scholarly journals Dual requirement for the yeast MMS19 gene in DNA repair and RNA polymerase II transcription.

1996 ◽  
Vol 16 (12) ◽  
pp. 6783-6793 ◽  
Author(s):  
S Lauder ◽  
M Bankmann ◽  
S N Guzder ◽  
P Sung ◽  
L Prakash ◽  
...  
Keyword(s):  
Dna Repair ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Excision Repair ◽  
Regulatory Element ◽  
Pol Ii ◽  
Cellular Processes ◽  
Nucleotide Excision ◽  
Damaged Dna

Genetic and biochemical studies of Saccharomyces cerevisiae have indicated the involvement of a large number of protein factors in nucleotide excision repair (NER) of UV-damaged DNA. However, how MMS19 affects this process has remained unclear. Here, we report on the isolation of the MMS19 gene and the determination of its role in NER and other cellular processes. Genetic and biochemical evidence indicates that besides its function in NER, MMS19 also affects RNA polymerase II (Pol II) transcription. mms19delta cells do not grow at 37 degrees C, and mutant extract exhibits a thermolabile defect in Pol II transcription. Thus, Mms19 protein resembles TFIIH in that it is required for both transcription and DNA repair. However, addition of purified Mms19 protein does not alleviate the transcriptional defect of the mms19delta extract, nor does it stimulate the incision of UV-damaged DNA reconstituted from purified proteins. Interestingly, addition of purified TFIIH corrects the transcriptional defect of the mms19delta extract. Mms19 is, however, not a component of TFIIH or of Pol II holoenzyme. These and other results suggest that Mms19 affects NER and transcription by influencing the activity of TFIIH as an upstream regulatory element. It is proposed that mutations in the human MMS19 counterpart could result in syndromes in which both NER and transcription are affected.

scholarly journals Requirement of ELC1 for RNA Polymerase II Polyubiquitylation and Degradation in Response to DNA Damage in Saccharomyces cerevisiae

2006 ◽  
Vol 26 (11) ◽  
pp. 3999-4005 ◽  
Author(s):  
Balazs Ribar ◽  
Louise Prakash ◽  
Satya Prakash
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Ubiquitin Ligase ◽  
Excision Repair ◽  
Uv Light ◽  
Yeast Cells ◽  
Pol Ii ◽  
Dna Damaging Agents ◽  
Nucleotide Excision

ABSTRACT Treatment of Saccharomyces cerevisiae and human cells with DNA-damaging agents such as UV light or 4-nitroquinoline-1-oxide induces polyubiquitylation of the largest RNA polymerase II (Pol II) subunit, Rpb1, which results in rapid Pol II degradation by the proteasome. Here we identify a novel role for the yeast Elc1 protein in mediating Pol II polyubiquitylation and degradation in DNA-damaged yeast cells and propose the involvement of a ubiquitin ligase, of which Elc1 is a component, in this process. In addition, we present genetic evidence for a possible involvement of Elc1 in Rad7-Rad16-dependent nucleotide excision repair (NER) of lesions from the nontranscribed regions of the genome and suggest a role for Elc1 in increasing the proficiency of repair of nontranscribed DNA, where as a component of the Rad7-Rad16-Elc1 ubiquitin ligase, it would promote the efficient turnover of the NER ensemble from the lesion site in a Rad23-19S proteasomal complex-dependent reaction.

scholarly journals Genome-wide distribution of Rad26 and Rad1-Rad10 reveals their relationship with Mediator and RNA polymerase II

2021 ◽  
Author(s):  
Diyavarshini Gopaul ◽  
Cyril Denby Wilkes ◽  
Arach Goldar ◽  
Nathalie Giordanengo Aiach ◽  
Marie-Bénédicte Barrault ◽  
...  
Keyword(s):  
Dna Repair ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Excision Repair ◽  
Genotoxic Stress ◽  
Wide Distribution ◽  
Yeast Genome ◽  
Yeast Saccharomyces Cerevisiae ◽  
Pol Ii ◽  
Genome Wide

