HITS-CLIP: panoramic views of protein-RNA regulation in living cells

Alternative isoform regulation in human tissue transcriptomes

Wang, E. T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S. F., Schroth, G. P., & Burge, C. B. (2008) · Nature · doi:10.1038/nature07509 · Cited by 5,181 · see citing works

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. S., & Weissman, J. S. (2009) · Science · doi:10.1126/science.1168978 · Cited by 3,853 · see citing works

The impact of microRNAs on protein output

Baek, D., Villén, J., Shin, C., Camargo, F. D., Gygi, S. P., & Bartel, D. P. (2008) · Nature · doi:10.1038/nature07242 · Cited by 3,592 · see citing works

Widespread changes in protein synthesis induced by microRNAs

Selbach, M., Schwanhäusser, B., Thierfelder, N., Fang, Z., Khanin, R., & Rajewsky, N. (2008) · Nature · doi:10.1038/nature07228 · Cited by 3,429 · see citing works

Genome-Wide Mapping of in Vivo Protein-DNA Interactions

Johnson, D. S., Mortazavi, A., Myers, R. M., & Wold, B. (2007) · Science · doi:10.1126/science.1141319 · Cited by 2,927 · see citing works

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

Hafner, M., Landthaler, M., Burger, L., Khorshid, M., Hausser, J., Berninger, P., Rothballer, A., Ascano, M., Jungkamp, A.-C., Munschauer, M., et al. (2010) · Cell · doi:10.1016/j.cell.2010.03.009 · Cited by 2,873 · see citing works

MEME: discovering and analyzing DNA and protein sequence motifs

Bailey, T. L., Williams, N., Misleh, C., & Li, W. W. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl198 · Cited by 2,671 · see citing works

Expansion of the eukaryotic proteome by alternative splicing

Nilsen, T. W., & Graveley, B. R. (2010) · Nature · doi:10.1038/nature08909 · Cited by 2,172 · see citing works

Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps

Chi, S. W., Zang, J. B., Mele, A., & Darnell, R. B. (2009) · Nature · doi:10.1038/nature08170 · Cited by 1,791 · see citing works

Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

Mayr, C., & Bartel, D. P. (2009) · Cell · doi:10.1016/j.cell.2009.06.016 · Cited by 1,613 · see citing works

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

Licatalosi, D. D., Mele, A., Fak, J. J., Ule, J., Kayikci, M., Chi, S. W., Clark, T. A., Schweitzer, A. C., Blume, J. E., Wang, X., et al. (2008) · Nature · doi:10.1038/nature07488 · Cited by 1,352 · see citing works

Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites

Sandberg, R., Neilson, J. R., Sarma, A., Sharp, P. A., & Burge, C. B. (2008) · Science · doi:10.1126/science.1155390 · Cited by 1,349 · see citing works

Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches

Chen, M., & Manley, J. L. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2777 · Cited by 1,284 · see citing works

RNA and Disease

Cooper, T. A., Wan, L., & Dreyfuss, G. (2009) · Cell · doi:10.1016/j.cell.2009.02.011 · Cited by 1,152 · see citing works

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

König, J., Zarnack, K., Rot, G., Curk, T., Kayikci, M., Zupan, B., Turner, D. J., Luscombe, N. M., & Ule, J. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1838 · Cited by 1,126 · see citing works

CLIP Identifies Nova-Regulated RNA Networks in the Brain

Ule, J., Jensen, K. B., Ruggiu, M., Mele, A., Ule, A., & Darnell, R. B. (2003) · Science · doi:10.1126/science.1090095 · Cited by 1,120 · see citing works

Microarray identification of FMRP-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome

Brown, V., Jin, P., Ceman, S., Darnell, J. C., O'Donnell, W. T., Tenenbaum, S. A., Jin, X., Feng, Y., Wilkinson, K. D., Keene, J. D., et al. (2001) · Cell · doi:10.1016/s0092-8674(01)00568-2 · Cited by 1,109 · see citing works

Fragile X Syndrome: Loss of Local mRNA Regulation Alters Synaptic Development and Function

Bassell, G. J., & Warren, S. T. (2008) · Neuron · doi:10.1016/j.neuron.2008.10.004 · Cited by 1,051 · see citing works

mRNA localization: Gene expression in the spatial dimension

Martin, K. C., & Ephrussi, A. (2009) · Cell · doi:10.1016/j.cell.2009.01.044 · Cited by 1,048 · see citing works

Predictive Identification of Exonic Splicing Enhancers in Human Genes

Fairbrother, W. G., Yeh, R., Sharp, P. A., & Burge, C. B. (2002) · Science · doi:10.1126/science.1073774 · Cited by 1,020 · see citing works

Fragile X mental retardation protein targets G quartet mRNAs important for neuronal function

Darnell, J. C., Jensen, K. B., Jin, P., Brown, V., Warren, S. T., & Darnell, R. B. (2001) · Cell · doi:10.1016/s0092-8674(01)00566-9 · Cited by 952 · see citing works

Deciphering the splicing code

Barash, Y., Calarco, J. A., Gao, W., Pan, Q., Wang, X., Ofer Shai, A., Blencowe, B. J., & Frey, B. J. (2010) · Nature · doi:10.1038/nature09000 · Cited by 891 · see citing works

Pre-mRNA Processing Reaches Back toTranscription and Ahead to Translation

Moore, M. J., & Proudfoot, N. J. (2009) · Cell · doi:10.1016/j.cell.2009.02.001 · Cited by 835 · see citing works

RNA processing and its regulation: global insights into biological networks

Licatalosi, D. D., & Darnell, R. B. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2673 · Cited by 760 · see citing works

An integrated software system for analyzing ChIP-chip and ChIP-seq data

Ji, H., Jiang, H., Ma, W., Johnson, D. S., Myers, R., & Wong, W. H. (2008) · Nature Biotechnology · doi:10.1038/nbt.1505 · Cited by 716 · see citing works

Lin-28 interaction with the Let-7 precursor loop mediates regulated microRNA processing

Newman, M. A., Thomson, J. M., & Hammond, S. M. (2008) · RNA · doi:10.1261/rna.1155108 · Cited by 691 · see citing works

Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System

Hogan, D. J., Riordan, D. P., Gerber, A. P., Herschlag, D., & Brown, P. O. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060255 · Cited by 609 · see citing works

In Vivo Cross-Linking and Immunoprecipitation for Studying Dynamic Protein:DNA Associations in a Chromatin Environment

Kuo, M., & Allis, C. D. (1999) · Methods · doi:10.1006/meth.1999.0879 · Cited by 601 · 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

Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex

Wang, Y., Juranek, S., Li, H., Sheng, G., Tuschl, T., & Patel, D. J. (2008) · Nature · doi:10.1038/nature07666 · Cited by 577 · see citing works

A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons

Boutz, P. L., Stoilov, P., Li, Q., Lin, C.-H., Chawla, G., Ostrow, K., Shiue, L., Ares, M., & Black, D. L. (2007) · Genes & Development · doi:10.1101/gad.1558107 · Cited by 577 · see citing works

