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Journal articles on the topic 'RNA-binding'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Muckstein, U., H. Tafer, J. Hackermuller, S. H. Bernhart, P. F. Stadler, and I. L. Hofacker. "Thermodynamics of RNA-RNA binding." Bioinformatics 22, no. 10 (2006): 1177–82. http://dx.doi.org/10.1093/bioinformatics/btl024.

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2

Hallegger, M., A. Taschner, and M. F. Jantsch. "RNA aptamers binding the double-stranded RNA-binding domain." RNA 12, no. 11 (2006): 1993–2004. http://dx.doi.org/10.1261/rna.125506.

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3

Muto, Yutaka, Chris Oubridge, and Kiyoshi Nagai. "RNA-binding proteins: TRAPping RNA bases." Current Biology 10, no. 1 (2000): R19—R21. http://dx.doi.org/10.1016/s0960-9822(99)00250-x.

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4

Kotelnikov, R. N., S. G. Shpiz, A. I. Kalmykova, and V. A. Gvozdev. "RNA-binding proteins in RNA interference." Molecular Biology 40, no. 4 (2006): 528–40. http://dx.doi.org/10.1134/s0026893306040054.

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5

Serin, Guillaume, Gérard Joseph, Laurence Ghisolfi, et al. "Two RNA-binding Domains Determine the RNA-binding Specificity of Nucleolin." Journal of Biological Chemistry 272, no. 20 (1997): 13109–16. http://dx.doi.org/10.1074/jbc.272.20.13109.

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6

Sastry, Srin, and Barbara M. Ross. "RNA-binding site in T7 RNA polymerase." Proceedings of the National Academy of Sciences 95, no. 16 (1998): 9111–16. http://dx.doi.org/10.1073/pnas.95.16.9111.

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Recent models of RNA polymerase transcription complexes have invoked the idea that enzyme-nascent RNA contacts contribute to the stability of the complexes. Although much progress on this topic has been made with the multisubunit Escherichia coli RNA polymerase, there is a paucity of information regarding the structure of single-subunit phage RNA polymerase transcription complexes. Here, we photo-cross-linked the RNA in a T7 RNA polymerase transcription complex and mapped a major contact site between amino acid residues 144 and 168 and probably a minor contact between residues 1 and 93. These

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7

Singh, Arunima. "RNA-binding protein kinetics." Nature Methods 18, no. 4 (2021): 335. http://dx.doi.org/10.1038/s41592-021-01122-6.

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8

SUGITA, Mamoru, and Masahiro SUGIURA. "Chloroplast RNA-binding Proteins." Nippon Nōgeikagaku Kaishi 71, no. 11 (1997): 1177–79. http://dx.doi.org/10.1271/nogeikagaku1924.71.1177.

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9

Larochelle, Stéphane. "RNA-binding proteome redux." Nature Methods 16, no. 3 (2019): 219. http://dx.doi.org/10.1038/s41592-019-0349-3.

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10

Laird-Offringa, Ite A., and Joel G. Belasco. "RNA-binding proteins tamed." Nature Structural & Molecular Biology 5, no. 8 (1998): 665–68. http://dx.doi.org/10.1038/1356.

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11

Goers, Emily S., Rodger B. Voelker, Devika P. Gates, and J. Andrew Berglund. "RNA Binding Specificity ofDrosophilaMuscleblind†." Biochemistry 47, no. 27 (2008): 7284–94. http://dx.doi.org/10.1021/bi702252d.

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12

Smith, Colin A., Valerie Calabro, and Alan D. Frankel. "An RNA-Binding Chameleon." Molecular Cell 6, no. 5 (2000): 1067–76. http://dx.doi.org/10.1016/s1097-2765(00)00105-2.

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13

Goodall, Greg, Jonathan Levy, Maria Mieszczak, and Witold Filipowicz. "Plant RNA-binding proteins." Molecular Biology Reports 14, no. 2-3 (1990): 137. http://dx.doi.org/10.1007/bf00360447.

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14

Nickelsen, J�rg. "Chloroplast RNA-binding proteins." Current Genetics 43, no. 6 (2003): 392–99. http://dx.doi.org/10.1007/s00294-003-0425-0.

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15

Shimada, Naohiko, Reiko Iwase, Tetsuji Yamaoka, and Akira Murakami. "Design of RNA-Binding Oligopeptides Based on Information of RNA-Binding Protein." Polymer Journal 35, no. 6 (2003): 507–12. http://dx.doi.org/10.1295/polymj.35.507.

