Extended References

Processing of Eukaryotic Pre-mRNA

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de Almeida, S. F., and M. Carmo-Fonseca. 2008. The CTD role in cotranscriptional RNA processing and surveillance. FEBS Lett. 582:1971–1976.

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Hocine, S., R. H. Singer, and D. Grünwald. 2010. RNA processing and export. Cold Spring Harb. Perspect. Biol. 2(12):a000752.

Houseley, J., and D. Tollervey. 2009. The many pathways of RNA degradation. Cell 136:763–776.

Lambowitz, A. M., and S. Zimmerly. 2004. Mobile group II introns. Annu. Rev. Genet. 38:1–35.

Moore, M. J., and N. J. Proudfoot. 2009. Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 136:688–700.

Pawlicki, J. M., and J. A. Steitz. 2010. Nuclear networking fashions pre-messenger RNA and primary microRNA transcripts for function. Trends Cell Biol. 20:52–61.

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Sharp, P. A. 2005. The discovery of split genes and RNA splicing. Trends Biochem. Sci. 30:279–281.

Shi, Y., and J. L. Manley. 2015. The end of the message: multiple protein-RNA interactions define the mRNA polyadenylation site. Genes Dev. 29:889–897.

Valadkhan, S. 2010. Role of the snRNAs in spliceosomal active site. RNA Biol. 7:345–353.

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Regulation of Pre-mRNA Processing

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Raponi, M., and D. Baralle. 2010. Alternative splicing: good and bad effects of translationally silent substitutions. FEBS J. 277:836–840.

Wang, E. T., et al. 2008. Alternative isoform regulation in human tissue transcriptomes. Nature 456:470–476.

Zheng, S., and D. L. Black. 2013. Alternative pre-mRNA splicing in neurons: growing up and extending its reach. Trends Genet. 29:442–448.

Zhong, X. Y., et al. 2009. SR proteins in vertical integration of gene expression from transcription to RNA processing to translation. Curr. Opin. Genet. Dev. 19:424–436.

Transport of mRNA Across the Nuclear Envelope

Cole, C. N., and J. J. Scarcelli. 2006. Transport of messenger RNA from the nucleus to the cytoplasm. Curr. Opin. Cell Biol. 18:299–306.

Field, M. C., L. Koreny, and M. P. Rout. 2014. Enriching the pore: splendid complexity from humble origins. Traffic 15:141–156.

Folkmann, A. W., et al. 2011. Dbp5, Gle1-IP6 and Nup159: a working model for mRNP export. Nucleus 2:540–548.

Grünwald, D., R. H. Singer, and M. Rout. 2011. Nuclear export dynamics of RNA-protein complexes. Nature 475:333–341.

Iglesias, N., and F. Stutz. 2008. Regulation of mRNP dynamics along the export pathway. FEBS Lett. 582:1987–1996.

Katahira, J., and Y. Yoneda. 2009. Roles of the TREX complex in nuclear export of mRNA. RNA Biol. 6:149–152.

Rodríguez-Navarro, S., and E. Hurt. 2011. Linking gene regulation to mRNA production and export. Curr. Opin. Cell Biol. 23:302–309.

Stewart, M. 2010. Nuclear export of mRNA. Trends Biochem. Sci. 35:609–617.

Wente, S. R., and M. P. Rout. 2010. The nuclear pore complex and nuclear transport. Cold Spring Harb. Perspect. Biol. 2(10):a000562.

Cytoplasmic Mechanisms of Post-transcriptional Control

Ambros, V. 2004. The functions of animal microRNAs. Nature 431:350–355.

Bar-Peled, L., and D. M. Sabatini. 2014. Regulation of mTORC1 by amino acids. Trends Cell Biol. 24:400–406.

Buchan, J. R., and R. Parker. 2009. Eukaryotic stress granules: the ins and outs of translation. Mol. Cell 36:932–941.

Carthew, R. W., and E. J. Sontheimer. 2009. Origins and mechanisms of miRNAs and siRNAs. Cell 136:642–655.

Doma, M. K., and R. Parker. 2007. RNA quality control in eukaryotes. Cell 131:660–668.

Eulalio, A., I. Behm-Ansmant, and E. Izaurralde. 2007. P bodies: at the crossroads of post-transcriptional pathways. Nat. Rev. Mol. Cell Biol. 8:9–22.

Fabian, M. R., N. Sonenberg, and W. Filipowicz. 2010. Regulation of mRNA translation and stability by microRNAs. Annu. Rev. Biochem. 79:351–379.

Ghildiyal, M., and P. D. Zamore. 2009. Small silencing RNAs: an expanding universe. Nat. Rev. Genet. 10:94–108.

Groppo, R., and J. D. Richter. 2009. Translational control from head to tail. Curr. Opin. Cell Biol. 21:444–451.

Hirokawa, N. 2006. mRNA transport in dendrites: RNA granules, motors, and tracks. J. Neurosci. 26:7139–7142.

Huntzinger, E., and E. Izaurralde. 2011. Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat. Rev. Genet. 12:99–110.

Ivshina, M., P. Lasko, and J. D. Richter. 2014. Cytoplasmic polyadenylation element binding proteins in development, health, and disease. Annu. Rev. Cell Dev. Biol. 30:393–415.

Jobson, R. W., and Y. L. Qiu. 2008. Did RNA editing in plant organellar genomes originate under natural selection or through genetic drift? Biol. Direct. 3:43.

Jonas, S., and E. Izaurralde. 2015. Towards a molecular understanding of microRNA-mediated gene silencing. Nat. Rev. Genet. 16:421–433.

Kato, M., et al. 2012. Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels. Cell 149:753–767.