An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells

Yeo, G. W., Coufal, N. G., Liang, T. Y., Peng, G. E., Fu, X.-D., & Gage, F. H. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1545 · Cited by 572 · 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

An RNA map predicting Nova-dependent splicing regulation

Ule, J., Stefani, G., Mele, A., Ruggiu, M., Wang, X., Taneri, B., Gaasterland, T., Blencowe, B. J., & Darnell, R. B. (2006) · Nature · doi:10.1038/nature05304 · Cited by 528 · see citing works

Nova regulates brain-specific splicing to shape the synapse

Ule, J., Ule, A., Spencer, J., Williams, A., Hu, J.-S., Cline, M., Wang, H., Clark, T., Fraser, C., Ruggiu, M., et al. (2005) · Nature Genetics · doi:10.1038/ng1610 · Cited by 509 · see citing works

A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart

Kalsotra, A., Xiao, X., Ward, A. J., Castle, J. C., Johnson, J. M., Burge, C. B., & Cooper, T. A. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0809045105 · Cited by 508 · see citing works

Genome-wide Analysis of PTB-RNA Interactions Reveals a Strategy Used by the General Splicing Repressor to Modulate Exon Inclusion or Skipping

Xue, Y., Zhou, Y., Wu, T., Zhu, T., Ji, X., Kwon, Y.-S., Zhang, C., Yeo, G., Black, D. L., Sun, H., et al. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.12.003 · Cited by 469 · see citing works

Formaldehyde-mediated DNA-protein crosslinking: a probe for in vivo chromatin structures.

Solomon, M. J., & Varshavsky, A. J. (1985) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.82.19.6470 · Cited by 462 · see citing works

The Centrality of RNA

Sharp, P. A. (2009) · Cell · doi:10.1016/j.cell.2009.02.007 · Cited by 452 · see citing works

Direct RNA sequencing

Ozsolak, F., Platt, A. R., Jones, D. R., Reifenberger, J. G., Sass, L. E., McInerney, P., Thompson, J. F., Bowers, J., Jarosz, M., & Milos, P. M. (2009) · Nature · doi:10.1038/nature08390 · Cited by 433 · see citing works

Nova-1 Regulates Neuron-Specific Alternative Splicing and Is Essential for Neuronal Viability

Jensen, K. B., Dredge, B. K., Stefani, G., Zhong, R., Buckanovich, R. J., Okano, H. J., Yang, Y. Y. L., & Darnell, R. B. (2000) · Neuron · doi:10.1016/s0896-6273(00)80900-9 · Cited by 426 · see citing works

Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA

Hendrickson, D. G., Hogan, D. J., McCullough, H. L., Myers, J. W., Herschlag, D., Ferrell, J. E., & Brown, P. O. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000238 · Cited by 418 · 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

A new function for the fragile X mental retardation protein in regulation of PSD-95 mRNA stability

Zalfa, F., Eleuteri, B., Dickson, K. S., Mercaldo, V., Rubeis, S. D., di Penta, A., Tabolacci, E., Chiurazzi, P., Neri, G., Grant, S. G. N., et al. (2007) · Nature Neuroscience · doi:10.1038/nn1893 · Cited by 364 · see citing works

Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs

Granneman, S., Kudla, G., Petfalski, E., & Tollervey, D. W. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0901997106 · Cited by 364 · see citing works

A sensitive method for the determination of protein-DNA binding specificities

Pollock, R. M., & Treisman, R. (1990) · Nucleic Acids Research · doi:10.1093/nar/18.21.6197 · Cited by 348 · see citing works

Defining the Sequence Specificity of DNA-Binding Proteins by Selecting Binding Sites from Random-Sequence Oligonucleotides: Analysis of Yeast GCN4 Protein

Oliphant, A., Brandl, C. J., & Struhl, K. (1989) · Molecular and Cellular Biology · doi:10.1128/mcb.9.7.2944-2949.1989 · Cited by 338 · see citing works

Posttranscriptional Regulation of miRNAs Harboring Conserved Terminal Loops

Michlewski, G., Guil, S., Semple, C. A. M., & Cáceres, J. F. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.10.013 · Cited by 337 · see citing works

Aberrant alternative splicing and extracellular matrix gene expression in mouse models of myotonic dystrophy

Du, H., Cline, M. S., Osborne, R. J., Tuttle, D. L., Clark, T. A., Donohue, J. P., Hall, M. P., Shiue, L., Swanson, M. S., Thornton, C. A., et al. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1720 · Cited by 332 · 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

A vertebrate RNA-binding protein Fox-1 regulates tissue-specific splicing via the pentanucleotide GCAUG

Jin, Y., Suzuki, H., Maegawa, S., Endo, H., Sugano, S., Hashimoto, K., Yasuda, K., & Inoue, K. (2003) · The EMBO Journal · doi:10.1093/emboj/cdg089 · Cited by 311 · see citing works

DNA Damage Regulates Alternative Splicing through Inhibition of RNA Polymerase II Elongation

Muñoz, M. J., Perez-Santángelo, S., Paronetto, M. P., de la Mata, M., Pelisch, F., Boireau, S., Glover-Cutter, K. M., Ben-Dov, C., Blaustein, M., Lozano, J. J., et al. (2009) · Cell · doi:10.1016/j.cell.2009.03.010 · Cited by 310 · see citing works

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcriptsPreprint

Sanford, J. R., Wang, X., Mort, M. E., VanDuyn, N., Cooper, D. N., Mooney, S. D., Edenberg, H. J., & Liu, Y. (2008) · Genome Research · doi:10.1101/gr.082503.108 · Cited by 309 · see citing works

A biochemical approach to identifying microRNA targets

Karginov, F. V., Conaco, C., Xuan, Z., Schmidt, B. H., Parker, J. S., Mandel, G., & Hannon, G. J. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0709971104 · Cited by 302 · see citing works

Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2

Zhang, C., Zhang, Z., Castle, J., Sun, S., Johnson, J., Krainer, A. R., & Zhang, M. Q. (2008) · Genes & Development · doi:10.1101/gad.1703108 · Cited by 300 · see citing works

Integrative Modeling Defines the Nova Splicing-Regulatory Network and Its Combinatorial Controls

Zhang, C., Frias, M. A., Mele, A., Ruggiu, M., Eom, T., Marney, C. B., Wang, H., Licatalosi, D. D., Fak, J. J., & Darnell, R. B. (2010) · Science · doi:10.1126/science.1191150 · Cited by 294 · see citing works

Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans

Zisoulis, D. G., Lovci, M., Wilbert, M. L., Hutt, K. R., Liang, T. Y., Pasquinelli, A. E., & Yeo, G. W.-M. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1745 · Cited by 290 · see citing works

Kissing complex RNAs mediate interaction between the Fragile-X mental retardation protein KH2 domain and brain polyribosomes

Darnell, J. C., Fraser, C. E., Mostovetsky, O., Stefani, G., Jones, T. A., Eddy, S. R., & Darnell, R. B. (2005) · Genes & Development · doi:10.1101/gad.1276805 · Cited by 287 · see citing works

SRprises along a Messenger’s Journey

Huang, Y., & STEITZ, J. A. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.02.020 · Cited by 280 · see citing works

RNA Gain-of-Function in Spinocerebellar Ataxia Type 8

Daughters, R. S., Tuttle, D. L., Gao, W., Ikeda, Y., Moseley, M. L., Ebner, T. J., Swanson, M. S., & Ranum, L. P. W. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000600 · Cited by 278 · see citing works

Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays

Tenenbaum, S. A. (2002) · Methods · doi:10.1016/s1046-2023(02)00022-1 · Cited by 269 · see citing works

From DNA sequence to transcriptional behaviour: a quantitative approach

Segal, E., & Widom, J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2591 · Cited by 262 · see citing works

Detecting protein-DNA interactions in vivo: distribution of RNA polymerase on specific bacterial genes.

