Methylation of histone H3 by Set1 and Set2 is required for deacetylation of nucleosomes in coding regions by histone deacetylase complexes (HDACs) Set3C and Rpd3C(S), respectively. We report that Set3C and Rpd3C(S) are co-transcriptionally recruited in the absence of Set1 and Set2, but in a manner stimulated by Pol II CTD kinase Cdk7/Kin28. Consistently, Rpd3C(S) and Set3C interact with Ser5-phosphorylated Pol II and histones in extracts, but only the histone interactions require H3 methylation. Moreover, reconstituted Rpd3C(S) binds specifically to Ser5-phosphorylated CTD peptides in vitro. Hence, whereas interaction with methylated H3 residues is required for Rpd3C(S) and Set3C deacetylation activities, their co-transcriptional recruitment is stimulated by the phosphorylated CTD. We further demonstrate that Rpd3, Hos2, and Hda1 have overlapping functions in deacetylating histones and suppressing co-transcriptional histone eviction. A strong correlation between increased acetylation and lower histone occupancy in HDA mutants implies that histone acetylation is a key determinant of nucleosome eviction.

Cyclin-dependent kinase BUR1/BUR2 appears to be the yeast ortholog of P-TEFb, which phosphorylates Ser2 of the RNA Pol II CTD, but the importance of BUR1/BUR2 in CTD phosphorylation is unclear. We show that BUR1/BUR2 is co-transcriptionally recruited to the 5′ end of ARG1 in a manner stimulated by interaction of the BUR1 C-terminus with CTD repeats phosphorylated on Ser5 by KIN28. Impairing BUR1/BUR2 function, or removing the CTD-interaction domain in BUR1, reduces Ser2 phosphorylation in bulk Pol II and eliminates the residual Ser2P in cells lacking the major Ser2 CTD kinase, CTK1. Impairing BUR1/BUR2 or CTK1 evokes a similar reduction of Ser2P in Pol II phosphorylated on Ser5, and in elongating Pol II near the ARG1 promoter. By contrast, CTK1 is responsible for the bulk of Ser2P in total Pol II and at promoter-distal sites. In addition to phosphorylating Ser2 near promoters, BUR1/BUR2 also stimulates Ser2P formation by CTK1 during transcription elongation.

Wild-type transcriptional activation by Gcn4p is dependent on multiple coactivators, including SAGA, SWI/SNF, Srb mediator, CCR4-NOT, and RSC, which are all recruited by Gcn4p to its target promoters in vivo. It was not known whether these coactivators are required for assembly of the preinitiation complex (PIC) or for subsequent steps in the initiation or elongation phase of transcription. We find that mutations in subunits of these coactivators reduce the recruitment of TATA binding protein (TBP) and RNA polymerase II (Pol II) by Gcn4p at ARG1, ARG4, and SNZ1, implicating all five coactivators in PIC assembly at Gcn4p target genes. Recruitment of Pol II at SNZ1 and ARG1 was eliminated by mutations in TBP or by deletion of the TATA box, indicating that TBP binding is a prerequisite for Pol II recruitment by Gcn4p. However, several mutations in SAGA subunits and deletion of SRB10 had a greater impact on promoter occupancy of Pol II versus TBP, suggesting that SAGA and Srb mediator can promote Pol II binding independently of their stimulatory effects on TBP recruitment. Our results reveal an unexpected complexity in the cofactor requirements for the enhancement of PIC assembly by a single activator protein.

