scholarly journals A Kinase-Independent Role for Cyclin-Dependent Kinase 19 in p53 Response

2017 ◽  
Vol 37 (13) ◽  
Author(s):  
K. Audrey Audetat ◽  
Matthew D. Galbraith ◽  
Aaron T. Odell ◽  
Thomas Lee ◽  
Ahwan Pandey ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Stress Responses ◽  
Cholesterol Metabolism ◽  
Genotoxic Stress ◽  
General Factor ◽  
Cyclin Dependent Kinase ◽  
Genome Wide ◽  
P53 Response ◽  
P53 Target Gene ◽  
Rna Polymerase Ii Transcription

ABSTRACT The human Mediator complex regulates RNA polymerase II transcription genome-wide. A general factor that regulates Mediator function is the four-subunit kinase module, which contains either cyclin-dependent kinase 8 (CDK8) or CDK19. Whereas CDK8 is linked to specific signaling cascades and oncogenesis, the cellular roles of its paralog, CDK19, are poorly studied. We discovered that osteosarcoma cells (SJSA) are naturally depleted of CDK8 protein. Whereas stable CDK19 knockdown was tolerated in SJSA cells, proliferation was reduced. Notably, proliferation defects were rescued upon the reexpression of wild-type or kinase-dead CDK19. Comparative RNA sequencing analyses showed reduced expression of mitotic genes and activation of genes associated with cholesterol metabolism and the p53 pathway in CDK19 knockdown cells. SJSA cells treated with 5-fluorouracil, which induces metabolic and genotoxic stress and activates p53, further implicated CDK19 in p53 target gene expression. To better probe the p53 response, SJSA cells (shCDK19 versus shCTRL) were treated with the p53 activator nutlin-3. Remarkably, CDK19 was required for SJSA cells to return to a proliferative state after nutlin-3 treatment, and this effect was kinase independent. These results implicate CDK19 as a regulator of p53 stress responses and suggest a role for CDK19 in cellular resistance to nutlin-3.

scholarly journals The telomeric Cdc13–Stn1–Ten1 complex regulates RNA polymerase II transcription

2019 ◽  
Vol 47 (12) ◽  
pp. 6250-6268 ◽  
Author(s):  
Olga Calvo ◽  
Nathalie Grandin ◽  
Antonio Jordán-Pla ◽  
Esperanza Miñambres ◽  
Noelia González-Polo ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Genome Stability ◽  
Elongation Factor ◽  
Yeast Saccharomyces Cerevisiae ◽  
Replication Fork Progression ◽  
Genome Wide ◽  
Length Regulation ◽  
Transcription Regulators ◽  
Rna Polymerase Ii Transcription

Abstract Specialized telomeric proteins have an essential role in maintaining genome stability through chromosome end protection and telomere length regulation. In the yeast Saccharomyces cerevisiae, the evolutionary conserved CST complex, composed of the Cdc13, Stn1 and Ten1 proteins, largely contributes to these functions. Here, we report genetic interactions between TEN1 and several genes coding for transcription regulators. Molecular assays confirmed this novel function of Ten1 and further established that it regulates the occupancies of RNA polymerase II and the Spt5 elongation factor within transcribed genes. Since Ten1, but also Cdc13 and Stn1, were found to physically associate with Spt5, we propose that Spt5 represents the target of CST in transcription regulation. Moreover, CST physically associates with Hmo1, previously shown to mediate the architecture of S-phase transcribed genes. The fact that, genome-wide, the promoters of genes down-regulated in the ten1-31 mutant are prefentially bound by Hmo1, leads us to propose a potential role for CST in synchronizing transcription with replication fork progression following head-on collisions.

scholarly journals Orphan Nuclear Receptor RORγ Modulates the Genome-Wide Binding of the Cholesterol Metabolic Genes during Mycotoxin-Induced Liver Injury

