Transcription-induced DNA supercoiling: New roles of intranucleosomal DNA loops in DNA repair and transcription

Герасимова, Н. Г.; Pestov, Nikolay A.; Kulaeva, Olga I.; Clark, David; Studitsky, Vasily M.

doi:10.1080/21541264.2016.1182240

Cited by 16 publications

(13 citation statements)

References 24 publications

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“…Our study shows that H2B K34ub by the MSL complex represents a new mechanism that promotes hexasome formation and this function is further enhanced by DNA torsional tension and histone chaperon NAP1. Since Pol II traversing through the nucleosome requires tightly coordinated displacement and reassembly of H2A-H2B dimers ( 9 ) and at the same time, generate positive or negative DNA torsional tensions ( 61 , 79 , 80 ), we envision a positive feedback regulation between the MSL complex and RNA Pol-II in productive transcription. In this model, the PAF1 complex recruits and stabilizes the MSL complex on chromatin ( 45 ), which in turn deposits H2B K34ub.…”

Section: Discussionmentioning

confidence: 99%

Effects of histone H2B ubiquitylation on the nucleosome structure and dynamics

Krajewski

Dou

2018

Nucleic Acids Research

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DNA in nucleosomes has restricted nucleosome dynamics and is refractory to DNA-templated processes. Histone post-translational modifications play important roles in regulating DNA accessibility in nucleosomes. Whereas most histone modifications function either by mitigating the electrostatic shielding of histone tails or by recruiting ‘reader’ proteins, we show that ubiquitylation of H2B K34, which is located in a tight space protected by two coils of DNA superhelix, is able to directly influence the canonical nucleosome conformation via steric hindrances by ubiquitin groups. H2B K34 ubiquitylation significantly enhances nucleosome dynamics and promotes generation of hexasomes both with symmetrically or asymmetrically modified nucleosomes. Our results indicate a direct mechanism by which a histone modification regulates the chromatin structural states.

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Section: Discussionmentioning

confidence: 99%

Effects of histone H2B ubiquitylation on the nucleosome structure and dynamics

Krajewski

Dou

2018

Nucleic Acids Research

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“…Negative and/or positive DNA supercoiling also builds up ahead of and/or behind RNAPII when the enzyme encounters “topological locks,” such as those generated by DNA–histone interactions . DNA topoisomerase (TOP)2 resolves some of these topological constraints by binding preferentially to nucleosome‐free DNA to generate transient, site‐specific DSBs on promoters . The latter creates a more permissive chromatin setting that is thought to facilitate access of transcription factors and the RNAPII at promoter and enhancer regions.…”

Section: Dna Damage: Linking Ner To Mrna Synthesismentioning

confidence: 99%

Nucleotide Excision Repair and Transcription‐Associated Genome Instability

et al. 2019

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Transcription is a potential threat to genome integrity, and transcription‐associated DNA damage must be repaired for proper messenger RNA (mRNA) synthesis and for cells to transmit their genome intact into progeny. For a wide range of structurally diverse DNA lesions, cells employ the highly conserved nucleotide excision repair (NER) pathway to restore their genome back to its native form. Recent evidence suggests that NER factors function, in addition to the canonical DNA repair mechanism, in processes that facilitate mRNA synthesis or shape the 3D chromatin architecture. Here, these findings are critically discussed and a working model that explains the puzzling clinical heterogeneity of NER syndromes highlighting the relevance of physiological, transcription‐associated DNA damage to mammalian development and disease is proposed.

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“…Reproduced with copyright permission ( Luger et al, 1997 ). (B) Schematic description of the nucleosome rolling action that results in the temporary removal of histones H2A and H2B ( Gerasimova et al, 2016 ). This temporary removal is essential for the RNA polymerase complex to transcribe genes and the histones are reassembled following the successful passing of the complex.…”

Section: Other Minor Groove Targeting Agentsmentioning

confidence: 99%

DNA Damage and Chromatin Conformation Changes Confer Nonhost Resistance: A Hypothesis Based on Effects of Anti-cancer Agents on Plant Defense Responses

Hadwiger

Tanaka

2018

Front. Plant Sci.

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Over the last decades, medical research has utilized DNA altering procedures in cancer treatments with the objective of killing cells or suppressing cell proliferation. Simultaneous research related to enhancing disease resistance in plants reported that alterations in DNA can enhance defense responses. These two opposite perspectives have in common their effects on the center for gene transcription, the nuclear chromatin. A review of selected research from both anticancer- and plant defense-related research provides examples of some specific DNA altering actions: DNA helical distortion, DNA intercalation, DNA base substitution, DNA single cleavage by DNases, DNA alkylation/methylation, and DNA binding/exclusion. The actions of the pertinent agents are compared, and their proposed modes of action are described in this study. Many of the DNA specific agents affecting resistance responses in plants, e.g., the model system using pea endocarp tissue, are indeed anticancer agents. The tumor cell death or growth suppression in cancer cells following high level treatments may be accompanied with chromatin distortions. Likewise, in plants, DNA-specific agents activate enhanced expression of many genes including defense genes, probably due to the chromatin alterations resulting from the agents. Here, we propose a hypothesis that DNA damage and chromatin structural changes are central mechanisms in initiating defense gene transcription during the nonhost resistance response in plants.

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Transcription-induced DNA supercoiling: New roles of intranucleosomal DNA loops in DNA repair and transcription

Cited by 16 publications

References 24 publications

Effects of histone H2B ubiquitylation on the nucleosome structure and dynamics

Effects of histone H2B ubiquitylation on the nucleosome structure and dynamics

Nucleotide Excision Repair and Transcription‐Associated Genome Instability

DNA Damage and Chromatin Conformation Changes Confer Nonhost Resistance: A Hypothesis Based on Effects of Anti-cancer Agents on Plant Defense Responses

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