scholarly journals HSFs drive stress type-specific transcription of genes and enhancers

2021 ◽  
Author(s):  
Samu V Himanen ◽  
Mikael C Puustinen ◽  
Alejandro J Da Silva ◽  
Anniina Vihervaara ◽  
Lea Sistonen
Keyword(s):  
Oxidative Stress ◽  
Heat Shock ◽  
Rna Polymerase Ii ◽  
Molecular Mechanisms ◽  
Gene Promoters ◽  
Heat Shock Factors ◽  
Pol Ii ◽  
Bona Fide ◽  
Stressed Cells ◽  
First Time

Reprogramming of transcription is critical for the survival under cellular stress. Heat shock has provided an excellent model to investigate nascent transcription in stressed cells, but the molecular mechanisms orchestrating RNA synthesis during other types of stress are unknown. We utilized PRO-seq and ChIP-seq to study how Heat Shock Factors, HSF1 and HSF2, coordinate transcription at genes and enhancers upon oxidative stress and heat shock. We show that pause-release of RNA polymerase II (Pol II) is a universal mechanism regulating gene transcription in stressed cells, while enhancers are activated at the level of Pol II recruitment. Moreover, besides functioning as conventional promoter-binding transcription factors, HSF1 and HSF2 bind to stress-induced enhancers to trigger Pol II pause-release from poised gene promoters. Importantly, HSFs act at distinct genes and enhancers in a stress type-specific manner. HSF1 binds to many chaperone genes upon oxidative and heat stress but activates them only in heat-shocked cells. Under oxidative stress, HSF1 and HSF2 trans-activate genes independently of each other, demonstrating, for the first time, that HSF2 is a bona fide transcription factor. Taken together, we show that HSFs function as multi-stress-responsive factors that activate specific genes and enhancers when encountering changes in temperature and redox state.

Mediator dynamics during heat shock in budding yeast

2021 ◽  
pp. gr.275750.121
Author(s):  
Debasish Sarkar ◽  
Z. Iris Zhu ◽  
Elisabeth R. Knoll ◽  
Emily Paul ◽  
David Landsman ◽  
...  
Keyword(s):  
Heat Shock ◽  
Rna Polymerase Ii ◽  
Budding Yeast ◽  
Core Promoter ◽  
Growth Conditions ◽  
Promoter Regions ◽  
Pol Ii ◽  
A Genome ◽  
Wide Scale ◽  
Stable Association

The Mediator complex is central to transcription by RNA polymerase II (Pol II) in eukaryotes. In budding yeast (Saccharomyces cerevisiae), Mediator is recruited by activators and associates with core promoter regions, where it facilitates pre-initiation complex (PIC) assembly, only transiently prior to Pol II escape. Interruption of the transcription cycle by inactivation or depletion of Kin28 inhibits Pol II escape and stabilizes this association. However, Mediator occupancy and dynamics have not been examined on a genome-wide scale in yeast grown in nonstandard conditions. Here we investigate Mediator occupancy following heat shock or CdCl2 exposure, with and without depletion of Kin28. We find that Pol II occupancy exhibits similar dependence on Mediator under normal and heat shock conditions. However, while Mediator association increases at many genes upon Kin28 depletion under standard growth conditions, little or no increase is observed at most genes upon heat shock, indicating a more stable association of Mediator after heat shock. Mediator remains associated upstream of the core promoter at genes repressed by heat shock or CdCl2 exposure whether or not Kin28 is depleted, suggesting that Mediator is recruited by activators but is unable to engage PIC components at these repressed targets. This persistent association is strongest at promoters that bind the HMGB family member Hmo1, and is reduced but not eliminated in hmo1∆ yeast. Finally, we show a reduced dependence on PIC components for Mediator occupancy at promoters after heat shock, further supporting altered dynamics or stronger engagement with activators under these conditions.

scholarly journals Molecular Mechanisms of Heat Shock Factors in Cancer

Cells ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 1202
Author(s):  
Mikael Christer Puustinen ◽  
Lea Sistonen
Keyword(s):  
Heat Shock ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Heat Shock Factors ◽  
Therapeutic Approaches ◽  
The Past ◽  
Cancer Types ◽  
Cellular Pathways ◽  
As Stress ◽  
Regulatory Functions