Nutrients ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 2539
Author(s):  
Kaiqi Li ◽  
Hao Li ◽  
Kexin Zhang ◽  
Jinying Zhang ◽  
Ping Hu ◽  
...  
Keyword(s):  
Liver Injury ◽  
Rna Polymerase Ii ◽  
Nuclear Receptor ◽  
Cholesterol Metabolism ◽  
Whole Body ◽  
Orphan Nuclear Receptor ◽  
Metabolism Regulation ◽  
Metabolic Genes ◽  
Genome Wide ◽  
A Genome

Maintaining lipid homeostasis is crucial to liver function, the key organ that governs the whole-body energy metabolism. In contrast, lipid dysregulation has been implicated in mycotoxin-induced liver injury, by which the pathophysiological regulation and the molecular components involved remain elusive. Here we focused on the potential roles of orphan nuclear receptor (NR) RORγ in lipid programming, and aimed to explore its action on cholesterol regulation in the liver of mycotoxin-exposed piglets. We found that liver tissues were damaged in the mycotoxin-exposed piglets compared to the healthy controls, revealed by histological analysis, elevated seral ALT, AST and ALP levels, and increased caspase 3/7 activities. Consistent with the transcriptomic finding of down-regulated cholesterol metabolism, we demonstrated that both cholesterol contents and cholesterol biosynthesis/transformation gene expressions in the mycotoxin-exposed livers were reduced, including HMGCS1, FDPS, SQLE, EBP, FDFT1 and VLDLR. Furthermore, we reported that RORγ binds to the cholesterol metabolic genes in porcine hepatocytes using a genome-wide ChIP-seq analysis, whereas mycotoxin decreased the RORγ binding occupancies genome-wide, especially at the cholesterol metabolic pathway. In addition, we revealed the enrichment of co-factors p300 and SRC, the histone marks H3K27ac and H3K4me2, together with RNA Polymerase II (Pol-II) at the locus of HMGCS1 in hepatocytes, which were reduced by mycotoxin-exposure. Our results provide a deep insight into the cholesterol metabolism regulation during mycotoxin-induced liver injury, and propose NRs as therapeutic targets for anti-mycotoxin treatments.

scholarly journals CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation

2020 ◽  
Vol 48 (14) ◽  
pp. 7712-7727
Author(s):  
Michael Tellier ◽  
Justyna Zaborowska ◽  
Livia Caizzi ◽  
Eusra Mohammad ◽  
Taras Velychko ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Elongation ◽  
Pol Ii ◽  
Terminal Domain ◽  
Carboxyl Terminal Domain ◽  
Genome Wide ◽  
A Genome ◽  
Carboxyl Terminal ◽  
Rna Polymerase Ii Transcription

Abstract Cyclin-dependent kinase 12 (CDK12) phosphorylates the carboxyl-terminal domain (CTD) of RNA polymerase II (pol II) but its roles in transcription beyond the expression of DNA damage response genes remain unclear. Here, we have used TT-seq and mNET-seq to monitor the direct effects of rapid CDK12 inhibition on transcription activity and CTD phosphorylation in human cells. CDK12 inhibition causes a genome-wide defect in transcription elongation and a global reduction of CTD Ser2 and Ser5 phosphorylation. The elongation defect is explained by the loss of the elongation factors LEO1 and CDC73, part of PAF1 complex, and SPT6 from the newly-elongating pol II. Our results indicate that CDK12 is a general activator of pol II transcription elongation and indicate that it targets both Ser2 and Ser5 residues of the pol II CTD.

Nuclear organization of RNA polymerase II transcription

2013 ◽  
Vol 91 (1) ◽  
pp. 22-30 ◽  
Author(s):  
Scott Davidson ◽  
Neil Macpherson ◽  
Jennifer A. Mitchell
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Unit ◽  
Nuclear Space ◽  
Protein Coding ◽  
Transcription Factories ◽  
3 Dimensional ◽  
Genome Wide ◽  
Evolving Model ◽  
Rna Polymerase Ii Transcription

