The essential WD repeat protein Swd2 has dual functions in RNA polymerase II transcription termination and lysine 4 methylation of histone H3.

The maturation of mRNA occurs cotranscriptionally in vivo and is facilitated by the recruitment of mRNA processing factors to the phosphorylated C-terminal domain (CTD) of the largest subunit of RNA polymerase II (RNAP II) (for a review, see reference 40). During transcription, the nascent pre-mRNA is capped at the 5′ end, introns are removed by splicing, and the 3′ end is cleaved and polyadenylated. The processing of the 3′ end promotes transcription termination and nuclear export, and acquisition of a poly(A) tail is essential for the production of functional mRNA. The cleavage and polyadenylation steps take place within a large complex of proteins that for the most part are highly conserved between yeast and mammals (13). In the yeast Saccharomyces cerevisiae, CF IA, Hrp1/Nab4, and CF II are sufficient for the cleavage reaction in vitro, while specific poly(A) addition requires CF IA, Hrp1, poly(A) binding protein, and the CPF complex, which is composed of CF II, poly(A) polymerase, and additional proteins. A subset of these components are important in causing RNAP II to terminate downstream of poly(A) sites or of genes encoding some snRNAs and snoRNAs (2, 5, 11, 33). Recent application of a tandem affinity purification strategy allowed several groups to isolate highly purified CPF from yeast whole-cell extract (10, 16, 21, 36). This complex contains the nine previously characterized CPF subunits (references 39 and 62 and references therein), several novel polypeptides (including Glc7, Pti1, Ssu72, and Swd2) with no previous links to the cleavage and polyadenylation machinery, and Ref2, an RNA-binding protein known to stimulate processing at weak poly(A) sites (46). Nedea et al. (36) proposed that these new proteins form a subcomplex of CPF called APT (for associated with Pta1) that is connected to core CPF by Pta1. Two of these APT subunits, Pti1 and Ref2, have minor roles in mRNA processing but are very important for maturation of snoRNA 3′ ends (9, 36, 46, 52) which are cleaved but not polyadenylated. Ssu72, a low-molecular-weight phosphatase (15, 30), is essential for 3′ end formation of both types of RNAP II transcripts (21, 36, 57) and also contributes to accurate initiation of RNAP II transcription (60). Glc7, the only type 1 serine/threonine protein phosphatase in S. cerevisiae, has been implicated in numerous nuclear and cytoplasmic processes, including transcription regulation and mRNA export (17, 56). The fourth APT subunit, Swd2, is a 37-kDa protein without a proven cellular function. It has six WD repeats, which are domains of about 40 amino acids that usually end with tryptophan-aspartic acid (WD). WD repeat proteins are thought to have circularized β-propeller-like structures, which can interact sequentially or simultaneously with several different proteins (53). The presence of Swd2 in the CPF complex suggests that it may be directly involved in mRNA or snoRNA 3′ end formation or may help coordinate 3′ end processing with other events in mRNA synthesis and utilization. Swd2 is also part of the Set1, or COMPASS, complex, which is composed of Set1, Bre2, Swd1, Swd2, Swd3, Spp1, Shg1, and Sdc1 (31, 34, 44). This complex, through its catalytic subunit Set1, adds one to three methyl groups specifically to lysine 4 of histone H3 (H3-K4) (6, 31, 34, 44). This function is required for position-dependent gene silencing at telomeres, the mating type locus, and ribosomal DNA (6, 8, 25, 38). Set1-mediated H3-K4 dimethylation in S. cerevisiae is found throughout the genome, while the trimethylated form is most prevalent in the coding regions of active or recently transcribed genes (3, 37, 48; reviewed in references 20 and 51) and may protect active coding regions from deacetylation (3). The purpose of the work described in this report is to examine the role of Swd2 in the processes of histone methylation, transcription, and mRNA 3′ end formation. Here we demonstrate that Swd2, as a bona fide member of the Set1 complex, is required for global histone H3-K4 methylation and other Set1-regulated events. In spite of its tight association with the CPF complex, Swd2 is not directly involved in pre-mRNA 3′ end processing. However, we show that Swd2 plays a role in RNAP II transcription termination that is not dependent on its function in histone methylation. We propose that Swd2, as part of CPF, helps to coordinate the activities of the transcription and 3′ end processing machineries.