Transcription is coupled with DNA repair, especially within nucleotide excision repair (NER). Mediator is a conserved coregulator playing a key role in RNA polymerase (Pol) II transcription. Mediator also links transcription and NER via a direct contact with Rad2/XPG endonuclease. In this work, we analyzed the genome-wide distribution of Rad26/CSB and that of Rad1-Rad10/XPF-ERCC1, addressing the question on a potential interplay of these proteins with Mediator and Pol II in yeast Saccharomyces cerevisiae. Our genome-wide analyses show that Rad1-Rad10 and Rad26 are present on the yeast genome in the absence of genotoxic stress, especially on highly transcribed regions, with Rad26 binding strongly correlating with that of Pol II. Moreover, we revealed that Rad1-Rad10 and Rad26 colocalize with Mediator on intergenic regions and physically interact with this complex. Using kin28 TFIIH mutant, we showed that Mediator stabilization on core promoters lead to an increase in Rad1-Rad10 chromatin binding, whereas Rad26 occupancy is less impacted by Mediator and follows mainly a decrease in Pol II transcription. Combined with multivariate analyses, our results reveal the interplay between Rad1-Rad10, Rad26, Mediator and Pol II, modulated by the binding dynamics of Mediator and Pol II transcription. In conclusion, we extend the Mediator link to Rad1-Rad10 and Rad26 NER proteins and reveal important differences in Mediator relationships with Rad2, Rad1-Rad10 and Rad26. Our work thus contributes to new concepts of the functional interplay between transcription and DNA repair, relevant for human diseases including cancer and XP/CS syndromes.

scholarly journals Recruitment of the putative transcription-repair coupling factor CSB/ERCC6 to RNA polymerase II elongation complexes.

1997 ◽  
Vol 17 (12) ◽  
pp. 6803-6814 ◽  
Author(s):  
D Tantin ◽  
A Kansal ◽  
M Carey
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Excision Repair ◽  
Coupling Factor ◽  
Pol Ii ◽  
Growth Defects ◽  
Cockayne's Syndrome ◽  
Nucleotide Excision ◽  
Rna Complex ◽  
Dna Template

Cockayne's syndrome (CS) is a disease characterized by developmental and growth defects, sunlight sensitivity, and a defect in transcription-coupled nucleotide excision repair. The two principle proteins involved in CS, CSA and CSB/ERCC6, have been hypothesized to bind RNA polymerase II (Pol II) and link transcription to DNA repair. We have tested CSA and CSB in assays designed to determine their role in transcription-coupled repair. Using a unique oligo(dC)-tailed DNA template, we provide biochemical evidence that CSB/ERCC6 interacts with Pol II molecules engaged in ternary complexes containing DNA and nascent RNA. CSB is a DNA-activated ATPase, and hydrolysis of the ATP beta-gamma phosphoanhydride bond is required for the formation of a stable Pol II-CSB-DNA-RNA complex. Unlike CSB, CSA does not directly bind Pol II.

scholarly journals Yeast RNA Polymerase II Transcription In Vitro Is Inhibited in the Presence of Nucleotide Excision Repair: Complementation of Inhibition by Holo-TFIIH and Requirement for RAD26

1998 ◽  
Vol 18 (5) ◽  
pp. 2668-2676 ◽  
Author(s):  
Zhaoyang You ◽  
William J. Feaver ◽  
Errol C. Friedberg
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Nucleotide Excision Repair ◽  
Excision Repair ◽  
Cell Extracts ◽  
Nucleotide Excision ◽  
Rnap Ii ◽  
Group B ◽  
Damaged Dna

ABSTRACT The Saccharomyces cerevisiae transcription factor IIH (TFIIH) is essential both for transcription by RNA polymerase II (RNAP II) and for nucleotide excision repair (NER) of damaged DNA. We have established cell extracts which support RNAP II transcription from the yeast CYC1 promoter or NER of transcriptionally silent damaged DNA on independent plasmid templates and substrates. When plasmid templates and substrates for both processes are simultaneously incubated with these extracts, transcription is significantly inhibited. This inhibition is strictly dependent on active NER and can be complemented with purified holo-TFIIH. These results suggest that in the presence of active NER, TFIIH is preferentially mobilized from the basal transcription machinery for use in NER. Inhibition of transcription in the presence of active NER requires theRAD26 gene, the yeast homolog of the human Cockayne syndrome group B gene (CSB).

scholarly journals Functional interplay between Mediator and RNA polymerase II in Rad2/XPG loading to the chromatin

2019 ◽  
Vol 47 (17) ◽  
pp. 8988-9004 ◽  
Author(s):  
Adrien Georges ◽  
Diyavarshini Gopaul ◽  
Cyril Denby Wilkes ◽  
Nathalie Giordanengo Aiach ◽  
Elizaveta Novikova ◽  
...  
Keyword(s):  
Dna Repair ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Excision Repair ◽  
Cellular Functions ◽  
Dynamic Interactions ◽  
Pol Ii ◽  
Core Promoters ◽  
Functional Dynamics ◽  
Genome Wide

