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Identification and Characterization of Elf1, a Conserved Transcription Elongation Factor in Saccharomyces cerevisiae

Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115,¹ Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 1L6,² Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario, Canada M5S 1A8³

Received 1 August 2005/ Returned for modification 19 August 2005/ Accepted 24 August 2005

	ABSTRACT

Top Abstract Introduction Materials and Methods Results Discussion References

 
In order to identify previously unknown transcription elongation factors, a genetic screen was carried out to identify mutations that cause lethality when combined with mutations in the genes encoding the elongation factors TFIIS and Spt6. This screen identified a mutation in YKL160W, hereafter named ELF1 (elongation factor 1). Further analysis identified synthetic lethality between an elf1 mutation and mutations in genes encoding several known elongation factors, including Spt4, Spt5, Spt6, and members of the Paf1 complex. Genome-wide synthetic lethality studies confirmed that elf1 specifically interacts with mutations in genes affecting transcription elongation. Chromatin immunoprecipitation experiments show that Elf1 is cotranscriptionally recruited over actively transcribed regions and that this association is partially dependent on Spt4 and Spt6. Analysis of elf1 mutants suggests a role for this factor in maintaining proper chromatin structure in regions of active transcription. Finally, purification of Elf1 suggests an association with casein kinase II, previously implicated in roles in transcription. Together, these results suggest an important role for Elf1 in the regulation of transcription elongation.

	INTRODUCTION

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Eukaryotic transcription is a complex process consisting of a series of steps involving initiation, elongation, and termination. Many recent studies have revealed the extent to which these steps are linked to each other, both functionally and physically (54, 71). While transcription initiation has been well studied and many of the fundamental mechanisms have been identified, an understanding of the control of transcription elongation in vivo is less clear. Some understanding of elongation has come from in vitro experiments examining the effects of various factors in modulating the elongation properties of RNA polymerase II (Pol II) (66). In the past few years many studies have also started to address the control of elongation in vivo and have identified many additional factors believed to play a role in this process (3, 69). In this paper, we describe a previously unstudied factor, Elf1 of Saccharomyces cerevisiae, that is functionally related to several other elongation factors and complexes, including TFIIS, Spt6, and the Paf1 complex.

TFIIS, the first eukaryotic elongation factor identified, was isolated nearly three decades ago based on its ability to induce long transcripts in an in vitro system (62). Further analysis of TFIIS revealed that it helps elongation in vitro by stimulating an RNA transcript cleavage activity of Pol II (13, 23). This activity allows backtracked (arrested) Pol II to cleave the 3' end of the nascent transcript, thus realigning the 3' end of the transcript with the Pol II catalytic site. Additional evidence suggests that TFIIS can help Pol II overcome a promoter-proximal pause (1, 50). Finally, recent evidence has shown that TFIIS is recruited along transcribed open reading frames, further suggesting a general role in elongation (51, 53).

Spt6 is one member of a class of elongation factors, initially identified in screens and selections for transcription mutants in S. cerevisiae, that includes Spt4, Spt5, Spt6, and Spt16. Spt4, which is nonessential for growth, and Spt5, which is essential, are components of the DSIF elongation factor which has been found to function both positively and negatively in regulating transcription elongation (21, 57, 72, 73, 76, 80). Spt6, an essential factor, genetically and physically interacts with Spt4 and Spt5 (31, 36, 73). Spt6 likely plays a role with chromatin-mediated transcription elongation, as it can assemble histones onto DNA in vitro (7) and spt6 mutations suppress loss of the Swi/Snf nucleosome remodeling complex (46, 73). Furthermore, Spt6 is also necessary for maintaining chromatin integrity in regions of active transcription in vivo, as spt6 mutations allow aberrant transcription initiation within coding regions (26). Spt6 likely plays non-chromatin-related roles in elongation as well, as human Spt6 has been shown to promote elongation on DNA templates in vitro (11). Spt16 interacts with Pob3 to form the CP/SPN complex in yeast (9, 14, 15). The mammalian homologue of this complex, FACT, was identified by its ability to facilitate transcription on a chromatin template in vitro (48). Similar to Spt6, Spt16 possesses histone chaperone activity (6) and mutation of spt16 also leads to aberrant transcription from within coding regions (26, 41). Current evidence suggests that FACT tracks along transcribed chromatin, destabilizing nucleosomes, and thereby facilitating elongation by Pol II (6, 16, 60).

The Paf1 complex, was identified through its physical interaction with Pol II (64, 65) and is composed of five proteins, including Paf1, Ctr9, Cdc73, Rtf1, and Leo1 (31, 44, 70). Initially thought to play a role in initiation, the Paf1 complex has also been shown to play important roles in elongation (10, 44, 70). The Paf1 complex is localized to transcribed regions and genetically interacts with several elongation factors (10, 31, 51, 70). Recent studies have found that the Paf1 complex is required for several histone modifications at active genes, including the methylation of lysines 4 and 36 of histone H3, catalyzed by Set1 and Set2, respectively (30, 32, 47).

