Termination of Transcription of Short Noncoding RNAs by RNA Polymerase II

Abstract

The RNA polymerase II transcription cycle is often divided into three major stages: initiation, elongation, and termination. Research over the last decade has blurred these divisions and emphasized the tightly regulated transitions that occur as RNA polymerase II synthesizes a transcript from start to finish. Transcription termination, the process that marks the end of transcription elongation, is regulated by proteins that interact with the polymerase, nascent transcript, and/or chromatin template. The failure to terminate transcription can cause accumulation of aberrant transcripts and interfere with transcription at downstream genes. Here, we review the mechanism, regulation, and physiological impact of a termination pathway that targets small noncoding transcripts produced by RNA polymerase II. We emphasize the Nrd1-Nab3-Sen1 pathway in yeast, in which the process has been extensively studied. The importance of understanding small RNA termination pathways is underscored by the need to control noncoding transcription in eukaryotic genomes.

Keywords: Nab3; Nrd1; Sen1; helicase; ribonucleoprotein.

Figure 1

The domain structure of the Nab3, Nrd1, and Sen1 proteins of Saccharomyces cerevisiae. The lengths of the proteins are indicated to the right (in amino acids). The boxes indicating domains are approximately to scale within their proteins. The Nrd1 interaction domain of Nab3 (NrdID; amino acids 204–248), the C-terminal domain (CTD) interaction domain of Nrd1 (CID; amino acids 6–151), and the Nab3 interaction domain of Nrd1 (NabID; amino acids 151–214) are those defined by Vasiljeva et al. (42). The extents of the RNA recognition motifs (RRMs) are those defined by the Saccharomyces Genome Database and GENE3D websites (amino acids 332–398 for Nrd1 and 327–403 for Nab3). The Q/P-rich, prion-like domains of Nrd1 (amino acids 516–575) and Nab3 (amino acids 565–794) are those described by Alberti et al. (34). The Sen1 ATPase helicase domain (ATPase-HD; amino acids 1,146–1,869) and a nuclear localization signal (NLS; amino acids 1,907–1,929) are as described by Chen et al. (61).

Figure 2

Association of the Nrd1–Nab3–Sen1 complex (NNS) with elongating RNA polymerase II (Pol II) is stabilized by interactions with the C-terminal domain (CTD) of Pol II and recognition sequences in the nascent transcript. The CTD interaction domain of Nrd1 binds preferentially to the phospho-Ser⁵ CTD, which is enriched at the 5′ ends of genes, providing a mechanistic explanation for the targeting of NNS to short transcripts. Interactions between Sen1 and Pol II have also been documented. The Nrd1–Nab3 heterodimer contributes RNA recognition motifs that recognize variations on the recognition sequences shown. The transition from a phospho-Ser⁵-enriched form to a phospho-Ser²-enriched form of Pol II (boxed gradients) occurs when the nascent transcript is ~450 nt long, defining a window of transcript susceptibility to NNS-mediated termination.