RNA-binding protein Nrd1 directs poly(A)-independent 3′-end formation of RNA polymerase II transcripts

Abstract

A eukaryotic chromosome contains many genes, each transcribed separately by RNA polymerase (pol) I, II or III. Transcription termination between genes prevents the formation of polycistronic RNAs and anti-sense RNAs, which are generally detrimental to the correct expression of genes. Terminating the transcription of protein-coding genes by pol II requires a group of proteins that also direct cleavage and polyadenylation of the messenger RNA in response to a specific sequence element, and are associated with the carboxyl-terminal domain of the largest subunit of pol II (refs 1, 2, 3, 4, 5, 6). By contrast, the cis-acting elements and trans-acting factors that direct termination of non-polyadenylated transcripts made by pol II, including small nucleolar and small nuclear RNAs, are not known. Here we show that read-through transcription from yeast small nucleolar RNA and small nuclear RNA genes into adjacent genes is prevented by a cis-acting element that is recognized, in part, by the essential RNA-binding protein Nrd1. The RNA-binding protein Nab3, the putative RNA helicase Sen1, and the intact C-terminal domain of pol II are also required for efficient response to the element. The same proteins are required for maintaining normal levels of Nrd1 mRNA, indicating that these proteins may control elongation of a subset of mRNA transcripts.

Transcription termination by nuclear RNA polymerases

“…Termination of the noncoding RNAs initiated upstream of the mRNA start site of the protein-coding genes regulates their expression. For instance, binding of Nrd1 and Nab3 to the 59-UTR and upstream coding region of NRD1 directs premature termination, resulting in negative autoregulation of Nrd1 levels (Steinmetz et al 2001;Arigo et al 2006a). Likewise, termination of CUTs initiated upstream of the IMD2 mRNA start site regulates IMD2 mRNA expression (Jenks et al 2008;Kuehner and Brow 2008;Thiebaut et al 2008).…”

“…For example, the regulatory region of the SER3 gene produces a CUT that represses transcription of SER3 (Martens et al 2004). Nrd1 complex-dependent termination was shown to recognize regulatory terminators called ''attenuators'' located in the 59-UTR of three characterized protein-coding genes-NRD1, HRP1 (or NAB4), and IMD2 (Steinmetz et al 2001(Steinmetz et al , 2006bArigo et al 2006a;Kuehner and Brow 2008). Termination of the noncoding RNAs initiated upstream of the mRNA start site of the protein-coding genes regulates their expression.…”

“…Importantly, NRD1 and SEN1 mutations cause strong termination defects at some snoRNAs (Kim et al 2006). Nrd1 and Nab3 recognize specific RNA sequences located downstream from the mature 39-end of sn/snoRNAs (GUAA/G and UCUU, respectively) Brow 1996, 1998;Conrad et al 2000;Steinmetz et al 2001;Carroll et al 2004Carroll et al , 2007, and mutations in these sites cause termination defects (Carroll et al 2004). Several snoRNA terminators contain multiple potential binding sites for Ndr1 and Nab3, which form a heterodimer (Carroll et al 2007).…”

“…Nrd1 (nuclear pre-mRNA down-regulation) is an essential nuclear RNA-binding protein that directs termination of snoRNA and some mRNA transcripts, in association with an interacting protein, the helicase Sen1 (Steinmetz and Brow 1996;Steinmetz et al 2001;Ursic et al 2004;Vasiljeva and Buratowski 2006). Nrd1 contains a CID (Meinhart and Cramer 2004;Meinhart et al 2005) that interacts with CTD phosphorylated at Ser5 (Conrad et al 2000;Gudipati et al 2008;Vasiljeva et al 2008a).…”

Posttranscriptional control of plant development

“…The β form, which is generated by polyadenylation within intron 3, is the most abundant form, but only the γ form can generate the functional FCA protein containing two RRM motifs and a WW domain [16,17• The molecular nature of the HUA and HEN genes suggests that these genes have a role in RNA metabolism. HUA2 encodes a novel protein [29] with a regulation of nuclear premRNA (RPR) domain that was first recognized in several metazoan nuclear RNAprocessing proteins [33,34]. The RPR domain mediates the interaction of these metazoan proteins with the largest subunit of the carboxy-terminal domain of RNA pol II [35].…”