Despite the large number of eukaryotic elongation factors recently identified, it seemed likely that not all had been discovered. In order to identify previously unknown elongation factors, we performed a genetic screen to identify mutations that cause lethality when combined with mutations in DST1, the gene encoding TFIIS, and SPT6. In this screen, we identified a mutation in a previously unstudied gene, YKL160W, that causes lethality in combination with mutations in DST1 and SPT6. The protein encoded by this gene is a member of a conserved family of zinc finger proteins of unknown function. In accordance with a role in transcription elongation, we have designated this gene as ELF1 (elongation factor 1). Genetic analysis reveals that elf1 genetically interacts with mutations in genes encoding many other elongation factors, including Spt4, Spt5, Spt6, and the Paf1 complex. Synthetic genetic array (SGA) analysis confirms that elf1 functionally interacts only with genes suggested to have roles in transcription elongation. Chromatin immunoprecipitation (ChIP) analysis demonstrates that Elf1 preferentially binds to the coding regions of genes compared to promoters. This localization to coding regions was found to be dependent on transcription and partially dependent on Spt4 and Spt6. Analysis of elf1 mutants suggests a role for this factor in maintaining proper chromatin structure in regions of active transcription. Finally, purification of Elf1 has revealed a physical association with casein kinase II (CKII). Together, these results provide strong evidence of an important role for Elf1 in transcription elongation.

	MATERIALS AND METHODS

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Yeast strains, plasmids, and media. All S. cerevisiae strains (Table 1) are isogenic to a GAL2⁺ derivative of S288C (78). To epitope tag Elf1, DNA sequence encoding 13 copies of the Myc epitope was integrated at the 3' end of the ELF1 coding region (37). The ELF1-13MYC gene is wild type with respect to an Spt phenotype, and it does not cause any synthetic defects in growth when crossed to any other mutation tested in this study. The Flag-tagged Spt4 construct was provided by G. Hartzog and has been previously described (36). The Ctr9-Myc construct has been previously described (25). The dst1::KANMX allele was constructed by a one-step PCR-mediated disruption which replaces the entire open reading frame with the KANMX4 cassette (8). The elf1::NATMX allele, referred to as elf1 throughout this paper, was constructed by a one-step PCR-mediated disruption which replaces the entire open reading frame with the NATMX4 cassette (20). The GAL1-FLO8-HIS3 reporter, to be described elsewhere, contains the HIS3 gene inserted out-of-frame into the 3' coding region of FLO8 such that wild-type HIS3 product is only expressed when transcription initiates from a cryptic promoter within the FLO8 gene. In addition, the FLO8 promoter has been replaced by the GAL1 promoter. All deletion mutants used from the yeast deletion set (InVitrogen) were confirmed by PCR. Plasmid pKC13 (gift of Kristine Johnson and Caroline Kane) contains the DST1 coding region under GAL1 control in the YEp435 vector (URA3⁺, 2µm plasmid). Western analysis with TFIIS antisera (a gift of C. Kane) revealed a significant level of TFIIS protein expressed from this plasmid under repressive growth conditions (glucose) and a greatly elevated level under inducing conditions (galactose). Plasmid pDP1 was constructed by addition of BamHI and EcoRI restriction sights to a PCR fragment containing ELF1 (–487 to +840 bp, where +1 = ATG and +436 = TAA) and ligated into pRS416 (45). Double mutant yeast strains were constructed by standard genetic methods. An elf1 mutant containing plasmid pDP1 was crossed to strains containing mutations in genes encoding a number of elongation factors. After sporulation and tetrad dissection, double mutant strains were identified and tested for growth on medium containing 5-fluoroorotic acid (5-FOA). In all cases, at least 10 tetrads were dissected and analyzed for growth. In most cases, strains used were in the FY (S288C) strain background and are listed in Table 1. However, strains containing leo1, rpb4, hir2, hir3, and hpc2 were obtained from the yeast deletion set, also in the S288C background (InVitrogen).

Identification of synthetic lethal mutations. To identify novel elongation factors, we performed a genetic screen to identify mutations causing synthetic lethality with mutations in dst1 and spt6-14. First, strain FY2371 (dst1 spt6-14) was transformed with plasmid pKC13, a high-copy-number plasmid containing the wild-type DST1⁺ and the URA3⁺ genes. This strain was then transformed with NotI-generated linear DNA fragments from an mTn3 transposon insertion library (59), and transformants were selected on medium lacking leucine. Approximately 20,000 transformants were replica plated to medium lacking leucine and medium containing 5-FOA. Initially, 28 synthetic lethal candidates were identified due to the lack of growth on 5-FOA-containing medium. These colonies were purified and retested for growth on 5-FOA. Many of the insertions were eliminated as candidates due to the instability of the transposon insertion, weakness of phenotype upon rechecking, or lack of linkage between the phenotype and the transposon insertion. Of these candidates, we found one strong synthetic lethal candidate where the phenotype was linked to the transposon insertion. We identified the genomic location of this insertion by vectorette PCR (34, 56). This insertion was located in the YKL160W/ELF1 gene and predicts a fusion of the first 62 amino acids with the lacZ gene from the transposon insertion.

