The pervasiveness of RNA synthesis in eukaryotes is largely the result of RNA polymerase II (Pol II)-mediated transcription, and termination of its activity is necessary to partition the genome and maintain the proper expression of neighbouring genes. Despite its ever-increasing biological significance, transcription termination remains one of the least understood processes in gene expression. However, recent mechanistic studies have revealed a striking convergence among several overlapping models of termination, including the poly(A)- and Sen1-dependent pathways, as well as new insights into the specificity of Pol II termination among its diverse gene targets. Broader knowledge of the role of Pol II carboxy-terminal domain phosphorylation in promoting alternative mechanisms of termination has also been gained.

Background: Rat1 is an exoribonuclease that functions in Pol II transcription termination. Results: Rat1 releases stalled Pol II in vitro, and Rtt103 restores termination activity to an exonucleolytic deficient Rat1 mutant. Conclusion: Exonucleolytic activity is not the Rat1 function that is ultimately responsible for dislodging Pol II. Significance: Understanding molecular details governing termination is key to understanding how it contributes to correct gene expression.

Summary Expansions of microsatellite repeats are responsible for numerous hereditary diseases in humans, including myotonic dystrophy and Friedreich’s ataxia. While the length of an expandable repeat is the main factor determining disease inheritance, recent data point to genomic trans-modifiers that can impact the likelihood of expansions and disease progression. Detection of these modifiers may lead to understanding and treating repeat expansion diseases. Here we describe a method for the rapid, genome-wide identification of trans-modifiers for repeat expansion in a yeast experimental system. Using this method, we found that missense mutations in the endoribonuclease subunit (Ysh1) of the mRNA cleavage and polyadenylation complex dramatically increase the rate of (GAA)n repeat expansions, but only when they are actively transcribed. These expansions correlate with slower transcription elongation caused by the ysh1 mutation. These results reveal a previously unsuspected interplay between RNA processing and repeat-mediated genome instability, confirming the validity of our approach.

SUMMARY 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 predominately 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.