Transcriptional elongation factor Paf1 core complex adopts a spirally wrapped solenoidal topology

Deng, Pujuan; Zhou, Yuqiao; Jiang, Junyi; Li, Haojie; Tian, Wei; Cao, Yinghua; Qin, Yan; Kim, Jae-Hoon; Roeder, Robert G.; Patel, Dinshaw J.; Wang, Zhanxin

doi:10.1073/pnas.1812256115

Cited by 21 publications

(17 citation statements)

References 29 publications

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“…To investigate the impact of Paf1C on the S. cerevisiae transcriptome, we used high-resolution whole-genome tiling arrays to measure steady state RNA levels in S. cerevisiae strains deleted for the PAF1 gene, which encodes a core member of Paf1C important for complex integrity (Mueller et al 2004;Deng et al 2018). Additionally, to assess the Paf1dependency of unstable ncRNAs in these experiments, we deleted TRF4 in both PAF1 and paf1D strains.…”

Section: Deletion Of Paf1 Affects Coding and Noncoding Transcripts Genome-widementioning

confidence: 99%

The Paf1 Complex Broadly Impacts the Transcriptome ofSaccharomyces cerevisiae

et al. 2019

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The Polymerase Associated Factor 1 complex (Paf1C) is a multifunctional regulator of eukaryotic gene expression important for the coordination of transcription with chromatin modification and post-transcriptional processes. In this study, we investigated the extent to which the functions of Paf1C combine to regulate the Saccharomyces cerevisiae transcriptome. While previous studies focused on the roles of Paf1C in controlling mRNA levels, here, we took advantage of a genetic background that enriches for unstable transcripts, and demonstrate that deletion of PAF1 affects all classes of Pol II transcripts including multiple classes of noncoding RNAs (ncRNAs). By conducting a de novo differential expression analysis independent of gene annotations, we found that Paf1 positively and negatively regulates antisense transcription at multiple loci. Comparisons with nascent transcript data revealed that many, but not all, changes in RNA levels detected by our analysis are due to changes in transcription instead of post-transcriptional events. To investigate the mechanisms by which Paf1 regulates protein-coding genes, we focused on genes involved in iron and phosphate homeostasis, which were differentially affected by PAF1 deletion. Our results indicate that Paf1 stimulates phosphate gene expression through a mechanism that is independent of any individual Paf1C-dependent histone modification. In contrast, the inhibition of iron gene expression by Paf1 correlates with a defect in H3 K36 trimethylation. Finally, we showed that one iron regulon gene, FET4, is coordinately controlled by Paf1 and transcription of upstream noncoding DNA. Together, these data identify roles for Paf1C in controlling both coding and noncoding regions of the yeast genome.

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Section: Deletion Of Paf1 Affects Coding and Noncoding Transcripts Genome-widementioning

confidence: 99%

The Paf1 Complex Broadly Impacts the Transcriptome ofSaccharomyces cerevisiae

et al. 2019

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show abstract

“…To investigate the impact of Paf1C on the S. cerevisiae transcriptome, we used 250 high-resolution whole-genome tiling arrays to measure steady state RNA levels in S. 251 cerevisiae strains deleted for the PAF1 gene, which encodes a core member of Paf1C 252 important for complex integrity (Mueller et al 2004;Deng et al 2018). Additionally, to assess the Paf1-dependency of unstable noncoding RNAs (ncRNAs) in these 254 experiments, we deleted TRF4 in both PAF1 and paf1∆ strains.…”

Section: Deletion Of Paf1 Affects Coding and Noncoding Transcripts Gementioning

confidence: 99%

The Paf1 complex broadly impacts the transcriptome ofSaccharomyces cerevisiae

Ellison

Lederer

Warner

et al. 2019

Preprint

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The Polymerase Associated Factor 1 complex (Paf1C) is a multifunctional regulator of eukaryotic gene expression important for the coordination of transcription with chromatin modification and post-transcriptional processes. In this study, we investigated the extent to which the functions of Paf1C combine to regulate the Saccharomyces cerevisiae transcriptome. While previous studies focused on the roles of Paf1C in controlling mRNA levels, here we took advantage of a genetic background that enriches for unstable transcripts and demonstrate that deletion of PAF1 affects all classes of Pol II transcripts including multiple classes of noncoding RNAs. By conducting a de novo differential expression analysis independent of gene annotations, we found that Paf1 positively and negatively regulates antisense transcription at multiple loci. Comparisons with nascent transcript data revealed that many, but not all, changes in RNA levels detected by our analysis are due to changes in transcription instead of posttranscriptional events. To investigate the mechanisms by which Paf1 regulates proteincoding genes, we focused on genes involved in iron and phosphate homeostasis, which were differentially affected by PAF1 deletion. Our results indicate that Paf1 stimulates phosphate gene expression through a mechanism that is independent of any individual Paf1C-dependent histone modification. In contrast, the inhibition of iron gene expression by Paf1 correlates with a defect in H3 K36 tri-methylation. Finally, we showed that one iron regulon gene, FET4, is coordinately controlled by Paf1 and transcription of upstream noncoding DNA. Together these data identify roles for Paf1C in controlling both coding and noncoding regions of the yeast genome.

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“…修饰, 并进一步更新了Paf1复合物的组装模式 [31] . 同年, Wang课题组 [32] 解析了嗜热真菌的Ctr9-Paf1-Cdc73 链DNA, 这与之前发现的Rtf1-Plus3结构域特异性结合单链DNA的结果一致 [26] .…”

Section: Paf1复合物的结构研究进展unclassified