Malignant transformation is accompanied by alterations in the key cellular pathways that regulate development, metabolism, proliferation and motility as well as stress resilience. The members of the transcription factor family, called heat shock factors (HSFs), have been shown to play important roles in all of these biological processes, and in the past decade it has become evident that their activities are rewired during tumorigenesis. This review focuses on the expression patterns and functions of HSF1, HSF2, and HSF4 in specific cancer types, highlighting the mechanisms by which the regulatory functions of these transcription factors are modulated. Recently developed therapeutic approaches that target HSFs are also discussed.

scholarly journals Cellular stress mechanisms of prenatal maternal stress: Heat shock factors and oxidative stress

2019 ◽  
Vol 709 ◽  
pp. 134368 ◽  
Author(s):  
Jonathan Dowell ◽  
Benjamin A. Elser ◽  
Rachel E. Schroeder ◽  
Hanna E. Stevens
Keyword(s):  
Oxidative Stress ◽  
Heat Shock ◽  
Maternal Stress ◽  
Cellular Stress ◽  
Heat Shock Factors ◽  
Prenatal Maternal Stress ◽  
And Oxidative Stress

scholarly journals Postrecruitment Regulation of RNA Polymerase II Directs Rapid Signaling Responses at the Promoters of Estrogen Target Genes

2008 ◽  
Vol 29 (5) ◽  
pp. 1123-1133 ◽  
Author(s):  
Miltiadis Kininis ◽  
Gary D. Isaacs ◽  
Leighton J. Core ◽  
Nasun Hah ◽  
W. Lee Kraus
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Target Genes ◽  
Elongation Factor ◽  
Estrogen Signaling ◽  
Gene Promoters ◽  
Pol Ii ◽  
Activator Proteins ◽  
Classical Models ◽  
Target Promoters

ABSTRACT Under classical models for signal-dependent transcription in eukaryotes, DNA-binding activator proteins regulate the recruitment of RNA polymerase II (Pol II) to a set of target promoters. However, recent studies, as well as our results herein, show that Pol II is widely distributed (i.e., “preloaded”) at the promoters of many genes prior to specific signaling events. How Pol II recruitment and Pol II preloading fit within a unified model of gene regulation is unclear. In addition, the mechanisms through which cellular signals activate preloaded Pol II across mammalian genomes remain largely unknown. We show here that the predominant genomic outcome of estrogen signaling is the postrecruitment regulation of Pol II activity at target gene promoters, likely through specific changes in Pol II phosphorylation rather than through recruitment of Pol II to the promoters. Furthermore, we show that negative elongation factor binds to estrogen target promoters in conjunction with preloaded Pol II and represses gene expression until the appropriate signal is received. Finally, our studies reveal that the estrogen-dependent activation of preloaded Pol II facilitates rapid gene regulatory responses which play important physiological roles in regulating estrogen signaling itself. Our results reveal a broad use of postrecruitment Pol II regulation by the estrogen signaling pathway, a mode of regulation that is likely to apply to a wide variety of signal-regulated pathways.

scholarly journals Kin28 depletion increases association of TFIID subunits Taf1 and Taf4 with promoters in Saccharomyces cerevisiae

2019 ◽  
Author(s):  
Elisabeth R. Knoll ◽  
Z. Iris Zhu ◽  
Debasish Sarkar ◽  
David Landsman ◽  
Randall H. Morse
Keyword(s):  
Transcription Factors ◽  
Rna Polymerase Ii ◽  
Mediator Complex ◽  
Gene Promoters ◽  
Initiation Complex ◽  
Pol Ii ◽  
Promoter Escape ◽  
General Transcription Factors ◽  
Promoter Occupancy ◽  
Encoding Genes

