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Genetics. 2014 Jul;197(3):839-49. doi: 10.1534/genetics.114.163279. Epub 2014 May 1.

Transcription-independent functions of an RNA polymerase II subunit, Rpb2, during genome rearrangement in the ciliate, Oxytricha trifallax.

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Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544.
Princeton Collaborative Proteomics and Mass Spectrometry Center, Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544.
Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544


The RNA polymerase II (Pol-II) holoenzyme, responsible for messenger RNA production, typically consists of 10-12 subunits. Our laboratory previously demonstrated that maternally deposited, long, noncoding, template RNAs are essential for programmed genome rearrangements in the ciliate Oxytricha trifallax. Here we show that such RNAs are bidirectionally transcribed and transported to the zygotic nucleus. The gene encoding the second-largest subunit of Pol-II, Rpb2, has undergone gene duplication, and the two paralogs, Rpb2-a and -b, display different expression patterns. Immunoprecipitation of double-stranded RNAs identified an association with Rpb2-a. Through immunoprecipitation and mass spectrometry, we show that Rpb2-a in early zygotes appears surprisingly unassociated with other Pol II subunits. A partial loss of function of Rpb2-a leads to an increase in expression of transposons and other germline-limited satellite repeats. We propose that evolutionary divergence of the Rpb2 paralogs has led to acquisition of transcription-independent functions during sexual reproduction that may contribute to the negative regulation of germline gene expression.


RNA polymerase; genome integrity; noncoding RNAs; transcription

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