Gilmour, D. S., & Lis, J. T. (1984) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.81.14.4275 · Cited by 260 · see citing works

The Neuronal RNA Binding Protein Nova-1 Recognizes Specific RNA Targets In Vitro and In Vivo

Buckanovich, R. J., & Darnell, R. B. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.6.3194 · Cited by 259 · see citing works

Isolation of microRNA targets by miRNP immunopurification

Easow, G., Teleman, A. A., & Cohen, S. M. (2007) · RNA · doi:10.1261/rna.563707 · Cited by 252 · see citing works

Splicing Regulation in Neurologic Disease

Licatalosi, D. D., & Darnell, R. B. (2006) · Neuron · doi:10.1016/j.neuron.2006.09.017 · Cited by 250 · see citing works

The neuronal RNA-binding protein Nova-2 is implicated as the autoantigen targeted in POMA patients with dementia

Yang, Y. Y. L., Yin, G. L., & Darnell, R. B. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.22.13254 · Cited by 219 · see citing works

RNA binding activity of the recessive parkinsonism protein DJ-1 supports involvement in multiple cellular pathways

van der Brug, M. P., Blackinton, J. G., Chandran, J. S., Hao, L.-Y., Lal, A., Mazan-Mamczarz, K., Martindale, J. L., Xie, C., Ahmad, R., Craig, K. J. T., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0708518105 · Cited by 214 · see citing works

Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein.

Oliphant, A., Brandl, C. J., & Struhl, K. (1989) · Molecular and Cellular Biology · doi:10.1128/mcb.9.7.2944 · Cited by 210 · see citing works

Myc‐Max heterodimers activate a DEAD box gene and interact with multiple E box‐related sites in vivo.

Grandori, C., Mac, J., Siebelt, F., Ayer, D. E., & Eisenman, R. N. (1996) · The EMBO Journal · doi:10.1002/j.1460-2075.1996.tb00808.x · Cited by 208 · see citing works

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

Dreyfuss, G., Choi, Y. D., & Adam, S. A. (1984) · Molecular and Cellular Biology · doi:10.1128/mcb.4.6.1104 · Cited by 204 · see citing works

Dose dependent decrease in extractability of DNA from bacteria following irradiation with ultraviolet light or with visible light plus dye

Smith, K. C. (1962) · Biochemical and Biophysical Research Communications · doi:10.1016/0006-291x(62)90255-3 · Cited by 198 · see citing works

RNA binding proteins and the regulation of neuronal synaptic plasticity

Ule, J., & Darnell, R. B. (2006) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2006.01.003 · Cited by 177 · see citing works

Nova2 Regulates Neuronal Migration through an RNA Switch in Disabled-1 Signaling

Yano, M., Hayakawa-Yano, Y., Mele, A., & Darnell, R. B. (2010) · Neuron · doi:10.1016/j.neuron.2010.05.007 · Cited by 176 · see citing works

Prp43 Bound at Different Sites on the Pre-rRNA Performs Distinct Functions in Ribosome Synthesis

Bohnsack, M. T., Martin, R., Granneman, S., Ruprecht, M., Schleiff, E., & Tollervey, D. W. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.09.039 · Cited by 175 · see citing works

Novel modes of splicing repression by PTB

Spellman, R., & Smith, C. W. J. (2006) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2005.12.003 · Cited by 160 · see citing works

Common Molecular Pathways Mediate Long-Term Potentiation of Synaptic Excitation and Slow Synaptic Inhibition

Huang, C. S., Shi, S.-H., Ule, J., Ruggiu, M., Barker, L. A., Darnell, R. B., Jan, Y. N., & Jan, L. Y. (2005) · Cell · doi:10.1016/j.cell.2005.07.033 · Cited by 157 · see citing works

The tetranucleotide UCAY directs the specific recognition of RNA by the Nova K-homology 3 domain

Jensen, K. B., Musunuru, K., Lewis, H. A., Burley, S. K., & Darnell, R. B. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.090553997 · Cited by 144 · see citing works

CLIP: Crosslinking and ImmunoPrecipitation of In Vivo RNA Targets of RNA-Binding Proteins

Jensen, K. B., & Darnell, R. B. (2008) · Methods in molecular biology · doi:10.1007/978-1-60327-475-3_6 · Cited by 143 · see citing works

U1-snRNP-A protein selects a ten nucleotide consensus sequence from a degenerate RNA pool presented in various structural contexts

Tsai, D. E., Harper, D. S., & Keene, J. D. (1991) · Nucleic Acids Research · doi:10.1093/nar/19.18.4931 · Cited by 143 · see citing works

Retinoic acid-gated sequence-specific translational control by RARα

Poon, M. M., & Chen, L. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0807740105 · Cited by 138 · see citing works

An intron with a constitutive transport element is retained in a Tap messenger RNA

Li, Y., Bor, Y.-C., Misawa, Y., Xue, Y., Rekosh, D. M., & Hammarskjöld, M. (2006) · Nature · doi:10.1038/nature05107 · Cited by 136 · see citing works

FMRP RNA targets: identification and validation

Darnell, J. C., Mostovetsky, O., & Darnell, R. B. (2005) · Genes Brain & Behavior · doi:10.1111/j.1601-183x.2005.00144.x · Cited by 132 · see citing works

Photo-induced joining of a transfer RNA with its cognate aminoacyl-transfer RNA synthetase

Schoemaker, H. J. P., & SCHIMMEL, P. R. (1974) · Journal of Molecular Biology · doi:10.1016/0022-2836(74)90112-0 · Cited by 132 · see citing works

Nova autoregulation reveals dual functions in neuronal splicing

Dredge, B. K., Stefani, G., Engelhard, C. C., & Darnell, R. B. (2005) · The EMBO Journal · doi:10.1038/sj.emboj.7600630 · Cited by 125 · see citing works

Crawling Out of the RNA World

Cech, T. R. (2009) · Cell · doi:10.1016/j.cell.2009.02.002 · Cited by 124 · see citing works

Nova Regulates GABA A Receptor γ2 Alternative Splicing via a Distal Downstream UCAU-Rich Intronic Splicing Enhancer

Dredge, B. K., & Darnell, R. B. (2003) · Molecular and Cellular Biology · doi:10.1128/mcb.23.13.4687-4700.2003 · Cited by 120 · see citing works