SGA analysis. SGA analysis was performed as previously described (74) with minor modifications. The S. cerevisiae deletion set was transferred from frozen stocks in 96-well containers to large YPD plates and grown as spots for 2 days at 30°C. The strains were then mated to lawns of the query strain L1095 on fresh YPD plates, incubated for 1 day, and then replica plated to YPD plates containing G418 and clonNAT to select for diploids. The diploids were replica plated to sporulation medium and incubated at 22°C for 5 days. MATa spores were selected by replica plating to SC-his-arg plates containing canavanine (50 mg/liter) for 2 days. Finally, strains were replica plated to haploid selection medium containing G418 and haploid selection medium containing G418 and clonNAT. Growth was scored for 3 days, and synthetic lethal candidates were identified by lack of growth on the medium containing G418 and clonNAT. From this analysis, 10 synthetic lethal candidates were identified. For nine of the candidates, we tested the possible synthetic lethality with elf1 by tetrad analysis. The tenth candidate (yml009w-B) was not tested, because this deletion removes a small portion of the essential gene, SPT5, and some alleles of SPT5 were already known to be synthetically lethal with elf1. Of the nine remaining candidates, only three were determined to be synthetically lethal with elf1 by tetrad analysis (cdc73, leo1, and rpb4). Five candidates were not synthetically lethal (rtf1, hir1, hir2, hir3, and hpc2), and one (bur2) germinated too poorly to allow any conclusion to be made. As previously pointed out, SGA analysis is subject to the identification of both false-negative and false-positive interactions (38, 74, 75). Using SGA analysis, we identified an interaction with mutations in three of the five known components of the Paf1 complex (cdc73, leo1, and rtf1). Lethality of elf1 with deletions of genes encoding the other two components of the Paf1 complex, paf1 and ctr9, was not able to be determined by SGA due to the sickness of these strains in the deletion set. In addition, another mutation known to be synthetically lethal with elf1, spt4, was not identified in the SGA analysis, likely because the spt4 strain is not healthy in the deletion set and thus could not be scored by SGA. In addition to false negatives, we also identified five false positives (see Table 3, below) for unknown reasons. There are several differences in the SGA method when compared to standard tetrad analysis that could account for these differences, including the use of synthetic complete media for germination or the requirement for sporulation and germination among patches of other wild-type and single mutant yeast cells.

View this table: [in this window] [in a new window]   TABLE 3. SGA analysis of elf1

Northern analysis. RNA isolation and Northern hybridization experiments were carried out as described previously (4, 72). Northern hybridization analysis was conducted using probes to FLO8 and SCR1. The FLO8 probe corresponds to the +1515 to +2326 region of the FLO8 gene. The SCR1 probe corresponds to the –221 to +452 region of the SCR1 gene. For each experiment, Northern analysis was performed in duplicate with similar results between the two experiments. Viability of all strains used for Northern analysis was approximately 100% for all times and temperatures used in the experiments.

Purification of Elf1 and mass spectrometry of associated proteins. Tandem affinity purification (TAP)-tagged Elf1 was purified on immunoglobulin G (IgG) and calmodulin columns from extracts of yeast cells (10 liters) grown in YPD medium to an optical density at 600 nm of 1.0 to 1.5 (19, 55). The cell pellets (7 to 10 g) were frozen in liquid nitrogen and lysed by grinding with dry ice in a Krups coffee grinder (model number 203-70). An equal volume of YEB (250 mM KCl, 100 mM HEPES-KOH, pH 7.9, 1 mM EDTA, 2.5 mM dithiothreitol [DTT]) was added and, following centrifugation in a Beckman Ti70 rotor at 4°C for 2 h at 34,000 rpm, the supernatant was dialyzed against IPP buffer (10 mM Tris-Cl, pH 7.9, 0.1% Triton X-100, 0.5 mM DTT, 0.2 mM EDTA, 20% glycerol, 100 mM NaCl). After dialysis, the extract was again centrifuged in a Ti70 rotor at 4°C for 30 min at 34,000 rpm and the supernatant was mixed for 3 h with 200 µl IgG-Sepharose (Pharmacia) equilibrated with IPP buffer. Following binding, the IgG-Sepharose was washed with 1 ml IPP buffer followed by 400 µl TEV protease cleavage buffer (50 mM Tris-Cl, pH 7.9, 1 mM DTT, 0.1% Triton X-100, 100 mM NaCl). The beads were then incubated overnight at 4°C with 100 U of TEV protease (Life Technologies) in 200 µl TEV cleavage buffer. The eluate was combined with a 200-µl wash with TEV cleavage buffer. To this was added 200 µl calmodulin binding buffer (10 mM Tris-Cl, pH 7.9, 10 mM ß-mercaptoethanol, 2 mM CaCl₂, 0.1% Triton X-100, 100 mM NaCl) and 200 µl of calmodulin beads (Pharmacia) equilibrated with the same buffer. After binding for 1 to 2 h at 4°C, the calmodulin beads were washed with 200 µl calmodulin binding buffer and 200 µl calmodulin wash buffer (10 mM Tris-Cl, pH 7.9, 10 mM ß-mercaptoethanol, 0.1 mM CaCl₂, 0.1% Triton X-100, 100 mM NaCl). The purified protein complexes were eluted from the calmodulin beads with 5x 100 µl calmodulin elution buffer (10 mM Tris-Cl, pH 7.9, 10 mM ß-mercaptoethanol, 3 mM EGTA, pH 8.0, 0.1% Triton X-100, 100 mM NaCl). The purified proteins were either directly reduced, alkylated, digested with trypsin, and analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS) on a Finnigan LCQ Deca tandem mass spectrometer or else separated by SDS-polyacrylamide gel electrophoresis (SDS-PAGE) on gels containing 10% polyacrylamide and stained with silver. After SDS-PAGE, protein bands were reduced, alkylated, and digested with trypsin, and purified peptide samples were spotted onto a target plate with a matrix of -cyano-4-hydroxycinnamic acid (Fluka). Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry analysis was conducted utilizing a Reflex IV (Bruker Daltonics, Billerica, MA) instrument in positive ion reflectron mode (39, 63). For tandem mass spectrometry, the trichloroacetic acid-precipitated protein was resuspended in 100 mM NH₄HCO₃-1 mM CaCl₂ buffer, pH 8.5, and digested overnight at 37°C with 2 µl of immobilized Poros trypsin beads (PerSeptive). The entire digest was fractionated as described previously (17) on a 7.5-cm (inner diameter, 100 µm) reverse-phase C₁₈ capillary column attached in-line to a Finnigan LCQ-Deca ion trap mass spectrometer by ramping a linear gradient from 2 to 60% solvent B in 90 min. Solvent A consisted of 5% acetonitrile, 0.5% acetic acid, and 0.02% heptafluorobutanoic acid, and solvent B consisted of acetonitrile-water (80:20) containing 0.5% acetic acid and 0.02% heptafluorobutanoic acid. The flow rate at the tip of the needle was set to 300 nl/min by programming the high-performance liquid chromatography pump and using a split line. The mass spectrometer cycled through four scans as the gradient progressed. The first was a full mass scan followed by successive tandem mass scans of the three most intense ions. A dynamic exclusion list was used to limit collection of tandem mass spectra for peptides that eluted over a long period of time. All tandem mass spectra were searched by using the SEQUEST computer algorithm against the complete yeast protein database. Each high-scoring peptide sequence was manually compared with the corresponding tandem mass spectrum to ensure that the match was correct.

