REFERENCES
- Ahn, S. H., M. Kim, and S. Buratowski. 2004. Phosphorylation of serine 2 within the RNA polymerase II C-terminal domain couples transcription and 3′ end processing. Mol. Cell 13:67–76.
- Andres, A. J., J. C. Fletcher, F. D. Karim, and C. S. Thummel. 1993. Molecular analysis of the initiation of insect metamorphosis: a comparative study of Drosophila ecdysteroid-regulated transcription. Dev. Biol. 160:388–404.
- Andrulis, E. D., E. Guzman, P. Doring, J. Werner, and J. T. Lis. 2000. High-resolution localization of Drosophila Spt5 and Spt6 at heat shock genes in vivo: roles in promoter proximal pausing and transcription elongation. Genes Dev. 14:2635–2649.
- Andrulis, E. D., J. Werner, A. Nazarian, H. Erdjument-Bromage, P. Tempst, and J. T. Lis. 2002. The RNA processing exosome is linked to elongating RNA polymerase II in Drosophila. Nature 420:837–841.
- Ashburner, M. 1978. Puffing of polytene chromosomes, p. 316-376. In M. Ashburner and T. R. F. Wright (ed.), The genetics and biology of Drosophila, vol. 2b. Academic Press, London, United Kingdom.
- Blackshear, P. J. 2002. Tristetraprolin and other CCCH tandem zinc-finger proteins in the regulation of mRNA turnover. Biochem. Soc. Trans. 30:945–952.
- Boehm, A. K., A. Saunders, J. Werner, and J. T. Lis. 2003. Transcription factor and polymerase recruitment, modification, and movement on dhsp70 in vivo in the minutes following heat shock. Mol. Cell. Biol. 23:7628–7637.
- Bonisch, C., C. Temme, B. Moritz, and E. Wahle. 2007. Degradation of hsp70 and other mRNAs in Drosophila via the 5′-3′ pathway and its regulation by heat shock. J. Biol. Chem. 282:21818–21828.
- Bousquet-Antonelli, C., C. Presutti, and D. Tollervey. 2000. Identification of a regulated pathway for nuclear pre-mRNA turnover. Cell 102:765–775.
- Burkard, K. T., and J. S. Butler. 2000. A nuclear 3′-5′ exonuclease involved in mRNA degradation interacts with poly(A) polymerase and the hnRNA protein Npl3p. Mol. Cell. Biol. 20:604–616.
- Ciais, D., M. T. Bohnsack, and D. Tollervey. 2008. The mRNA encoding the yeast ARE-binding protein Cth2 is generated by a novel 3′ processing pathway. Nucleic Acids Res. 36:3075–3084.
- Couttet, P., M. Fromont-Racine, D. Steel, R. Pictet, and T. Grange. 1997. Messenger RNA deadenylylation precedes decapping in mammalian cells. Proc. Natl. Acad. Sci. USA 94:5628–5633.
- D'Avino, P. P., S. Crispi, L. C. Polito, and M. Furia. 1995. The role of the BR-C locus on the expression of genes located at the ecdysone-regulated 3C puff of Drosophila melanogaster. Mech. Dev. 49:161–171.
- Fridell, R. A., A. M. Pret, and L. L. Searles. 1990. A retrotransposon 412 insertion within an exon of the Drosophila melanogaster vermilion gene is spliced from the precursor RNA. Genes Dev. 4:559–566.
- Fridell, R. A., and L. L. Searles. 1994. Evidence for a role of the Drosophila melanogaster suppressor of sable gene in the pre-mRNA splicing pathway. Mol. Cell. Biol. 14:859–867.
- Gatfield, D., L. Unterholzner, F. D. Ciccarelli, P. Bork, and E. Izaurralde. 2003. Nonsense-mediated mRNA decay in Drosophila: at the intersection of the yeast and mammalian pathways. EMBO J. 22:3960–3970.
- Geyer, P. K., A. J. Chien, V. G. Corces, and M. M. Green. 1991. Mutations in the su(s) gene affect RNA processing in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 88:7116–7120.
