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Sutcu HH, Rassinoux P, Donnio LM, Neuillet D, Vianna F, Gabillot O, Mari PO, Baldeyron C, Giglia-Mari G. Decline of DNA damage response along with myogenic differentiation. Life Sci Alliance 2024; 7:e202302279. [PMID: 37993260 PMCID: PMC10665522 DOI: 10.26508/lsa.202302279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 11/24/2023] Open
Abstract
DNA integrity is incessantly confronted to agents inducing DNA lesions. All organisms are equipped with a network of DNA damage response mechanisms that will repair DNA lesions and restore proper cellular activities. Despite DNA repair mechanisms have been revealed in replicating cells, still little is known about how DNA lesions are repaired in postmitotic cells. Muscle fibers are highly specialized postmitotic cells organized in syncytia and they are vulnerable to age-related degeneration and atrophy after radiotherapy treatment. We have studied the DNA repair capacity of muscle fiber nuclei and compared it with the one measured in proliferative myoblasts here. We focused on the DNA repair mechanisms that correct ionizing radiation (IR)-induced lesions, namely the base excision repair, the nonhomologous end joining, and the homologous recombination (HR). We found that in the most differentiated myogenic cells, myotubes, these DNA repair mechanisms present weakened kinetics of recruitment of DNA repair proteins to IR-damaged DNA. For base excision repair and HR, this decline can be linked to reduced steady-state levels of key proteins involved in these processes.
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Affiliation(s)
- Haser H Sutcu
- https://ror.org/01ha22c77 Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SERAMED/LRAcc, Fontenay-aux-Roses, France
| | - Phoebe Rassinoux
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM) CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, Lyon, France
| | - Lise-Marie Donnio
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM) CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, Lyon, France
| | - Damien Neuillet
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM) CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, Lyon, France
| | - François Vianna
- https://ror.org/01ha22c77 Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SDOS/LMDN, Saint-Paul-Lez-Durance, France
| | - Olivier Gabillot
- https://ror.org/01ha22c77 Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SERAMED/LRAcc, Fontenay-aux-Roses, France
| | - Pierre-Olivier Mari
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM) CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, Lyon, France
| | - Céline Baldeyron
- https://ror.org/01ha22c77 Institut de Radioprotection et de Sûreté Nucléaire (IRSN), PSE-SANTE/SERAMED/LRAcc, Fontenay-aux-Roses, France
| | - Giuseppina Giglia-Mari
- Pathophysiology and Genetics of Neuron and Muscle (INMG-PGNM) CNRS UMR 5261, INSERM U1315, Université Claude Bernard Lyon 1, Lyon, France
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2
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Steurer B, Janssens RC, Geijer ME, Aprile-Garcia F, Geverts B, Theil AF, Hummel B, van Royen ME, Evers B, Bernards R, Houtsmuller AB, Sawarkar R, Marteijn J. DNA damage-induced transcription stress triggers the genome-wide degradation of promoter-bound Pol II. Nat Commun 2022; 13:3624. [PMID: 35750669 PMCID: PMC9232492 DOI: 10.1038/s41467-022-31329-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 06/10/2022] [Indexed: 01/22/2023] Open
Abstract
The precise regulation of RNA Polymerase II (Pol II) transcription after genotoxic stress is crucial for proper execution of the DNA damage-induced stress response. While stalling of Pol II on transcription-blocking lesions (TBLs) blocks transcript elongation and initiates DNA repair in cis, TBLs additionally elicit a response in trans that regulates transcription genome-wide. Here we uncover that, after an initial elongation block in cis, TBLs trigger the genome-wide VCP-mediated proteasomal degradation of promoter-bound, P-Ser5-modified Pol II in trans. This degradation is mechanistically distinct from processing of TBL-stalled Pol II, is signaled via GSK3, and contributes to the TBL-induced transcription block, even in transcription-coupled repair-deficient cells. Thus, our data reveal the targeted degradation of promoter-bound Pol II as a critical pathway that allows cells to cope with DNA damage-induced transcription stress and enables the genome-wide adaptation of transcription to genotoxic stress.