	RESULTS

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Identification of a mutation that causes lethality in combination with mutations in DST1 and SPT6. To identify previously unstudied genes involved in transcription elongation in S. cerevisiae, we performed a genetic screen for mutations that cause inviability when combined with mutations in genes known to encode elongation factors. Specifically, we screened for mutations that cause inviability when combined with both dst1 and spt6-14 (described in Materials and Methods). From this screen, we identified one mutation in YKL160W, a previously uncharacterized gene. This gene is hereafter referred to as ELF1, and the mutation is referred to as elf1-1::Tn3. To determine the phenotype of elf1-1::Tn3 when combined with either dst1 or spt6-14 individually, we constructed elf1-1::Tn3 dst1 and elf1-1::Tn3 spt6-14 double mutants. The elf1-1::Tn3 dst1 double mutant had very little defect in growth. In contrast, the elf1-1::Tn3 spt6-14 mutant was extremely sick. Thus, the elf1-1::Tn3 and spt6-14 mutations contribute the majority of the growth defect initially observed in our screen. Later in this paper, we show that elf1 spt6-14 double mutants are inviable and that elf1 dst1 double mutants are viable but have mutant phenotypes.

Elf1 is a member of a conserved eukaryotic family of zinc finger proteins. The ELF1 gene of S. cerevisiae is predicted to encode a small protein of 145 amino acids. BLAST analysis (2) reveals that the predicted Elf1 protein is conserved in other sequenced eukaryotic genomes, including other yeasts, human, Drosophila melanogaster, Caenorhabditis elegans, and Arabidopsis thaliana (Fig. 1). The conservation of Elf1 occurs in the region corresponding to the N-terminal half of the S. cerevisiae protein. These hypothetical proteins are short (often less than 100 amino acids) and contain a C4 zinc-binding region. The four cysteine residues of the potential zinc-binding domain are completely conserved in all homologues, and this conserved domain has been termed DUF701 (domain of unknown function 701) (40). To date, only the C. elegans homologue has been functionally characterized; in RNA inhibition experiments, no significant growth defect was observed (24). Two genome-wide localization screens (22, 33) have suggested that Elf1 is localized to the nucleus, consistent with our localization analysis of an Elf1-green fluorescent protein fusion (data not shown). Interestingly, Elf1 was also identified in one of those studies to be associated with meiotic chromosomes (33). The conservation of Elf1 strongly suggests that it plays an important role throughout eukaryotes.

View larger version (35K): [in this window] [in a new window]   FIG. 1. Elf1 is a conserved member of a zinc finger family of uncharacterized proteins. Homologues of Elf1 were identified by standard protein BLAST analysis. Full-length homologous protein sequences from several eukaryotic organisms were then aligned using ClustalW. Identical residues are noted by an asterisk, conserved substitutions are noted by a colon, and semiconservative substitutions are noted by a period. The four conserved cysteines of the zinc finger domain are noted by arrows above the alignment. Abbreviations: YEAST, Saccharomyces cerevisiae; SCHPO, Schizosaccharomyces pombe; HUMAN, Homo sapiens; MUS, Mus musculus; CAEEL, Caenorhabditis elegans; DROME, Drosophila melanogaster; ARATH, Arabidopsis thaliana.

elf1 causes mild sensitivity to 6-AU and genetically interacts with dst1.

elf1

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elf1 dst1

elf1 dst1

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lys2-128

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View larger version (29K): [in this window] [in a new window]   FIG. 2. The elf1 mutation causes mild sensitivity to 6AU and genetically interacts with dst1. Yeast strains were spotted onto plates in a series of 10-fold dilutions. Strains were grown on SC-ura or SC medium for 2 days, medium containing 6AU (50 µg/ml) for 5 days, or medium containing MPA (20 µg/ml) for 3 days.

elf1 genetically interacts with mutations in the genes encoding the Spt4, Spt5, Spt6, and Spt16 elongation factors.

elf1

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By crosses, we first combined elf1 with spt4, spt5, and spt6 mutations. Genetic and biochemical results have implicated the Spt4, Spt5, and Spt6 proteins functioning through effects on transcription elongation and chromatin structure (82). By crosses, we tested elf1 combined with a complete deletion of the nonessential SPT4 gene and with several different missense mutations in the essential SPT5 and SPT6 genes. Our results demonstrate that an elf1 spt4 double mutant is inviable (Fig. 3A; Table 2). Consistent with these results, an elf1 mutation was independently identified in a screen for mutations that cause lethality when combined with spt4 (G. Hartzog and J. Speer, personal communication). We tested elf1 with three different spt5 mutations and observed inviability for two of the combinations (Table 2). The third combination is described below. We also tested four different spt6 alleles: three combinations resulted in synthetic lethality, and the fourth double mutant grew extremely poorly (Fig. 3A; Table 2). From these results, we conclude that, in general, elf1 causes lethality when combined with spt4, spt5, and spt6 mutations.

