regulation of cap-dependent translation by eIF4E inhibitory proteins

Richter, J. D., & Sonenberg, N. (2005) · Nature · doi:10.1038/nature03205 · Cited by 972 · see citing works

The spliceosome deposits multiple proteins 20–24 nucleotides upstream of mRNA exon–exon junctions

Hir, H. L., Izaurralde, E., Maquat, L. E., & Moore, M. J. (2000) · The EMBO Journal · doi:10.1093/emboj/19.24.6860 · Cited by 970 · see citing works

Recruitment of human muscleblind proteins to (CUG)n expansions associated with myotonic dystrophy

Miller, J. W., Urbinati, C. R., Teng‐umnuay, P., Stenberg, M. G., Byrne, B. J., Thornton, C. A., & Swanson, M. S. (2000) · The EMBO Journal · doi:10.1093/emboj/19.17.4439 · Cited by 937 · see citing works

Short GCG expansions in the PABP2 gene cause oculopharyngeal muscular dystrophy

Brais, B., Bouchard, J.-P., Xie, Y., Rochefort, D. L., Chrétien, N., Tomé, F. M. S., Lafrentére, R. G., Rommens, J. M., Uyama, E., Nohira, O., et al. (1998) · Nature Genetics · doi:10.1038/ng0298-164 · Cited by 804 · see citing works

Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs

Matera, A. G., Terns, R. M., & Terns, M. P. (2007) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2124 · Cited by 752 · see citing works

RNA stabilization by the AU‐rich element binding protein, HuR, an ELAV protein

Peng, S., Chen, C. A., Xu, N., & Shyu, A. (1998) · The EMBO Journal · doi:10.1093/emboj/17.12.3461 · Cited by 739 · see citing works

Spatial regulation of β-actin translation by Src-dependent phosphorylation of ZBP1

Hüttelmaier, S., Zenklusen, D., Lederer, M., Dictenberg, J., Lorenz, M., Meng, X.-H., Bassell, G., Condeelis, J., & Singer, R. (2005) · Nature · doi:10.1038/nature04115 · Cited by 681 · see citing works

RNA editing of AMPA receptor subunit GluR-B: A base-paired intron-exon structure determines position and efficiency

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Extensive Association of Functionally and Cytotopically Related mRNAs with Puf Family RNA-Binding Proteins in Yeast

Gerber, A. P., Herschlag, D., & Brown, P. O. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020079 · Cited by 651 · see citing works

The dsRNA protein kinase PKR: Virus and cell control

García, M. A., Meurs, E. F., & Esteban, M. (2007) · Biochimie · doi:10.1016/j.biochi.2007.03.001 · Cited by 644 · see citing works

CLIP: A method for identifying protein–RNA interaction sites in living cells

Ule, J., Jensen, K. B., Mele, A., & Darnell, R. B. (2005) · Methods · doi:10.1016/j.ymeth.2005.07.018 · Cited by 597 · see citing works

The multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a

Guil, S., & Cáceres, J. F. (2007) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1250 · Cited by 567 · see citing works

Characterization of a β-Actin mRNA Zipcode-Binding Protein

Ross, A. F., Oleynikov, Y., Kislauskis, E., Taneja, K. L., & Singer, R. H. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.4.2158 · Cited by 563 · see citing works

TAP, the human homolog of Mex67p, mediates CTE-dependent RNA export from the nucleus

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HuD, a paraneoplastic encephalomyelitis antigen, contains RNA-binding domains and is homologous to Elav and sex-lethal

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Comparative genomics and evolution of proteins involved in RNA metabolism

Anantharaman, V. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.7.1427 · Cited by 541 · see citing works

CPEB: a life in translation

Richter, J. D. (2007) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2007.04.004 · Cited by 526 · see citing works

The protein Aly links pre-messenger-RNA splicing to nuclear export in metazoans

Zhou, Z., Luo, M., Sträßer, K., Katahira, J., Hurt, E., & Reed, R. (2000) · Nature · doi:10.1038/35030160 · Cited by 517 · see citing works

A conserved RNA-binding protein that regulates sexual fates in the C. elegans hermaphrodite germ line

Zhang, B., Gallegos, M. E., Puoti, A., Durkin, E., Fields, S., Kimble, J. E., & Wickens, M. (1997) · Nature · doi:10.1038/37297 · Cited by 510 · see citing works

A three-hybrid system to detect RNA-protein interactions in vivo.

