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van’t Sant LJ, Birkisdóttir MB, Ozinga RA, Gyenis Á, Hoeijmakers JH, Vermeij WP, Jaarsma D. Gene expression changes in cerebellum induced by dietary restriction. Front Mol Neurosci 2023; 16:1185665. [PMID: 37293544 PMCID: PMC10244750 DOI: 10.3389/fnmol.2023.1185665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/03/2023] [Indexed: 06/10/2023] Open
Abstract
Background Dietary restriction (DR) is a well-established universal anti-aging intervention, and is neuroprotective in multiple models of nervous system disease, including models with cerebellar pathology. The beneficial effects of DR are associated with a rearrangement of gene expression that modulate metabolic and cytoprotective pathways. However, the effect of DR on the cerebellar transcriptome remained to be fully defined. Results Here we analyzed the effect of a classical 30% DR protocol on the transcriptome of cerebellar cortex of young-adult male mice using RNAseq. We found that about 5% of expressed genes were differentially expressed in DR cerebellum, the far majority of whom showing subtle expression changes. A large proportion of down-regulated genes are implicated in signaling pathways, in particular pathways associated with neuronal signaling. DR up regulated pathways in large part were associated with cytoprotection and DNA repair. Analysis of the expression of cell-specific gene sets, indicated a strong enrichment of DR down genes in Purkinje cells, while genes specifically associated with granule cells did not show such a preferential down-regulation. Conclusion Our data show that DR may have a clear effect on the cerebellar transcriptome inducing a mild shift from physiology towards maintenance and repair, and having cell-type specific effects.
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Affiliation(s)
| | - María B. Birkisdóttir
- Department of Neuroscience, Erasmus MC, Rotterdam, Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Rutger A. Ozinga
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Ákos Gyenis
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine, Institute for Genome Stability in Ageing and Disease, University of Cologne, Cologne, Germany
| | - Jan H.J. Hoeijmakers
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), Faculty of Medicine, Institute for Genome Stability in Ageing and Disease, University of Cologne, Cologne, Germany
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Wilbert P. Vermeij
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Dick Jaarsma
- Department of Neuroscience, Erasmus MC, Rotterdam, Netherlands
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2
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Birkisdóttir MB, van Galen I, Brandt RMC, Barnhoorn S, van Vliet N, van Dijk C, Nagarajah B, Imholz S, van Oostrom CT, Reiling E, Gyenis Á, Mastroberardino PG, Jaarsma D, van Steeg H, Hoeijmakers JHJ, Dollé MET, Vermeij WP. Corrigendum: The use of progeroid DNA repair-deficient mice for assessing anti-aging compounds, illustrating the benefits of nicotinamide riboside. Front Aging 2022; 3:1086552. [PMID: 36506463 PMCID: PMC9727279 DOI: 10.3389/fragi.2022.1086552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/24/2022]
Abstract
[This corrects the article DOI: 10.3389/fragi.2022.1005322.].
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Affiliation(s)
- María B. Birkisdóttir
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,Oncode Institute, Utrecht, Netherlands
| | - Ivar van Galen
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,Oncode Institute, Utrecht, Netherlands
| | - Renata M. C. Brandt
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Sander Barnhoorn
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Nicole van Vliet
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Claire van Dijk
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands,Department of Hematology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Bhawani Nagarajah
- Centre for Health Protection, National Institute for Public Health and the Environment, (RIVM), Bilthoven, Netherlands
| | - Sandra Imholz
- Centre for Health Protection, National Institute for Public Health and the Environment, (RIVM), Bilthoven, Netherlands
| | - Conny T. van Oostrom
- Centre for Health Protection, National Institute for Public Health and the Environment, (RIVM), Bilthoven, Netherlands
| | - Erwin Reiling
- Centre for Health Protection, National Institute for Public Health and the Environment, (RIVM), Bilthoven, Netherlands
| | - Ákos Gyenis
- Faculty of Medicine, CECAD, Institute for Genome Stability in Aging and Disease, University of Cologne, Cologne, Germany
| | - Pier G. Mastroberardino
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands,IFOM-The FIRC Institute of Molecular Oncology, Milan, Italy,Department of Life, Health, and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Dick Jaarsma
- Department of Neuroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Harry van Steeg
- Centre for Health Protection, National Institute for Public Health and the Environment, (RIVM), Bilthoven, Netherlands
| | - Jan H. J. Hoeijmakers
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,Oncode Institute, Utrecht, Netherlands,Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands,Faculty of Medicine, CECAD, Institute for Genome Stability in Aging and Disease, University of Cologne, Cologne, Germany
| | - Martijn E. T. Dollé
- Centre for Health Protection, National Institute for Public Health and the Environment, (RIVM), Bilthoven, Netherlands,*Correspondence: Wilbert P. Vermeij, ; Martijn E. T. Dollé,
| | - Wilbert P. Vermeij
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,Oncode Institute, Utrecht, Netherlands,*Correspondence: Wilbert P. Vermeij, ; Martijn E. T. Dollé,
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3