View larger version (49K): [in this window] [in a new window]   FIG. 3. elf1 genetically interacts with mutations in the genes encoding the transcription elongation factors Spt4, Spt5, Spt6, and the Paf1 complex. (A) Deletion of elf1 is lethal in combination with mutations in SPT4, SPT6, or Paf1 complex genes. elf1 strains were transformed with plasmid pDP1 containing ELF1+ on a CEN URA3 plasmid and mated to spt4, spt6-1004, cdc73, or paf1 strains. Diploids were sporulated and dissected, and representative spores from the resulting complete tetrads were patched onto YPD. Patches were replica plated to medium lacking uracil for 1 day and medium containing 5FOA for 2 days. (B) Deletion of elf1 suppresses spt5-242 phenotypes. spt5-242 is a Cs– Spt– mutation that can be suppressed by mutations in Pol II or other elongation factors that impair elongation (21). elf1 strongly suppresses the Cs– phenotype and modestly suppresses the Spt– phenotype of spt5-242. The Spt– phenotype was scored by observing growth on medium lacking lysine and using the lys2-128 allele. Yeast strains were spotted in a series of 10-fold serial dilutions onto YPD for 2 days at 30°C, YPD at 14°C for 9 days, SC for 2 days, or SC-lys for 4 days.

View this table: [in this window] [in a new window]   TABLE 2. elf1 genetically interacts with mutations encoding several transcription factors

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We next tested to see whether an elf1 mutation interacted with an spt16 mutation. We observed no significant growth defect when elf1 was combined with the spt16-197 mutation, although there was a slight synthetic Spt^– phenotype (Table 2 and data not shown). Thus, mutations in elf1 interact strongly with mutations in SPT4, SPT5, and SPT6 but only cause a mild phenotype when combined with a mutation in SPT16. However, it is possible that other alleles of spt16 might cause more severe defects than the spt16-197 mutation.

elf1 genetically interacts with mutations in the genes encoding the Paf1 complex. We next tested for genetic interactions between elf1 and null mutations in the genes encoding components of the Paf1 complex. We found that an elf1 mutation causes synthetic lethality when combined with deletion mutations in four of the five Paf1 complex genes, paf1, cdc73, ctr9, and leo1. In agreement with this result, elf1 was identified in a large-scale SGA screen to genetically interact with a mutation in the gene encoding the Cdc73 component of the Paf1 complex (75). In contrast, when elf1 was combined with rtf1, the double mutant was viable, although it displayed both Spt^– and Ts^– phenotypes (Table 2). Together, the strong genetic interactions of elf1 with mutations in the genes encoding the elongation factors Spt4, Spt5, Spt6, and the Paf1 complex further support an important role for Elf1 in transcription elongation.

SGA analysis identifies additional mutations that genetically interact with elf1. To examine the genetic interactions of elf1 with deletions of all of the nonessential genes of S. cerevisiae, we performed SGA analysis (74). In this approach, elf1 was combined with the approximately 4,700 deletions contained within the yeast deletion set. This analysis led to the identification of 10 candidate mutations that were initially scored as causing synthetic lethality with elf1 (Table 3). Of these 10 candidates, 9 merited further investigation (see Materials and Methods) and were tested for synthetic lethality with elf1 by standard tetrad analysis. These crosses demonstrated that only three of the nine mutations, cdc73, leo1, and rpb4, actually caused synthetic lethality with elf1, while some of the others, while viable, caused other mutant phenotypes (Table 3). As previously pointed out by others (38, 74, 75), analysis of genetic interactions by SGA often leads to false positives (see Materials and Methods). Of the three cases of synthetic lethality, two of them, cdc73 and leo1, had been identified by the direct tests described in an earlier section. Consistent with our results, elf1 was also identified in a large-scale SGA screen to genetically interact with cdc73 (75).

The third mutation identified by SGA to cause synthetic lethality with elf1 was rpb4. RPB4 encodes a nonessential subunit of Pol II (79). Based on this interaction, we also tested whether elf1 confers synthetic phenotypes when combined with three different alleles in the essential Pol II genes RPB1 and RPB2 that confer a 6AU^S phenotype. We found that these three mutations, rpb1-221, rpb2-7, and rpb2-10 (21, 52), cause increased sickness and sensitivity to MPA when combined with an elf1 mutation (data not shown). Thus, 6AU^S mutations in the genes encoding subunits of the Pol II complex can lead to an increased requirement for the Elf1 elongation factor.