Transcription occurs at distinct nuclear compartments termed transcription factories that are specialized for transcription by 1 of the 3 polymerase complexes (I, II, or III). Protein-coding genes appear to move in and out of RNA polymerase II (RNAPII) compartments as they are expressed and silenced. In addition, transcription factories are sites where several transcription units, either from the same chromosome or different chromosomes, are transcribed. Chromosomes occupy distinct territories in the interphase nucleus with active genes preferentially positioned on the periphery or even looped out of the territory. These chromosome territories have been observed to intermingle in the nucleus, and multiple interactions among different chromosomes have been identified in genome-wide studies. Deep sequencing of the transcriptome and RNAPII associated on DNA obtained by chromatin immunoprecipitation have revealed a plethora of noncoding transcription and intergenic accumulations of RNAPII that must also be considered in models of genome function. The organization of transcription into distinct regions of the nucleus has changed the way we view transcription with the evolving model for silencing or activation of gene expression involving physical relocation of the transcription unit to a silencing or activation compartment, thus, highlighting the need to consider the process of transcription in the 3-dimensional nuclear space.

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 The telomeric Cdc13-Stn1-Ten1 complex regulates RNA polymerase II transcription

2018 ◽  
Author(s):  
Olga Calvo ◽  
Nathalie Grandin ◽  
Antonio Jordán-Pla ◽  
Esperanza Miñambres ◽  
Noelia González-Polo ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Genome Stability ◽  
Elongation Factor ◽  
Replication Fork Progression ◽  
Genome Wide ◽  
Length Regulation ◽  
Transcription Regulators ◽  
Telomere Length Regulation ◽  
Rna Polymerase Ii Transcription

SummarySpecialized telomeric proteins have an essential role in maintaining genome stability through chromosome end protection and telomere length regulation. In the yeast Saccharomyces cerevisiae, the evolutionary conserved CST complex, composed of the Cdc13, Stn1 and Ten1 proteins, largely contributes to these functions. Here, we report the existence of genetic interactions between TEN1 and several genes coding for transcription regulators. Molecular assays confirmed this novel function of Ten1 and further established that it regulates the occupancies of RNA polymerase II and the Spt5 elongation factor within transcribed genes. Since Ten1, but also Cdc13 and Stn1, were found to physically associate with Spt5, we propose that Spt5 represents the target of CST in transcription regulation. Moreover, CST physically associates with Hmo1, previously shown to mediate the architecture of S phase-transcribed genes. The fact that, genome-wide, the promoters of genes down-regulated in the ten1-31 mutant are prefentially bound by Hmo1, leads us to propose a potential role for CST in synchronizing transcription with replication fork progression following head-on collisions.

scholarly journals Genome-wide R-loop analysis defines unique roles for DDX5, XRN2, and PRMT5 in DNA/RNA hybrid resolution

2020 ◽  
Vol 3 (10) ◽  
pp. e202000762
Author(s):  
Oscar D Villarreal ◽  
Sofiane Y Mersaoui ◽  
Zhenbao Yu ◽  
Jean-Yves Masson ◽  
Stéphane Richard
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Start Site ◽  
Transcription Initiation ◽  
Transcription Termination ◽  
Start Site ◽  
Loop Gain ◽  
Transcription Start ◽  
Genome Wide ◽  
Rna Polymerase Ii Transcription

DDX5, XRN2, and PRMT5 have been shown to resolve DNA/RNA hybrids (R-loops) at RNA polymerase II transcription termination sites at few genomic loci. Herein, we perform genome-wide R-loop mapping using classical DNA/RNA immunoprecipitation and high-throughput sequencing (DRIP-seq) of loci regulated by DDX5, XRN2, and PRMT5. We observed hundreds to thousands of R-loop gains and losses at transcribed loci in DDX5-, XRN2-, and PRMT5-deficient U2OS cells. R-loop gains were characteristic of highly transcribed genes located at gene-rich regions, whereas R-loop losses were observed in low-density gene areas. DDX5, XRN2, and PRMT5 shared many R-loop gain loci at transcription termination sites, consistent with their coordinated role in RNA polymerase II transcription termination. DDX5-depleted cells had unique R-loop gain peaks near the transcription start site that did not overlap with those of siXRN2 and siPRMT5 cells, suggesting a role for DDX5 in transcription initiation independent of XRN2 and PRMT5. Moreover, we observed that the accumulated R-loops at certain loci in siDDX5, siXRN2, and siPRMT5 cells near the transcription start site of genes led to antisense intergenic transcription. Our findings define unique and shared roles of DDX5, XRN2, and PRMT5 in DNA/RNA hybrid regulation.