SenGupta, D. J., Zhang, B., Kraemer, B. C., Pochart, P., Fields, S., & Wickens, M. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.16.8496 · Cited by 510 · see citing works

Liver Disintegration in the Mouse Embryo Caused by Deficiency in the RNA-editing Enzyme ADAR1

Hartner, J. C., Schmittwolf, C., Kispert, A., Müller, A. M., Higuchi, M., & Seeburg, P. H. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m311347200 · Cited by 508 · see citing works

Stress-induced Apoptosis Associated with Null Mutation of ADAR1 RNA Editing Deaminase Gene

Wang, Q., Miyakoda, M., Yang, W., Khillan, J. S., Stachura, D. L., Weiss, M. J., & Nishikura, K. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m310162200 · Cited by 501 · 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

RNA-MEDIATED NEUROMUSCULAR DISORDERS

Ranum, L. P. W., & Cooper, T. A. (2006) · Annual Review of Neuroscience · doi:10.1146/annurev.neuro.29.051605.113014 · Cited by 472 · see citing works

The poly(C)-binding proteins: A multiplicity of functions and a search for mechanisms

Makeyev, A. V., & Liebhaber, S. A. (2002) · RNA · doi:10.1017/s1355838202024627 · Cited by 469 · see citing works

Expansion of a CUG trinucleotide repeat in the 3′ untranslated region of myotonic dystrophy protein kinase transcripts results in nuclear retention of transcripts

Davis, B. M., McCurrach, M. E., Taneja, K. L., Singer, R. H., & Housman, D. E. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.14.7388 · Cited by 468 · see citing works

Identification of a (CUG)n Triplet Repeat RNA-Binding Protein and Its Expression in Myotonic Dystrophy

Timchenko, L., Miller, J. W., Timchenko, N. A., DeVore, D. R., Datar, K. V., Lin, L., Roberts, R., Caskey, C. T., & Swanson, M. S. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.22.4407 · Cited by 465 · see citing works

Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease

Mandel, C. R., Kaneko, S., Zhang, H., Gebauer, D., Vethantham, V., Manley, J. L., & Tong, L. (2006) · Nature · doi:10.1038/nature05363 · Cited by 458 · see citing works

CPEB is a specificity factor that mediates cytoplasmic polyadenylation during Xenopus oocyte maturation

Hake, L. E., & Richter, J. D. (1994) · Cell · doi:10.1016/0092-8674(94)90547-9 · Cited by 454 · see citing works

Increased Steady-State Levels of CUGBP1 in Myotonic Dystrophy 1 Are Due to PKC-Mediated Hyperphosphorylation

Kuyumcu-Martinez, N. M., Wang, G., & Cooper, T. A. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.07.027 · Cited by 445 · see citing works

The Mex67p‐mediated nuclear mRNA export pathway is conserved from yeast to human

Katahira, J., Sträßer, K., Podtelejnikov, A. V., Mann, M., Jung, J. U., & Hurt, E. (1999) · The EMBO Journal · doi:10.1093/emboj/18.9.2593 · Cited by 441 · see citing works

Structure of the Exon Junction Core Complex with a Trapped DEAD-Box ATPase Bound to RNA

Andersen, C. B. F., Ballut, L., Johansen, J., Chamieh, H., Nielsen, K. H., Oliveira, C. L. P., Pedersen, J. S., Séraphin, B., Hir, H. L., & Andersen, G. R. (2006) · Science · doi:10.1126/science.1131981 · Cited by 437 · see citing works

Mechanistic links between nonsense-mediated mRNA decay and pre-mRNA splicing in mammalian cells

Lejeune, F., & Maquat, L. E. (2005) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2005.03.002 · Cited by 430 · see citing works

The Crystal Structure of the Exon Junction Complex Reveals How It Maintains a Stable Grip on mRNA

Bono, F., Ebert, J., Lorentzen, E., & Conti, E. (2006) · Cell · doi:10.1016/j.cell.2006.08.006 · Cited by 423 · see citing works