The RNA-binding protein Rrm4 is essential for polarity inUstilago maydisand shuttles along microtubules

Becht, P., König, J., & Feldbrügge, M. (2006) · Journal of Cell Science · doi:10.1242/jcs.03287 · Cited by 118 · see citing works

Rescuing Z ⁺ agrin splicing in <i>Nova</i> null mice restores synapse formation and unmasks a physiologic defect in motor neuron firing

Ruggiu, M., Herbst, R., Kim, N., Jevsek, M., Fak, J. J., Mann, M. A., Fischbach, G., Burden, S. J., & Darnell, R. B. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0813112106 · Cited by 113 · see citing works

Identification of Nuclear and Cytoplasmic mRNA Targets for the Shuttling Protein SF2/ASF

Sanford, J. R., Coutinho, P., Hackett, J. A., Wang, X., Ranahan, W. P., & Cáceres, J. F. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003369 · Cited by 113 · see citing works

Cross-linking of Deoxyribonucleic Acid to Protein following Ultra-Violet Irradiation of Different Cells

Alexander, P. M., & Moroson, H. (1962) · Nature · doi:10.1038/194882a0 · Cited by 106 · see citing works

The fungal RNA‐binding protein Rrm4 mediates long‐distance transport of ubi1 and rho3 mRNAs

König, J., Baumann, S. J., Koepke, J., Pohlmann, T., Zarnack, K., & Feldbrügge, M. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.145 · Cited by 99 · see citing works

Mechanisms of RNA-mediated Disease

O'Rourke, J. R., & Swanson, M. S. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.r800025200 · Cited by 96 · see citing works

MADS: A new and improved method for analysis of differential alternative splicing by exon-tiling microarrays

Xing, Y., Stoilov, P., Kapur, K., Han, A., Jiang, H., Shen, S., Black, D. L., & Wong, W. H. (2008) · RNA · doi:10.1261/rna.1070208 · Cited by 94 · see citing works

CLIP: Construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo

Wang, Z., Tollervey, J. R., Briese, M., Turner, D., & Ule, J. (2009) · Methods · doi:10.1016/j.ymeth.2009.02.021 · Cited by 90 · see citing works

Characterization of Heterogeneous Nuclear RNA-Protein Complexes In Vivo with Monoclonal Antibodies

Dreyfuss, G., Choi, Y. D., & Adam, S. A. (1984) · Molecular and Cellular Biology · doi:10.1128/mcb.4.6.1104-1114.1984 · Cited by 88 · see citing works

Rapid RNA sequencing: nucleases from Staphylococcus aureus and Neurospora crassa discriminate between uridine and cytidine

Krupp, G., & Gross, H. J. (1979) · Nucleic Acids Research · doi:10.1093/nar/6.11.3481 · Cited by 83 · see citing works

Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors

Gama‐Carvalho, M., Barbosa‐Morais, N. L., Brodsky, A. S., Silver, P. A., & Carmo‐Fonseca, M. (2006) · Genome biology · doi:10.1186/gb-2006-7-11-r113 · Cited by 79 · see citing works

[19] Intra-RNA and RNA—protein cross-linking techniques in Escherichia coli ribosomes

Brimacombe, R. L. C., Stiege, W., Kyriatsoulis, A., & Maly, P. (1988) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(88)64050-x · Cited by 75 · see citing works

Structure of nuclear ribonucleoprotein: identification of proteins in contact with poly(A)+ heterogeneous nuclear RNA in living HeLa cells.

Mayrand, S. H., Setyono, B., Greenberg, J. R., & Pederson, T. (1981) · The Journal of Cell Biology · doi:10.1083/jcb.90.2.380 · Cited by 75 · see citing works

[32] Immunoprecipitation of ribonucleoproteins using autoantibodies

STEITZ, J. A. (1989) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(89)80118-1 · Cited by 74 · see citing works

Nuclear ribonucleoprotein particles probed in living cells.

Mayrand, S. H., & Pederson, T. (1981) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.78.4.2208 · Cited by 74 · see citing works

A two-tracked approach to analyze RNA–protein crosslinking sites in native, nonlabeled small nuclear ribonucleoprotein particles

Urlaub, H. (2002) · Methods · doi:10.1016/s1046-2023(02)00020-8 · Cited by 71 · see citing works

The neuronal splicing factor Nova co-localizes with target RNAs in the dendrite

Racca, C. (2010) · Frontiers in Neural Circuits · doi:10.3389/neuro.04.005.2010 · Cited by 69 · see citing works

Post-Transcriptional Regulation of UV Induced TNF-α Expression

Leverkus, M., Yaar, M., Eller, M. S., Tang, E. H., & Gilchrest, B. A. (1998) · Journal of Investigative Dermatology · doi:10.1046/j.1523-1747.1998.00154.x · Cited by 69 · see citing works

UV Radiation Regulates Mi-2 through Protein Translation and Stability

Burd, C. J., Kinyamu, H. K., Miller, F. W., & Archer, T. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m805383200 · Cited by 65 · see citing works

Specificity of photochemical crosslinking in protein-nucleic acid complexes: identification of the interacting residues in RNase-pyrimidine nucleotide complex

Havron, A., & Sperling, J. M. (1977) · Biochemistry · doi:10.1021/bi00644a038 · Cited by 65 · see citing works

Heterogeneity of deoxynucleoprotein particles as evidenced by ultracentrifugation in cesium chloride density gradient

Ilyin, Y. V., & Georgiev, G. P. (1969) · Journal of Molecular Biology · doi:10.1016/0022-2836(69)90395-7 · Cited by 61 · see citing works

Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data

Wang, Y., Zhang, X., & Xia, Y. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp625 · Cited by 49 · see citing works

A role for a bacterial ortholog of the Ro autoantigen in starvation-induced rRNA degradation

Wurtmann, E. J., & Wolin, S. L. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000307107 · Cited by 45 · see citing works

A single C. elegans PUF protein binds RNA in multiple modes

Koh, Y. Y., Opperman, L., Stumpf, C. R., Mandan, A., Keleş, S., & Wickens, M. (2009) · RNA · doi:10.1261/rna.1545309 · Cited by 45 · see citing works

Evidence for RNA-RNA cross-link formation in Escherichia coli ribosomes

Zwieb, C. W., Ross, A., Rinke, J., Meinke, M., & Brimacombe, R. L. C. (1978) · Nucleic Acids Research · doi:10.1093/nar/5.8.2705 · Cited by 43 · see citing works

Direct cloning of DNA that interacts in vivo with a specific protein: application to RNA polymerase II and sites of pausing in Drosophila

Law, A. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.4.919 · Cited by 37 · see citing works

Developing Global Insight into RNA RegulationPreprint

Darnell, R. B. (2006) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2006.71.002 · Cited by 36 · see citing works

Feed-Forward Regulation of a Cell Fate Determinant by an RNA-Binding Protein Generates Asymmetry in Yeast

Wolf, J. J., Dowell, R. D., Mahony, S., Rabani, M., Gifford, D. K., & Fink, G. R. (2010) · Genetics · doi:10.1534/genetics.110.113944 · Cited by 36 · see citing works