AbstractIn eukaryotes, transcription of mRNA-encoding genes by RNA polymerase II (Pol II) begins with assembly of the pre-initiation complex (PIC), comprising Pol II and the general transcription factors. Although the pathway of PIC assembly is well established, the mechanism of assembly and the dynamics of PIC components are not fully understood. For example, only recently has it been shown in yeast that the Mediator complex, which assists in pre-initiation complex formation at promoters of essentially all genes transcribed by Pol II, normally occupies promoters only transiently. This was inferred from studies showing that inhibiting Pol II promoter escape by depleting or inactivating Kin28 resulted in increased promoter occupancy by Mediator, as measured by chromatin immunoprecipitation (ChIP). Here we show that two subunits of TFIID, Taf1 and Taf4, similarly show increased occupancy as measured by ChIP upon depletion or inactivation of Kin28. In contrast, TBP occupancy is unaffected by depletion of Kin28, thus revealing an uncoupling of Taf and TBP occupancy during the transcription cycle. Increased Taf1 occupancy upon Kin28 depletion is suppressed by depletion of TBP, while depletion of TBP in the presence of Kin28 has little effect on Taf1 occupancy. Taf1 occupancy relative to TBP is higher at TFIID-dominated promoters and promoters having consensus TATA elements than at SAGA-dominated promoters and promoters lacking consensus TATA elements, consistent with prior work, and the increase in Taf occupancy upon depletion of Kin28 is more pronounced at TFIID-dominated promoters. Our results support the suggestion, based on recent structural studies, that TFIID may not remain bound to gene promoters through the transcription initiation cycle.Author SummaryTranscription of mRNA-encoding genes by RNA polymerase II (Pol II) begins when the pre-initiation complex, a large complex comprising Pol II and several general transcription factors, including the TATA-binding protein (TBP)-containing TFIID complex, assembles at gene promoters. Although the major steps in the pathway of PIC assembly have been identified, the mechanism of assembly in vivo and the dynamics of PIC components are not fully understood. In this work we have used a yeast strain that is engineered to allow inhibition of promoter escape by Pol II by administration of a chemical, in order to “freeze” the assembled PIC and thus determine whether this condition increases the promoter occupancy of TBP and two TBP-associated factors (Tafs) that are components of TFIID. This approach was used recently to demonstrate that the Mediator complex, which facilitates PIC assembly, normally binds only transiently to gene promoters. We find that Tafs, like Mediator, show increased occupancy when Pol II promoter escape is inhibited, whereas TBP binding is constant. These results imply that binding of TBP and Tafs is uncoupled during the transcription cycle, and that Taf occupancy is at least partially interrupted upon Pol II promoter escape.

scholarly journals Stress-Induced Transcriptional Memory Accelerates Promoter-Proximal Pause-Release and Decelerates Termination over Mitotic Divisions

2019 ◽  
Author(s):  
Anniina Vihervaara ◽  
Dig Bijay Mahat ◽  
Samu V. Himanen ◽  
Malin A.H. Blom ◽  
John T. Lis ◽  
...  
Keyword(s):  
Heat Shock ◽  
Rna Polymerase Ii ◽  
Transcriptional Response ◽  
Regulatory Elements ◽  
List Type ◽  
Pol Ii ◽  
Daughter Cells ◽  
Heat Shocks ◽  
Transcriptional Memory ◽  
Pol Ii Pausing

SummaryHeat shock triggers an instant reprogramming of gene and enhancer transcription, but whether cells encode a memory to stress, at the level of nascent transcription, has remained unknown. Here, we measured transcriptional response to acute heat stress in unconditioned cells and in daughters of cells that had been exposed to a single or multiple heat shocks. Tracking RNA Polymerase II (Pol II) genome-wide at nucleotide-resolution revealed that cells precisely remember their transcriptional identity throughout stress, restoring Pol II distribution at gene bodies and enhancers upon recovery. However, single heat shock primed faster gene-induction in the daughter cells by increasing promoter-proximal Pol II pausing, and accelerating the pause-release. In repeatedly stressed cells, both basal and inducible transcription was refined, and pre-mRNA processing decelerated, which retained transcripts on chromatin and reduced recycling of the transcription machinery. These results mechanistically uncovered how the steps of pause-release and termination maintain transcriptional memory over mitosis.Highlights-Cell type-specific transcription precisely recovers after heat-induced reprogramming-Single heat shock primes genes for accelerated induction over mitotic divisionsviaincreased promoter-proximal Pol II pausing and faster pause-release-Multiple heat shocks refine basal and inducible transcription over mitotic divisions to support survival of the daughter cells-Decelerated termination at active genes reduces recycling of Pol II to heat-activated promoters and enhancers-HSF1 increases the rate of promoter-proximal pause-releaseviadistal and proximal regulatory elements

scholarly journals Mechanism of DNA alkylation-induced transcriptional stalling, lesion bypass, and mutagenesis