Reversible cross-linking combined with immunoprecipitation to study RNA–protein interactions in vivo

Niranjanakumari, S. (2002) · Methods · doi:10.1016/s1046-2023(02)00021-x · Cited by 410 · see citing works

Splicing enhances translation in mammalian cells: an additional function of the exon junction complexPreprint

Nott, A., Hir, H. L., & Moore, M. J. (2004) · Genes & Development · doi:10.1101/gad.1163204 · Cited by 408 · see citing works

Maskin Is a CPEB-Associated Factor that Transiently Interacts with eIF-4E

Stebbins-Boaz, B., Cao, Q., de Moor, C. D., Méndez, R., & Richter, J. (1999) · Molecular Cell · doi:10.1016/s1097-2765(00)80230-0 · Cited by 404 · see citing works

REF, an evolutionarily conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export

Stutz, F., Bachi, A., Doerks, T., Kos‐Braun, I. C., Séraphin, B., Wilm, M. S., Peer Bork, B., & Izaurralde, E. (2000) · RNA · doi:10.1017/s1355838200000078 · Cited by 382 · see citing works

A-to-I Pre-mRNA Editing in Drosophila Is Primarily Involved in Adult Nervous System Function and Integrity

Palladino, M. J., Keegan, L. P., O’Connell, M. A., & Reenan, R. A. (2000) · Cell · doi:10.1016/s0092-8674(00)00049-0 · Cited by 379 · see citing works

Nervous System Targets of RNA Editing Identified by Comparative Genomics

Hoopengardner, B., Bhalla, T., Staber, C., & Reenan, R. (2003) · Science · doi:10.1126/science.1086763 · Cited by 376 · see citing works

Human, Drosophila, and C.elegans TDP43: Nucleic Acid Binding Properties and Splicing Regulatory Function

Ayala, Y. M., Pantano, S., D’Ambrogio, A., Buratti, E., Brindisi, A., Marchetti, C., Romano, M., & Baralle, F. E. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.02.038 · Cited by 375 · see citing works

Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis

Jurica, M. S., Licklider, L. J., Gygi, S. P., Grigorieff, N., & Moore, M. J. (2002) · RNA · doi:10.1017/s1355838202021088 · Cited by 370 · see citing works

Evidence for reassociation of RNA-binding proteins after cell lysis: Implications for the interpretation of immunoprecipitation analyses

Mili, S., & STEITZ, J. A. (2004) · RNA · doi:10.1261/rna.7151404 · Cited by 369 · see citing works

Quality control of mRNA 3′-end processing is linked to the nuclear exosome

Hilleren, P. J., McCarthy, T., Rosbash, M., Parker, R., & Jensen, T. H. (2001) · Nature · doi:10.1038/35097110 · Cited by 364 · see citing works

An eIF4AIII-containing complex required for mRNA localization and nonsense-mediated mRNA decay

Palacios, I. M., Gatfield, D., Johnston, D. S., & Izaurralde, E. (2004) · Nature · doi:10.1038/nature02351 · Cited by 362 · see citing works

Asymmetric Accumulation of Ash1p in Postanaphase Nuclei Depends on a Myosin and Restricts Yeast Mating-Type Switching to Mother Cells

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The exon junction core complex is locked onto RNA by inhibition of eIF4AIII ATPase activity

Ballut, L., Marchadier, B., Baguet, A., Tomasetto, C., Séraphin, B., & Hir, H. L. (2005) · Nature Structural & Molecular Biology · doi:10.1038/nsmb990 · Cited by 357 · see citing works

Symplekin and xGLD-2 Are Required for CPEB-Mediated Cytoplasmic Polyadenylation

Barnard, D. C., Ryan, K., Manley, J. L., & Richter, J. D. (2004) · Cell · doi:10.1016/j.cell.2004.10.029 · Cited by 334 · see citing works

Pre-mRNA Splicing Imprints mRNA in the Nucleus with a Novel RNA-Binding Protein that Persists in the Cytoplasm

Kataoka, N., Yong, J., Kim, V. N., Velázquez, F., Perkinson, R. A., Wang, F., & Dreyfuss, G. (2000) · Molecular Cell · doi:10.1016/s1097-2765(00)00065-4 · Cited by 331 · see citing works

HuR binding to cytoplasmic mRNA is perturbed by heat shock

Gallouzi, I., Brennan, C. M., Stenberg, M. G., Swanson, M. S., Eversole, A., Maizels, N., & STEITZ, J. A. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.7.3073 · Cited by 326 · see citing works

Physical change in cytoplasmic messenger ribonucleoproteins in cells treated with inhibitors of mRNA transcription.

