All cells respond to stress and do so in part by altering gene expression. When eukaryotic cells are subjected to the stress of heat shock, general RNA polymerase II transcription decreases at the same time as transcription of a set of heat shock specific genes increases. We are performing a series of genomic studies to understand mechanisms by which heat shock causes global changes in the mRNA transcription program in human and mouse cells. Another profound cellular stress that causes global changes in transcription is viral infection. We are using herpes simplex virus type 1 (HSV-1) as a model system to study how infection of mammalian cells causes a global decrease in RNA polymerase II occupancy on the host cell genome, while co-opting the polymerase to transcribe its genes. Interestingly, using ChIP-seq of RNA polymerase II we observed many genes that respond differently to HSV-1 infection and heat shock (two examples are shown in the figure below).

Effects of heat shock and HSV-1 infection

Among the factors involved in regulating transcription during heat shock are two non-coding RNAs (mouse B2 RNA and human Alu RNA). Levels of these ncRNAs increase during heat shock and other cellular stresses. 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. We are studying the function of B2 RNA and Alu RNA as transcriptional repressors genome-wide during heat shock.

B2 and Alu RNA repress transcription

Relevant research publications:

  • Cardiello, J.F., Goodrich, J.A., Kugel, J.F. (2018). Heat shock causes a reversible increase in RNA polymerase II occupancy downstream of mRNA genes, consistent with a global loss in transcriptional termination. Mol. Cell. Biol. 38: e00181-18
  • Abrisch, R.G., Eidem, T.M., Yakovchuk, P., Kugel, J.F., and Goodrich, J.A.  (2016).  Infection by Herpes Simplex Virus Type-1 causes near-complete loss of RNA polymerase II occupancy on the host cell genome.  J. Virology.  90: 2503-2513.
  • 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.  (2011).  B2 RNA represses TFIIH phosphorylation of RNA polymerase II.  Transcription.  2: 45-49.
  • Wagner, S.D., Kugel, J.F., and Goodrich, J.A.  (2010).  TFIIF facilitates dissociation of RNA polymerase II from ncRNAs that lack a repression domain.  Mol. Cell. Biol.  30: 91-97.
  • 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.
  • Mariner, P.D., Walters, R.D., Espinoza, C.A., Drullinger, L.F., Wagner, S.D., Kugel, J.F., and Goodrich, J.A.  (2008).  Human Alu ncRNA is a modular transacting repressor of mRNA transcription during heat shock.  Mol. Cell.  29: 499-509.
  • 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.