Mechanisms of DNA damage, repair, and mutagenesis

In the paper

“However, robust DNA repair and damage-bypass mechanisms faithfully protect the DNA by either removing or tolerating the damage to ensure an overall survival.”

In the paper

“Other times, the replicative polymerases incorrectly incorporate uracil in the DNA or end up with a compromised fidelity because of the alterations of the relative and absolute concentrations of dNTPs and rNTPs within the cell’s environment [Andersen et al., 2005; Vertessy and Toth, 2009; Kumar et al., 2011; Clausen et al., 2013; Buckland et al., 2014; Potenski and Klein, 2014].”

What the sources say

• Not checked yetcites Andersen et al., 2005
• Not checked yetcites Vertessy and Toth, 2009
• Not checked yetcites Kumar et al., 2011

In the paper

“Deviations in this fine-tuning are known to destabilize cellular metabolic homeostasis, as exemplified in diverse cancers where disruption or deregulation of DNA repair pathways results in genome instability.”

In the paper

“TOP1, for example, transiently nicks the supercoiled DNA and facilitates rotation of the broken strand around the TOP1-bound DNA strand to relax the DNA. Thereafter, TOP1 religates the breaks by aligning the 5′-OH group of the DNA with the tyrosine-DNA phosphodiester bond to resolve the complex [Stewart et al., 1998; Carey et al., 2003].”

What the sources say

• Not checked yetcites Stewart et al., 1998
• Not checked yetcites Carey et al., 2003

In the paper

“Not surprisingly, in many cancers, DNA repair, DNA damage tolerance and DDR pathways are disrupted or deregulated, which increases mutagenesis and genomic instability, thereby promoting cancer progression [Bouwman and Jonkers, 2012; Ghosal and Chen, 2013; Wolters and Schumacher, 2013].”

What the sources say

• Not checked yetcites Bouwman and Jonkers, 2012
• Not checked yetcites Ghosal and Chen, 2013
• Not checked yetcites Wolters and Schumacher, 2013

In the paper

“These incorrectly paired/incorporated nucleotides that escape proofreading and MMR become mutations in the next round of replication and are a major source of spontaneous mutagenesis.”

In the paper

“While deaminated cytosine is rapidly removed from DNA by uracil-DNA glycosylase, the G:T base pair resulting from deamination of 5-methylcytosine is instead a substrate for the thymine DNA glycosylase (TDG) and the relatively slow MMR process [Lindahl, 1979; Wiebauer and Jiricny, 1990; Waters and Swann, 1998].”

What the sources say

• Not checked yetcites Lindahl, 1979
• Not checked yetcites Wiebauer and Jiricny, 1990
• Not checked yetcites Waters and Swann, 1998

In the paper

“At low levels, ROS species perform important cellular functions such as serving as cellular messengers in redox signaling reactions and effecting important defense responses to invading pathogens by the immune system [Errol C. Friedberg, 2005; Segal, 2005; Malle et al., 2007].”

What the sources say

• Not checked yetcites Errol C. Friedberg, 2005
• Not checked yetcites Segal, 2005
• Not checked yetcites Malle et al., 2007

In the paper

“These electrophilic •OH radicals react with DNA bases by 1) adding to their double bonds, 2) abstracting hydrogen atoms from their methyl groups, and 3) attacking the sugar residue in their immediate vicinity [Breen and Murphy, 1995; Winterbourn, 2008].”

What the sources say

• Not checked yetcites Breen and Murphy, 1995
• Not checked yetcites Winterbourn, 2008

In the paper

“In a human cell, about 10,000 abasic sites are created per day; both extreme pH conditions and high temperatures positively impact their generation [Lindahl, 1993; Tropp, 2011].”

What the sources say

• Not checked yetcites Lindahl, 1993
• Not checked yetcites Tropp, 2011

In the paper

“Amongst these ROS species, the •OH radical, produced as a byproduct of a Fenton’s reaction of H2O2 with Fe2+, is by far the most reactive, and is capable of damaging DNA, proteins and lipids [Imlay et al., 1988; Dizdaroglu et al., 1991].”

What the sources say

• Not checked yetcites Imlay et al., 1988
• Not checked yetcites Dizdaroglu et al., 1991

In the paper

“Interestingly, these base deamination events occur at a much higher frequency in single-stranded versus double-stranded DNA and are often exacerbated by transient single strandedness during active replication, transcription and recombination [Lindahl, 1993; Yonekura et al., 2009].”

