Budding Yeast CTDK-I Is Required for DNA Damage-Induced Transcription

Ostapenko, Denis; Solomon, Mark J.

doi:10.1128/ec.2.2.274-283.2003

Cited by 44 publications

(47 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The selective binding of Hrr25 to 2,5P repeats suggests a role in DNA damage responses for RNAPII carrying repeats phosphorylated in this pattern. This suggestion is in line with published studies showing that ctk1⌬ strains are sensitive to certain DNA damaging agents (Ostapenko and Solomon 2003). On the other hand, PCTD-associated Hrr25 may be involved in other processes.…”

Section: Not Just Rna Processing Anymore: Many More Pcaps and Functionssupporting

confidence: 80%

Phosphorylation and functions of the RNA polymerase II CTD

Phatnani¹,

Greenleaf²

2006

Genes Dev.

660

704

View full text Add to dashboard Cite

The C-terminal repeat domain (CTD), an unusual extension appended to the C terminus of the largest subunit of RNA polymerase II, serves as a flexible binding scaffold for numerous nuclear factors; which factors bind is determined by the phosphorylation patterns on the CTD repeats. Changes in phosphorylation patterns, as polymerase transcribes a gene, are thought to orchestrate the association of different sets of factors with the transcriptase and strongly influence functional organization of the nucleus. In this review we appraise what is known, and what is not known, about patterns of phosphorylation on the CTD of RNA polymerases II at the beginning, the middle, and the end of genes; the proposal that doubly phosphorylated repeats are present on elongating polymerase is explored. We discuss briefly proteins known to associate with the phosphorylated CTD at the beginning and ends of genes; we explore in more detail proteins that are recruited to the body of genes, the diversity of their functions, and the potential consequences of tethering these functions to elongating RNA polymerase II. We also discuss accumulating structural information on phosphoCTD-binding proteins and how it illustrates the variety of binding domains and interaction modes, emphasizing the structural flexibility of the CTD. We end with a number of open questions that highlight the extent of what remains to be learned about the phosphorylation and functions of the CTD.

show abstract

Section: Not Just Rna Processing Anymore: Many More Pcaps and Functionssupporting

confidence: 80%

Phosphorylation and functions of the RNA polymerase II CTD

Phatnani¹,

Greenleaf²

2006

Genes Dev.

660

704

View full text Add to dashboard Cite

show abstract

“…Analogously, the identification of Hrr25 as a PCAP suggests a role for CTDK-I in modulating DNA damage responses. Indeed, like hrr25Δ cells, ctk1Δ cells are unable to efficiently induce RNR gene transcription upon exposure to DNA damaging agents (67). Do the splicing factors found in the current or previous work to be PCTD-associated (Prp40, Snu56, Ssd1) therefore entail a role for CTDK-I in splicing?…”

Section: Functional Implications For Ctd Phosphorylation By Ctdk-imentioning

confidence: 74%

“…Specifically, hrr25Δ cells were shown to be defective in the transcriptional induction of RNR gene expression upon exposure to HU (66); fittingly, ctk1Δ cells display the same defect in DNA damage responses (67).…”

Section: (3) Hrr25 and Dna Transactionsmentioning

confidence: 99%

Expanding the Functional Repertoire of CTD Kinase I and RNA Polymerase II: Novel PhosphoCTD-Associating Proteins in the Yeast Proteome

2004

View full text Add to dashboard Cite

CTD kinase I (CTDK-I) of Saccharomyces cerevisiae is required for normal phosphorylation of the C-terminal repeat domain (CTD) on elongating RNA polymerase II. To elucidate cellular roles played by this kinase and the hyperphosphorylated CTD (phosphoCTD) it generates, we systematically searched yeast extracts for proteins that bound to the phosphoCTD made by CTDK-I in vitro. Initially, using a combination of far-western blotting and phosphoCTD affinity chromatography, we discovered a set of novel phosphoCTD-associating proteins (PCAPs) implicated in a variety of nuclear functions. We identified the phosphoCTD-interacting domains of a number of these PCAPs, and in several test cases (namely, Set2, Ssd1, and Hrr25) adduced evidence that phosphoCTD binding is functionally important in vivo. Employing surface plasmon resonance (BIACORE) analysis, we found that recombinant versions of these and other PCAPs bind preferentially to CTD repeat peptides carrying SerPO 4 residues at positions 2 and 5 of each seven amino acid repeat, consistent with the positional specificity of CTDK-I in vitro [Jones, J. C., et al. (2004) J. Biol. Chem. 279, 24957-24964]. Subsequently, we used a synthetic CTD peptide with three doubly phosphorylated repeats (2,5P) as an affinity matrix, greatly expanding our search for PCAPs. This resulted in identification of approximately 100 PCAPs and associated proteins representing a wide range of functions (e.g., transcription, RNA processing, chromatin structure, DNA metabolism, protein synthesis and turnover, RNA degradation, snRNA modification, and snoRNP biogenesis). The varied nature of these PCAPs and associated proteins points to an unexpectedly diverse set of connections between Pol II elongation and other processes, conceptually expanding the role played by CTD phosphorylation in functional organization of the nucleus.The carboxyl-terminal repeat domain (CTD) 1 of the largest subunit of eukaryotic RNA polymerase II (Pol II) comprises tandem repeats of the consensus heptapeptide YSPTSPS. This highly conserved sequence, which is repeated 26 times in yeast and 52 times in mammals, is essential for viability. Phosphorylation of the CTD regulates the activities of the polymerase: only Pol II with an unphosphorylated CTD (Pol IIA) is thought to be able to assemble into preinitiation complexes at the promoter, whereas elongating polymerase has a hyperphosphorylated CTD (Pol IIO) (1,2). The serines at positions 2 and 5 within the heptad repeat represent major sites of phosphorylation during transcription. † Supported by National Institutes of Health Grant GM40505.© 2004 American Chemical Society * To whom correspondence should be addressed. . E-mail: arno@biochem.duke.edu. 1 Abbreviations: CTDK-I, CTD kinase I; Pol II, RNA polymerase II; CTD, C-terminal repeat domain; phosphoCTD, hyperphosphorylated CTD; PCTD, phosphoCTD; PCAP, phosphoCTD-associating protein; PCID, phosphoCTD-interacting domain; SGD, Saccharomyces Genome Database; SPR, surface plasmon resonance; RU, response units. NIH Publi...