Kidner, C. A., and R. A. Martienssen. 2005. The developmental role of microRNA in plants. Curr. Opin. Plant Biol. 8:38–44.

Leung, A. K., and P. A. Sharp. 2010. MicroRNA functions in stress responses. Mol. Cell 40:205–215.

Lodish, H. F., et al. 2008. Micromanagement of the immune system by microRNAs. Nat. Rev. Immunol. 8:120–130.

Maquat, L. E., W. Y. Tarn, and O. Isken. 2010. The pioneer round of translation: features and functions. Cell 142:368–374.

Martin, K. C., and A. Ephrussi. 2009. mRNA localization: gene expression in the spatial dimension. Cell 136:719–730.

Mello, C. C., and D. Conte Jr. 2004. Revealing the world of RNA interference. Nature 431:338–342. C. C. Mello’s Nobel Prize lecture can be viewed at http://nobelprize.org/nobel_prizes/medicine/laureates/2006/mello-lecture.html.

Michels, A. A. 2011. MAF1: a new target of mTORC1. Biochem. Soc. T. 39:487–491.

Mihaylova, M. M., and R. J. Shaw. 2011. The AMPK signalling pathway coordinates cell growth, autophagy and metabolism. Nat. Cell Biol. 13:1016–1023.

Parker, R., and H. Song. 2004. The enzymes and control of eukaryotic mRNA turnover. Nat. Struct. Mol. Biol. 11:121–127.

Richter, J. D., and N. Sonenberg. 2005. Regulation of cap-dependent translation by eIF4E inhibitory proteins. Nature 433:477–480.

Ruvkun, G. B. 2004. The tiny RNA world. Harvey Lect. 99:1–21.

Shaw, R. J. 2008. mTOR signaling: RAG GTPases transmit the amino acid signal. Trends Biochem. Sci. 33:565–568.

Simpson, L., et al. 2004. Mitochondrial proteins and complexes in Leishmania and Trypanosoma involved in U-insertion/deletion RNA editing. RNA 10:159–170.

Siomi, M. C., et al. 2011. PIWI-interacting small RNAs: the vanguard of genome defence. Nat. Rev. Mol. Cell Biol. 12:246–258.

Willis, I. M., and R. D. Moir. 2007. Integration of nutritional and stress signaling pathways by Maf1. Trends Biochem. Sci. 32:51–53.

Wullschleger, S., R. Loewith, and M. N. Hall. 2006. TOR signaling in growth and metabolism. Cell 124:471–484.

Zhang, H., J. M. Maniar, and A. Z. Fire. 2011. “Inc-miRs”: functional intron-interrupted miRNA genes. Genes Dev. 25:1589–1594. A. Z. Fire’s Nobel Prize lecture can be viewed at http://nobelprize.org/nobel_prizes/medicine/laureates/2006/fire-lecture.html.

Zoncu, R., A. Efeyan, and D. M. Sabatini. 2011. mTOR: from growth signal integration to cancer, diabetes and ageing. Nat. Rev. Mol. Cell Biol. 12:21–35.

Processing of rRNA and tRNA

Evans, D., S. M. Marquez, and N. R. Pace. 2006. RNase P: interface of the RNA and protein worlds. Trends Biochem. Sci. 31:333–341.

Fatica, A., and D. Tollervey. 2002. Making ribosomes. Curr. Opin. Cell Biol. 14:313–318.

Hage, A. E., and D. Tollervey. 2004. A surfeit of factors: why is ribosome assembly so much more complicated in eukaryotes than bacteria? RNA Biol. 1:10–15.

Hamma, T., and A. R. Ferré-D’Amaré. 2010. The box H/ACA ribonucleoprotein complex: interplay of RNA and protein structures in post-transcriptional RNA modification. J. Biol. Chem. 285:805–809.

Handwerger, K. E., and J. G. Gall. 2006. Subnuclear organelles: new insights into form and function. Trends Cell Biol. 16:19–26.

Hopper, A. K., and H. Y. Huang. 2015. Quality control pathways for nucleus-encoded eukaryotic tRNA biosynthesis and subcellular trafficking. Mol. Cell Biol. 35:2052–2058.

Januszyk, K., and C. D. Lima. 2014. The eukaryotic RNA exosome. Curr. Opin. Struct. Biol. 24:132–140.

Kressler, D., E. Hurt, and J. Bassler. 2010. Driving ribosome assembly. Biochim. Biophys. Acta 1803:673–683.

Liang, B., and H. Li. 2011. Structures of ribonucleoprotein particle modification enzymes. Quart. Rev. Biophys. 44:95–122.

Marvin, M. C., and D. R. Engelke. 2009. RNase P: increased versatility through protein complexity? RNA Biol. 6:40–42.

Nizami, Z., S. Deryusheva, and J. G. Gall. 2010. The Cajal body and histone locus body. Cold Spring Harb. Perspect. Biol. 2:a000653.

Phizicky, E. M., and A. K. Hopper. 2010. tRNA biology charges to the front. Genes 24:1832–1860.

Schmid, M., and T. H. Jensen. 2008. The exosome: a multipurpose RNA-decay machine. Trends Biochem. Sci. 33:501–510.

Stahley, M. R., and S. A. Strobel. 2006. RNA splicing: group I intron crystal structures reveal the basis of splice site selection and metal ion catalysis. Curr. Opin. Struct. Biol. 16:319–326.

Tschochner, H., and E. Hurt. 2003. Pre-ribosomes on the road from the nucleolus to the cytoplasm. Trends Cell Biol. 13:255–263.

Turowski, T. W., and D. Tollervey. 2015. Cotranscriptional events in eukaryotic ribosome synthesis. Wiley Interdiscip. Rev. RNA 6:129–139.