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Birkisdóttir MB, van Galen I, Brandt RMC, Barnhoorn S, van Vliet N, van Dijk C, Nagarajah B, Imholz S, van Oostrom CT, Reiling E, Gyenis Á, Mastroberardino PG, Jaarsma D, van Steeg H, Hoeijmakers JHJ, Dollé MET, Vermeij WP. The use of progeroid DNA repair-deficient mice for assessing anti-aging compounds, illustrating the benefits of nicotinamide riboside. Front Aging 2022; 3:1005322. [PMID: 36313181 PMCID: PMC9596940 DOI: 10.3389/fragi.2022.1005322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/14/2022] [Indexed: 11/06/2022]
Abstract
Despite efficient repair, DNA damage inevitably accumulates with time affecting proper cell function and viability, thereby driving systemic aging. Interventions that either prevent DNA damage or enhance DNA repair are thus likely to extend health- and lifespan across species. However, effective genome-protecting compounds are largely lacking. Here, we use Ercc1 Δ/- and Xpg -/- DNA repair-deficient mutants as two bona fide accelerated aging mouse models to test propitious anti-aging pharmaceutical interventions. Ercc1 Δ/- and Xpg -/- mice show shortened lifespan with accelerated aging across numerous organs and tissues. Previously, we demonstrated that a well-established anti-aging intervention, dietary restriction, reduced DNA damage, and dramatically improved healthspan, strongly extended lifespan, and delayed all aging pathology investigated. Here, we further utilize the short lifespan and early onset of signs of neurological degeneration in Ercc1 Δ/- and Xpg -/- mice to test compounds that influence nutrient sensing (metformin, acarbose, resveratrol), inflammation (aspirin, ibuprofen), mitochondrial processes (idebenone, sodium nitrate, dichloroacetate), glucose homeostasis (trehalose, GlcNAc) and nicotinamide adenine dinucleotide (NAD+) metabolism. While some of the compounds have shown anti-aging features in WT animals, most of them failed to significantly alter lifespan or features of neurodegeneration of our mice. The two NAD+ precursors; nicotinamide riboside (NR) and nicotinic acid (NA), did however induce benefits, consistent with the role of NAD+ in facilitating DNA damage repair. Together, our results illustrate the applicability of short-lived repair mutants for systematic screening of anti-aging interventions capable of reducing DNA damage accumulation.
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Affiliation(s)
- María B. Birkisdóttir
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,Oncode Institute, Utrecht, Netherlands
| | - Ivar van Galen
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,Oncode Institute, Utrecht, Netherlands
| | - Renata M. C. Brandt
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Sander Barnhoorn
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Nicole van Vliet
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Claire van Dijk
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands,Department of Hematology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Bhawani Nagarajah
- Centre for Health Protection, National Institute for Public Health and the Environment, (RIVM), Bilthoven, Netherlands
| | - Sandra Imholz
- Centre for Health Protection, National Institute for Public Health and the Environment, (RIVM), Bilthoven, Netherlands
| | - Conny T. van Oostrom
- Centre for Health Protection, National Institute for Public Health and the Environment, (RIVM), Bilthoven, Netherlands
| | - Erwin Reiling
- Centre for Health Protection, National Institute for Public Health and the Environment, (RIVM), Bilthoven, Netherlands
| | - Ákos Gyenis
- Faculty of Medicine, CECAD, Institute for Genome Stability in Aging and Disease, University of Cologne, Cologne, Germany
| | - Pier G. Mastroberardino
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands,IFOM-The FIRC Institute of Molecular Oncology, Milan, Italy,Department of Life, Health, and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Dick Jaarsma
- Department of Neuroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Harry van Steeg
- Centre for Health Protection, National Institute for Public Health and the Environment, (RIVM), Bilthoven, Netherlands
| | - Jan H. J. Hoeijmakers
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,Oncode Institute, Utrecht, Netherlands,Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands,Faculty of Medicine, CECAD, Institute for Genome Stability in Aging and Disease, University of Cologne, Cologne, Germany
| | - Martijn E. T. Dollé
- Centre for Health Protection, National Institute for Public Health and the Environment, (RIVM), Bilthoven, Netherlands,*Correspondence: Wilbert P. Vermeij, ; Martijn E. T. Dollé,
| | - Wilbert P. Vermeij
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands,Oncode Institute, Utrecht, Netherlands,*Correspondence: Wilbert P. Vermeij, ; Martijn E. T. Dollé,
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4
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Borsos BN, Huliák I, Majoros H, Ujfaludi Z, Gyenis Á, Pukler P, Boros IM, Pankotai T. Human p53 interacts with the elongating RNAPII complex and is required for the release of actinomycin D induced transcription blockage. Sci Rep 2017; 7:40960. [PMID: 28102346 PMCID: PMC5244413 DOI: 10.1038/srep40960] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 12/14/2016] [Indexed: 12/30/2022] Open
Abstract
The p53 tumour suppressor regulates the transcription initiation of selected genes by binding to specific DNA sequences at their promoters. Here we report a novel role of p53 in transcription elongation in human cells. Our data demonstrate that upon transcription elongation blockage, p53 is associated with genes that have not been reported as its direct targets. p53 could be co-immunoprecipitated with active forms of DNA-directed RNA polymerase II subunit 1 (RPB1), highlighting its association with the elongating RNA polymerase II. During a normal transcription cycle, p53 and RPB1 are localised at distinct regions of selected non-canonical p53 target genes and this pattern of localisation was changed upon blockage of transcription elongation. Additionally, transcription elongation blockage induced the proteasomal degradation of RPB1. Our results reveal a novel role of p53 in human cells during transcription elongation blockage that may facilitate the removal of RNA polymerase II from DNA.