Abstract Transcription and maintenance of genome integrity are fundamental cellular functions. Deregulation of transcription and defects in DNA repair lead to serious pathologies. The Mediator complex links RNA polymerase (Pol) II transcription and nucleotide excision repair via Rad2/XPG endonuclease. However, the functional interplay between Rad2/XPG, Mediator and Pol II remains to be determined. In this study, we investigated their functional dynamics using genomic and genetic approaches. In a mutant affected in Pol II phosphorylation leading to Mediator stabilization on core promoters, Rad2 genome-wide occupancy shifts towards core promoters following that of Mediator, but decreases on transcribed regions together with Pol II. Specific Mediator mutations increase UV sensitivity, reduce Rad2 recruitment to transcribed regions, lead to uncoupling of Rad2, Mediator and Pol II and to colethality with deletion of Rpb9 Pol II subunit involved in transcription-coupled repair. We provide new insights into the functional interplay between Rad2, Mediator and Pol II and propose that dynamic interactions with Mediator and Pol II are involved in Rad2 loading to the chromatin. Our work contributes to the understanding of the complex link between transcription and DNA repair machineries, dysfunction of which leads to severe diseases.

scholarly journals Mechanism of RNA polymerase II stalling by DNA alkylation

2017 ◽  
Vol 114 (46) ◽  
pp. 12172-12177 ◽  
Author(s):  
Stefano Malvezzi ◽  
Lucas Farnung ◽  
Claudia M. N. Aloisi ◽  
Todor Angelov ◽  
Patrick Cramer ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Anticancer Agents ◽  
Excision Repair ◽  
Minor Groove ◽  
Dna Alkylation ◽  
Drug Induced ◽  
Rna Pol Ii ◽  
Pol Ii

Several anticancer agents that form DNA adducts in the minor groove interfere with DNA replication and transcription to induce apoptosis. Therapeutic resistance can occur, however, when cells are proficient in the removal of drug-induced damage. Acylfulvenes are a class of experimental anticancer agents with a unique repair profile suggesting their capacity to stall RNA polymerase (Pol) II and trigger transcription-coupled nucleotide excision repair. Here we show how different forms of DNA alkylation impair transcription by RNA Pol II in cells and with the isolated enzyme and unravel a mode of RNA Pol II stalling that is due to alkylation of DNA in the minor groove. We incorporated a model for acylfulvene adducts, the stable 3-deaza-3-methoxynaphtylethyl-adenosine analog (3d-Napht-A), and smaller 3-deaza-adenosine analogs, into DNA oligonucleotides to assess RNA Pol II transcription elongation in vitro. RNA Pol II was strongly blocked by a 3d-Napht-A analog but bypassed smaller analogs. Crystal structure analysis revealed that a DNA base containing 3d-Napht-A can occupy the +1 templating position and impair closing of the trigger loop in the Pol II active center and polymerase translocation into the next template position. These results show how RNA Pol II copes with minor-groove DNA alkylation and establishes a mechanism for drug resistance.

Structural Biology of RNA Polymerase II Transcription: 20 Years On

2020 ◽  
Vol 36 (1) ◽  
pp. 1-34 ◽  
Author(s):  
Sara Osman ◽  
Patrick Cramer
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Focal Point ◽  
Dna Lesions ◽  
Cellular Regulation ◽  
Pol Ii ◽  
Associated Proteins ◽  
Rna Polymerase Ii Transcription

Gene transcription by RNA polymerase II (Pol II) is the first step in the expression of the eukaryotic genome and a focal point for cellular regulation during development, differentiation, and responses to the environment. Two decades after the determination of the structure of Pol II, the mechanisms of transcription have been elucidated with studies of Pol II complexes with nucleic acids and associated proteins. Here we provide an overview of the nearly 200 available Pol II complex structures and summarize how these structures have elucidated promoter-dependent transcription initiation, promoter-proximal pausing and release of Pol II into active elongation, and the mechanisms that Pol II uses to navigate obstacles such as nucleosomes and DNA lesions. We predict that future studies will focus on how Pol II transcription is interconnected with chromatin transitions, RNA processing, and DNA repair.

Nucleotide excision repair in the yeast Saccharomyces cerevisiae : its relationship to specialized mitotic recombination and RNA polymerase II basal transcription

1995 ◽  
Vol 347 (1319) ◽  
pp. 63-68 ◽  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Nucleotide Excision Repair ◽  
Excision Repair ◽  
Gene Products ◽  
Basal Transcription ◽  
Yeast Saccharomyces Cerevisiae ◽  
Nucleotide Excision ◽  
Yeast Genes

Nucleotide excision repair (ner) in eukaryotes is a biochemically complex process involving multiple gene products. The budding yeast Saccharomyces cerevisiae is an informative model for this process. Multiple genes and in some cases gene products that are indispensable for ner have been isolated from this organism. Homologues of many of these yeast genes are structurally and functionally conserved in higher organisms, including humans. The yeast Rad1/Rad10 heterodimeric protein complex is an endonuclease that is believed to participate in damage-specific incision of DNA during ner . This endonuclease is also required for specialized types of recombination. The products of the RAD3, SSL2(RAD25) SSL1 and TFB1 genes have dual roles in ner and in RNA polymerase II-dependent basal transcription.

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