Another class of mutations identified by the elf1 SGA analysis included the HIR/HPC genes. These four genes, HIR1, HIR2, HIR3/HPC1, and HPC2, were initially identified due to their roles in the regulation of histone gene transcription (49, 81). More recently, the HIR genes have been implicated in transcription elongation due to synthetic lethal interactions with mutations in spt16 and genes encoding members of the Paf1 complex (16). Although SGA analysis suggested that elf1 is synthetically lethal with mutations in the HIR/HPC genes, tetrad analysis demonstrated that the double mutants between elf1 and deletions in the HIR genes were all viable and healthy (Table 3). However, when we tested the elf1 hir/hpc double mutants, we found several synthetic phenotypes, including Ts^– and Spt^– phenotypes. Thus, there are genetic interactions present between elf1 and mutations in the HIR genes, although not lethality as implied by SGA analysis. Taken together, our results from SGA analysis have identified only genetic interactions between elf1 and mutations in genes implicated as playing a role in transcription elongation, further highlighting an important and specific role for Elf1 in transcription elongation.

Elf1 is localized to regions of active transcription. The genetic interactions of elf1 suggested that Elf1 might play a direct role in transcription elongation. To test if Elf1 is associated with transcribed regions in vivo, we performed ChIP experiments using a functional, 13xMyc-tagged version of Elf1 (see Materials and Methods). In these experiments, we tested the physical association of Elf1 with PMA1 and GAL1, two genes commonly used for such studies (25, 27, 28). PMA1 is a highly transcribed gene, and GAL1 is regulated by carbon source, allowing us to test whether Elf1 ChIP is dependent upon ongoing transcription. Our results show that Elf1 is localized at high levels over the coding region of PMA1 and of GAL1 when it is induced (Fig. 4A and B). Furthermore, Elf1 is present at reduced levels over the TATA regions and at low levels over the UAS regions of these genes (Fig. 4A and B). Comparison of the distribution of Elf1 to that of Pol II shows that the level of Elf1 association is lower than Pol II over the promoter region compared to the coding regions, suggesting that Elf1 is recruited to genes subsequent to Pol II recruitment (Fig. 4A and B). This pattern is similar to that observed for Spt16 (41) and Spt6 (25, 27). The localization of Elf1 to the GAL1 coding region is dependent on transcription, as we only observed the association of Elf1 with GAL1 upon the induction of transcription with galactose (Fig. 4B). Additionally, Elf1 appeared to be present at similar levels to Pol II over the 3' UTR of both GAL1 and PMA1, similar to what has previously been observed for the elongation factors Spt4, Spt5, Spt6, and Spt16 (25, 27) and in contrast to other elongation factors, including the Paf1 and the TREX complexes, that show low levels of association over the 3' UTR (25, 27). Taken together, these results suggest that Elf1 is preferentially localized to regions of active transcription.

View larger version (32K): [in this window] [in a new window]   FIG. 4. Elf1 is preferentially localized to transcribed regions of active genes. (A) Elf1 is localized to the transcribed region of PMA1. Yeast cells containing the Elf1-13Myc and Rpb3-HA epitope-tagged proteins were grown at 30°C to mid-log in YPD medium. Cells were cross-linked with 1% formaldehyde and lysed, and the chromatin was sheared by sonication to an average size of 400 bp. Elf1-13Myc was immunoprecipitated using the A14 anti-Myc antibody, and Rpb3-HA was immunoprecipitated using the 12CA5 anti-HA antibody. Radiolabeled PCR products were obtained with primers specific to the PMA1 UAS, TATA, 5' ORF, 3' ORF, or 3' UTRs and were visualized on 6% polyacrylamide gels. As a control for DNA binding specificity, each PCR contained primers to amplify a nontranscribed region of chromosome V that is not contained in any open reading frames (28). ChIP values are represented as the fold enrichment of the specific PCR product compared to this control region. The locations of primer sets used for ChIP analysis are represented as lines below the schematic of the PMA1 gene. Results were obtained for at least three independent experiments, and the average and standard error are plotted on the graph. (B) Elf1 is localized across the GAL1 transcribed region upon transcriptional induction. Yeast cells containing Elf1-13Myc and Rpb3-HA epitope-tagged proteins were grown at 30°C to mid-log in medium containing 2% raffinose. Transcription of GAL1 was induced by the addition of 2% galactose for 2 hours. Chromatin immunoprecipitations were performed as described for panel A in at least three independent experiments, with the resulting averages and standard errors plotted on the graph.

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paf1

paf1

View larger version (21K): [in this window] [in a new window]   FIG. 5. Elf1 localization to PMA1 is partially dependent on the Spt4 and Spt6 elongation factors. (A) Elf1 localization at PMA1 in several elongation mutants. ChIP experiments were performed as described for Fig. 4A for wild-type, spt4, rtf1, paf1, spt6-1004, or spt16-197 strains at 30°C. ChIP results for Elf1-13Myc (top panel) and Rpb3-HA (bottom panel) are shown. The results from at least three independent experiments are shown. (B) Localization of Spt4 and Ctr9 to PMA1 is not affected in an elf1 mutant. Wild-type or elf1 strains containing Spt4-Flag, Ctr9-Myc, and Rpb3-HA were subjected to ChIP analysis as described for Fig. 4A. Ctr9-Myc was immunoprecipitated using the A14 anti-Myc antibody, and Spt4-Flag was immunoprecipitated using the M2 anti-Flag antibody. The results from at least three independent experiments are shown.

elf1

elf1

elf1

Evidence that Elf1 affects chromatin structure in actively transcribed regions. The genetic interactions of elf1 with elongation factors and its localization to actively transcribed regions are consistent with a role for Elf1 in transcription elongation. Based on the synthetic lethality observed between elf1 and mutations in SPT4 and SPT6 and the fact that the localization of Elf1 is partially dependent on Spt4 and Spt6, we hypothesized that Elf1 is performing a role related to these proteins in vivo. Recent studies have suggested a role for Spt6 in controlling chromatin structure over transcribed sequences, as spt6 mutations were found to cause defects in chromatin structure in actively transcribed regions. These defects allow transcription initiation from cryptic promoters within some coding regions (26).

