Professor   16a Mudd Hall Biology Johns Hopkins University 3400 N. Charles Street Baltimore, MD 21218-2685   Email: KLB@jhu.edu Office 410 516-7289 Lab 410 516-8236 Departmental fax 410 516-5213   B.S. University of Michigan Ph.D. University of California, Berkeley Postdoctoral University of California, Berkeley The Salk Institute

Research Interests

Retroviral RNA Processing, Avian Leukosis Virus Tumorigenesis, micro-RNAs

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. 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 micro-RNA that is over-expressed in 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 long 3' UTR.

NMR structure of  NRS pseudo-5' splice site

Representative Publications

Withers, J.B., Ashvetiya, T., and Beemon, K.L. 2012.  Exclusion of exon 2 is a common mRNA splice variant of primate telomerase reverse transcriptases. PLOS One.

Bolisetty, M.T., Blomberg, J., Benachenhou, F., Sperber, G.O., and Beemon, K.L. 2012.  Unexpected diversity and expression of avian endogenous retroviruses. Mbio vol. 3, issue 5 e00344-12. Supplementary data: Consensus sequences of avian ERVs

Bolisetty, M.T. and Beemon, K.L. 2012.  Splicing of internal large exons is defined by novel cis-acting sequence elements. Nucleic Acids Res. doi:10.1093/nar/gks652

Withers, J.B. and Beemon, K.L. 2011.  The structure and function of the Rous sarcoma virus RNA stability element. Journal of Cellular Biochemistry doi: 10.1002/jcb.23272

Beemon, K.L. and Rosenberg, N.E. 2011.  Mechanisms of Oncogenesis by Avian and Murine Retroviruses. pp. 677-704 in Cancer-associated Viruses (Robertson, E.S., ed.) Springer.

Withers, J.B. and Beemon, K.L. 2010.  Structural features in the Rous sarcoma virus RNA stability element are necessary for sensing the correct termination codon. Retrovirology 7:65-80.

Bolisetty MT, Dy G, Tam W, Beemon KL. 2009.  Reticuloendotheliosis virus strain T induces miR-155 which targets JARID2 and promotes cell survival. J. Virology 83:12009-12017

Weil, J.E., Hadjithomas, M., and K.L. Beemon. 2009. Structural characterization of the Rous sarcoma virus RNA stability element. J Virol. 83:2119-29.

Yang, F, Xian, R.R., Li, Y., Polony, T. and Beemon, K.L. 2007.  Telomerase reverse transcriptase expression elevated by avian leukosis virus integration in B cell lymphomas. Proc. Natl. Acad. Sci. USA. 104:18952-7.

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.

Lab Members

Postdoctoral Fellows:

Scott Johnson
Mohan Bolisetty

Graduate Students:

James Justice
Bao Lin Quek

Undergraduate Student:

Anthony Gacita

Technician:

YingYing Li