"B2 RNA binds directly to RNA polymerase II to repress transcript synthesis".

Celso A Espinoza ^{1, 2}, Tiffany A Allen ^{1, 2}, Aaron R Hieb ¹, Jennifer F Kugel ¹, and James A Goodrich ¹

¹ Department of Chemistry and Biochemistry, University of Colorado at Boulder, 215 UCB, Boulder, Colorado 80309-0215, USA.

² These authors contributed equally to this work.

Correspondence should be addressed to:
Jennifer F Kugel:    jennifer.kugel@colorado.edu or
James A Goodrich:    james.goodrich@colorado.edu

B2 RNA is a small noncoding RNA polymerase III transcript that represses mRNA transcription in
response to heat shock in mouse cells. Here we define the mechanism by which B2 RNA inhibits RNA
polymerase II (Pol II) transcription. Using a purified Pol II transcription system, we found that B2 RNA
potently inhibits transcription by binding to core Pol II with high affinity and specificity. Through this
interaction, B2 RNA assembles into preinitiation complexes at the promoter and blocks RNA synthesis.
Once B2 RNA is removed from preinitiation complexes, transcriptional activity is restored. Our studies
describe a previously unobserved mechanism of transcriptional repression by a small RNA and suggest
that B2 RNA associates with Pol II at promoters in heat shocked cells to actively inhibit transcription.

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