show abstract

“…We speculate that CTD hyperphosphorylation may have multiple roles-promoting transcription of stress promoters, such as heat shock protein 70, where polymerases are poised early in elongation (54), facilitating DNA damage repair (39,55), and transiently shutting down transcription of vulnerable snRNAs until danger has passed. Consistent with this hypothesis, artificial recruitment of P-TEFb to an snRNA promoter impairs transcription (58).…”

Section: Discussionmentioning

confidence: 99%

Role of the C-Terminal Domain of RNA Polymerase II in U2 snRNA Transcription and 3′ Processing

Jacobs

Ogiwara

Weiner

2004

Molecular and Cellular Biology

View full text Add to dashboard Cite

U small nuclear RNAs (snRNAs) and mRNAs are both transcribed by RNA polymerase II (Pol II), but the snRNAs have unusual TATA-less promoters and are neither spliced nor polyadenylated; instead, 3 processing is directed by a highly conserved 3 end formation signal that requires initiation from an snRNA promoter. Here we show that the C-terminal domain (CTD) of Pol II is required for efficient U2 snRNA transcription, as it is for mRNA transcription. However, CTD kinase inhibitors, such as 5,6-dichloro-1-␤-D-ribofuranosylbenzimidazole (DRB) and 1-(5-isoquinolinesulfonyl)-2-methylpiperazine (H7), that block mRNA elongation do not affect U2 transcription, although 3 processing of the U2 primary transcript is impaired. We show further that U2 transcription is preferentially inhibited by low doses of UV irradiation or actinomycin D, which induce CTD kinase activity, and that UV inhibition can be rescued by treatment with DRB or H7. We propose that Pol II complexes transcribing snRNAs and mRNAs have distinct CTD phosphorylation patterns. mRNA promoters recruit factors including kinases that hyperphosphorylate the CTD, and the CTD in turn recruits proteins needed for mRNA splicing and polyadenylation. We predict that snRNA promoters recruit factors including a CTD kinase(s) whose snRNA-specific phosphorylation pattern recruits factors required for promoter-coupled 3 end formation.RNAs that encode proteins are transcribed by RNA polymerase II (Pol II) in almost all eukaryotes. In contrast, untranslated RNAs are transcribed by all three RNA polymerases: 5.8, 18, and 28S rRNA by Pol I; 5S rRNA, tRNA, and U6 small nuclear RNA (snRNA) by Pol III (56); and the other U snRNAs, which function in mRNA splicing and various RNA processing events, by Pol II (27). Kinetoplastid protozoa, a class of early diverging eukaryotes, are exceptions to these rules. Kinetoplastid snRNAs are transcribed not by Pol II but by Pol III (65), and certain mRNAs, including the immunologically important variant surface glycoprotein message, are hybrids of a U snRNA-like spliced leader transcribed by Pol II and a protein-coding mRNA body transcribed by Pol I (19).Although U snRNAs and mRNAs are both transcribed by Pol II in mammals, the genes are very different. U snRNA promoters have no TATA box and rely instead upon a dedicated U snRNA-specific promoter consisting of a highly conserved proximal sequence element (PSE) and an enhancer-like distal sequence element spaced one nucleosome apart (27). In addition, U snRNA genes are short (typically only a few hundred base pairs) and lack introns, whereas genes encoding mRNAs can span megabases and usually contain many introns. Also, U snRNA genes are typically present in multiple copies in higher eukaryotes-the human U1 and U2 genes are tandemly repeated (6, 40, 66, 68)-whereas most protein-coding genes are present in only one or a few copies per haploid genome.U snRNA processing also differs from mRNA processing. U snRNAs are neither spliced nor polyadenylated; instead, formation of the first U snRNA interme...

show abstract

Budding Yeast CTDK-I Is Required for DNA Damage-Induced Transcription

Cited by 44 publications

References 43 publications

Phosphorylation and functions of the RNA polymerase II CTD

Phosphorylation and functions of the RNA polymerase II CTD

Expanding the Functional Repertoire of CTD Kinase I and RNA Polymerase II: Novel PhosphoCTD-Associating Proteins in the Yeast Proteome

Role of the C-Terminal Domain of RNA Polymerase II in U2 snRNA Transcription and 3′ Processing

Contact Info

Product

Resources

About