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16

Stefl, Richard, Ming Xu, Lenka Skrisovska, Ronald B. Emeson, and Frédéric H. T. Allain. "Structure and Specific RNA Binding of ADAR2 Double-Stranded RNA Binding Motifs." Structure 14, no. 2 (2006): 345–55. http://dx.doi.org/10.1016/j.str.2005.11.013.

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17

Windbichler, Nikolai, and Renée Schroeder. "Isolation of specific RNA-binding proteins using the streptomycin-binding RNA aptamer." Nature Protocols 1, no. 2 (2006): 637–40. http://dx.doi.org/10.1038/nprot.2006.95.

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18

Gonzalez-Rivera, Juan C., Asuka A. Orr, Sean M. Engels, et al. "Computational evolution of an RNA-binding protein towards enhanced oxidized-RNA binding." Computational and Structural Biotechnology Journal 18 (2020): 137–52. http://dx.doi.org/10.1016/j.csbj.2019.12.003.

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19

Tuccinardi, Tiziano. "Binding-interaction prediction of RNA-binding ligands." Future Medicinal Chemistry 3, no. 6 (2011): 723–33. http://dx.doi.org/10.4155/fmc.11.25.

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20

Zhu, J., K. Gopinath, A. Murali, et al. "RNA-binding proteins that inhibit RNA virus infection." Proceedings of the National Academy of Sciences 104, no. 9 (2007): 3129–34. http://dx.doi.org/10.1073/pnas.0611617104.

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21

Fu, Yuan, and Anne Baranger. "MBNL1-RNA Interactions: Binding-Induced Rna Conformational Changes." Biophysical Journal 102, no. 3 (2012): 75a. http://dx.doi.org/10.1016/j.bpj.2011.11.438.

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22

Jolma, Arttu, Jilin Zhang, Estefania Mondragón, et al. "Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences." Genome Research 30, no. 7 (2020): 962–73. http://dx.doi.org/10.1101/gr.258848.119.

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23

Brooks, Roman, Christian R. Eckmann, and Michael F. Jantsch. "The double-stranded RNA-binding domains ofXenopus laevisADAR1 exhibit different RNA-binding behaviors." FEBS Letters 434, no. 1-2 (1998): 121–26. http://dx.doi.org/10.1016/s0014-5793(98)00963-6.

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24

Kobayashi, Takahiko, Junich Ishida, Yuichi Shimizu, et al. "Decreased RNA-binding motif 5 expression is associated with tumor progression in gastric cancer." Tumor Biology 39, no. 3 (2017): 101042831769454. http://dx.doi.org/10.1177/1010428317694547.

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RNA-binding motif 5 is a putative tumor suppressor gene that modulates cell cycle arrest and apoptosis. We recently demonstrated that RNA-binding motif 5 inhibits cell growth through the p53 pathway. This study evaluated the clinical significance of RNA-binding motif 5 expression in gastric cancer and the effects of altered RNA-binding motif 5 expression on cancer biology in gastric cancer cells. RNA-binding motif 5 protein expression was evaluated by immunohistochemistry using the surgical specimens of 106 patients with gastric cancer. We analyzed the relationships of RNA-binding motif 5 expr

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25

Burd, C. G., E. L. Matunis, and G. Dreyfuss. "The multiple RNA-binding domains of the mRNA poly(A)-binding protein have different RNA-binding activities." Molecular and Cellular Biology 11, no. 7 (1991): 3419–24. http://dx.doi.org/10.1128/mcb.11.7.3419-3424.1991.

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The poly(A)-binding protein (PABP) is the major mRNA-binding protein in eukaryotes, and it is essential for viability of the yeast Saccharomyces cerevisiae. The amino acid sequence of the protein indicates that it consists of four ribonucleoprotein consensus sequence-containing RNA-binding domains (RBDs I, II, III, and IV) and a proline-rich auxiliary domain at the carboxyl terminus. We produced different parts of the S. cerevisiae PABP and studied their binding to poly(A) and other ribohomopolymers in vitro. We found that none of the individual RBDs of the protein bind poly(A) specifically or

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26

Burd, C. G., E. L. Matunis, and G. Dreyfuss. "The multiple RNA-binding domains of the mRNA poly(A)-binding protein have different RNA-binding activities." Molecular and Cellular Biology 11, no. 7 (1991): 3419–24. http://dx.doi.org/10.1128/mcb.11.7.3419.