Comparison of Femtosecond Laser and Continuous Wave UV Sources for Protein–Nucleic Acid Crosslinking

Fecko, C. J., Munson, K. M., Saunders, A., Sun, G., Begley, T. P., Lis, J. T., & Webb, W. W. (2007) · Photochemistry and Photobiology · doi:10.1111/j.1751-1097.2007.00179.x · Cited by 31 · see citing works

MIWI-independent small RNAs (MSY-RNAs) bind to the RNA-binding protein, MSY2, in male germ cells

Xu, M., Medvedev, S., Yang, J., & Hecht, N. B. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0903944106 · Cited by 26 · see citing works

Ultraviolet radiation (UVR) activates p38 MAP kinase and induces post‐transcriptional stabilization of the C/EBPδ mRNA in G0 growth arrested mammary epithelial cells

Li, B., Si, J., & DeWille, J. W. (2007) · Journal of Cellular Biochemistry · doi:10.1002/jcb.21554 · Cited by 22 · see citing works

RNA Processing: Redrawing the Map of Charted Territory

Corrionero, A., & Valcárcel, J. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.12.004 · Cited by 15 · see citing works

Site-specific crosslinking of human microRNPs to RNA targets

Kirino, Y., & Mourelatos, Z. P. (2008) · RNA · doi:10.1261/rna.1133808 · Cited by 13 · see citing works

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data

Li, J.-H., Liu, S., Zhou, H., Qu, L., & Yang, J.-H. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1248 · Cited by 5,587 · see citing works

FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism

Darnell, J. C., Van Driesche, S. J., Zhang, C., Hung, K. Y. S., Mele, A., Fraser, C. E., Stone, E. F., Chen, C., Fak, J. J., Chi, S. W., et al. (2011) · Cell · doi:10.1016/j.cell.2011.06.013 · Cited by 2,072 · see citing works

The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3

McHugh, C. A., Chen, C., Chow, A. Y., Surka, C., Tran, C., McDonel, P. E., Pandya‐Jones, A., Blanco, M. R., Burghard, C. P., Moradian, A., et al. (2015) · Nature · doi:10.1038/nature14443 · Cited by 1,163 · see citing works

Hfq and its constellation of RNA

Vogel, J., & Luisi, B. F. (2011) · Nature Reviews Microbiology · doi:10.1038/nrmicro2615 · Cited by 1,020 · see citing works

A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulationPreprint

Ke, S., Alemu, E. A., Mertens, C., Gantman, E. C., Fak, J. J., Mele, A., Haripal, B., Zucker-Scharff, I., Moore, M. J., Park, C. Y., et al. (2015) · Genes & Development · doi:10.1101/gad.269415.115 · Cited by 815 · see citing works

Functional consequences of developmentally regulated alternative splicing

Kalsotra, A., & Cooper, T. A. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3052 · Cited by 729 · see citing works

A network-biology perspective of microRNA function and dysfunction in cancer

Bracken, C. P., Scott, H. S., & Goodall, G. J. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.134 · Cited by 668 · see citing works

Protein–RNA interactions: new genomic technologies and perspectives

König, J., Zarnack, K., Luscombe, N. M., & Ule, J. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3141 · Cited by 555 · see citing works

Advances and Trends in Omics Technology Development

Dai, X., & Shen, L. (2022) · Frontiers in Medicine · doi:10.3389/fmed.2022.911861 · Cited by 567 · see citing works

The translation of translational control by FMRP: therapeutic targets for FXS

Darnell, J. C., & Klann, E. (2013) · Nature Neuroscience · doi:10.1038/nn.3379 · Cited by 491 · see citing works

Alternative Splicing in the Mammalian Nervous System: Recent Insights into Mechanisms and Functional Roles

Raj, B., & Blencowe, B. J. (2015) · Neuron · doi:10.1016/j.neuron.2015.05.004 · Cited by 475 · see citing works

The genomic binding sites of a noncoding RNA

Simon, M. D., Wang, C. I., Kharchenko, P. V., West, J. A., Chapman, B., Alekseyenko, A. A., Borowsky, M. L., Kuroda, M. I., & Kingston, R. E. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1113536108 · Cited by 444 · see citing works

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data

Zhang, C., & Darnell, R. B. (2011) · Nature Biotechnology · doi:10.1038/nbt.1873 · Cited by 405 · see citing works

The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest

Trendel, J., Schwarzl, T., Horos, R., Prakash, A., Bateman, A. G., Hentze, M. W., & Krijgsveld, J. (2018) · Cell · doi:10.1016/j.cell.2018.11.004 · Cited by 400 · see citing works

Global Mapping of Small RNA-Target Interactions in Bacteria

Melamed, S., Peer, A., Faigenbaum-Romm, R., Gatt, Y. E., Reiss, N., Bar, A., Altuvia, Y., Argaman, L., & Margalit, H. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.07.026 · Cited by 397 · see citing works

Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expressionPreprint

Lianoglou, S., Garg, V., Yang, J. L., Leslie, C. S., & Mayr, C. (2013) · Genes & Development · doi:10.1101/gad.229328.113 · Cited by 389 · see citing works

HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism

Weyn-Vanhentenryck, S. M., Mele, A., Yan, Q., Sun, S., Farny, N., Zhang, Z., Xue, C., Herre, M., Silver, P. A., Zhang, M. Q., et al. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.02.005 · Cited by 333 · see citing works

The neurogenetics of alternative splicing

Vuong, C. K., Black, D. L., & Zheng, S. (2016) · Nature Reviews Neuroscience · doi:10.1038/nrn.2016.27 · Cited by 340 · see citing works

An alternative mode of microRNA target recognition

Chi, S. W., Hannon, G. J., & Darnell, R. B. (2012) · Nature Structural &amp; Molecular Biology · doi:10.1038/nsmb.2230 · Cited by 328 · see citing works

Long noncoding RNAs: an emerging link between gene regulation and nuclear organization

Quinodoz, S. A., & Guttman, M. (2014) · Trends in Cell Biology · doi:10.1016/j.tcb.2014.08.009 · Cited by 316 · see citing works

Integrative Modeling Defines the Nova Splicing-Regulatory Network and Its Combinatorial Controls

Zhang, C., Frias, M. A., Mele, A., Ruggiu, M., Eom, T., Marney, C. B., Wang, H., Licatalosi, D. D., Fak, J. J., & Darnell, R. B. (2010) · Science · doi:10.1126/science.1191150 · Cited by 294 · see citing works

Global RNA recognition patterns of post‐transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo

Holmqvist, E., Wright, P. R., Li, L., Bischler, T., Barquist, L., Reinhardt, R., Backofen, R., & Vogel, J. (2016) · The EMBO Journal · doi:10.15252/embj.201593360 · Cited by 285 · see citing works

Understanding splicing regulation through RNA splicing maps

Witten, J. T., & Ule, J. (2011) · Trends in Genetics · doi:10.1016/j.tig.2010.12.001 · Cited by 276 · see citing works

EBV and human microRNAs co‐target oncogenic and apoptotic viral and human genes during latency

