Reviews - 3i4m mentioned but not cited (3)
- Structural basis of DNA lesion recognition for eukaryotic transcription-coupled nucleotide excision repair. Wang W, Xu J, Chong J, Wang D. DNA Repair (Amst) 71 43-55 (2018)
- Molecular basis of transcriptional pausing, stalling, and transcription-coupled repair initiation. Oh J, Xu J, Chong J, Wang D. Biochim Biophys Acta Gene Regul Mech 1864 194659 (2021)
- Cas6 processes tight and relaxed repeat RNA via multiple mechanisms: A hypothesis. Sefcikova J, Roth M, Yu G, Li H. Bioessays 39 (2017)
Articles - 3i4m mentioned but not cited (4)
- Molecular basis of transcriptional mutagenesis at 8-oxoguanine. Damsma GE, Cramer P. J Biol Chem 284 31658-31663 (2009)
- Intrinsic translocation barrier as an initial step in pausing by RNA polymerase II. Imashimizu M, Kireeva ML, Lubkowska L, Gotte D, Parks AR, Strathern JN, Kashlev M. J Mol Biol 425 697-712 (2013)
- 3dDNA: A Computational Method of Building DNA 3D Structures. Zhang Y, Xiong Y, Xiao Y. Molecules 27 5936 (2022)
- 8-Oxo-guanine DNA damage induces transcription errors by escaping two distinct fidelity control checkpoints of RNA polymerase II. Konovalov KA, Pardo-Avila F, Tse CKM, Oh J, Wang D, Huang X. J Biol Chem 294 4924-4933 (2019)
Reviews citing this publication (17)
- Mammalian transcription-coupled excision repair. Vermeulen W, Fousteri M. Cold Spring Harb Perspect Biol 5 a012625 (2013)
- Transcriptional mutagenesis: causes and involvement in tumour development. Brégeon D, Doetsch PW. Nat Rev Cancer 11 218-227 (2011)
- Structural basis of transcription elongation. Martinez-Rucobo FW, Cramer P. Biochim Biophys Acta 1829 9-19 (2013)
- Molecular basis of transcriptional fidelity and DNA lesion-induced transcriptional mutagenesis. Xu L, Da L, Plouffe SW, Chong J, Kool E, Wang D. DNA Repair (Amst) 19 71-83 (2014)
- RNA polymerase II transcriptional fidelity control and its functional interplay with DNA modifications. Xu L, Wang W, Chong J, Shin JH, Xu J, Wang D. Crit Rev Biochem Mol Biol 50 503-519 (2015)
- Transcriptional mutagenesis and its potential roles in the etiology of cancer and bacterial antibiotic resistance. Morreall JF, Petrova L, Doetsch PW. J Cell Physiol 228 2257-2261 (2013)
- UVSSA and USP7, a new couple in transcription-coupled DNA repair. Schwertman P, Vermeulen W, Marteijn JA. Chromosoma 122 275-284 (2013)
- Transcriptional mutagenesis by 8-oxodG in α-synuclein aggregation and the pathogenesis of Parkinson's disease. Basu S, Basu S, Je G, Kim YS. Exp Mol Med 47 e179 (2015)
- Transcription elongation. Heterogeneous tracking of RNA polymerase and its biological implications. Imashimizu M, Shimamoto N, Oshima T, Kashlev M. Transcription 5 e28285 (2014)
- Mechanism of transcription-coupled DNA modification recognition. Shin JH, Xu L, Wang D. Cell Biosci 7 9 (2017)
- The Structural Basis of Transcription: 10 Years After the Nobel Prize in Chemistry. Hantsche M, Cramer P. Angew Chem Int Ed Engl 55 15972-15981 (2016)
- RNA polymerase pausing, stalling and bypass during transcription of damaged DNA: from molecular basis to functional consequences. Agapov A, Olina A, Kulbachinskiy A. Nucleic Acids Res 50 3018-3041 (2022)
- RNA polymerase between lesion bypass and DNA repair. Deaconescu AM. Cell Mol Life Sci 70 4495-4509 (2013)
- Structural and biochemical analysis of DNA lesion-induced RNA polymerase II arrest. Oh J, Xu J, Chong J, Wang D. Methods 159-160 29-34 (2019)
- Polymerases and DNA Repair in Neurons: Implications in Neuronal Survival and Neurodegenerative Diseases. Li X, Cao G, Liu X, Tang TS, Guo C, Liu H. Front Cell Neurosci 16 852002 (2022)
- Towards molecular systems biology of gene transcription and regulation. Cramer P. Biol Chem 391 731-735 (2010)
- The Role of DNA Damage and Repair in Idiopathic Pulmonary Fibrosis. Zhu J, Liu L, Ma X, Cao X, Chen Y, Qu X, Ji M, Liu H, Liu C, Qin X, Xiang Y. Antioxidants (Basel) 11 2292 (2022)
Articles citing this publication (23)
- Molecular basis of RNA polymerase III transcription repression by Maf1. Vannini A, Ringel R, Kusser AG, Berninghausen O, Kassavetis GA, Cramer P. Cell 143 59-70 (2010)
- Mechanism of translesion transcription by RNA polymerase II and its role in cellular resistance to DNA damage. Walmacq C, Cheung AC, Kireeva ML, Lubkowska L, Ye C, Gotte D, Strathern JN, Carell T, Cramer P, Kashlev M. Mol Cell 46 18-29 (2012)
