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Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays
Open accessAbstract
Genomic array technologies provide a means for profiling global changes in gene expression under a variety of conditions. However, it has been difficult to assess whether transcriptional or posttranscriptional regulation is responsible for these changes. Additionally, fluctuations in gene expression in a single cell type within a complex tissue like a tumor may be masked by overlapping profiles of all cell types in the population. In this paper, we describe the use of cDNA arrays to identify subsets of mRNAs contained in endogenous messenger ribonucleoprotein complexes (mRNPs) that are cell type specific. We identified mRNA subsets from P19 embryonal carcinoma stem cells by using mRNA-binding proteins HuB, eIF-4E, and PABP that are known to play a role in translation. The mRNA profiles associated with each of these mRNPs were unique and represented gene clusters that differed from total cellular RNA. Additionally, the composition of mRNAs detected in HuB–mRNP complexes changed dramatically after induction of neuronal differentiation with retinoic acid. We suggest that the association of structurally related mRNAs into mRNP complexes is dynamic and may help regulate posttranscriptional events such as mRNA turnover and translation. Recovering proteins specifically associated with mRNP complexes to identify and profile endogenously clustered mRNAs should provide insight into structural and functional relationships among gene transcripts and/or their protein products. We have termed this approach to functional genomics ribonomic s and suggest that it will provide a useful paradigm for organizing genomic information in a biologically relevant manner.
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Cites
AU-rich elements: characterization and importance in mRNA degradation
Chen, C.-Y. A., & Shyu, A.-B. (1995) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)89102-1 · Cited by 1,948
A conserved family of elav-like genes in vertebrates.
Good, P. J. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.10.4557 · Cited by 319
Aranda-Abreu, G. E., Behar, L., Chung, S., Furneaux, H., & Ginzburg, I. (1999) · The Journal of Neuroscience · doi:10.1523/jneurosci.19-16-06907.1999 · Cited by 142
Paraneoplastic Encephalomyelitis Antigens Bind to the AU-rich Elements of mRNA
Liu, J., Dalmau, J., Szabo, A., Rosenfeld, M., Huber, J., & Furneaux, H. (1995) · Neurology · doi:10.1212/wnl.45.3.544 · Cited by 122
Cited by
John, B., Enright, A. J., Aravin, A., Tuschl, T., Sander, C., & Marks, D. S. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020363 · Cited by 3,796
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
A census of human RNA-binding proteins
Gerstberger, S., Hafner, M., & Tuschl, T. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3813 · Cited by 2,032
Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)
Van Nostrand, E. L., Pratt, G. A., Shishkin, A. A., Gelboin-Burkhart, C., Fang, M. Y., Sundararaman, B., Blue, S. M., Nguyen, T. B., Surka, C., Elkins, K., et al. (2016) · Nature Methods · doi:10.1038/nmeth.3810 · Cited by 1,397
RNA regulons: coordination of post-transcriptional events
Keene, J. D. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2111 · Cited by 1,321
Self-citationGlobal signatures of protein and mRNA expression levels
de Sousa Abreu, R., Penalva, L. O., Marcotte, E. M., & Vogel, C. (2009) · Molecular BioSystems · doi:10.1039/b908315d · Cited by 1,248
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
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
Self-citationGenome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae
Arava, Y., Wang, Y., Storey, J. D., Liu, C. L., Brown, P. O., & Herschlag, D. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0635171100 · Cited by 663
Deciphering molecular interactions by proximity labeling
Qin, W., Cho, K. F., Cavanagh, P. E., & Ting, A. Y. (2021) · Nature Methods · doi:10.1038/s41592-020-01010-5 · Cited by 671
Mukherjee, N., Corcoran, D. L., Nusbaum, J. D., Reid, D. W., Georgiev, S., Hafner, M., Ascano, M., Tuschl, T., Ohler, U., & Keene, J. D. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.06.007 · Cited by 654
Self-citationRBPDB: a database of RNA-binding specificities
Cook, K. B., Kazan, H., Zuberi, K., Morris, Q., & Hughes, T. R. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1069 · Cited by 638
MicroRNA regulation by RNA-binding proteins and its implications for cancer
van Kouwenhove, M., Kedde, M., & Agami, R. (2011) · Nature Reviews Cancer · doi:10.1038/nrc3107 · Cited by 617
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
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
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
RNA cargoes associating with FMRP reveal deficits in cellular functioning in Fmr1 null mice
Miyashiro, K. Y., Beckel-Mitchener, A., Purk, T. P., Becker, K. G., Barret, T., Liu, L., Carbonetto, S., Weiler, I. J., Greenough, W. T., & Eberwine, J. (2003) · Neuron · doi:10.1016/s0896-6273(03)00034-5 · Cited by 495
Rajasekhar, V. K., Viale, A., Socci, N. D., Wiedmann, M., Hu, X., & Holland, E. C. (2003) · Molecular Cell · doi:10.1016/s1097-2765(03)00395-2 · Cited by 420
Puig, S., Askeland, E., & Thiele, D. J. (2005) · Cell · doi:10.1016/j.cell.2004.11.032 · Cited by 382
The regulation of mRNA stability in mammalian cells: 2.0
Wu, X., & Brewer, G. (2012) · Gene · doi:10.1016/j.gene.2012.03.021 · Cited by 239
Coupling and coordination in gene expression processes: a systems biology view
Komili, S., & Silver, P. A. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2223 · Cited by 218
Morris, A. R., Mukherjee, N., & Keene, J. D. (2008) · Molecular and Cellular Biology · doi:10.1128/mcb.00155-08 · Cited by 155
Self-citationPioglitazone prevents alcohol-induced fatty liver in rats through up-regulation of c-Met
Tomita, K., Azuma, T., Kitamura, N., Nishida, J., Tamiya, G., Oka, A., Inokuchi, S., Nishimura, T., Suematsu, M., & Ishii, H. (2004) · Gastroenterology · doi:10.1053/j.gastro.2003.12.008 · Cited by 141
Quattrone, A., Pascale, A., Nogues, X., Zhao, W., Gusev, P., Pacini, A., & Alkon, D. L. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.191388398 · Cited by 137
Bolognani, F., Contente-Cuomo, T., & Perrone-Bizzozero, N. I. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp863 · Cited by 113
Mansfield, K. D., & Keene, J. D. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1114 · Cited by 112
Self-citationAronov, S., Aranda, G., Behar, L., & Ginzburg, I. (2002) · Journal of Cell Science · doi:10.1242/jcs.00058 · Cited by 112
The ribonome: a dominant force in co‐ordinating gene expression
Mansfield, K. D., & Keene, J. D. (2009) · Biology of the Cell · doi:10.1042/bc20080055 · Cited by 102
Self-citationCalarco, J. A., Zhen, M., & Blencowe, B. J. (2011) · RNA · doi:10.1261/rna.2603911 · Cited by 72
Functional Interactions Between microRNAs and RNA Binding Proteins
Jiang, P., & Coller, H. (2012) · MicroRNA e · doi:10.2174/2211536611201010070 · Cited by 62
Differential translation and fragile X syndrome
Vanderklish, P. W., & Edelman, G. M. (2005) · Genes, Brain and Behavior · doi:10.1111/j.1601-183x.2005.00134.x · Cited by 59
Metadata
- Authors
- Tenenbaum, S. A., Carson, C. C., Lager, P. J., & Keene, J. D.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2000-12-19
- Volume
- 97
- Issue
- 26
- Pages
- 14085-14090
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2001320847
- Cited by
- 396
- References
- 4
- FWCI
- 4.73
- Type
- journal article
- Language
- en
- Open access
- green
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