My lab studies retroviral gene expression at the post-transcriptional level. An unusual feature of all retroviruses is that their primary RNA transcript is both a major viral mRNA, encoding capsid proteins, and a pre-mRNA. In addition, this unspliced RNA is packaged into viral particles as genomic RNA. We study control of retroviral RNA splicing, stability, and export. We have identified a Negative Regulator of Splicing (NRS) RNA element within the avian retroviral RNA intron, which helps maintain a portion of the primary transcripts as unspliced mRNA and genomic RNA. We are currently exploring the 3D structure of the NRS RNA (see Figure below) and the mechanism of its splicing suppression. The NRS behaves like a defective 5' splice site, binding all of the splicing snRNPs, and interacting with 3' splice sites. It appears to compete with the authentic 5' splice site for interactions with 3' splice sites. While the NRS pseudo-spliceosome contains all of the splicing snRNPs, their arrangement is aberrant. We have observed the pRP8 splicing scaffold protein is not localized in the pseudo-spliceosome. Recently, we have also found that the NRS promotes polyadenylation in vitro. Inactivating mutations in the NRS of an avian leukosis virus have been associated with rapid-onset chicken lymphomas, involving viral integration into the c-myb locus. These tumors have been characterized by transcriptional profiling using chicken microarrays. We are also investigating possible additional integration sites. In several tumors, we have found viral integrations upstream of the telomerase reverase transcriptase (TERT) and associated over-expression of TERT and telomerase activity. We are also studying the role of micro-RNAs in tumors. We are identifying targets of mir155 (bic), a miRNA that is over-expressed in metastatic chicken and human tumors. In addition, we are exploring the mechanism of nonsense-mediated RNA decay (NMD), induced by premature termination codons in the gag gene of unspliced retroviral RNAs. This is particularly interesting because NMD in higher organisms is thought to be coupled to splicing, and the deposition of exon-junction complexes. We have shown that NMD of unspliced viral RNAs is dependent on Upf1 and translation. Further, we have observed a stability element downstream of the normal gag termination codon. When these downstream sequences are removed, the RNA undergoes NMD. We think these stability sequences may be necessary to stabilize RNAs having a 7 kb 3' UTR, which is much longer than normal. 
NMR structure of NRS pseudo-5' splice site Wilusz JE, Beemon KL. (2006). The negative regulator of splicing element of rous sarcoma virus promotes polyadenylation. J Virol. 80(19):9634-40. Weil, J.E. and Beemon, K.L. (2006). A 3' UTR sequence stabilizes termination codons in the unspliced RNA of Rous sarcoma virus. RNA 12:102-10. Giles, K.E. and Beemon, K.L. (2005). Retroviral splicing suppressor sequesters a 3' splice site in a 50S aberrant splicing complex. Mol Cell Biol 25:4397-405. Cabello-Villegas, J., Giles, K.E., Soto, A.M., Ping, Y., Mougin, A., Beemon, K.L. and Wang, Y-X. (2004). Solution structure of the pseudo-5' splice site of a retroviral splicing suppressor. RNA 10: 1388-1398. LeBlanc, J.J. and K.L. Beemon. (2004). Unspliced Rous sarcoma virus genomic RNAs are translated and subjected to nonsense-mediated mRNA decay before packaging. J. Virol. 78:5139-5146. Giles K.E., M. Caputi, and K.L. Beemon K.L. (2004). Packaging and reverse transcription of snRNAs by retroviruses may generate pseudogenes.RNA 10: 299-307. Polony, T.S., S.J. Bowers, P.E. Neiman, and K.L. Beemon. (2003). Silent point mutation in an avian retrovirus RNA processing element promotes c-myb associated short-latency lymphomas. J. Virol. 77:9378-9387. Neiman, P.E., J.J. Grbic, T. Polony, R. Kimmel, S.J. Bowers, J. Delrow, and K.L. Beemon. (2003). Functional genomic analysis reveals distinct neoplastic phenotypes associated with c-myb mutation in the bursa of Fabricius. Oncogene 22:1073-1086. Caputi, M., Kendzior, R.J., and Beemon, K.L. (2002). A nonsense mutation in the fibrillin-1 gene of a Marfan syndrome patient induces NMD and disrupts an SC35-dependent splicing enhancer. Genes Dev. 16:1754-1759.
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