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Affiliation(s)
- Barbara Steurer
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Roel C Janssens
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marit E Geijer
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Bart Geverts
- Department of Pathology, Optical Imaging Centre, Erasmus MC, Rotterdam, The Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Barbara Hummel
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Martin E van Royen
- Department of Pathology, Optical Imaging Centre, Erasmus MC, Rotterdam, The Netherlands
| | - Bastiaan Evers
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - René Bernards
- Oncode Institute, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Adriaan B Houtsmuller
- Department of Pathology, Optical Imaging Centre, Erasmus MC, Rotterdam, The Netherlands
| | - Ritwick Sawarkar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- MRC, University of Cambridge, Cambridge, UK
| | - Jurgen Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
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3
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Oh J, Jia T, Xu J, Chong J, Dervan PB, Wang D. RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder. Proc Natl Acad Sci U S A 2022; 119:e2114065119. [PMID: 35022237 PMCID: PMC8784135 DOI: 10.1073/pnas.2114065119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/07/2021] [Indexed: 02/06/2023] Open
Abstract
Elongating RNA polymerase II (Pol II) can be paused or arrested by a variety of obstacles. These obstacles include DNA lesions, DNA-binding proteins, and small molecules. Hairpin pyrrole-imidazole (Py-Im) polyamides bind to the minor groove of DNA in a sequence-specific manner and induce strong transcriptional arrest. Remarkably, this Py-Im-induced Pol II transcriptional arrest is persistent and cannot be rescued by transcription factor TFIIS. In contrast, TFIIS can effectively rescue the transcriptional arrest induced by a nucleosome barrier. The structural basis of Py-Im-induced transcriptional arrest and why TFIIS cannot rescue this arrest remain elusive. Here we determined the X-ray crystal structures of four distinct Pol II elongation complexes (Pol II ECs) in complex with hairpin Py-Im polyamides as well as of the hairpin Py-Im polyamides-dsDNA complex. We observed that the Py-Im oligomer directly interacts with RNA Pol II residues, introduces compression of the downstream DNA duplex, prevents Pol II forward translocation, and induces Pol II backtracking. These results, together with biochemical studies, provide structural insight into the molecular mechanism by which Py-Im blocks transcription. Our structural study reveals why TFIIS fails to promote Pol II bypass of Py-Im-induced transcriptional arrest.
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Affiliation(s)
- Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Tiezheng Jia
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Jun Xu
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Jenny Chong
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Peter B Dervan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125;
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093;
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
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4
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Agapov A, Olina A, Kulbachinskiy A. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3018-3041. [PMID: 35323981 PMCID: PMC8989532 DOI: 10.1093/nar/gkac174] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 02/26/2022] [Accepted: 03/03/2022] [Indexed: 11/14/2022] Open
Abstract
Cellular DNA is continuously transcribed into RNA by multisubunit RNA polymerases (RNAPs). The continuity of transcription can be disrupted by DNA lesions that arise from the activities of cellular enzymes, reactions with endogenous and exogenous chemicals or irradiation. Here, we review available data on translesion RNA synthesis by multisubunit RNAPs from various domains of life, define common principles and variations in DNA damage sensing by RNAP, and consider existing controversies in the field of translesion transcription. Depending on the type of DNA lesion, it may be correctly bypassed by RNAP, or lead to transcriptional mutagenesis, or result in transcription stalling. Various lesions can affect the loading of the templating base into the active site of RNAP, or interfere with nucleotide binding and incorporation into RNA, or impair RNAP translocation. Stalled RNAP acts as a sensor of DNA damage during transcription-coupled repair. The outcome of DNA lesion recognition by RNAP depends on the interplay between multiple transcription and repair factors, which can stimulate RNAP bypass or increase RNAP stalling, and plays the central role in maintaining the DNA integrity. Unveiling the mechanisms of translesion transcription in various systems is thus instrumental for understanding molecular pathways underlying gene regulation and genome stability.