To determine if Elf1 plays related roles, we employed a phenotypic assay based on the observation that spt6 mutations cause transcription initiation to start internally within the 3' coding region of the FLO8 gene (26). We made use of a reporter construct in which the 3' end of FLO8 has been replaced with the HIS3 gene (GAL1-FLO8-HIS3) (see Materials and Methods). In this construct, HIS3 can be expressed only upon transcription initiation from the FLO8 internal start site. When we analyzed an elf1 strain for internal initiation, by testing for growth on medium lacking histidine, we found that it was able to grow when GAL1-FLO8-HIS3 transcription levels are high (growth on galactose) but not when they are low (growth on glucose) (Fig. 6A). This result suggests that cells lacking elf1 are defective in maintaining proper chromatin structure at the GAL1-FLO8-HIS3 gene, thus allowing transcription to occur from a normally cryptic promoter within the coding region.

View larger version (51K): [in this window] [in a new window]   FIG. 6. Elf1 is necessary for maintaining proper chromatin structure in actively transcribed regions. (A) elf1 mutations allow use of a cryptic TATA element within the GAL1-FLO8-HIS3 reporter. Wild-type and elf1 strains containing the GAL1-FLO8-HIS3 reporter construct were patched onto YPD medium. Strains were then replica plated to synthetic complete medium, medium lacking histidine and containing glucose, and medium lacking histidine and containing galactose as the carbon source. Strains were scored for growth at 30°C for either 1 or 3 days. (B) Mutations in elf1 are Ts– in combination with rtf1 or hir1 mutations. elf1 strains were crossed to rtf1 and hir1 mutants. Diploids were sporulated and dissected, and representative spores from the resulting complete tetrads were spotted onto YPD medium at 30°C or 39°C for 2 days. (C) elf1 hir1 mutants allow transcription to initiate from within the endogenous FLO8 coding region. Wild-type, elf1, hir1, elf11 hir1, rtf1, and elf1 rtf1 strains were grown in YPD to mid-log at 30°C. Strains were shifted to 39°C by addition of an equal volume of YPD medium prewarmed to 48°C. Strains were then incubated at 39°C, and cells were collected at 2 and 4 h after the temperature shift. Northern analysis was performed using probes to the 3' region of FLO8 (+1515 to +2326) and also to the SCR1 loading control.

elf1

elf1

elf1

elf1 rtf1

elf1 hir1

elf1 hir1

elf1 rtf1

elf1 hir1

elf1 rtf1

Elf1 associates with casein kinase II. In order to further characterize S. cerevisiae Elf1, we purified it using a C-terminal TAP tag (55) containing a calmodulin-binding peptide and Staphylococcus aureus protein A, separated by a TEV protease cleavage site. The tagged protein was then purified on IgG and calmodulin columns and analyzed by SDS-PAGE followed by staining with silver. Protein bands absent from a control preparation and corresponding to the tagged protein and any associated proteins were then identified by MALDI-TOF mass spectrometry (Fig. 7). Elf1-TAP copurified substoichiometrically with subunits of casein kinase II (CKII). We were able to detect the two largest components of CKII (Cka1 and Ckb1) using MALDI-TOF mass spectrometry on trypsin-digested silver-stained gel bands, but not its two smaller subunits (Cka2 and Ckb2), which coelectrophoresed with the much more abundant Elf1 polypeptide. Cka2 and Ckb2 were, however, detected by trypsin digestion and liquid chromatography/tandem mass spectrometry (LC-MS/MS) analysis of the entire purified protein preparation. Consistent with this association, Elf1 contains seven potential CKII sites in its carboxy-terminal end at positions S86, S95, S101, T109, S117, S124, and S142.

View larger version (38K): [in this window] [in a new window]   FIG. 7. Purification of Elf1. Purification of Elf1 was carried out with strains containing either an untagged protein or a TAP-tagged version of Elf1. The protein complex was purified and was then analyzed by SDS-PAGE and silver staining. Elf1 and the two largest subunits of CKII (Cka1 and Ckb1) were identified by trypsin digestion and MALDI-TOF. In the mass spectrum, there were 6 (35% coverage), 16 (43% coverage), and 10 (39% coverage) peptides used to identify Elf1, Cka1, and Ckb1, respectively. The two smaller subunits of CKII, which comigrate with Elf1-TAP, were identified (along with Cka1, Ckb1, and Elf1) by using gel-free LC-MS/MS. The + indicates the position of TEV protease. Other detectable bands are present in both lanes, including those at around 70 kDa that are likely the heat shock proteins Ssa1 and Ssb1, present in most purifications (N. Krogan and J. Greenblatt, unpublished results).

	DISCUSSION

Top Abstract Introduction Materials and Methods Results Discussion References

elf1

elf1

elf1

elf1

The conservation of Elf1 throughout eukaryotes also suggests an important role for this protein in transcription. All Elf1 homologues identified so far are quite small and contain a conserved C4 putative zinc finger domain. The C4 zinc fingers are the most abundant class of zinc-binding domains and are found in a number of proteins associated with the transcriptional machinery, including Spt4, TFIIS, and Rpb9 (29). In the only other case where a role for an Elf1 homologue has been examined, C. elegans, no phenotype was detected after treatment with ELF1-specific RNA inhibition (24). This result is similar to our finding in S. cerevisiae, where an elf1 mutation alone causes no detectable growth defect and only modest phenotypes under standard laboratory growth conditions. More detailed analysis in other organisms will be required to assess the general role of Elf1 in transcription.

