Regulation of RNA Polymerase II by non-coding RNAs

All cells respond to stress, and do so in part by altering gene expression. When eukaryotic cells are subjected to heat shock, general RNA polymerase II transcription decreases at the same time as transcription of a set of heat shock specific genes increases. Two non-coding RNAs (mouse B2 RNA and human Alu RNA) are transcriptionally upregulated upon heat shock. We have found that these ncRNAs bind RNA polymerase II with high affinity (low nM) and block the formation of functional initiation complexes in vitro. Our studies show that each of the ncRNAs binds the catalytic cleft of RNA polymerase II and that it is recruited with the polymerase into complexes assembling at promoters where it keeps the polymerase from properly engaging the DNA. Surprisingly, B2 RNA serves as a substrate and a template for the RNA-dependent RNA polymerase (RdRP) activity of RNA polymerase II. Specifically, RNA polymerase II adds 18 nucleotides of defined sequence to the 3' end of B2 RNA, which results in a dramatic decrease in the stability of the ncRNA in cells. We are now studying the function of B2 RNA and Alu RNA as transcriptional repressors genome-wide during heat shock, investigating the roles of these ncRNAs in controlling host cell transcription during herpes virus infection, and determining the general role of the RNA polymerase II RdRP activity in mammalian cells.

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Publications:

Ponicsan, S.L., Houel, S., Old, W.M., Ahn, N.G., Goodrich, J.A., Kugel, J.F. (2013). The non-coding B2 RNA binds to the DNA cleft and active site region of RNA polymerase II. J. Mol. Biol. Epub ahead of print.

Wagner, S.D., Yakovchuk, P., Gilman, B., Poniscan, S.L., Drullinger, L.F., Kugel, J.F., Goodrich, J.A. (2013). Mammalian RNA polymerase II acts as an RNA-dependent RNA polymerase to extend and destabilize a non-coding RNA. EMBO J. Epub ahead of print.

Yakovchuk, P., Goodrich, J.A., Kugel, J.F. (2011) B2 RNA represses TFIIH phosphorylation of RNA polymerase II.. Transcription. Jan;2(1):45-49

Yakovchuk, P., Gilman B., Goodrich, J.A., Kugel, J.F. (2010) RNA polymerase II and TAFs undergo a slow isomerization after the polymerase is recruited to promoter-bound TFIID.. J Mol Biol. 397(1):57-68

Wagner, S.D., Kugel, J.F., Goodrich, J.A. (2010) TFIIF facilitates dissociation of RNA polymerase II from noncoding RNAs that lack a repression domain.. Mol Cell Biol.30(1):91-7

Yakovchuk, P., Goodrich, J.A., Kugel, J.F. (2009) B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes. Proc Natl Acad Sci U S A. 106(14):5569-74

Espinoza, C.A., Goodrich, J.A., and Kugel, J.F. (2007). Characterization of the structure, function and mechanism of B2 RNA, an ncRNA repressor of RNA polymerase II transcription. RNA. 13: 583-596.

Goodrich, J.A. and Kugel, J.F. (2006). Noncoding RNA regulators of RNA polymerase II transcription. Nature Rev. Mol. Cell Biol. 7: 612-616.

Espinoza, C.A., Allen, T.A., Hieb, A.R., Kugel, J.F., and Goodrich, J.A. (2004). B2 RNA binds directly to RNA polymerase II to repress transcript synthesis. Nature Struct. Mol. Biol. 11: 822-829.

Allen, T.A., Von Kaenel, S., Goodrich, J.A., and Kugel, J.F. (2004). The SINE encoded mouse B2 RNA represses mRNA transcription in response to heat shock. Nature Struct. Mol. Biol. 11: 816-821.

Kugel, J.F. and Goodrich, J.A. (1998). Promoter escape limits the rate of transcription from the adenovirus major late promoter on negatively supercoiled templates. Proc. Natl. Acad. Sci. 95: 9232-9237.