Riley, K. J.-L., Rabinowitz, G. S., Yario, T. A., Luna, J. M., Darnell, R. B., & STEITZ, J. A. (2012) · The EMBO Journal · doi:10.1038/emboj.2012.63 · Cited by 281 · see citing works

Competition between target sites of regulators shapes post-transcriptional gene regulation

Jens, M., & Rajewsky, N. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3853 · Cited by 255 · see citing works

Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis

Moore, M. J., Zhang, C., Gantman, E. C., Mele, A., Darnell, J. C., & Darnell, R. B. (2014) · Nature Protocols · doi:10.1038/nprot.2014.012 · Cited by 251 · see citing works

RIP: RNA Immunoprecipitation

Gagliardi, M., & Matarazzo, M. R. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-6380-5_7 · Cited by 247 · see citing works

TRIBE: Hijacking an RNA-Editing Enzyme to Identify Cell-Specific Targets of RNA-Binding Proteins

McMahon, A., Rahman, R., Jin, H., Shen, J. L., Fieldsend, A., Luo, W., & Rosbash, M. (2016) · Cell · doi:10.1016/j.cell.2016.03.007 · Cited by 241 · see citing works

Dissecting the expression landscape of RNA-binding proteins in human cancers

Kechavarzi, B., & Janga, S. C. (2014) · Genome biology · doi:10.1186/gb-2014-15-1-r14 · Cited by 242 · see citing works

Sensing of viral and endogenous RNA by ZBP1/DAI induces necroptosis

Maelfait, J., Liverpool, L., Bridgeman, A., Ragan, K. B., Upton, J. W., & Rehwinkel, J. (2017) · The EMBO Journal · doi:10.15252/embj.201796476 · Cited by 237 · see citing works

The importance of CELF control: molecular and biological roles of the CUG‐BP, Elav‐like family of RNA‐binding proteins

Dasgupta, T., & Ladd, A. N. (2011) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.107 · Cited by 225 · see citing works

Neuronal Elav-like (Hu) proteins regulate RNA splicing and abundance to control glutamate levels and neuronal excitability

Ince-Dunn, G., Okano, H. J., Jensen, K. B., Park, W.-Y., Zhong, R., Ule, J., Mele, A., Fak, J. J., Yang, C., Zhang, C., et al. (2012) · Neuron · doi:10.1016/j.neuron.2012.07.009 · Cited by 212 · see citing works

CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex

Saulière, J., Murigneux, V., Wang, Z., Marquenet, E., Barbosa, I., Tonquèze, O. L., Audic, Y., Paillard, L., Crollius, H. R., & Hir, H. L. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2420 · Cited by 199 · see citing works

Noncoding RNAs: Master Regulators of Inflammatory Signaling

Chew, C. L., Conos, S. A., Unal, B., & Tergaonkar, V. (2017) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2017.11.003 · Cited by 194 · see citing works

Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain

Licatalosi, D. D., Yano, M., Fak, J. J., Mele, A., Grabinski, S. E., Zhang, C., & Darnell, R. B. (2012) · Genes &amp; Development · doi:10.1101/gad.191338.112 · Cited by 193 · see citing works

Nova2 Regulates Neuronal Migration through an RNA Switch in Disabled-1 Signaling

Yano, M., Hayakawa-Yano, Y., Mele, A., & Darnell, R. B. (2010) · Neuron · doi:10.1016/j.neuron.2010.05.007 · Cited by 176 · see citing works

CLIP Tool Kit (CTK): a flexible and robust pipeline to analyze CLIP sequencing data

Shah, A., Qian, Y., Weyn‐Vanhentenryck, S. M., & Zhang, C. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw653 · Cited by 182 · see citing works

RNA Protein Interaction in Neurons

Darnell, R. B. (2013) · Annual Review of Neuroscience · doi:10.1146/annurev-neuro-062912-114322 · Cited by 181 · see citing works

Alternative splicing: decoding an expansive regulatory layer

Irimia, M., & Blencowe, B. J. (2012) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2012.03.005 · Cited by 177 · see citing works

Methods for comprehensive experimental identification of RNA-protein interactions

McHugh, C. A., Russell, P. H., & Guttman, M. (2014) · Genome biology · doi:10.1186/gb4152 · Cited by 164 · see citing works

Advances and challenges in the detection of transcriptome‐wide protein– RNA interactions

Wheeler, E. C., Nostrand, E. L. V., & Yeo, G. W.-M. (2017) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1436 · Cited by 164 · see citing works

Long non-coding RNA and RNA-binding protein interactions in cancer: Experimental and machine learning approaches

Shaath, H., Vishnubalaji, R., Elango, R., Kardousha, A., Islam, Z., Qureshi, R., Alam, T., Kolatkar, P. R., & Alajez, N. M. (2022) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2022.05.013 · Cited by 157 · see citing works

PureCLIP: capturing target-specific protein–RNA interaction footprints from single-nucleotide CLIP-seq data

Krakau, S., Richard, H., & Marsico, A. (2017) · Genome biology · doi:10.1186/s13059-017-1364-2 · Cited by 156 · see citing works

Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7

Meyer, K., Köster, T., Nolte, C., Weinholdt, C., Lewinski, M., Große, I., & Staiger, D. (2017) · Genome biology · doi:10.1186/s13059-017-1332-x · Cited by 148 · see citing works

Loss of the multifunctional RNA-binding protein RBM47 as a source of selectable metastatic traits in breast cancer

Vanharanta, S., Marney, C. B., Shu, W., Valiente, M., Zou, Y., Mele, A., Darnell, R. B., & Massagué, J. (2014) · eLife · doi:10.7554/elife.02734 · Cited by 143 · see citing works

Functional roles of alternative splicing factors in human disease

Cieply, B. W., & Carstens, R. P. (2015) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1276 · Cited by 142 · see citing works

DExD/H-box RNA helicases in ribosome biogenesis

Martin, R., Straub, A. U., Doebele, C., & Bohnsack, M. T. (2013) · RNA Biology · doi:10.4161/rna.21879 · Cited by 140 · see citing works

Auto-regulatory feedback by RNA-binding proteins

Müller-McNicoll, M., Roßbach, O., Hui, J., & Medenbach, J. (2019) · Journal of Molecular Cell Biology · doi:10.1093/jmcb/mjz043 · Cited by 140 · see citing works

Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain

Scheckel, C., Drapeau, E., Frias, M. A., Park, C. Y., Fak, J., Zucker-Scharff, I., Kou, Y., Haroutunian, V., Ma'ayan, A., Buxbaum, J. D., et al. (2016) · eLife · doi:10.7554/elife.10421 · Cited by 139 · see citing works

Defining the RNA interactome by total RNA‐associated protein purification

Shchepachev, V., Bresson, S. M., Spanos, C., Petfalski, E., Fischer, L., Rappsilber, J., & Tollervey, D. W. (2019) · Molecular Systems Biology · doi:10.15252/msb.20188689 · Cited by 139 · see citing works

Influenza virus non-structural protein NS1: interferon antagonism and beyond

Marc, D. (2014) · Journal of General Virology · doi:10.1099/vir.0.069542-0 · Cited by 138 · see citing works