What the sources say

• Not checked yetcites Lindahl, 1993
• Not checked yetcites Yonekura et al., 2009

In the paper

“Most AP sites are effectively removed by AP endonucleases that cleave at their 5′ end and allow the BER pathway to repair them. Alternatively, AP sites can be bypassed by TLS polymerases [Chan et al., 2013].”

What the sources say

• Not checked yetcites Chan et al., 2013

In the paper

“Ordinarily, the deleterious consequences of ROS are regulated in cells by 1) restricting respiration in the mitochondrial compartment, thereby protecting other cellular components, 2) protecting DNA by complexing it with histones, and 3) quenching of surplus ROS species by the anti-oxidant enzymes superoxide dismutase, catalase, and peroxiredoxin [Riley, 1994; Mates et al., 1999; Mates and Sanchez”

What the sources say

• Not checked yetcites Riley, 1994
• Not checked yetcites Mates et al., 1999
• Not checked yetcites Mates and Sanchez-Jimenez, 1999

In the paper

“Cytosine and 5-methyl cytosine are the most frequently deaminated, but 5-methyl cytosine is deaminated three to four times more frequently than cytosine [Lindahl, 1979].”

What the sources say

• Not checked yetcites Lindahl, 1979

In the paper

“Another biologically significant and major oxidative base lesion formed from hydroxylation of the C-8 residue of guanine is the saturated imidazole ring 7,8 dihydro-8-oxoguanine (8-oxo-G) (Figure 1C). 8-oxo-guanine pairs incorrectly with adenine instead of cytosine, thereby adding to the overall mutational load, and is further oxidized to other deleterious secondary DNA lesions because of its low”

What the sources say

• Not checked yetcites Kasai and Nishimura, 1984
• Not checked yetcites Cheng et al., 1992 source
• Not checked yetcites Cadet et al., 1999

In the paper

“Base deamination is a major source of spontaneous mutagenesis in human cells, where cytosine (C), adenine (A), guanine (G), and 5-methyl cytosine (5mC) in DNA lose their exocyclic amine to become uracil (U), hypoxanthine, xanthine and thymine (T), respectively (Figure 1B).”

In the paper

“Paradoxically, cytosine deamination is also a normal route for somatic hypermutagenesis during antibody development due to the action of the deaminase enzymes AID (activation-induced deaminase) and APOBEC1 (Apolipoprotein B mRNA editing enzyme catalytic polypeptide 1), which mediate host defense against reteroviruses [Goff, 2003; Blanc and Davidson, 2010; Chandra et al., 2015].”

What the sources say

• Not checked yetcites Goff, 2003
• Not checked yetcites Blanc and Davidson, 2010
• Not checked yetcites Chandra et al., 2015

In the paper

“The most conspicuous of the ROS species are the superoxide radicals (•O2−), hydrogen peroxide (H2O2), and the hydroxyl radical (•OH) [Tropp, 2011].”

What the sources say

• Not checked yetcites Tropp, 2011

In the paper

“Reactive oxygen species (ROS) are the typical byproducts of the electron transport chain (ETC) during cellular respiration in aerobic organisms, and are additionally derived from catabolic oxidases, anabolic processes and peroxisomal metabolism [Henle and Linn, 1997].”

What the sources say

• Not checked yetcites Henle and Linn, 1997

In the paper

“About 1 adduct per 106 – 107 parent DNA bases results from lipid peroxidation events and the number of mutagenic adducts are expected to be even higher for metal storage diseases such as Wilson’s disease and hemochromatosis [Carmichael et al., 1995; Luczaj and Skrzydlewska, 2003; Broedbaek et al., 2009].”

What the sources say

• Not checked yetcites Carmichael et al., 1995
• Not checked yetcites Luczaj and Skrzydlewska, 2003
• Not checked yetcites Broedbaek et al., 2009

In the paper

“The DDR is a collection of mechanisms that sense DNA damage, signal its presence and promote subsequent repair [Harper and Elledge, 2007].”