scholarly journals A CSB-PAF1C axis restores processive transcription elongation after DNA damage repair

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Diana van den Heuvel ◽  
Cornelia G. Spruijt ◽  
Román González-Prieto ◽  
Angela Kragten ◽  
Michelle T. Paulsen ◽  
...  
Keyword(s):  
Dna Damage ◽  
Rna Polymerase Ii ◽  
Transcription Elongation ◽  
Genotoxic Stress ◽  
Dna Lesions ◽  
Damage Repair ◽  
Genome Wide ◽  
A Genome ◽  
Processivity Factor ◽  
Dependent Pathway

AbstractBulky DNA lesions in transcribed strands block RNA polymerase II (RNAPII) elongation and induce a genome-wide transcriptional arrest. The transcription-coupled repair (TCR) pathway efficiently removes transcription-blocking DNA lesions, but how transcription is restored in the genome following DNA repair remains unresolved. Here, we find that the TCR-specific CSB protein loads the PAF1 complex (PAF1C) onto RNAPII in promoter-proximal regions in response to DNA damage. Although dispensable for TCR-mediated repair, PAF1C is essential for transcription recovery after UV irradiation. We find that PAF1C promotes RNAPII pause release in promoter-proximal regions and subsequently acts as a processivity factor that stimulates transcription elongation throughout genes. Our findings expose the molecular basis for a non-canonical PAF1C-dependent pathway that restores transcription throughout the human genome after genotoxic stress.

scholarly journals Cdk9 and H2Bub1 signal to Clr6-CII/Rpd3S to suppress aberrant antisense transcription

2020 ◽  
Author(s):  
Miriam Sansó ◽  
Pabitra K Parua ◽  
Daniel Pinto ◽  
J Peter Svensson ◽  
Viviane Pagé ◽  
...  
Keyword(s):  
Fission Yeast ◽  
Rna Polymerase Ii ◽  
Elongation Factor ◽  
Antisense Transcription ◽  
Cyclin Dependent Kinase ◽  
Coding Regions ◽  
Gene Coding ◽  
Genome Wide ◽  
Cleavage And Polyadenylation ◽  
Yeast Genes

Abstract Mono-ubiquitylation of histone H2B (H2Bub1) and phosphorylation of elongation factor Spt5 by cyclin-dependent kinase 9 (Cdk9) occur during transcription by RNA polymerase II (RNAPII), and are mutually dependent in fission yeast. It remained unclear whether Cdk9 and H2Bub1 cooperate to regulate the expression of individual genes. Here, we show that Cdk9 inhibition or H2Bub1 loss induces intragenic antisense transcription of ∼10% of fission yeast genes, with each perturbation affecting largely distinct subsets; ablation of both pathways de-represses antisense transcription of over half the genome. H2Bub1 and phospho-Spt5 have similar genome-wide distributions; both modifications are enriched, and directly proportional to each other, in coding regions, and decrease abruptly around the cleavage and polyadenylation signal (CPS). Cdk9-dependence of antisense suppression at specific genes correlates with high H2Bub1 occupancy, and with promoter-proximal RNAPII pausing. Genetic interactions link Cdk9, H2Bub1 and the histone deacetylase Clr6-CII, while combined Cdk9 inhibition and H2Bub1 loss impair Clr6-CII recruitment to chromatin and lead to decreased occupancy and increased acetylation of histones within gene coding regions. These results uncover novel interactions between co-transcriptional histone modification pathways, which link regulation of RNAPII transcription elongation to suppression of aberrant initiation.

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