The Transcription Elongation Factor Bur1-Bur2 Interacts with Replication Protein A and Maintains Genome Stability during Replication Stress

Clausing, Emanuel; Mayer, Andreas; Chanarat, Sittinan; Müller, Bárbara; Germann, Susanne Manuela; Cramer, Patrick; Lisby, Michael; Sträßer, Katja

doi:10.1074/jbc.m110.193292

Cited by 20 publications

(30 citation statements)

References 38 publications

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“…However, expression defects of DDR genes were excluded as a causative mechanism, since depletion of Cdk9 did not show any changes in expression of DDR genes in their transcriptional genomewide microarray. Consistently, transcriptional changes of DDR genes were also not observed for the kinase-dead mutant of Bur1 (yeast homolog of Cdk9) (Clausing et al 2010). Our data show the down-regulation of many key DDR genes in expression microarrays after knockdown of CycK or Cdk12 (Supplemental Table S4).…”

Section: Discussionsupporting

confidence: 66%

The Cyclin K/Cdk12 complex maintains genomic stability via regulation of expression of DNA damage response genes

Blažek¹,

Kohoutek²,

et al. 2011

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Various cyclin-dependent kinase (Cdk) complexes have been implicated in the regulation of transcription. In this study, we identified a 70-kDa Cyclin K (CycK) that binds Cdk12 and Cdk13 to form two different complexes (CycK/Cdk12 or CycK/Cdk13) in human cells. The CycK/Cdk12 complex regulates phosphorylation of Ser2 in the C-terminal domain of RNA polymerase II and expression of a small subset of human genes, as revealed in expression microarrays. Depletion of CycK/Cdk12 results in decreased expression of predominantly long genes with high numbers of exons. The most prominent group of down-regulated genes are the DNA damage response genes, including the critical regulators of genomic stability: BRCA1 (breast and ovarian cancer type 1 susceptibility protein 1), ATR (ataxia telangiectasia and Rad3-related), FANCI, and FANCD2. We show that CycK/ Cdk12, rather than CycK/Cdk13, is necessary for their expression. Nuclear run-on assays and chromatin immunoprecipitations with RNA polymerase II on the BRCA1 and FANCI genes suggest a transcriptional defect in the absence of CycK/Cdk12. Consistent with these findings, cells without CycK/Cdk12 induce spontaneous DNA damage and are sensitive to a variety of DNA damage agents. We conclude that through regulation of expression of DNA damage response genes, CycK/Cdk12 protects cells from genomic instability. The essential role of CycK for organisms in vivo is further supported by the result that genetic inactivation of CycK in mice causes early embryonic lethality.

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Section: Discussionsupporting

confidence: 66%

The Cyclin K/Cdk12 complex maintains genomic stability via regulation of expression of DNA damage response genes

Blažek¹,

Kohoutek²,

et al. 2011

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“…We observed synthetic genetic interactions between ssDNA binding domain mutants of Rfa1 and two positive elongation factors: Spt4 and Bur2 (Figures 5D and S3C) and Rfa1 physically interacts with the Bur1/Bur2 kinase complex (Clausing et al, 2010). These same RFA1 mutant alleles confer partial resistance to mycophenolic acid (Figure 5E), a phenotype also seen with mutations in factors that are normally inhibitory for RNApII elongation (Carrozza et al, 2005; Keogh et al, 2005).…”

Section: Discussionmentioning

confidence: 98%

Sub1 and RPA Associate with RNA Polymerase II at Different Stages of Transcription

et al. 2011

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Summary Single stranded DNA binding proteins play many roles in nucleic acid metabolism, but their importance during transcription remains unclear. Quantitative proteomic analysis of RNA polymerase II (RNApII) pre-initiation complexes (PICs) identified Sub1 and the Replication Protein A complex (RPA), both of which bind single-stranded DNA (ssDNA). Sub1, homolog of mammalian coactivator PC4, exhibits strong genetic interactions with factors necessary for promoter melting. Sub1 localizes near the transcription bubble in vitro and binds to promoters in vivo dependent upon PIC assembly. In contrast, RPA localizes to transcribed regions of active genes, strongly correlated with transcribing RNApII but independently of replication. RFA1 interacts genetically with transcription elongation factor genes. Interestingly, RPA levels increase at active promoters in cells carrying a Sub1 deletion or ssDNA binding mutant, suggesting competition for a common binding site. We propose that Sub1 and RPA interact with the non-template strand of RNApII complexes during initiation and elongation, respectively.

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“…Its activities in replication require an intact CDK9 kinase domain; therefore, identifying the substrates of CDK9-CYCLIN K will be essential to understand its function. Notably, this activity in the DDR appears to be evolutionarily conserved, since yeast CDK9-cyclin proteins also participate in the DDR [126]. …”

Section: Atr Signalingmentioning

confidence: 99%

ATR signalling: more than meeting at the fork

Nam

Chen

2011

Biochemical Journal

272

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Synopsis Preservation of genome integrity via the DNA damage response is critical to prevent disease. Ataxia-telangiectasia mutated and Rad3-related (ATR) is essential for life and functions as a master regulator of the DNA damage response, especially during DNA replication. ATR controls and coordinates DNA replication origin firing, replication fork stability, cell cycle checkpoints, and DNA repair. Since its identification 15 years ago, a model of ATR activation and signaling has emerged that involves localization to sites of DNA damage and activation through protein-protein interactions. Recent research has added an increasingly detailed understanding of the canonical ATR pathway, and an appreciation that the canonical model does not fully capture the complexity of ATR regulation. Here we review the ATR signaling process, focusing on mechanistic findings garnered from the identification of new ATR interacting proteins and substrates. We discuss how to incorporate these new insights into a model of ATR regulation, and point out the significant gaps in our understanding of this essential genome maintenance pathway.

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The Transcription Elongation Factor Bur1-Bur2 Interacts with Replication Protein A and Maintains Genome Stability during Replication Stress

Cited by 20 publications

References 38 publications

The Cyclin K/Cdk12 complex maintains genomic stability via regulation of expression of DNA damage response genes

The Cyclin K/Cdk12 complex maintains genomic stability via regulation of expression of DNA damage response genes

Sub1 and RPA Associate with RNA Polymerase II at Different Stages of Transcription

ATR signalling: more than meeting at the fork

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