- Glisovic, T., J. L. Bachorik, J. Yong, and G. Dreyfuss. 2008. RNA-binding proteins and post-transcriptional gene regulation. FEBS Lett. 582:1977–1986.
- Graham, A. C., D. L. Kiss, and E. D. Andrulis. 2006. Differential distribution of exosome subunits at the nuclear lamina and in cytoplasmic foci. Mol. Biol. Cell 17:1399–1409.
- Hackett, R. W., and J. T. Lis. 1981. DNA sequence analysis reveals extensive homologies of regions preceding hsp70 and alphabeta heat shock genes in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 78:6196–6200.
- Hirose, Y., and Y. Ohkuma. 2007. Phosphorylation of the C-terminal domain of RNA polymerase II plays central roles in the integrated events of eucaryotic gene expression. J. Biochem. 141:601–608.
- Houseley, J., K. Kotovic, A. El Hage, and D. Tollervey. 2007. Trf4 targets ncRNAs from telomeric and rDNA spacer regions and functions in rDNA copy number control. EMBO J. 26:4996–5006.
- Houseley, J., J. LaCava, and D. Tollervey. 2006. RNA-quality control by the exosome. Nat. Rev. Mol. Cell Biol. 7:529–539.
- Houseley, J., and D. Tollervey. 2009. The many pathways of RNA degradation. Cell 136:763–776.
- Kaminker, J. S., C. M. Bergman, B. Kronmiller, J. Carlson, R. Svirskas, S. Patel, E. Frise, D. A. Wheeler, S. E. Lewis, G. M. Rubin, M. Ashburner, and S. E. Celniker. 2002. The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective. Genome Biol. 3: RESEARCH0084.
- Kim, N., J. Kim, D. Park, C. Rosen, D. Dorsett, and J. Yim. 1996. Structure and expression of wild-type and suppressible alleles of the Drosophila purple gene. Genetics 142:1157–1168.
- Kuan, Y. S., P. Brewer-Jensen, and L. L. Searles. 2004. Suppressor of sable, a putative RNA-processing protein, functions at the level of transcription. Mol. Cell. Biol. 24:3734–3746.
- LaCava, J., J. Houseley, C. Saveanu, E. Petfalski, E. Thompson, A. Jacquier, and D. Tollervey. 2005. RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 121:713–724.
- Lehmann, M., and G. Korge. 1995. Ecdysone regulation of the Drosophila Sgs-4 gene is mediated by the synergistic action of ecdysone receptor and SEBP 3. EMBO J. 14:716–726.
- Lis, J. T., D. Ish-Horowicz, and S. M. Pinchin. 1981. Genomic organization and transcription of the alpha beta heat shock DNA in Drosophila melanogaster. Nucleic Acids Res. 9:5297–5310.
- Matunis, E. L., R. Kelley, and G. Dreyfuss. 1994. Essential role for a heterogeneous nuclear ribonucleoprotein (hnRNP) in oogenesis: hrp40 is absent from the germ line in the dorsoventral mutant squid. Proc. Natl. Acad. Sci. USA 91:2781–2784.
- Matunis, E. L., M. J. Matunis, and G. Dreyfuss. 1993. Association of individual hnRNP proteins and snRNPs with nascent transcripts. J. Cell Biol. 121:219–228.
- Moore, M. J. 2005. From birth to death: the complex lives of eukaryotic mRNAs. Science 309:1514–1518.
- Murray, M. V., M. A. Turnage, K. J. Williamson, W. R. Steinhauer, and L. L. Searles. 1997. The Drosophila suppressor of sable protein binds to RNA and associates with a subset of polytene chromosome bands. Mol. Cell. Biol. 17:2291–2300.
- Muskavitch, M. A., and D. S. Hogness. 1980. Molecular analysis of a gene in a developmentally regulated puff of Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 77:7362–7366.
- Narita, T., Y. Yamaguchi, K. Yano, S. Sugimoto, S. Chanarat, T. Wada, D. K. Kim, J. Hasegawa, M. Omori, N. Inukai, M. Endoh, T. Yamada, and H. Handa. 2003. Human transcription elongation factor NELF: identification of novel subunits and reconstitution of the functionally active complex. Mol. Cell. Biol. 23:1863–1873.
