We found that a mouse non-coding RNA, B2 RNA, binds RNA polymerase II with high affinity in the catalytic cleft of RNA polymerase II. We further discovered that 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 level of this ncRNA in the nuclei of cells. We are now studying the general role of the RNA polymerase II RdRP activity in mammalian cells.

B2 RNA extension is templatedModel of Pol II RdRP activity

Relevant research publications:

  • Eidem, T.M., Kugel, J.F., Goodrich, J.A. (2016). Noncoding RNAs: regulators of the mammalian transcription machinery. J. Mol. Biol. 428: 2652-2659
  • Ponicsan, S.L., Kugel, J.F., and Goodrich, J.A.  (2015).  Repression of RNA polymerase II transcription by B2 RNA depends on a specific pattern of structural regions in the RNA.  Non-coding RNA.  1: 4-16.
  • Kassube, S.A., Fang, J., Grob, P., Yakovchuk, P., Goodrich, J.A., and Nogales, E.  (2013).  Structural insights into transcriptional repression by ncRNAs that bind to human Pol II.  J. Mol. Biol. 425: 3639-3648.
  • Ponicsan, S.L., Houel, S., Old, W.M., Ahn, N.G., Goodrich, J.A., and 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.  425: 3625-3638.
  • Wagner, S.D., Yakovchuk, P., Gilman, B., Ponicsan, 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.  32: 781-790.
  • Yakovchuk, P., Goodrich, J.A., and 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. USA.  106: 5569-5574.
  • 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.
  • 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.