Abstract
Current models of transcription termination factor recruitment to the RNA polymerase II (Pol II) transcription complex rely exclusively on the direct interaction between the termination factor and phosphorylated isoforms of the Pol II C-terminal domain (CTD). Here, we report that the Pol II flap loop is needed for physical interaction of Pol II with the Pcf11/Clp1 subcomplex of cleavage factor IA (CF IA), which functions in both 3? end processing and Pol II termination, and for proper termination of short RNAs in vitro and in vivo. Deletion of the flap loop reduces the in vivo interaction of Pol II with CF IA but increases the association of Nrd1 during stages of the transcription cycle when the CTD is predominantly Ser5 phosphorylated. We propose a model in which the flap loop coordinates a binding equilibrium between the competing termination factors Pcf11 and Nrd1 to Pol II during termination of short RNA synthesis.
Highlights
polymerase II (Pol II) is responsible for transcribing all protein-coding RNAs as well as some non-coding RNAs, such as small nucleolar RNAs, in eukaryotes
We find that the flap loop mediates interaction of Cleavage Factor IA (CF IA) with Pol II, thereby providing the first evidence that structural features of the Pol II body are important for termination factor binding
This feature is conserved in eukaryotes, raising the possibility that it contributes to proper Pol II termination (Kuehner et al, 2011)
Summary
Pol II is responsible for transcribing all protein-coding RNAs (mRNAs) as well as some non-coding RNAs, such as small nucleolar RNAs (snoRNAs), in eukaryotes. In a manner that is dependent upon the stage of transcription, the CTD is differentially phosphorylated at serines in positions 2, 5 and 7 and tyrosine at position 1 (Mayer et al, 2012; Heidemann, et al, 2013) These differential phosphorylation patterns help recruit and subsequently release specific classes of accessory factors to the Pol II transcription complex in ways that influence transcription initiation, elongation, termination and RNA processing (Hsin and Manley, 2012). Evidence accumulated over the last decade points to the importance of specific protein-CTD interactions in choosing between two main termination pathways and facilitating proper Pol II termination. These two pathways include the poly(A)-dependent pathway (the Rat pathway) and the poly(A)-independent pathway (Sen1/Nrd pathway)
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