- Ni, Z., B. E. Schwartz, J. Werner, J. R. Suarez, and J. T. Lis. 2004. Coordination of transcription, RNA processing, and surveillance by P-TEFb kinase on heat shock genes. Mol. Cell 13:55–65.
- Norvell, A., R. L. Kelley, K. Wehr, and T. Schupbach. 1999. Specific isoforms of squid, a Drosophila hnRNP, perform distinct roles in Gurken localization during oogenesis. Genes Dev. 13:864–876.
- O'Connell, P. O., and M. Rosbash. 1984. Sequence, structure, and codon preference of the Drosophila ribosomal protein 49 gene. Nucleic Acids Res. 12:5495–5513.
- Phatnani, H. P., and A. L. Greenleaf. 2006. Phosphorylation and functions of the RNA polymerase II CTD. Genes Dev. 20:2922–2936.
- Ross, J. 1995. mRNA stability in mammalian cells. Microbiol. Rev. 59:423–450.
- Roth, K. M., M. K. Wolf, M. Rossi, and J. S. Butler. 2005. The nuclear exosome contributes to autogenous control of NAB2 mRNA levels. Mol. Cell. Biol. 25:1577–1585.
- Saunders, A., J. Werner, E. D. Andrulis, T. Nakayama, S. Hirose, D. Reinberg, and J. T. Lis. 2003. Tracking FACT and the RNA polymerase II elongation complex through chromatin in vivo. Science 301:1094–1096.
- Simon, J. A., and J. T. Lis. 1987. A germline transformation analysis reveals flexibility in the organization of heat shock consensus elements. Nucleic Acids Res. 15:2971–2988.
- Simon, J. A., C. A. Sutton, R. B. Lobell, R. L. Glaser, and J. T. Lis. 1985. Determinants of heat shock-induced chromosome puffing. Cell 40:805–817.
- So, W. V., and M. Rosbash. 1997. Post-transcriptional regulation contributes to Drosophila clock gene mRNA cycling. EMBO J. 16:7146–7155.
- Thiebaut, M., E. Kisseleva-Romanova, M. Rougemaille, J. Boulay, and D. Libri. 2006. Transcription termination and nuclear degradation of cryptic unstable transcripts: a role for the nrd1-nab3 pathway in genome surveillance. Mol. Cell 23:853–864.
- Turnage, M. A., P. Brewer-Jensen, W. L. Bai, and L. L. Searles. 2000. Arginine-rich regions mediate the RNA binding and regulatory activities of the protein encoded by the Drosophila melanogaster suppressor of sable gene. Mol. Cell. Biol. 20:8198–8208.
- Vasiljeva, L., and S. Buratowski. 2006. Nrd1 interacts with the nuclear exosome for 3′ processing of RNA polymerase II transcripts. Mol. Cell 21:239–248.
- Voelker, R. A., W. Gibson, J. P. Graves, J. F. Sterling, and M. T. Eisenberg. 1991. The Drosophila suppressor of sable gene encodes a polypeptide with regions similar to those of RNA-binding proteins. Mol. Cell. Biol. 11:894–905.
- Weeks, J. R., S. E. Hardin, J. Shen, J. M. Lee, and A. L. Greenleaf. 1993. Locus-specific variation in phosphorylation state of RNA polymerase II in vivo: correlations with gene activity and transcript processing. Genes Dev. 7:2329–2344.
- Wolin, S. L., and K. M. Reinisch. 2006. The Ro 60 kDa autoantigen comes into focus: interpreting epitope mapping experiments on the basis of structure. Autoimmun. Rev. 5:367–372.
- Wyers, F., M. Rougemaille, G. Badis, J. C. Rousselle, M. E. Dufour, J. Boulay, B. Regnault, F. Devaux, A. Namane, B. Seraphin, D. Libri, and A. Jacquier. 2005. Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121:725–737.
- Yost, H. J., and S. Lindquist. 1986. RNA splicing is interrupted by heat shock and is rescued by heat shock protein synthesis. Cell 45:185–193.