- Dynamics of pyrophosphate ion release and its coupled trigger loop motion from closed to open state in RNA polymerase II. Da LT, Wang D, Huang X. J Am Chem Soc 134 2399-2406 (2012)
- A movie of RNA polymerase II transcription. Cheung AC, Cramer P. Cell 149 1431-1437 (2012)
- 8-Oxo-7,8-dihydroguanine in DNA does not constitute a barrier to transcription, but is converted into transcription-blocking damage by OGG1. Kitsera N, Stathis D, Lühnsdorf B, Müller H, Carell T, Epe B, Khobta A. Nucleic Acids Res 39 5926-5934 (2011)
- Structures of E. coli σS-transcription initiation complexes provide new insights into polymerase mechanism. Liu B, Zuo Y, Steitz TA. Proc Natl Acad Sci U S A 113 4051-4056 (2016)
- Mechanism of RNA polymerase II bypass of oxidative cyclopurine DNA lesions. Walmacq C, Wang L, Chong J, Scibelli K, Lubkowska L, Gnatt A, Brooks PJ, Wang D, Kashlev M. Proc Natl Acad Sci U S A 112 E410-9 (2015)
- Combined exercise and insulin-like growth factor-1 supplementation induces neurogenesis in old rats, but do not attenuate age-associated DNA damage. Koltai E, Zhao Z, Lacza Z, Cselenyak A, Vacz G, Nyakas C, Boldogh I, Ichinoseki-Sekine N, Radak Z. Rejuvenation Res 14 585-596 (2011)
- Whole transcriptome analysis reveals a role for OGG1-initiated DNA repair signaling in airway remodeling. Aguilera-Aguirre L, Hosoki K, Bacsi A, Radák Z, Sur S, Hegde ML, Tian B, Saavedra-Molina A, Brasier AR, Ba X, Boldogh I. Free Radic Biol Med 89 20-33 (2015)
- RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-π and CH-π interactions. Oh J, Fleming AM, Xu J, Chong J, Burrows CJ, Wang D. Proc Natl Acad Sci U S A 117 9338-9348 (2020)
- Mechanism of DNA alkylation-induced transcriptional stalling, lesion bypass, and mutagenesis. Xu L, Wang W, Wu J, Shin JH, Wang P, Unarta IC, Chong J, Wang Y, Wang D. Proc Natl Acad Sci U S A 114 E7082-E7091 (2017)
- RNA polymerase II senses obstruction in the DNA minor groove via a conserved sensor motif. Xu L, Wang W, Gotte D, Yang F, Hare AA, Welch TR, Li BC, Shin JH, Chong J, Strathern JN, Dervan PB, Wang D. Proc Natl Acad Sci U S A 113 12426-12431 (2016)
- Lineage-specific variations in the trigger loop modulate RNA proofreading by bacterial RNA polymerases. Esyunina D, Turtola M, Pupov D, Bass I, Klimašauskas S, Belogurov G, Kulbachinskiy A. Nucleic Acids Res 44 1298-1308 (2016)
- RNA polymerase II acts as a selective sensor for DNA lesions and endogenous DNA modifications. Shin JH, Xu L, Wang D. Transcription 7 57-62 (2016)
- Gre-family factors modulate DNA damage sensing by Deinococcus radiodurans RNA polymerase. Agapov A, Esyunina D, Kulbachinskiy A. RNA Biol 16 1711-1720 (2019)
- Oxidized base 8-oxoguanine, a product of DNA repair processes, contributes to dendritic cell activation. Pázmándi K, Sütő M, Fekete T, Varga A, Boldizsár E, Boldogh I, Bácsi A. Free Radic Biol Med 143 209-220 (2019)
- Recognition and excision properties of 8-halogenated-7-deaza-2'-deoxyguanosine as 8-oxo-2'-deoxyguanosine analogues and Fpg and hOGG1 inhibitors. Yin Y, Sasaki S, Taniguchi Y. Chembiochem 16 1190-1198 (2015)
- Understanding the Molecular Basis of RNA Polymerase II Transcription. Zhang S, Wang D. Isr J Chem 53 (2013)
- Autologous hematopoietic stem cell transplantation in lymphoma patients is associated with a decrease in the double strand break repair capacity of peripheral blood lymphocytes. Lacoste S, Bhatia S, Chen Y, Bhatia R, O'Connor TR. PLoS One 12 e0171473 (2017)
- Role of the trigger loop in translesion RNA synthesis by bacterial RNA polymerase. Agapov A, Ignatov A, Turtola M, Belogurov G, Esyunina D, Kulbachinskiy A. J Biol Chem 295 9583-9595 (2020)
- Structural Molecular Biology-A Personal Reflection on the Occasion of John Kendrew's 100th Birthday. Cramer P. J Mol Biol 429 2603-2610 (2017)
- A comprehensive mechanism for 5-carboxylcytosine-induced transcriptional pausing revealed by Markov state models. Konovalov KA, Wang W, Wang G, Goonetilleke EC, Gao X, Wang D, Huang X. J Biol Chem 296 100735 (2021)
- Transcriptional mutagenesis of α-synuclein caused by DNA oxidation in Parkinson's disease pathogenesis. Basu S, Song M, Adams L, Jeong I, Je G, Guhathakurta S, Jiang J, Boparai N, Dai W, Cardozo-Pelaez F, Tatulian SA, Han KY, Elliott J, Baum J, McLean PJ, Dickson DW, Kim YS. Acta Neuropathol 146 685-705 (2023)