Dreyfuss, G., Adam, S. A., & Choi, Y. D. (1984) · Molecular and Cellular Biology · doi:10.1128/mcb.4.3.415 · Cited by 326 · see citing works

Nova, the paraneoplastic Ri antigen, is homologous to an RNA-binding protein and is specifically expressed in the developing motor system

Buckanovich, R. J., Posner, J. B., & Darnell, R. B. (1993) · Neuron · doi:10.1016/0896-6273(93)90077-5 · Cited by 318 · see citing works

Opposing polymerase-deadenylase activities regulate cytoplasmic polyadenylation.

Kim, J. H., & Richter, J. (2006) · Molecules and Cells · doi:10.1016/j.molcel.2006.08.016 · Cited by 305 · see citing works

Role of the Nonsense-Mediated Decay Factor hUpf3 in the Splicing-Dependent Exon-Exon Junction Complex

Kim, V. N., Kataoka, N., & Dreyfuss, G. (2001) · Science · doi:10.1126/science.1062829 · Cited by 299 · see citing works

Why is Hu where? Shuttling of early-response-gene messenger RNA subsets

Keene, J. D. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.1.5 · Cited by 294 · see citing works

3′-End processing of pre-mRNA in eukaryotes

Wahle, E., & Rüegsegger, U. (1999) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.1999.tb00400.x · Cited by 294 · see citing works

eIF4A3 is a novel component of the exon junction complex

CHAN, C. C., Dostie, J., Diem, M. D., Feng, W., Mann, M., Rappsilber, J., & Dreyfuss, G. (2004) · RNA · doi:10.1261/rna.5230104 · Cited by 292 · see citing works

Y14 and hUpf3b Form an NMD-Activating Complex

Gehring, N. H., Neu‐Yilik, G., Schell, T., Hentze, M. W., & Kulozik, A. E. (2003) · Molecular Cell · doi:10.1016/s1097-2765(03)00142-4 · Cited by 291 · see citing works

Identification of alternative splicing regulators by RNA interference in Drosophila

Park, J. W., Parisky, K. M., Celotto, A. M., Reenan, R. A., & Graveley, B. R. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0407004101 · Cited by 290 · see citing works

Arginine methylation facilitates the nuclear export of hnRNP proteinsPreprint

Shen, E. C., Henry, M. F., Weiss, V. H., Valentini, S. R., Silver, P. A., & Lee, M. S. (1998) · Genes & Development · doi:10.1101/gad.12.5.679 · Cited by 289 · see citing works

Editor meets silencer: crosstalk between RNA editing and RNA interference

Nishikura, K. (2006) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2061 · Cited by 281 · see citing works

eIF4AIII binds spliced mRNA in the exon junction complex and is essential for nonsense-mediated decay

Shibuya, T., Tange, T. Ø., Sonenberg, N., & Moore, M. J. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb750 · Cited by 274 · see citing works

Nuclear mRNA Export Requires Complex Formation between Mex67p and Mtr2p at the Nuclear Pores

Santos-Rosa, H., Moreno, H., Simos, G., Segref, A., Fahrenkrog, B., Panté, N., & Hurt, E. (1998) · Molecular and Cellular Biology · doi:10.1128/mcb.18.11.6826 · Cited by 264 · see citing works

Mutations of the RNA-Specific Adenosine Deaminase Gene (DSRAD) Are Involved in Dyschromatosis Symmetrica Hereditaria

Miyamura, Y., Suzuki, T., Kono, M., Inagaki, K., Ito, S., Suzuki, N., & Tomita, Y. (2003) · The American Journal of Human Genetics · doi:10.1086/378209 · Cited by 259 · see citing works