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Affiliation(s)
- Barbara N Borsos
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, 6726, Hungary
| | - Ildikó Huliák
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, 6726, Hungary
| | - Hajnalka Majoros
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, 6726, Hungary
| | - Zsuzsanna Ujfaludi
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, 6726, Hungary
| | - Ákos Gyenis
- Department of Molecular Genetics, Erasmus University Medical Centre, Rotterdam, PO Box 2040, 3000 CA, The Netherlands
| | - Peter Pukler
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, 6726, Hungary
| | - Imre M Boros
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, 6726, Hungary.,Institute of Biochemistry, Biological Research Centre, Szeged, 6726, Hungary
| | - Tibor Pankotai
- Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, 6726, Hungary
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5
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Vermeij WP, Dollé MET, Reiling E, Jaarsma D, Payan-Gomez C, Bombardieri CR, Wu H, Roks AJM, Botter SM, van der Eerden BC, Youssef SA, Kuiper RV, Nagarajah B, van Oostrom CT, Brandt RMC, Barnhoorn S, Imholz S, Pennings JLA, de Bruin A, Gyenis Á, Pothof J, Vijg J, van Steeg H, Hoeijmakers JHJ. Restricted diet delays accelerated ageing and genomic stress in DNA-repair-deficient mice. Nature 2016; 537:427-431. [PMID: 27556946 PMCID: PMC5161687 DOI: 10.1038/nature19329] [Citation(s) in RCA: 189] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 07/25/2016] [Indexed: 12/27/2022]
Abstract
Mice deficient in the DNA excision-repair gene Ercc1 (Ercc1∆/-) show numerous accelerated ageing features that limit their lifespan to 4-6 months. They also exhibit a 'survival response', which suppresses growth and enhances cellular maintenance. Such a response resembles the anti-ageing response induced by dietary restriction (also known as caloric restriction). Here we report that a dietary restriction of 30% tripled the median and maximal remaining lifespans of these progeroid mice, strongly retarding numerous aspects of accelerated ageing. Mice undergoing dietary restriction retained 50% more neurons and maintained full motor function far beyond the lifespan of mice fed ad libitum. Other DNA-repair-deficient, progeroid Xpg-/- (also known as Ercc5-/-) mice, a model of Cockayne syndrome, responded similarly. The dietary restriction response in Ercc1∆/- mice closely resembled the effects of dietary restriction in wild-type animals. Notably, liver tissue from Ercc1∆/- mice fed ad libitum showed preferential extinction of the expression of long genes, a phenomenon we also observed in several tissues ageing normally. This is consistent with the accumulation of stochastic, transcription-blocking lesions that affect long genes more than short ones. Dietary restriction largely prevented this declining transcriptional output and reduced the number of γH2AX DNA damage foci, indicating that dietary restriction preserves genome function by alleviating DNA damage. Our findings establish the Ercc1∆/- mouse as a powerful model organism for health-sustaining interventions, reveal potential for reducing endogenous DNA damage, facilitate a better understanding of the molecular mechanism of dietary restriction and suggest a role for counterintuitive dietary-restriction-like therapy for human progeroid genome instability syndromes and possibly neurodegeneration in general.