Silencing of the miR-17∼92 Cluster Family Inhibits Medulloblastoma Progression

Murphy, B. L., Obad, S., Bihannic, L., Ayrault, O., Zindy, F., Kauppinen, S., & Roussel, M. F. (2013) · Cancer Research · doi:10.1158/0008-5472.can-13-0927 · Cited by 136 · see citing works

SomamiR 2.0: a database of cancer somatic mutations altering microRNA–ceRNA interactions

Bhattacharya, A., & Cui, Y. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1220 · Cited by 134 · see citing works

Cytoplasmic RNA-Binding Proteins and the Control of Complex Brain FunctionPreprint

Darnell, J. C., & Richter, J. D. (2012) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a012344 · Cited by 124 · see citing works

Deciphering the mRNP Code: RNA-Bound Determinants of Post-Transcriptional Gene Regulation

Gehring, N. H., Wahle, E., & Fischer, U. (2017) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2017.02.004 · Cited by 127 · see citing works

Stem-Loop Recognition by DDX17 Facilitates miRNA Processing and Antiviral Defense

Moy, R. H., Cole, B. S., Yasunaga, A., Gold, B., Shankarling, G. S., Varble, A., Molleston, J. M., tenOever, B. R., Lynch, K. W., & Cherry, S. R. (2014) · Cell · doi:10.1016/j.cell.2014.06.023 · Cited by 125 · see citing works

DoRiNA 2.0—upgrading the doRiNA database of RNA interactions in post-transcriptional regulation

Blin, K., Dieterich, C., Wurmus, R., Rajewsky, N., Landthaler, M., & Akalin, A. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1180 · Cited by 123 · see citing works

Modeling RNA-Binding Protein Specificity In Vivo by Precisely Registering Protein-RNA Crosslink Sites

Feng, H., Bao, S., Rahman, M. A., Weyn‐Vanhentenryck, S. M., Khan, A., Wong, J., Shah, A., Flynn, E. D., Krainer, A. R., & Zhang, C. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.02.002 · Cited by 119 · see citing works

A deep learning framework to predict binding preference of RNA constituents on protein surface

Lam, J. H., Li, Y., Zhu, L., Umarov, R. K., Jiang, H., Héliou, A., Sheong, F. K., Liu, T., Long, Y., Li, Y., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12920-0 · Cited by 121 · see citing works

Binding specificities of human RNA-binding proteins toward structured and linear RNA sequencesPreprint

Jolma, A., Zhang, J., Mondragón, E., Morgunova, E. Y., Kivioja, T., Laverty, K. U., Yin, Y., Zhu, F., Bourenkov, G. P., Morris, Q., et al. (2020) · Genome Research · doi:10.1101/gr.258848.119 · Cited by 121 · see citing works

Advances in the characterization of RNA‐binding proteins

Marchese, D., de Groot, N. S., Lorenzo-Gotor, N., Livi, C. M., & Tartaglia, G. G. (2016) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1378 · Cited by 119 · see citing works

NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure

Eom, T., Zhang, C., Wang, H., Lay, K., Fak, J., Noebels, J. L., & Darnell, R. B. (2013) · eLife · doi:10.7554/elife.00178 · Cited by 118 · see citing works

Non-coding RNAs: long non-coding RNAs and microRNAs in endocrine-related cancers

Klinge, C. M. (2018) · Endocrine Related Cancer · doi:10.1530/erc-17-0548 · Cited by 111 · see citing works

Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies

Barquist, L., & Vogel, J. (2015) · Annual Review of Genetics · doi:10.1146/annurev-genet-112414-054804 · Cited by 108 · see citing works

Centromeric Transcription Regulates Aurora-B Localization and Activation

Blower, M. D. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.04.054 · Cited by 108 · 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

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

Genome-wide identification of miRNA targets by PAR-CLIP

Hafner, M., Lianoglou, S., Tuschl, T., & Betel, D. (2012) · Methods · doi:10.1016/j.ymeth.2012.08.006 · Cited by 102 · see citing works

Long Non-Coding RNAs: A Novel Paradigm for Toxicology

Dempsey, J. L., & Cui, J. Y. (2016) · Toxicological Sciences · doi:10.1093/toxsci/kfw203 · Cited by 102 · see citing works

ELAVL1 Primarily Couples mRNA Stability with the 3’UTRs of Interferon Stimulated Genes

Rothamel, K. L., Arcos, S., Kim, B., Reasoner, C., Lisy, S. M., Mukherjee, N., & Ascano, M. (2020) · Cell Reports · doi:10.1016/j.celrep.2021.109178 · Cited by 89 · see citing works

Microexons: discovery, regulation, and function

Ustianenko, D., Weyn‐Vanhentenryck, S. M., & Zhang, C. (2017) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1418 · Cited by 98 · see citing works

Bioinformatics Method to Predict Two Regulation Mechanism: TF–miRNA–mRNA and lncRNA–miRNA–mRNA in Pancreatic Cancer

Song, Y., Yang, L., Zhao, X., Song, W., Wang, W., & Zheng, S. (2014) · Cell Biochemistry and Biophysics · doi:10.1007/s12013-014-0142-y · Cited by 94 · see citing works

Leveraging the complementary nature of RNA‐Seq and shotgun proteomics data

Wang, X., Liu, Q., & Zhang, B. (2014) · PROTEOMICS · doi:10.1002/pmic.201400184 · Cited by 92 · see citing works

Identification of RNA-binding protein targets with HyperTRIBE

Rahman, R., Xu, W., Jin, H., & Rosbash, M. (2018) · Nature Protocols · doi:10.1038/s41596-018-0020-y · Cited by 94 · see citing works

A Pleiotropic RNA-Binding Protein Controls Distinct Cell Cycle Checkpoints to Drive Resistance of p53-Defective Tumors to Chemotherapy

Cannell, I. G., Merrick, K. A., Morandell, S., Zhu, C., Braun, C. J., Grant, R. A., Cameron, E. R., Tsao, M., Hemann, M. T., & Yaffe, M. B. (2015) · Cancer Cell · doi:10.1016/j.ccell.2015.09.009 · Cited by 88 · see citing works

Denaturing purifications demonstrate that PRC2 and other widely reported chromatin proteins do not appear to bind directly to RNA in vivo

Guo, J. K., Blanco, M. R., Walkup, W. G., Bonesteele, G., Urbinati, C. R., Banerjee, A. K., Chow, A. Y., Ettlin, O., Strehle, M. M., Peyda, P., et al. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.01.026 · Cited by 88 · see citing works

Protein-RNA networks revealed through covalent RNA marks

Lapointe, C. P., Wilinski, D., Saunders, H. A. J., & Wickens, M. (2015) · Nature Methods · doi:10.1038/nmeth.3651 · Cited by 87 · see citing works

PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis

Chen, B., Yun, J., Kim, M. S., Mendell, J. T., & Xie, Y. (2014) · Genome biology · doi:10.1186/gb-2014-15-1-r18 · Cited by 85 · see citing works

A deep neural network approach for learning intrinsic protein-RNA binding preferences