REF proteins mediate the export of spliced and unspliced mRNAs from the nucleus

Rodrigues, J. P., Rode, M., Gatfield, D., Blencowe, B. J., Carmo‐Fonseca, M., & Izaurralde, E. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.98.3.1030 · Cited by 250 · see citing works

Structure of Pumilio Reveals Similarity between RNA and Peptide Binding Motifs

Edwards, T. A., Pyle, S. E., Wharton, R. P., & Aggarwal, A. K. (2001) · Cell · doi:10.1016/s0092-8674(01)00318-x · Cited by 250 · see citing works

Crystal 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

Magoh, a human homolog of Drosophila mago nashi protein, is a component of the splicing‐dependent exon–exon junction complex

Kataoka, N., Diem, M. D., Kim, V. N., et al. (2001) · The EMBO Journal · doi:10.1093/emboj/20.22.6424 · Cited by 242 · see citing works

Engineering RNA sequence specificity of Pumilio repeats

Cheong, C.-G., & Hall, T. M. T. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0606294103 · Cited by 232 · see citing works

Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome

Keene, J. D. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.111145598 · Cited by 230 · see citing works

Real-Time Visualization of ZBP1 Association with β-Actin mRNA during Transcription and Localization

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Dissolution of the maskin–eIF4E complex by cytoplasmic polyadenylation and poly(A)‐binding protein controls cyclin B1 mRNA translation and oocyte maturation

Cao, Q., & Richter, J. D. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf353 · Cited by 219 · see citing works

PKR—A protein kinase regulated by double-stranded RNA

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Translation Is Required to Remove Y14 from mRNAs in the Cytoplasm

Dostie, J., & Dreyfuss, G. (2002) · Current Biology · doi:10.1016/s0960-9822(02)00902-8 · Cited by 215 · see citing works

She2p, a novel RNA‐binding protein tethers ASH1 mRNA to the Myo4p myosin motor via She3p

Böhl, F., Kruse, C., Frank, A., Ferring, D., & Jansen, R. (2000) · The EMBO Journal · doi:10.1093/emboj/19.20.5514 · Cited by 209 · see citing works

Characterisation of Two Major Cellular Poly(rC)-Binding Human Proteins, Each Containing Three K-homologous (KH) Domains

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Characterization of heterogeneous nuclear RNA-protein complexes in vivo with monoclonal antibodies.

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The protein Mago provides a link between splicing and mRNA localization

Hir, H. L., Gatfield, D., Kos‐Braun, I. C., et al. (2001) · EMBO Reports · doi:10.1093/embo-reports/kve245 · Cited by 204 · see citing works

An interaction between U2AF 65 and CF Im links the splicing and 3′ end processing machineries

Millevoi, S., Loulergue, C., Dettwiler, S., Karaa, Z. S., Keller, W., Antoniou, M. N., & Vagner, S. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7601331 · Cited by 203 · see citing works

Direct Interactions between Subunits of CPSF and the U2 snRNP Contribute to the Coupling of Pre-mRNA 3′ End Processing and Splicing

Kyburz, A., Friedlein, A., Langen, H., & Keller, W. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.05.037 · Cited by 198 · see citing works

A nuclear translation-like factor eIF4AIII is recruited to the mRNA during splicing and functions in nonsense-mediated decay

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Evidence that polyadenylation factor CPSF-73 is the mRNA 3′ processing endonuclease

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The Y14 protein communicates to the cytoplasm the position of exon–exon junctions

Kim, V. N., Yong, J., Kataoka, N., Abel, L., Diem, M. D., & Dreyfuss, G. (2001) · The EMBO Journal · doi:10.1093/emboj/20.8.2062 · Cited by 181 · see citing works

mRNA polyadenylation and its coupling to other RNA processing reactions and to transcription

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

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Specificity of RNA Binding by CPEB: Requirement for RNA Recognition Motifs and a Novel Zinc Finger

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Purification of the cleavage and polyadenylation factor involved in the 3'-processing of messenger RNA precursors.

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ADAR Gene Family and A-to-I RNA Editing: Diverse Roles in Posttranscriptional Gene Regulation

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