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The poly(A)-binding protein (PABP) is the major mRNA-binding protein in eukaryotes, and it is essential for viability of the yeast Saccharomyces cerevisiae. The amino acid sequence of the protein indicates that it consists of four ribonucleoprotein consensus sequence-containing RNA-binding domains (RBDs I, II, III, and IV) and a proline-rich auxiliary domain at the carboxyl terminus. We produced different parts of the S. cerevisiae PABP and studied their binding to poly(A) and other ribohomopolymers in vitro. We found that none of the individual RBDs of the protein bind poly(A) specifically or

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27

Maticzka, Daniel, Sita J. Lange, Fabrizio Costa, and Rolf Backofen. "GraphProt: modeling binding preferences of RNA-binding proteins." Genome Biology 15, no. 1 (2014): R17. http://dx.doi.org/10.1186/gb-2014-15-1-r17.

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28

Yu, Hui, Jing Wang, Quanhu Sheng, Qi Liu, and Yu Shyr. "beRBP: binding estimation for human RNA-binding proteins." Nucleic Acids Research 47, no. 5 (2018): e26-e26. http://dx.doi.org/10.1093/nar/gky1294.

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Abstract Identifying binding targets of RNA-binding proteins (RBPs) can greatly facilitate our understanding of their functional mechanisms. Most computational methods employ machine learning to train classifiers on either RBP-specific targets or pooled RBP–RNA interactions. The former strategy is more powerful, but it only applies to a few RBPs with a large number of known targets; conversely, the latter strategy sacrifices prediction accuracy for a wider application, since specific interaction features are inevitably obscured through pooling heterogeneous datasets. Here, we present beRBP, a

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29

Sohrabi-Jahromi, Salma, and Johannes Söding. "Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins." Bioinformatics 37, Supplement_1 (2021): i308—i316. http://dx.doi.org/10.1093/bioinformatics/btab300.

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Abstract Motivation Understanding how proteins recognize their RNA targets is essential to elucidate regulatory processes in the cell. Many RNA-binding proteins (RBPs) form complexes or have multiple domains that allow them to bind to RNA in a multivalent, cooperative manner. They can thereby achieve higher specificity and affinity than proteins with a single RNA-binding domain. However, current approaches to de novo discovery of RNA binding motifs do not take multivalent binding into account. Results We present Bipartite Motif Finder (BMF), which is based on a thermodynamic model of RBPs with

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30

Ottoz, Diana S. M., and Luke E. Berchowitz. "The role of disorder in RNA binding affinity and specificity." Open Biology 10, no. 12 (2020): 200328. http://dx.doi.org/10.1098/rsob.200328.

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Most RNA-binding modules are small and bind few nucleotides. RNA-binding proteins typically attain the physiological specificity and affinity for their RNA targets by combining several RNA-binding modules. Here, we review how disordered linkers connecting RNA-binding modules govern the specificity and affinity of RNA–protein interactions by regulating the effective concentration of these modules and their relative orientation. RNA-binding proteins also often contain extended intrinsically disordered regions that mediate protein–protein and RNA–protein interactions with multiple partners. We di

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31

Ciafrè, Silvia Anna, and Silvia Galardi. "microRNAs and RNA-binding proteins." RNA Biology 10, no. 6 (2013): 934–42. http://dx.doi.org/10.4161/rna.24641.

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32

DeLisle, A. J. "RNA-Binding Protein from Arabidopsis." Plant Physiology 102, no. 1 (1993): 313–14. http://dx.doi.org/10.1104/pp.102.1.313.

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33

Tang, Lei. "Examining global RNA-binding proteomes." Nature Methods 16, no. 2 (2019): 144. http://dx.doi.org/10.1038/s41592-019-0321-2.

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34

Strack, Rita. "Predicting RNA–protein binding affinity." Nature Methods 16, no. 6 (2019): 460. http://dx.doi.org/10.1038/s41592-019-0445-4.

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35

Surendranath, Kalpana. "RNA Binding Proteins and Osteosarcoma." Cancer Research and Cellular Therapeutics 7, no. 2 (2023): 01–09. http://dx.doi.org/10.31579/2640-1053/146.

