Molecular and physiological consequences of faulty eukaryotic ribonucleotide excision repair

Kellner, Vanessa; Luke, Brian

doi:10.15252/embj.2019102309

Cited by 46 publications

(48 citation statements)

References 124 publications

(277 reference statements)

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“…The loss of RNase H2 activity is linked to Aicardi-Goutieres syndrome in humans (18). If RNase H2 is unable to remove these ribonucleotides (19), they can have both favorable (20,21) and lethal biological consequences (22). Recent investigations have shown that ribonucleotides are deleterious lesions that can lead to mutations, large deletions, replication stress, strand breaks (topoisomerase-1 mediated repair), chromosomal rearrangements, loss of hereditary information, and disruption of transcription processes (1,(23)(24)(25)(26).…”

Section: Introductionmentioning

confidence: 99%

Impact of 1,N6-ethenoadenosine, a damaged ribonucleotide in DNA, on translesion synthesis and repair

Ghodke

Guengerich

2020

Journal of Biological Chemistry

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Incorporation of ribonucleotides into DNA can severely diminish genome integrity. However, how ribonucleotides instigate DNA damage is poorly understood. In DNA, they can promote replication stress and genomic instability and have been implicated in several diseases. We report here the impact of the ribonucleotide rATP and of its naturally occurring damaged analog 1,N6-ethenoadenosine (1,N6-ϵrA) on translesion synthesis (TLS), mediated by human DNA polymerase η (hpol η), and on RNase H2–mediated incision. Mass spectral analysis revealed that 1,N6-ϵrA in DNA generates extensive frameshifts during TLS, which can lead to genomic instability. Moreover, steady-state kinetic analysis of the TLS process indicated that deoxypurines (i.e. dATP and dGTP) are inserted predominantly opposite 1,N6-ϵrA. We also show that hpol η acts as a reverse transcriptase in the presence of damaged ribonucleotide 1,N6-ϵrA but has poor RNA primer extension activities. Steady-state kinetic analysis of reverse transcription and RNA primer extension showed that hpol η favors the addition of dATP and dGTP opposite 1,N6-ϵrA. We also found that RNase H2 recognizes 1,N6-ϵrA but has limited incision activity across from this lesion, which can lead to the persistence of this detrimental DNA adduct. We conclude that the damaged and unrepaired ribonucleotide 1,N6-ϵrA in DNA exhibits mutagenic potential and can also alter the reading frame in an mRNA transcript because 1,N6-ϵrA is incompletely incised by RNase H2.

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Section: Introductionmentioning

confidence: 99%

Impact of 1,N6-ethenoadenosine, a damaged ribonucleotide in DNA, on translesion synthesis and repair

Ghodke

Guengerich

2020

Journal of Biological Chemistry

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“…suggested that GLOE-seq labels sites at which DNA is nicked during removal of mis-incorporated ribonucleotides [36]. To test this idea, we generated TrAEL-seq libraries from rnh201 Δ and rnh202 Δ mutants that lack key components of RNase H2, the main enzyme that cleaves DNA at mis-incorporated ribonucleotides, along with a wild-type control [68, 69]. Strikingly, both read polarity bias and RFD plots for these mutants are equivalent to wild-type, showing that the leading strand bias of TrAEL-seq reads is not caused by RNase H2 and therefore is unlikely to arise through excision of mis-incorporated ribonucleotides (Fig.…”

Section: Resultsmentioning

confidence: 99%

Genome-wide analysis of DNA replication and DNA double strand breaks by TrAEL-seq

Kara

Krueger

Rugg‐Gunn

et al. 2020

Preprint

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Understanding the distribution of sites at which replication forks stall, and the ensuing fork processing events, requires genome-wide methods sensitive to both changes in replication fork structure and the formation of recombinogenic DNA ends. Here we describe Tr ansferase- A ctivated E nd L igation seq uencing (TrAEL-seq), a method that captures single stranded DNA 3’ ends genome-wide and with base pair resolution. TrAEL-seq labels DNA breaks, and profiles both stalled and processive replication forks in yeast and mammalian cells. Replication forks stalling at defined barriers and expressed genes are detected by TrAEL-seq with exceptional signal-to-noise, most likely through labelling of DNA 3’ ends exposed during fork reversal. TrAEL-seq also labels unperturbed processive replication forks to yield maps of replication fork direction similar to those obtained by Okazaki fragment sequencing, however TrAEL-seq is performed on asynchronous populations of wild-type cells without incorporation of labels, cell sorting, or biochemical purification of replication intermediates, rendering TrAEL-seq simpler and more widely applicable than existing replication fork direction profiling methods. The specificity of TrAEL-seq for DNA 3’ ends also allows accurate detection of double strand break sites after the initiation of DNA end resection, which we demonstrate by genome-wide mapping of meiotic double strand break hotspots in a dmc1 Δ mutant. Overall, TrAEL-seq provides a flexible and robust methodology with high sensitivity and resolution for studying DNA replication and repair, which will be of significant use in determining mechanisms of genome instability.

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“…PARP senses the single-stranded DNA breaks (SSBs) by activating unligated fragments as a trigger for the replication of unperturbed S-phase cells (47). PARP1 is the main responder to DNA damage in the repair pathway, which initiates almost 90% of PAR chains through PARylation catalyzed by PARPs (48). The catalyzed PAR chains initiate the DNA repair process by recruiting a series of targeted DNA repair effectors and chromatin remodeling effectors (49).…”

Section: Mechanism Of Parp1 Actionmentioning

confidence: 99%

New Perspectives for Resistance to PARP Inhibitors in Triple-Negative Breast Cancer

Han

et al. 2020

Front. Oncol.

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Poly (ADP-ribose) polymerase (PARP) inhibitors are a therapeutic milestone exerting a synthetic lethal effect in the treatment of cancer involving BRCA1/2 mutation. Theoretically, PARP inhibitors (PARPi) eliminate tumor cells by disrupting DNA damage repair through either PARylation or the homologous recombination (HR) pathway. However, resistance to PARPi greatly hinders therapeutic effectiveness in triple-negative breast cancer (TNBC). Owing to the high heterogeneity and few genetic targets in TNBC, there has been limited therapeutic progress in the past decades. In view of this, there is a need to circumvent resistance to PARPi and develop potential treatment strategies for TNBC. We present, herein, a review of the scientific progress and explore the mechanisms underlying PARPi resistance in TNBC. The complicated mechanisms of PARPi resistance, including drug exporter formation, loss of poly (ADP-ribose) glycohydrolase (PARG), HR reactivation, and restoration of replication fork stability, are discussed in detail in this review. Additionally, we also discuss new combination therapies with PARPi that can improve the clinical response in TNBC. The new perspectives for PARPi bring novel challenges and opportunities to overcome PARPi resistance in breast cancer.

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Molecular and physiological consequences of faulty eukaryotic ribonucleotide excision repair

Cited by 46 publications

References 124 publications

Impact of 1,N6-ethenoadenosine, a damaged ribonucleotide in DNA, on translesion synthesis and repair

Impact of 1,N6-ethenoadenosine, a damaged ribonucleotide in DNA, on translesion synthesis and repair

Genome-wide analysis of DNA replication and DNA double strand breaks by TrAEL-seq

New Perspectives for Resistance to PARP Inhibitors in Triple-Negative Breast Cancer

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