Our analysis of ELF1 reveals a number of interesting similarities with SPT4. First, the proteins encoded by these genes are both small and contain a C4 zinc finger domain. Second, both elf1 and spt4 mutations also cause Spt^– and 6AU^s phenotypes, although the elf1 phenotypes are considerably more modest than those caused by spt4. Third, although both elf1 and spt4 mutations cause no detectable growth defects on their own, both mutations cause inviability when combined with a similar set of mutations in other genes encoding elongation factors. For example, both elf1 and spt4 are lethal in combination with mutations in the genes encoding several of the Paf1 complex members (our results and reference 70), as well as in combination with mutations in SPT5 and SPT6 (our results and reference 73). Finally, ChIP analysis of Elf1 reveals similarities to Spt4 as well as to Spt5, Spt6, and Spt16, all of which are present at levels comparable to that of Pol II across genes and into the 3' UTR of genes (25, 27). This localization contrasts with that of the Paf1 and TREX complexes, which show decreased binding past the polyadenylation site (25, 27). The significance of these observations and the effects of these proteins on termination are unclear, but they further highlight the similarities between Spt4 and Elf1.

The physical association of Elf1 and CKII suggests that modification by phosphorylation may play a role in Elf1 function. Consistent with this, Elf1 has been shown to be phosphorylated in vitro in the presence of [³²P]ATP and yeast extract (M. Constanzo and B. Andrews, personal communication). Aside from the physical association of Elf1 and CKII, there is no evidence for a stable association of Elf1 with additional proteins. While many elongation factors are present in stable complexes, Elf1 was not identified as a protein partner in global TAP purifications (18, 31). In our attempts to identify Elf1-interacting proteins, we purified Elf1 using the TAP tag under many different salt conditions (100 to 350 mM NaCl, 200 to 500 mM KO-acetate, and 250 mM KCl) and did not detect any other proteins that copurify with Elf1 besides CKII (data not shown). Additionally, Elf1 did not coimmunoprecipitate with Pol II or several other elongation factors, including Spt4, Spt5, Spt6, Rtf1, and Chd1 (data not shown). The relevant physical association of Elf1 with other proteins, whether they are stable or transient, may only occur when it is associated with chromatin, and this might be missed by standard purification approaches.

We have yet to determine how Elf1 is recruited to actively transcribed regions. Results from our chromatin immunoprecipitation experiments suggest that Elf1 can be recruited to significant levels independently of other elongation factors, although its recruitment is partially dependent on Spt4 and Spt6. One possibility is that Elf1 interacts directly with Pol II and that Spt4 and Spt6 help to stabilize this association. Alternatively, Elf1 may associate with elongating Pol II through some elongation factor not tested here. Another possibility still is that Elf1 is recruited by an altered chromatin structure occurring in the wake of transcription. Further studies are needed to understand the associations of Elf1 along actively transcribed chromatin.

Our experiments suggest that Elf1 plays a role in elongation by maintaining proper chromatin structure in regions of active transcription. There are several pieces of evidence supporting this idea. Mutations in elf1 cause a weak Spt^– phenotype, a phenotype shared by mutations in the genes encoding several other chromatin elongation factors and within the genes encoding the histones themselves (77). We also found that this phenotype was exacerbated in elf1 mutants when combined with mutations in genes encoding other elongation factors and regulators of histone transcription. The Spt phenotype has been hypothesized for some spt mutants to be due to defects in chromatin structure during elongation, allowing differential use of TATA elements (26). This is supported by the observation that in the elf1 hir1 mutant with enhanced Ts^– and Spt^– phenotypes, we also see an increased level of short transcripts initiating from a cryptic promoter within the FLO8 coding region. We hypothesize that the synthetic lethality of elf1 observed in combination with mutations in SPT4, SPT5, and SPT6 is likely due to the inability of these strains to maintain chromatin integrity in actively transcribing regions of the genome. Further analysis of elf1 mutants alone and in combination with other elongation mutants will provide clues into the function of this conserved elongation factor and new insights regarding the mechanisms of elongation through chromatin in vivo. Given the conservation of Elf1 and its probable role in chromatin structure, Elf1 may also be involved in other chromatin-related processes, such as DNA repair, replication, and recombination.

	ACKNOWLEDGMENTS

 
We thank Grant Hartzog, Kristina Johnson, and Caroline Kane for providing strains, plasmids, and antisera and Grant Hartzog for sharing unpublished results. We also thank G. Zhong and X. Guo for technical help and Affinium Pharmaceuticals for help with mass spectrometry.

This work was supported by NIH grant GM32967 to F.W. and by grants to J.F.G. from the Canadian Institute of Health Research, the Ontario Genomics Institute, and the National Cancer Institute of Canada with funds from the Canadian Cancer Society. D.P. was supported by Regulation of Gene Expression in Prokaryotes and Eukaryotes and Genetics of Cancer and Inherited Diseases training grants from the NIH. N.J.K. was supported by a doctoral fellowship from the Canadian Institute of Health Research.

	FOOTNOTES

 
* Corresponding author. Mailing address: Department of Genetics, Harvard Medical School, Boston, MA 02115. Phone: (617) 432-7768. Fax: (617) 432-6506. E-mail: winston{at}genetics.med.harvard.edu.

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