The Paf1 complex (Paf1C) interacts with RNA polymerase II (Pol II) and promotes histone methylation of transcribed coding sequences, but the mechanism of Paf1C recruitment is unknown. We show that Paf1C is not recruited directly by the activator Gcn4p but is dependent on preinitiation complex assembly and Ser5 carboxy-terminal domain phosphorylation for optimal association with ARG1 coding sequences. Importantly, Spt4p is required for Paf1C occupancy at ARG1 (and other genes) and for Paf1C association with Ser5-phosphorylated Pol II in cell extracts, whereas Spt4p-Pol II association is independent of Paf1C. Since spt4⌬ does not reduce levels of Pol II at ARG1, Ser5 phosphorylation, or Paf1C expression, it appears that Spt4p (or its partner in DSIF, Spt5p) provides a platform on Pol II for recruiting Paf1C following Ser5 phosphorylation and promoter clearance. spt4⌬ reduces trimethylation of Lys4 on histone H3, demonstrating a new role for yeast DSIF in promoting a Paf1C-dependent function in elongation.Transcription by RNA polymerase II (Pol II) is a multistep process that includes preinitiation complex (PIC) assembly, open complex formation, initiation, promoter clearance, elongation, and termination. Phosphorylation of Ser5 in the Pol II carboxy-terminal domain (CTD) by the kinase subunit of TFIIH (Kin28p) stimulates promoter clearance and the transition from initiation to elongation. Ser5 phosphorylation also mediates cotranscriptional capping of mRNA by enhancing the recruitment and activity of the capping enzyme (reviewed in reference 42). Phosphorylation of Ser2 in the CTD by Ctk1p is restricted to elongating Pol II, and there is evidence that Ser2 phosphorylation increases, while Ser5 phosphorylation decreases, as Pol II moves from the promoter (13). Consistent with this, Ser2 phosphorylation stimulates recruitment of 3Ј-end processing factors (1, 10).CTD phosphorylation is also required for methylation of histones in the coding sequences. Set1p complex (COMPASS) methylates Lys4 in histone H3 (H3-K4) near the 5Ј ends of transcribed genes (27, 37). Set1p associates with Ser5-phosphorylated Pol II and is recruited to the 5Ј ends of transcribed genes dependent on Kin28p (27). Set2p methylates H3-K36 throughout the open reading frame (ORF) (16, 52), and CTD Ser2 phosphorylation stimulates recruitment of Set2p (16,18,52). Interactions of Set1p and Set2p with phosphorylated Pol II and the attendant methylation events also depend on Paf1 complex (Paf1C) (14,16,27,51). Paf1C further stimulates Set1p function by promoting H2B ubiquitylation by Rad6p/ Bre1p complex (7, 26, 49, 51), a prerequisite for H3-K4 methylation (4, 44).Paf1C was first identified in yeast as a group of proteins associated with unphosphorylated Pol II (47) and consists of five core subunits: Paf1p, Cdc73p, Rtf1p, Leo1p, and Ctr9p (12,15,24,39,40,43). Paf1C forms a stoichiometric complex with Pol II (39), and deletion of Rtf1p or Cdc73p dissociates the remaining Paf1C subunits from chromatin (25). Unlike the Pol II-associated mediator, which i...

Paf1 complex (Paf1C) is a transcription elongation factor whose recruitment is stimulated by Spt5 and the CDKs Kin28 and Bur1, which phosphorylate the Pol II C-terminal domain (CTD) on Serines 2, 5, and 7. Bur1 promotes Paf1C recruitment by phosphorylating C-terminal repeats (CTRs) in Spt5, and we show that Kin28 enhances Spt5 phosphorylation by promoting Bur1 recruitment. It was unclear, however, whether CTD phosphorylation by Kin28 or Bur1 also stimulates Paf1C recruitment. We find that Paf1C and its Cdc73 subunit bind diphosphorylated CTD repeats (pCTD) and phosphorylated Spt5 CTRs (pCTRs) in vitro, and that cdc73 mutations eliminating both activities reduce Paf1C recruitment in vivo. Phosphomimetic (acidic) substitutions in the Spt5 CTR sustain high-level Paf1C recruitment in otherwise wild-type cells, but not following inactivation of Bur1 or Kin28. Furthermore, inactivating the pCTD/pCTR-interaction domain (PCID) in Cdc73 decreases Paf1C-dependent histone methylation in cells containing non-phosphorylatable Spt5 CTRs. These results identify an Spt5 pCTR-independent pathway of Paf1C recruitment requiring Kin28, Bur1, and the Cdc73 PCID. We propose that pCTD repeats and Spt5 pCTRs provide separate interaction surfaces that cooperate to ensure high-level Paf1C recruitment.

GCN2 stimulates translation of GCN4 mRNA in amino acid‐starved cells by phosphorylating translation initiation factor 2. GCN2 is activated by binding of uncharged tRNA to a domain related to histidyl‐tRNA synthetase (HisRS). The HisRS‐like region contains two dimerization domains (HisRS‐N and HisRS‐C) required for GCN2 function in vivo but dispensable for dimerization by full‐length GCN2. Residues corresponding to amino acids at the dimer interface of Escherichia coli HisRS were required for dimerization of recombinant HisRS‐N and for tRNA binding by full‐length GCN2, suggesting that HisRS‐N dimerization promotes tRNA binding and kinase activation. HisRS‐N also interacted with the protein kinase (PK) domain, and a deletion impairing this interaction destroyed GCN2 function without reducing tRNA binding; thus, HisRS‐N–PK interaction appears to stimulate PK function. The C‐terminal domain of GCN2 (C‐term) interacted with the PK domain in a manner disrupted by an activating PK mutation (E803V). These results suggest that the C‐term is an autoinhibitory domain, counteracted by tRNA binding. We conclude that multiple domain interactions, positive and negative, mediate the activation of GCN2 by uncharged tRNA.

