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

Abstract

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.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 3Ј end of the nascent transcript, thus realigning the 3Ј end of the transcript with the Pol II catalytic site. Additional evidence suggests that TFIIS can help Pol II overcome a promoterproximal 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 elongat...

Chromatin and Transcription in Yeast

“…This level of cryptic initiation is likely an underestimate of the true level, as this study looked only at coding strands, and the method of detection would have found cryptic initiation only in genes transcribed at low levels Lickwar et al 2009). Cryptic initiation has also been observed in several other mutants, including spt16 and set2 (Kaplan et al 2003;Mason and Struhl 2003;Carrozza et al 2005;Prather et al 2005;Nourani et al 2006;Li et al 2007b;Xiao et al 2007;Cheung et al 2008;Imbeault et al 2008), with spt6 and spt16 mutants having the strongest effects .…”

“…However, there may be other mechanisms for repression of cryptic promoters, as many mutants that allow cryptic initiation have normal levels of H3K36 methylation . In spt6 mutants, cryptic initiation may be caused by multiple reasons in addition to loss of H3K36 methylation, including an inability to reassemble nucleosomes in the wake of elongating RNAPII (Kaplan et al 2003) and defective recruitment of two factors, Spt2 and Elf1, that each contribute to the repression of cryptic promoters (Prather et al 2005;Nourani et al 2006).…”

Potential role of the histone chaperone, CAF-1, in transcription

“…Their recruitment profile was further analyzed by normalization with pol II (Fig. 1B, bottom panel), and resembled the association pattern of the elongation factors, Spt2, Spt4, Spt5, Spt6, Spt16, and Elf1, all involved in chromatin dynamics, whose association persists over the 3'UTR (14,(16)(17)(18).…”

Aging by epigenetics—A consequence of chromatin damage?

“…Significantly, at least one of these, the histone chaperone HIRA, has been shown to increase in expression or undergo some level of regulation in aging baboon skin [40,41]. Although the HIRA histone chaperone may have some functions linked to transcription activation [42][43][44][45][46][47][48], this chaperone is known to have an evolutionarily conserved role in heterochromatin formation [49][50][51][52][53][54][55][56].…”