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Affiliation(s)
- W P Vermeij
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - M E T Dollé
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), PO Box 1, 3720 BA Bilthoven, The Netherlands
| | - E Reiling
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, The Netherlands.,Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), PO Box 1, 3720 BA Bilthoven, The Netherlands
| | - D Jaarsma
- Department of Neuroscience, Erasmus University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - C Payan-Gomez
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, The Netherlands.,Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Carrera 24, 63C-69 Bogotá, Colombia
| | - C R Bombardieri
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - H Wu
- Department of Internal Medicine, Division of Vascular Medicine and Pharmacology, Erasmus University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - A J M Roks
- Department of Internal Medicine, Division of Vascular Medicine and Pharmacology, Erasmus University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - S M Botter
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, The Netherlands.,Laboratory for Orthopedic Research, Balgrist University Hospital, Forchstrasse 340, 8008, Zürich, Switzerland
| | - B C van der Eerden
- Department of Internal Medicine, Erasmus University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - S A Youssef
- Dutch Molecular Pathology Center, Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, PO Box 80125, 3508 TC Utrecht, The Netherlands
| | - R V Kuiper
- Dutch Molecular Pathology Center, Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, PO Box 80125, 3508 TC Utrecht, The Netherlands
| | - B Nagarajah
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), PO Box 1, 3720 BA Bilthoven, The Netherlands
| | - C T van Oostrom
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), PO Box 1, 3720 BA Bilthoven, The Netherlands
| | - R M C Brandt
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - S Barnhoorn
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - S Imholz
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), PO Box 1, 3720 BA Bilthoven, The Netherlands
| | - J L A Pennings
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), PO Box 1, 3720 BA Bilthoven, The Netherlands
| | - A de Bruin
- Dutch Molecular Pathology Center, Department of Pathobiology, Faculty of Veterinary Medicine, Utrecht University, PO Box 80125, 3508 TC Utrecht, The Netherlands.,Department of Pediatrics, Division Molecular Genetics, University Medical Center Groningen, PO Box 30001, 9700 RB Groningen, The Netherlands
| | - Á Gyenis
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - J Pothof
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - J Vijg
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
| | - H van Steeg
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), PO Box 1, 3720 BA Bilthoven, The Netherlands.,Department of Human Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - J H J Hoeijmakers
- Department of Molecular Genetics, Erasmus University Medical Center Rotterdam, PO Box 2040, 3000 CA Rotterdam, The Netherlands.,CECAD Forschungszentrum, Universität zu Köln, Joseph-Stelzmann-Straße 26, 50931 Köln, Germany
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6
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Gyenis Á, Umlauf D, Újfaludi Z, Boros I, Ye T, Tora L. UVB induces a genome-wide acting negative regulatory mechanism that operates at the level of transcription initiation in human cells. PLoS Genet 2014; 10:e1004483. [PMID: 25058334 PMCID: PMC4109906 DOI: 10.1371/journal.pgen.1004483] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 05/19/2014] [Indexed: 11/19/2022] Open
Abstract
Faithful transcription of DNA is constantly threatened by different endogenous and environmental genotoxic effects. Transcription coupled repair (TCR) has been described to stop transcription and quickly remove DNA lesions from the transcribed strand of active genes, permitting rapid resumption of blocked transcription. This repair mechanism has been well characterized in the past using individual target genes. Moreover, numerous efforts investigated the fate of blocked RNA polymerase II (Pol II) during DNA repair mechanisms and suggested that stopped Pol II complexes can either backtrack, be removed and degraded or bypass the lesions to allow TCR. We investigated the effect of a non-lethal dose of UVB on global DNA-bound Pol II distribution in human cells. We found that the used UVB dose did not induce Pol II degradation however surprisingly at about 93% of the promoters of all expressed genes Pol II occupancy was seriously reduced 2-4 hours following UVB irradiation. The presence of Pol II at these cleared promoters was restored 5-6 hours after irradiation, indicating that the negative regulation is very dynamic. We also identified a small set of genes (including several p53 regulated genes), where the UVB-induced Pol II clearing did not operate. Interestingly, at promoters, where Pol II promoter clearance occurs, TFIIH, but not TBP, follows the behavior of Pol II, suggesting that at these genes upon UVB treatment TFIIH is sequestered for DNA repair by the TCR machinery. In agreement, in cells where the TCR factor, the Cockayne Syndrome B protein, was depleted UVB did not induce Pol II and TFIIH clearance at promoters. Thus, our study reveals a UVB induced negative regulatory mechanism that targets Pol II transcription initiation on the large majority of transcribed gene promoters, and a small subset of genes, where Pol II escapes this negative regulation.
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Affiliation(s)
- Ákos Gyenis
- Cellular signaling and nuclear dynamics program, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - David Umlauf
- Cellular signaling and nuclear dynamics program, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
| | - Zsuzsanna Újfaludi
- University of Szeged, Faculty of Sciences and Informatics, Department of Biochemistry and Molecular Biology, Szeged, Hungary
| | - Imre Boros
- University of Szeged, Faculty of Sciences and Informatics, Department of Biochemistry and Molecular Biology, Szeged, Hungary
| | - Tao Ye
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
- Microarrays and deep sequencing platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Làszlò Tora
- Cellular signaling and nuclear dynamics program, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, Illkirch, France
- * E-mail:
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