2017 ◽  
Vol 114 (34) ◽  
pp. E7082-E7091 ◽  
Author(s):  
Liang Xu ◽  
Wei Wang ◽  
Jiabin Wu ◽  
Ji Hyun Shin ◽  
Pengcheng Wang ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Molecular Mechanisms ◽  
Minor Groove ◽  
Dna Lesions ◽  
Dna Alkylation ◽  
Lesion Bypass ◽  
Pol Ii ◽  
The Impact

Alkylated DNA lesions, induced by both exogenous chemical agents and endogenous metabolites, interfere with the efficiency and accuracy of DNA replication and transcription. However, the molecular mechanisms of DNA alkylation-induced transcriptional stalling and mutagenesis remain unknown. In this study, we systematically investigated how RNA polymerase II (pol II) recognizes and bypasses regioisomeric O2-, N3-, and O4-ethylthymidine (O2-, N3-, and O4-EtdT) lesions. We observed distinct pol II stalling profiles for the three regioisomeric EtdT lesions. Intriguingly, pol II stalling at O2-EtdT and N3-EtdT sites is exacerbated by TFIIS-stimulated proofreading activity. Assessment for the impact of the EtdT lesions on individual fidelity checkpoints provided further mechanistic insights, where the transcriptional lesion bypass routes for the three EtdT lesions are controlled by distinct fidelity checkpoints. The error-free transcriptional lesion bypass route is strongly favored for the minor-groove O2-EtdT lesion. In contrast, a dominant error-prone route stemming from GMP misincorporation was observed for the major-groove O4-EtdT lesion. For the N3-EtdT lesion that disrupts base pairing, multiple transcriptional lesion bypass routes were found. Importantly, the results from the present in vitro transcriptional studies are well correlated with in vivo transcriptional mutagenesis analysis. Finally, we identified a minor-groove–sensing motif from pol II (termed Pro-Gate loop). The Pro-Gate loop faces toward the minor groove of RNA:DNA hybrid and is involved in modulating the translocation of minor-groove alkylated DNA template after nucleotide incorporation opposite the lesion. Taken together, this work provides important mechanistic insights into transcriptional stalling, lesion bypass, and mutagenesis of alkylated DNA lesions.

scholarly journals RNA-Dependent Replication and Transcription of Hepatitis Delta Virus RNA Involve Distinct Cellular RNA Polymerases

2000 ◽  
Vol 20 (16) ◽  
pp. 6030-6039 ◽  
Author(s):  
Lucy E. Modahl ◽  
Thomas B. Macnaughton ◽  
Nongliao Zhu ◽  
Deborah L. Johnson ◽  
Michael M. C. Lai
Keyword(s):  
Rna Polymerase Ii ◽  
Hepatitis Delta Virus ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Full Length ◽  
Supporting Evidence ◽  
Mrna Transcription ◽  
Hepatitis Delta ◽  
Pol Ii ◽  
Delta Virus

ABSTRACT Cellular DNA-dependent RNA polymerase II (pol II) has been postulated to carry out RNA-dependent RNA replication and transcription of hepatitis delta virus (HDV) RNA, generating a full-length (1.7-kb) RNA genome and a subgenomic-length (0.8-kb) mRNA. However, the supporting evidence for this hypothesis was ambiguous because the previous experiments relied on DNA-templated transcription to initiate HDV RNA synthesis. Furthermore, there is no evidence that the same cellular enzyme is involved in the synthesis of both RNA species. In this study, we used a novel HDV RNA-based transfection approach, devoid of any artificial HDV cDNA intermediates, to determine the enzymatic and metabolic requirements for the synthesis of these two RNA species. We showed that HDV subgenomic mRNA transcription was inhibited by a low concentration of α-amanitin (<3 μg/ml) and could be partially restored by an α-amanitin-resistant mutant pol II; however, surprisingly, the synthesis of the full-length (1.7-kb) antigenomic RNA was not affected by α-amanitin to a concentration higher than 25 μg/ml. By several other criteria, such as the differing requirement for the de novo-synthesized hepatitis delta antigen and temperature dependence, we further showed that the metabolic requirements of subgenomic HDV mRNA synthesis are different from those for the synthesis of genomic-length HDV RNA and cellular pol II transcripts. The synthesis of the two HDV RNA species could also be uncoupled under several different conditions. These findings provide strong evidence that pol II, or proteins derived from pol II transcripts, is involved in mRNA transcription from the HDV RNA template. In contrast, the synthesis of the 1.7-kb HDV antigenomic RNA appears not to be dependent on pol II. These results reveal that there are distinct molecular mechanisms for the synthesis of these two RNA species.