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Affiliation(s)
- Aleksei Agapov
- Correspondence may also be addressed to Aleksei Agapov. Tel: +7 499 196 0015; Fax: +7 499 196 0015;
| | - Anna Olina
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute” Moscow 123182, Russia
| | - Andrey Kulbachinskiy
- To whom correspondence should be addressed. Tel: +7 499 196 0015; Fax: +7 499 196 0015;
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5
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DNA Repair in Haploid Context. Int J Mol Sci 2021; 22:ijms222212418. [PMID: 34830299 PMCID: PMC8620282 DOI: 10.3390/ijms222212418] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/08/2021] [Accepted: 11/14/2021] [Indexed: 12/15/2022] Open
Abstract
DNA repair is a well-covered topic as alteration of genetic integrity underlies many pathological conditions and important transgenerational consequences. Surprisingly, the ploidy status is rarely considered although the presence of homologous chromosomes dramatically impacts the repair capacities of cells. This is especially important for the haploid gametes as they must transfer genetic information to the offspring. An understanding of the different mechanisms monitoring genetic integrity in this context is, therefore, essential as differences in repair pathways exist that differentiate the gamete’s role in transgenerational inheritance. Hence, the oocyte must have the most reliable repair capacity while sperm, produced in large numbers and from many differentiation steps, are expected to carry de novo variations. This review describes the main DNA repair pathways with a special emphasis on ploidy. Differences between Saccharomyces cerevisiae and Schizosaccharomyces pombe are especially useful to this aim as they can maintain a diploid and haploid life cycle respectively.
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6
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Agapov A, Esyunina D, Kulbachinskiy A. Gre-family factors modulate DNA damage sensing by Deinococcus radiodurans RNA polymerase. RNA Biol 2019; 16:1711-1720. [PMID: 31416390 DOI: 10.1080/15476286.2019.1656027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Deinococcus radiodurans is a highly stress resistant bacterium that encodes universal as well as lineage-specific factors involved in DNA transcription and repair. However, the effects of DNA lesions on RNA synthesis by D. radiodurans RNA polymerase (RNAP) have never been studied. We investigated the ability of this RNAP to transcribe damaged DNA templates and demonstrated that various lesions significantly affect the efficiency and fidelity of RNA synthesis. DNA modifications that disrupt correct base-pairing can strongly inhibit transcription and increase nucleotide misincorporation by D. radiodurans RNAP. The universal transcription factor GreA and Deinococcus-specific factor Gfh1 stimulate RNAP stalling at various DNA lesions, depending on the type of the lesion and the presence of Mn2+ ions, abundant divalent cations in D. radiodurans. Furthermore, Gfh1 stimulates the action of the Mfd translocase, which removes transcription elongation complexes paused at the sites of DNA lesions. Thus, Gre-family factors in D. radiodurans might have evolved to increase the efficiency of DNA damage recognition by the transcription and repair machineries in this bacterium.
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Affiliation(s)
- Aleksei Agapov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
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7
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What happens at the lesion does not stay at the lesion: Transcription-coupled nucleotide excision repair and the effects of DNA damage on transcription in cis and trans. DNA Repair (Amst) 2018; 71:56-68. [PMID: 30195642 DOI: 10.1016/j.dnarep.2018.08.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Unperturbed transcription of eukaryotic genes by RNA polymerase II (Pol II) is crucial for proper cell function and tissue homeostasis. However, the DNA template of Pol II is continuously challenged by damaging agents that can result in transcription impediment. Stalling of Pol II on transcription-blocking lesions triggers a highly orchestrated cellular response to cope with these cytotoxic lesions. One of the first lines of defense is the transcription-coupled nucleotide excision repair (TC-NER) pathway that specifically removes transcription-blocking lesions thereby safeguarding unperturbed gene expression. In this perspective, we outline recent data on how lesion-stalled Pol II initiates TC-NER and we discuss new mechanistic insights in the TC-NER reaction, which have resulted in a better understanding of the causative-linked Cockayne syndrome and UV-sensitive syndrome. In addition to these direct effects on lesion-stalled Pol II (effects in cis), accumulating evidence shows that transcription, and particularly Pol II, is also affected in a genome-wide manner (effects in trans). We will summarize the diverse consequences of DNA damage on transcription, including transcription inhibition, induction of specific transcriptional programs and regulation of alternative splicing. Finally, we will discuss the function of these diverse cellular responses to transcription-blocking lesions and their consequences on the process of transcription restart. This resumption of transcription, which takes place either directly at the lesion or is reinitiated from the transcription start site, is crucial to maintain proper gene expression following removal of the DNA damage.
