Reversible DNA–Protein Cross‐Linking at Epigenetic DNA Marks

Ji, Shaofei; Shao, Hongzhao; Han, Qiyuan; Seiler, Charles E.; Tretyakova, Natalia

doi:10.1002/ange.201708286

Cited by 26 publications

(26 citation statements)

References 29 publications

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“…Thus, modulation of the catalytic activity of three TET enzymes by differential isoform expression, posttranslational modifications, interacting factors, and site-specific recruitment could constitute an additional layer of epigenetic regulation. Interestingly, 5fC was recently revealed to possess novel characteristics such as the ability to distort the DNA double helix (Raiber et al, 2015) and directly mediate DNA-protein crosslinks (Ji et al, 2017;Li et al, 2017) , with potentially far reaching consequences on transcriptional regulation and chromatin remodeling (Raiber et al, 2017) . In this context, our observation that 5fC formation is largely TET2-dependent might also have novel implications for the understanding of Tet2 mutations in cancerogenesis.…”

Section: Our Analysis Of Global Cytosine Modification Levels Inmentioning

confidence: 99%

Distinct and stage-specific contributions of TET1 and TET2 to stepwise cytosine oxidation in the transition from naive to primed pluripotency

Mulholland

Traube

Parsa

et al. 2018

Preprint

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The TET-oxidized cytosine derivatives, 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC), are considered DNA demethylation intermediates as well as stable epigenetic marks in mammals. We compared modified cytosine and enzyme levels in TET-knockout cells during naive pluripotency exit and found distinct and differentiation-dependent contributions of TET1 and TET2 to 5hmC and 5fC formation. The divergent modified cytosine levels argue for independent consecutive oxidation steps in vivo with broad implications for epigenetic regulation.

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Section: Our Analysis Of Global Cytosine Modification Levels Inmentioning

confidence: 99%

Distinct and stage-specific contributions of TET1 and TET2 to stepwise cytosine oxidation in the transition from naive to primed pluripotency

Mulholland

Traube

Parsa

et al. 2018

Preprint

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“…Thus, the absence of CMG slowing down at a lagging-strand streptavidin barrier may be due to the linker escaping through the narrow channel between MCM ZF domains. To test this possibility, we used 5-formylcytosine (5fC) modification to form a DPC lacking a linker between DNA and streptavidin (Ji et al, 2017;Li et al, 2017) ( Figure 7a). We generated a fork substrate containing a single 5fC-streptavidin crosslink on the lagging-strand template in the middle of 60-bp parental duplex (Supplementary Figure 6).…”

Section: Cmg Bypasses a Protein Directly Crosslinked To The Excluded mentioning

confidence: 99%

Mechanism of RPA-Facilitated Processive DNA Unwinding by the Eukaryotic CMG Helicase

Kose

Xie

Cameron

et al. 2019

Preprint

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The DNA double helix is unwound by the Cdc45/Mcm2-7/GINS (CMG) complex at the eukaryotic replication fork. While isolated CMG unwinds duplex DNA very slowly, its fork unwinding rate is stimulated by an order of magnitude by single-stranded DNA binding protein, RPA. However, the molecular mechanism by which RPA enhances CMG helicase activity remained elusive. Here, we demonstrate that engagement of CMG with parental double-stranded DNA (dsDNA) at the replication fork impairs its helicase activity, explaining the slow DNA unwinding by isolated CMG. Using single-molecule and ensemble biochemistry, we show that binding of RPA to the excluded DNA strand prevents duplex engagement by the helicase and speeds up CMG-mediated DNA unwinding. When stalled due to dsDNA interaction, DNA rezipping-induced helicase backtracking re-establishes productive helicase-fork engagement underscoring the significance of plasticity in helicase action. Together, our results elucidate the dynamics of CMG at the replication fork and reveal how other replisome components can mediate proper DNA engagement by the replicative helicase to achieve efficient fork progression. steric exclusion, a mechanism shared by all known replicative helicases (Egelman et al., 1995;Fu et al., 2011;Kaplan, 2000;Lee et al., 2014;Yardimci et al., 2012b).Using single-molecule magnetic-tweezers, we earlier found that individual Drosophila CMG complexes exhibit forward and backward motion while unwinding dsDNA (Burnham et al., 2019), similar to E1 and T7 gp4 helicases (Johnson et al., 2007;Lee et al., 2014;Syed et al., 2014). Furthermore, the helicase often enters long-lived paused states leading to an average unwinding rate of 0.1-0.5 base pairs per second (bps −1 ), which is approximately two orders of magnitude slower than eukaryotic replication fork rates observed in vivo (Anglana et al., 2003;Raghuraman et al., 2001). However, recent single-molecule work with yeast CMG suggests that the helicase translocates on ssDNA at 5-10 bps -1 (Wasserman et al., 2019). Single-molecule trajectories by other replicative helicases such as DnaB and gp4 suggest that helicase pausing during dsDNA unwinding is a general property of these enzymes (Ribeck et al., 2010;. However, it is not clear why replicative helicases frequently halt whilst moving at the fork and how higher speeds are achieved by the entire replisome.The rate of DNA unwinding by E.coli DnaB and T7 gp4 is substantially enhanced when engaged with their corresponding replicative polymerases (Kim et al., 1996;Stano et al., 2005) suggesting that rate of fork progression in eukaryotes may also depend on DNA synthesis.Likewise, uncoupling of CMG from the leading-strand polymerase leads to fork slowing in an in vitro purified yeast system (Taylor and Yeeles, 2019). 5-10 fold reduction in helicase speed was also observed in Xenopus egg extracts when DNA synthesis was inhibited by aphidicolin (Sparks et al., 2019). However, this decrease in CMG translocation rate is not sufficient to account for the approximate 100-fold lowe...

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“…In these studies, 5fC was found to recruit transcriptional regulators and DNA repair-associated proteins [27,67]. Recently the formation of reversible covalent crosslinks between 5fC DNA and lysine/arginine residues of histone proteins in the nucleosome core particle have been reported [68,69]. Moreover, the availability of synthetic DNA enabled the development and benchmarking of specific labeling methods, a selection of which is discussed in this Review.…”

Section: Structural and Biophysical Properties Of 5fc And Recognitionmentioning

confidence: 99%

Chemoselective labeling and site‐specific mapping of 5‐formylcytosine as a cellular nucleic acid modification

2018

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DNA methylation has a profound impact on the regulation of gene expression in normal cell development, and aberrant methylation has been recognized as a key factor in the pathogenesis of human diseases such as cancer. The discovery of modified nucleobases arising from 5-methylcytosine (5mC) through consecutive oxidation to give 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC) has stimulated intense research efforts regarding the biological functions of these epigenetic marks. This Review focuses on the sensitive detection and quantitation of 5fC in DNA and RNA by chemoselective labeling, which aims at discriminating between 5fC and its thymine counterpart 5-formyluracil (5fU), and summarizes single-base resolution sequencing methods for locus-specific mapping of 5mC and its oxidized derivatives.

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Reversible DNA–Protein Cross‐Linking at Epigenetic DNA Marks

Cited by 26 publications

References 29 publications

Distinct and stage-specific contributions of TET1 and TET2 to stepwise cytosine oxidation in the transition from naive to primed pluripotency

Distinct and stage-specific contributions of TET1 and TET2 to stepwise cytosine oxidation in the transition from naive to primed pluripotency

Mechanism of RPA-Facilitated Processive DNA Unwinding by the Eukaryotic CMG Helicase

Chemoselective labeling and site‐specific mapping of 5‐formylcytosine as a cellular nucleic acid modification

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