scholarly journals Activity of chimeric U small nuclear RNA (snRNA)/mRNA genes in transfected protoplasts of Nicotiana plumbaginifolia: U snRNA 3'-end formation and transcription initiation can occur independently in plants.

1993 ◽  
Vol 13 (10) ◽  
pp. 6403-6415 ◽  
Author(s):  
S Connelly ◽  
W Filipowicz
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Transcription Initiation ◽  
Gene Promoter ◽  
Nicotiana Plumbaginifolia ◽  
Gene Promoters ◽  
Coding Region ◽  
Pol Ii ◽  
U2 Snrna ◽  
Snrna Gene

Formation of the 3' ends of RNA polymerase II (Pol II)-specific U small nuclear RNAs (U snRNAs) in vertebrate cells is dependent upon transcription initiation from the U snRNA gene promoter. Moreover, U snRNA promoters are unable to direct the synthesis of functional polyadenylated mRNAs. In this work, we have investigated whether U snRNA 3'-end formation and transcription initiation are also coupled in plants. We have first characterized the requirements for 3'-end formation of an Arabidopsis U2 snRNA expressed in transfected protoplasts of Nicotiana plumbaginifolia. We found that the 3'-end-adjacent sequence CA (N)3-10AGTNNAA, conserved in plant Pol II-specific U snRNA genes, is essential for the 3'-end formation of U2 transcripts and, similar to the vertebrate 3' box, is highly tolerant to mutation. The 3'-flanking regions of an Arabidopsis U5 and a maize U2 snRNA gene can effectively substitute for the Arabidopsis U2 3'-end formation signal, indicating that these signals are functionally equivalent among different Pol II-transcribed snRNA genes. The plant U snRNA 3'-end formation signal can be recognized irrespective of whether transcription initiation occurs at U snRNA or mRNA gene promoters, although efficiency of 3' box utilization is higher when transcription initiation occurs at the U snRNA promoter. Moreover, transcripts initiated from the U2 gene promoter can be spliced and polyadenylated. Transcription from a Pol III-specific plant U snRNA gene promoter is not compatible with polyadenylation. Finally, we reveal that initiation at a Pol II-specific plant U snRNA gene promoter can occur in the absence of the snRNA coding region and a functional snRNA 3'-end formation signal, demonstrating that these sequences play no role in determining the RNA polymerase specificity of plant U snRNA genes.

scholarly journals Regulation of expression of human RNA polymerase II-transcribed snRNA genes

Open Biology ◽  
2017 ◽  
Vol 7 (6) ◽  
pp. 170073 ◽  
Author(s):  
Joana Guiro ◽  
Shona Murphy
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Molecular Mechanisms ◽  
Mrna Splicing ◽  
Regulation Of Expression ◽  
Protein Coding ◽  
Pol Ii ◽  
Protein Coding Genes ◽  
Non Coding Rnas ◽  
Rna Genes

In addition to protein-coding genes, RNA polymerase II (pol II) transcribes numerous genes for non-coding RNAs, including the small-nuclear (sn)RNA genes. snRNAs are an important class of non-coding RNAs, several of which are involved in pre-mRNA splicing. The molecular mechanisms underlying expression of human pol II-transcribed snRNA genes are less well characterized than for protein-coding genes and there are important differences in expression of these two gene types. Here, we review the DNA features and proteins required for efficient transcription of snRNA genes and co-transcriptional 3′ end formation of the transcripts.

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