Ben-Bassat, I., Chor, B., & Orenstein, Y. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty600 · Cited by 89 · see citing works

Deciphering the Plant Splicing Code: Experimental and Computational Approaches for Predicting Alternative Splicing and Splicing Regulatory Elements

Reddy, A. S. N., Rogers, M. F., Richardson, D. N., Hamilton, M., & Ben‐Hur, A. (2012) · Frontiers in Plant Science · doi:10.3389/fpls.2012.00018 · Cited by 87 · see citing works

Mechanistic implications of enhanced editing by a HyperTRIBE RNA-binding protein

Xu, W., Rahman, R., & Rosbash, M. (2017) · RNA · doi:10.1261/rna.064691.117 · Cited by 88 · see citing works

Approaches for Understanding the Mechanisms of Long Noncoding RNA Regulation of Gene ExpressionPreprint

McDonel, P. E., & Guttman, M. (2019) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a032151 · Cited by 84 · see citing works

Genome-Wide Analysis of miRNA-mRNA Interactions in Marrow Stromal Cells

Balakrishnan, I., Yang, X., Brown, J., Ramakrishnan, A., Torok‐Storb, B., Kabos, P., Hesselberth, J. R., & Pillai, M. M. (2013) · Stem Cells · doi:10.1002/stem.1531 · Cited by 80 · see citing works

The METTL5-TRMT112 N6-methyladenosine methyltransferase complex regulates mRNA translation via 18S rRNA methylation

Sepich‐Poore, C., Zheng, Z., Schmitt, E., Wen, K., Zhang, Z. S., Cui, X., Dai, Q., Zhu, A. C., Zhang, L., Castillo, A. S., et al. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.101590 · Cited by 80 · see citing works

Systematic Identification of Regulatory Elements in Conserved 3′ UTRs of Human Transcripts

Oikonomou, P., Goodarzi, H., & Tavazoie, S. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.03.001 · Cited by 84 · see citing works

Role of the N6-methyladenosine RNA mark in gene regulation and its implications on development and disease

Chandola, U., Das, R., & Panda, B. (2014) · Briefings in Functional Genomics · doi:10.1093/bfgp/elu039 · Cited by 80 · see citing works

A HuD‐ZBP1 ribonucleoprotein complex localizes GAP‐43 mRNA into axons through its 3′ untranslated region AU‐rich regulatory element

Yoo, S., Kim, H. H., Kim, P., Donnelly, C. J., Kalinski, A. L., Vuppalanchi, D., Park, M. M., Lee, S. J., Merianda, T. T., Perrone‐Bizzozero, N. I., et al. (2013) · Journal of Neurochemistry · doi:10.1111/jnc.12266 · Cited by 79 · see citing works

New directions in poly(ADP‐ribose) polymerase biology

Bock, F. J., & Chang, P. (2016) · FEBS Journal · doi:10.1111/febs.13737 · Cited by 78 · see citing works

De Novo Prediction of PTBP1 Binding and Splicing Targets Reveals Unexpected Features of Its RNA Recognition and Function

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

cTag-PAPERCLIP Reveals Alternative Polyadenylation Promotes Cell-Type Specific Protein Diversity and Shifts Araf Isoforms with Microglia Activation

Hwang, H.-W., Saito, Y., Park, C. Y., Blachère, N. E., Tajima, Y., Fak, J. J., Zucker-Scharff, I., & Darnell, R. B. (2017) · Neuron · doi:10.1016/j.neuron.2017.08.024 · Cited by 74 · see citing works

A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins

Jarmoskaite, I., Denny, S. K., Vaidyanathan, P. P., Becker, W. R., Andreasson, J. O. L., Layton, C. J., Kappel, K., Shivashankar, V., Sreenivasan, R., Das, R., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.04.012 · Cited by 73 · see citing works

Silica-based solid-phase extraction of cross-linked nucleic acid–bound proteins

Asencio, C., Chatterjee, A., & Hentze, M. W. (2018) · Life Science Alliance · doi:10.26508/lsa.201800088 · Cited by 73 · see citing works

RNAcompete methodology and application to determine sequence preferences of unconventional RNA-binding proteins

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

Coordinate regulation of alternative pre-mRNA splicing events by the human RNA chaperone proteins hnRNPA1 and DDX5Preprint

Lee, Y. J., Wang, Q., & Rio, D. C. (2018) · Genes & Development · doi:10.1101/gad.316034.118 · Cited by 69 · see citing works

The “Observer Effect” in Genome-wide Surveys of Protein-RNA Interactions

Riley, K. J.-L., & STEITZ, J. A. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.01.030 · Cited by 68 · see citing works

Progressive impairment of muscle regeneration in muscleblind-like 3 isoform knockout mice

Poulos, M. G., Batra, R., Li, M., Yuan, Y., Zhang, C., Darnell, R. B., & Swanson, M. S. (2013) · Human Molecular Genetics · doi:10.1093/hmg/ddt209 · Cited by 69 · see citing works

Prediction of clustered RNA-binding protein motif sites in the mammalian genome

Zhang, C., Lee, K., Swanson, M. S., & Darnell, R. B. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt421 · Cited by 65 · see citing works

HITS-CLIP reveals key regulators of nuclear receptor signaling in breast cancer

Pillai, M. M., Gillen, A. E., Yamamoto, T. M., Kline, E. C., Brown, J., Flory, K., Hesselberth, J. R., & Kabos, P. (2014) · Breast Cancer Research and Treatment · doi:10.1007/s10549-014-3004-9 · Cited by 68 · see citing works

Unraveling the Pathways to Neuronal Homeostasis and Disease: Mechanistic Insights into the Role of RNA-Binding Proteins and Associated Factors

Ravanidis, S., Kattan, F.-G., & Doxakis, E. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19082280 · Cited by 65 · see citing works

RNA-binding protein hnRNPLL regulates mRNA splicing and stability during B-cell to plasma-cell differentiation

Chang, X., Li, B., & Rao, A. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1422490112 · Cited by 63 · see citing works

CLIP: viewing the RNA world from an RNA-protein interactome perspective

Zhang, Y., Xie, S., Xu, H. M., & Qu, L. (2015) · Science China Life Sciences · doi:10.1007/s11427-014-4764-5 · Cited by 20 · see citing works

Understanding RNA Regulation Through Analysis of CLIP-Seq Data

Wang, T. (2015)

Journal of Visualized Experiments www.jove.com Video Article iCLIP- Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

König, J., Kathi, Z., Rot, G., Curk, T., Kayikci, M., Zupan, B., Turner, D. J., Luscombe, N. M., & Ule, J. (2013)

Video Article iCLIP- Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

König, J., Kathi, Z., Rot, G., Curk, T., Kayikci, M., Zupan, B., Turner, D., Luscombe, N. M., & Ule, J. (2016)

Mapping transcriptome‐wide protein‐RNA interactions to elucidate RNA regulatory programs

Hannigan, M. M., Zagore, L. L., & Licatalosi, D. D. (2018) · Quantitative Biology · doi:10.1007/s40484-018-0145-6 · Cited by 13 · see citing works