Abstract
A post-transcriptional operon is a set of monocistronic mRNAs encoding functionally related proteins that are co-regulated by a group of RNA-binding proteins and/or small non-coding RNAs so that protein expression is coordinated at the post-transcriptional level. The post-transcriptional operon model (PTO) is used to describe data from an assortment of methods (e.g. RIP-Chip, CLIP-Chip, miRNA profiling, ribosome profiling) that globally address the functionality of mRNA. Several examples of post-transcriptional operons have been documented in the literature and demonstrate the usefulness of the model in identifying new participants in cellular pathways as well as in deepening our understanding of cellular responses.
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References
Tenenbaum, S. A., Carson, C. C., Lager, P. J., Keene, J. D. (2000) Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc Natl Acad Sci USA 97, 14085–14090.
Keene, J. D. (2001) Ribonucleoprotein infrastructure regulating the flow of genetic information between the genome and the proteome. Proc Natl Acad Sci USA 98, 7018–7024.
Keene, J. D., Tenenbaum, S. A. (2002) Eukaryotic mRNPs may represent posttranscriptional operons. Mol Cell 9, 1161–1167.
Keene, J. D. (2007) RNA regulons: coordination of post-transcriptional events. Nat Rev Genet 8, 533–543.
Mansfield, K. D., Keene, J. D. (2009) The ribonome: a dominant force in co-ordinating gene expression. Biol Cell 101, 169–181.
Neil, H., Malabat, C., ubenton-Carafa, Y., Xu, Z., Steinmetz, L. M., Jacquier, A. (2009) Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature 457, 1038–1042.
He, Y., Vogelstein, B., Velculescu, V. E., Papadopoulos, N., Kinzler, K. W. (2008) The antisense transcriptomes of human cells. Science 322, 1855–1857.
Oliver, B., Parisi, M., Clark, D. (2002) Gene expression neighborhoods. J Biol 1, 4.
Carninci, P. (2009) Molecular biology: the long and short of RNAs. Nature 457, 974–975.
Seila, A. C., Calabrese, J. M., Levine, S. S., Yeo, G. W., Rahl, P. B., Flynn, R. A., Young, R. A., Sharp, P. A. (2008) Divergent transcription from active promoters. Science 322, 1849–1851.
Maniatis, T., Reed, R. (2002) An extensive network of coupling among gene expression machines. Nature 416, 499–506.
Moore, M. J., Proudfoot, N. J. (2009) Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 136, 688–700.
Gerstein, M. B., Bruce, C., Rozowsky, J. S., Zheng, D., Du, J., Korbel, J. O., Emanuelsson, O., Zhang, Z. D., Weissman, S., Snyder, M. (2007) What is a gene, post-ENCODE? History and updated definition. Genome Res 17, 669–681.
Pan, Q., Shai, O., Lee, L. J., Frey, B. J., Blencowe, B. J. (2008) Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 40, 1413–1415.
Wang, E. T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S. F., Schroth, G. P., Burge, C. B. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470–476.
Ji, Z., Lee, J. Y., Pan, Z., Jiang, B., Tian, B. (2009) Progressive lengthening of 3′ untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc Natl Acad Sci USA 106, 7028–7033.
Sandberg, R., Neilson, J. R., Sarma, A., Sharp, P. A., Burge, C. B. (2008) Proliferating cells express mRNAs with shortened 3′ untranslated regions and fewer microRNA target sites. Science 320, 1643–1647.
Moore, M. J. (2005) From birth to death: the complex lives of eukaryotic mRNAs. Science 309, 1514–1518.
Diehn, M., Bhattacharya, R., Botstein, D., Brown, P. O. (2006) Genome-scale identification of membrane-associated human mRNAs. PLoS Genet 2, e11.
Halbeisen, R. E., Galgano, A., Scherrer, T., Gerber, A. P. (2008) Post-transcriptional gene regulation: from genome-wide studies to principles. Cell Mol Life Sci 65, 798–813.
St Johnston, D. (2005) Moving messages: the intracellular localization of mRNAs. Nat Rev Mol Cell Biol 6, 363–375.
Gilbert, W. V., Zhou, K., Butler, T. K., Doudna, J. A. (2007) Cap-independent translation is required for starvation-induced differentiation in yeast. Science 317, 1224–1227.
Ingolia, N. T., Ghaemmaghami, S., Newman, J. R., Weissman, J. S. (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218–223.
Keene, J. D., Komisarow, J. M., Friedersdorf, M. B. (2006) RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat Protoc 1, 302–307.
Baroni, T. E., Chittur, S. V., George, A. D., Tenenbaum, S. A. (2008) Advances in RIP-chip analysis: RNA-binding protein immunoprecipitation-microarray profiling. Methods Mol Biol 419, 93–108.
Tian, Q., Stepaniants, S. B., Mao, M., Weng, L., Feetham, M. C., Doyle, M. J., Yi, E. C., Dai, H., Thorsson, V., Eng, J., et al. (2004) Integrated genomic and proteomic analyses of gene expression in Mammalian cells. Mol Cell Proteomics 3, 960–969.
Lunde, B. M., Moore, C., Varani, G. (2007) RNA-binding proteins: modular design for efficient function. Nat Rev Mol Cell Biol 8, 479–490.
Gerber, A. P., Herschlag, D., Brown, P. O. (2004) Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol 2, E79.
Saint-Georges, Y., Garcia, M., Delaveau, T., Jourdren, L., Le, C. S., Lemoine, S., Tanty, V., Devaux, F., Jacq, C. (2008) Yeast mitochondrial biogenesis: a role for the PUF RNA-binding protein Puf3p in mRNA localization. PLoS One 3, e2293.
Townley-Tilson, W. H., Pendergrass, S. A., Marzluff, W. F., Whitfield, M. L. (2006) Genome-wide analysis of mRNAs bound to the histone stem-loop binding protein. RNA 12, 1853–1867.
Barreau, C., Paillard, L., Osborne, H. B. (2005) AU-rich elements and associated factors: are there unifying principles? Nucleic Acids Res 33, 7138–7150.
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Tenenbaum, S.A., Christiansen, J., Nielsen, H. (2011). The Post-transcriptional Operon. In: Nielsen, H. (eds) RNA. Methods in Molecular Biology, vol 703. Humana Press. https://doi.org/10.1007/978-1-59745-248-9_16
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DOI: https://doi.org/10.1007/978-1-59745-248-9_16
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