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8
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Structural basis of DNA lesion recognition for eukaryotic transcription-coupled nucleotide excision repair. DNA Repair (Amst) 2018; 71:43-55. [PMID: 30174298 DOI: 10.1016/j.dnarep.2018.08.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Eukaryotic transcription-coupled nucleotide excision repair (TC-NER) is a pathway that removes DNA lesions capable of blocking RNA polymerase II (Pol II) transcription from the template strand. This process is initiated by lesion-arrested Pol II and the recruitment of Cockayne Syndrome B protein (CSB). In this review, we will focus on the lesion recognition steps of eukaryotic TC-NER and summarize the recent research progress toward understanding the structural basis of Pol II-mediated lesion recognition and Pol II-CSB interactions. We will discuss the roles of CSB in both TC-NER initiation and transcription elongation. Finally, we propose an updated model of tripartite lesion recognition and verification for TC-NER in which CSB ensures Pol II-mediated recognition of DNA lesions for TC-NER.
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9
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Abstract
RNA polymerase II (Pol II) catalyzes the transcription of DNA to RNA in the nucleus. DNA alkylating cancer drugs can stall transcription; however, the basis for Pol II stalling when encountering a DNA template with minor-groove alkylation adducts has remained elusive due to its inherent chemical instability. We characterized the behavior of Pol II in transcription over minor-groove alkylation adducts and uncovered a previously unobserved mode of Pol II stalling wherein clashes between DNA adducts and the mobile trigger loop of RNA Pol II prevent translocation of the enzyme after nucleotide insertion. These results provide a molecular basis for how DNA damage in transcribed portions of the genome initiates DNA repair contributing to drug resistance. Several anticancer agents that form DNA adducts in the minor groove interfere with DNA replication and transcription to induce apoptosis. Therapeutic resistance can occur, however, when cells are proficient in the removal of drug-induced damage. Acylfulvenes are a class of experimental anticancer agents with a unique repair profile suggesting their capacity to stall RNA polymerase (Pol) II and trigger transcription-coupled nucleotide excision repair. Here we show how different forms of DNA alkylation impair transcription by RNA Pol II in cells and with the isolated enzyme and unravel a mode of RNA Pol II stalling that is due to alkylation of DNA in the minor groove. We incorporated a model for acylfulvene adducts, the stable 3-deaza-3-methoxynaphtylethyl-adenosine analog (3d-Napht-A), and smaller 3-deaza-adenosine analogs, into DNA oligonucleotides to assess RNA Pol II transcription elongation in vitro. RNA Pol II was strongly blocked by a 3d-Napht-A analog but bypassed smaller analogs. Crystal structure analysis revealed that a DNA base containing 3d-Napht-A can occupy the +1 templating position and impair closing of the trigger loop in the Pol II active center and polymerase translocation into the next template position. These results show how RNA Pol II copes with minor-groove DNA alkylation and establishes a mechanism for drug resistance.
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10
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Wang W, Xu L, Hu L, Chong J, He C, Wang D. Epigenetic DNA Modification N 6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing. J Am Chem Soc 2017; 139:14436-14442. [PMID: 28933854 PMCID: PMC5812728 DOI: 10.1021/jacs.7b06381] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
N6-Methyladenine (N6-mA or 6 mA) is an epigenetic DNA modification in eukaryotic genomes. In contrast to the well-established roles of 5-methylcytosine for epigenetic regulation of gene expression, the functional roles of N6-mA remain elusive. In particular, the impact of N6-mA modification of the DNA template on RNA polymerase II (pol II) transcription elongation is not known. In this work, using the Saccharomyces cerevisiae pol II transcriptional elongation system as a model, we investigated the molecular mechanism of pol II recognition and processing of N6-mA sites via both biochemical and structural approaches. We found that N6-mA causes site-specific pol II pausing/stalling. Structural analysis revealed that while N6-mA can reach the +1 template position, the stability of the N6-mA and UTP base pairing is compromised. Taken together, we reveal that the presence of the 6-methyl group on adenine reduces incorporation efficiency and promotes backtracking translocation. Our studies with yeast pol II provide molecular insights into understanding the impacts of N6-mA on pol II transcription dynamics in different organisms.
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Affiliation(s)
- Wei Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093-0625, United States
| | - Liang Xu
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093-0625, United States
- Department of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Lulu Hu
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Jenny Chong
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093-0625, United States
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, United States
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093-0625, United States
- Department of Cellular & Molecular Medicine, School of Medicine, University of California, San Diego, La Jolla, California 92093-0625, United States
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11
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Mechanism of DNA alkylation-induced transcriptional stalling, lesion bypass, and mutagenesis. Proc Natl Acad Sci U S A 2017; 114:E7082-E7091. [PMID: 28784758 DOI: 10.1073/pnas.1708748114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
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.
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