Chaperones, nucleosome remodeling complexes, and histone acetyltransferases have been implicated in nucleosome disassembly at promoters of particular yeast genes, but whether these cofactors function ubiquitously, as well as the impact of nucleosome eviction on transcription genome-wide, is poorly understood. We used chromatin immunoprecipitation of histone H3 and RNA polymerase II (Pol II) in mutants lacking single or multiple cofactors to address these issues for about 200 genes belonging to the Gcn4 transcriptome, of which about 70 exhibit marked reductions in H3 promoter occupancy on induction by amino acid starvation. Examining four target genes in a panel of mutants indicated that SWI/SNF, Gcn5, the Hsp70 cochaperone Ydj1, and chromatin-associated factor Yta7 are required downstream from Gcn4 binding, whereas Asf1/Rtt109, Nap1, RSC, and H2AZ are dispensable for robust H3 eviction in otherwise wild-type cells. Using ChIP-seq to interrogate all 70 exemplar genes in single, double, and triple mutants implicated Gcn5, Snf2, and Ydj1 in H3 eviction at most, but not all, Gcn4 target promoters, with Gcn5 generally playing the greatest role and Ydj1 the least. Remarkably, these three cofactors cooperate similarly in H3 eviction at virtually all yeast promoters. Defective H3 eviction in cofactor mutants was coupled with reduced Pol II occupancies for the Gcn4 transcriptome and the most highly expressed uninduced genes, but the relative Pol II levels at most genes were unaffected or even elevated. These findings indicate that nucleosome eviction is crucial for robust transcription of highly expressed genes but that other steps in gene activation are more rate-limiting for most other yeast genes.

) or the RNA component of RNase MRP encoded by NME1. Here we show that overexpression of the tRNA pseudouridine 55 synthase encoded by PUS4 also leads to translational derepression of GCN4 (Gcd ؊ phenotype) independently of eIF2 phosphorylation. Surprisingly, the Gcd ؊ phenotype of high-copy-number PUS4 (hcPUS4) did not require PUS4 enzymatic activity, and several lines of evidence indicate that PUS4 overexpression did not diminish functional initiator tRNA Met levels. The presence of hcPUS4 or hcNME1 led to the accumulation of certain tRNA precursors, and their Gcd ؊ phenotypes were reversed by overexpressing the RNA component of RNase P (RPR1), responsible for 5-end processing of all tRNAs. Consistently, overexpression of a mutant pre-tRNA Tyr that cannot be processed by RNase P had a Gcd ؊ phenotype. Interestingly, the Gcd ؊ phenotype of hcPUS4 also was reversed by overexpressing LOS1, required for efficient nuclear export of tRNA, and los1⌬ cells have a Gcd ؊ phenotype. Overproduced PUS4 appears to impede 5-end processing or export of certain tRNAs in the nucleus in a manner remedied by increased expression of RNase P or LOS1, respectively. The mutant tRNA Val* showed nuclear accumulation in otherwise wild-type cells, suggesting a defect in export to the cytoplasm. We propose that yeast contains a nuclear surveillance system that perceives defects in processing or export of tRNA and evokes a reduction in translation initiation at the step of initiator tRNA Met binding to the ribosome.Starvation of yeast cells for amino acids or purines leads to increased expression of GCN4, a transcriptional activator of amino acid biosynthetic enzymes (general amino acid control). GCN4 expression is stimulated at the translational level by a mechanism involving four short upstream open reading frames (uORFs) in its mRNA leader. During growth on amino acidreplete medium, scanning ribosomes translate the first uORF (uORF1) and reinitiate downstream at uORF2, uORF3, or uORF4 but cannot reinitiate again at the GCN4 start codon. In amino acid-starved cells, eukaryotic translation initiation factor 2 (eIF2) is phosphorylated on its ␣ subunit by protein kinase GCN2, and the phosphorylated eIF2 inhibits the guanine nucleotide exchange factor for eIF2, known as eIF2B. Consequently, formation of the ternary complex containing eIF2, GTP, and initiator methionyl-tRNA (Met-tRNA i Met ) is reduced, impairing delivery of tRNA i Met to the ribosome. In GCN4 mRNA, the ensuing delay in rebinding of ternary complex to 40S ribosomes which have translated uORF1 allows them to scan past uORF2 to uORF4 and reinitiate downstream at the GCN4 start codon instead (25,26). Thus, GCN4 translation is induced under conditions of diminished ternarycomplex formation.It is thought that GCN2 is activated in amino acid-starved cells by uncharged tRNAs (34,42,43,54) which accumulate under these conditions and bind to a regulatory domain in GCN2 homologous to histidyl-tRNA synthetases (55,57,58). Because starvation for any of several amino acids elicits activat...