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Osteosarcoma, the most prevalent form of bone cancer, is primarily attributed to the abnormal behavior of bone-forming mesenchymal stem cells and its occurrence as the third most common cancer among children is of concern. Recent investigations have uncovered the novel roles of RNA- binding proteins (RBPs) in addition to controlling mRNA processing and translation, with notable mutations observed in various malignancies, including osteosarcoma. Although the exact mechanisms linking RBPs and osteosarcoma remain elusive, multiple studies have indicated the critical involvement of specific RBPs i

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36

Berens, Christian, Alison Thain, and Renée Schroeder. "A tetracycline-binding RNA aptamer." Bioorganic & Medicinal Chemistry 9, no. 10 (2001): 2549–56. http://dx.doi.org/10.1016/s0968-0896(01)00063-3.

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37

Zamore, Phillip D., Maria L. Zapp та Michael R. Green. "RNA binding: βS and basics". Nature 348, № 6301 (1990): 485–86. http://dx.doi.org/10.1038/348485a0.

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38

Antson, Alfred A. "Single stranded RNA binding proteins." Current Opinion in Structural Biology 10, no. 1 (2000): 87–94. http://dx.doi.org/10.1016/s0959-440x(99)00054-8.

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39

Nafisi, Sh, A. Shadaloi, A. Feizbakhsh, and H. A. Tajmir-Riahi. "RNA binding to antioxidant flavonoids." Journal of Photochemistry and Photobiology B: Biology 94, no. 1 (2009): 1–7. http://dx.doi.org/10.1016/j.jphotobiol.2008.08.001.

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40

Luo, Zheng, Qin Yang, and Li Yang. "RNA Structure Switches RBP Binding." Molecular Cell 64, no. 2 (2016): 219–20. http://dx.doi.org/10.1016/j.molcel.2016.10.006.

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41

Purnell, B. A. "Noncoding RNA helps protein binding." Science 350, no. 6263 (2015): 923–25. http://dx.doi.org/10.1126/science.350.6263.923-o.

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42

Holmqvist, Erik, and Jörg Vogel. "RNA-binding proteins in bacteria." Nature Reviews Microbiology 16, no. 10 (2018): 601–15. http://dx.doi.org/10.1038/s41579-018-0049-5.

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43

ARNEZ, JOHN G., and JEAN CAVARELLI. "Structures of RNA-binding proteins." Quarterly Reviews of Biophysics 30, no. 3 (1997): 195–240. http://dx.doi.org/10.1017/s0033583597003351.

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44

Toth, Miklos. "RNA binding proteins in epilepsy." Gene Function & Disease 2, no. 2-3 (2001): 95–98. http://dx.doi.org/10.1002/1438-826x(200110)2:2/3<95::aid-gnfd95>3.0.co;2-i.

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45

De Conti, Laura, Marco Baralle, and Emanuele Buratti. "Neurodegeneration and RNA-binding proteins." Wiley Interdisciplinary Reviews: RNA 8, no. 2 (2016): e1394. http://dx.doi.org/10.1002/wrna.1394.

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46

Copeland, Paul R., and Donna M. Driscoll. "RNA binding proteins and selenocysteine." BioFactors 14, no. 1-4 (2001): 11–16. http://dx.doi.org/10.1002/biof.5520140103.

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47

Shi, De-Li. "RNA-Binding Proteins in Cardiomyopathies." Journal of Cardiovascular Development and Disease 11, no. 3 (2024): 88. http://dx.doi.org/10.3390/jcdd11030088.

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The post-transcriptional regulation of gene expression plays an important role in heart development and disease. Cardiac-specific alternative splicing, mediated by RNA-binding proteins, orchestrates the isoform switching of proteins that are essential for cardiomyocyte organization and contraction. Dysfunctions of RNA-binding proteins impair heart development and cause the main types of cardiomyopathies, which represent a heterogenous group of abnormalities that severely affect heart structure and function. In particular, mutations of RBM20 and RBFOX2 are associated with dilated cardiomyopathy

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48

Tiwari, Prakriti, Emre Deniz, and Akyut Üren. "BPS2025 - Characterizing Ezrin RNA binding." Biophysical Journal 124, no. 3 (2025): 88a. https://doi.org/10.1016/j.bpj.2024.11.535.

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49

Rouda, Susan, and Emmanuel Skordalakes. "Structure of the RNA-Binding Domain of Telomerase: Implications for RNA Recognition and Binding." Structure 15, no. 11 (2007): 1403–12. http://dx.doi.org/10.1016/j.str.2007.09.007.

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50

Ginisty, Hervé, François Amalric, and Philippe Bouvet. "Two Different Combinations of RNA-binding Domains Determine the RNA Binding Specificity of Nucleolin." Journal of Biological Chemistry 276, no. 17 (2001): 14338–43. http://dx.doi.org/10.1074/jbc.m011120200.

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