What the sources say

• Not checked yetcites Harper and Elledge, 2007

In the paper

“However, DNA repair pathways (Figure 4) effectively remove most DNA lesions, which could otherwise result in the formation of mutations or block metabolic processes such as replication and transcription thereby causing senescence and cell death as we discuss below.”

In the paper

“While the BER pathway repairs the oxidized bases, the breaks in the DNA backbone are repaired by the single strand break repair (SSBR) pathways or the double strand break repair (DSBR) pathways [Henner et al., 1983a; Demple and Harrison, 1994].”

What the sources say

• Not checked yetcites Henner et al., 1983a
• Not checked yetcites Demple and Harrison, 1994

In the paper

“There are 9 human homologs of E. coli AlkB, which are designated as ALKBH1-8 (Alkylation Repair Homologs) and FTO (Fat Mass and Obesity associated) in human cells [Kurowski et al., 2003; Gerken et al., 2007; Sanchez-Pulido and Andrade-Navarro, 2007; Yi and He, 2013].”

What the sources say

• Not checked yetcites Kurowski et al., 2003
• Not checked yetcites Gerken et al., 2007
• Not checked yetcites Sanchez-Pulido and Andrade-Navarro, 2007

In the paper

“At least 11 different DNA glycosylases can recognize and excise a damaged base from undistorted helices, as well as ones flipped out from the major groove [Huffman et al., 2005; Krokan and Bjoras, 2013].”

What the sources say

• Not checked yetcites Huffman et al., 2005
• Not checked yetcites Krokan and Bjoras, 2013

In the paper

“In contrast, N3-methyladenine is only partly cytotoxic due to inhibition of DNA synthesis, while the N7-methylguanine residue is essentially harmless unless it undergoes a spontaneous cleavage to generate an AP site or opens the imidazole ring to form formamidopyrimidine [Loveless, 1969; Loechler et al., 1984; Larson et al., 1985; Preston et al., 1986; Preston et al., 1987; O’Connor et al., 1988;”

What the sources say

• Not checked yetcites Loveless, 1969
• Not checked yetcites Loechler et al., 1984
• Not checked yetcites Larson et al., 1985

In the paper

“O6-methylguanine and the related residues O4-methylthymine and O4-ethylthymine are highly mutagenic, producing G:C→A:T and T:A→C:G transition mutations, respectively.”

In the paper

“In short patch repair, the abasic site is the substrate for the AP endonuclease (APE1 in human cells), which cleaves the phosphodiester bond 5′ to the abasic site and generates a hydroxyl residue at the 3′-end while leaving a deoxyribose phosphate (dRP) at the 5′-end. This repair gap is tailored by the 5′-dRP lyase activity of POL β (gap tailoring), followed by filling the single nucleotide gap by”

What the sources say

• Not checked yetcites Almeida and Sobol, 2007

In the paper

“For repair of UV-induced CPDs, the ultraviolet-damaged DNA damage−binding protein (UV–DDB) complex, consisting of DDB1 (XPE−binding factor) and the GG−NER−specific protein DDB2, directly binds to UV−radiation−induced lesions and then stimulates the binding of XPC [Chu and Chang, 1988; Wakasugi et al., 2002; Scrima et al., 2008].”

What the sources say

• Not checked yetcites Chu and Chang, 1988
• Not checked yetcites Wakasugi et al., 2002
• Not checked yetcites Scrima et al., 2008

In the paper

“XPC bound to the lesion becomes the substrate for the transcription initiation factor II H (TFIIH) complex, a transcription initiation and repair factor composed of ten protein subunits that can switch functions in both transcription initiation and in NER [Yokoi et al., 2000; Volker et al., 2001; Compe and Egly, 2012].”

What the sources say

• Not checked yetcites Yokoi et al., 2000
• Not checked yetcites Volker et al., 2001
• Not checked yetcites Compe and Egly, 2012

In the paper

“MMR is also implicated in a variety of cellular processes including microsatellite stability, meiotic and mitotic recombination, DNA-damage signaling, apoptosis, class-switch recombination, somatic hypermutation and triplet-repeat expansion [Jiricny, 2006; Jiricny, 2013; Chatterjee et al., 2016a].”

What the sources say

• Not checked yetcites Jiricny, 2006
• Not checked yetcites Jiricny, 2013
• Not checked yetcites Chatterjee et al., 2016a

In the paper

“Of the eight known MSH (MutS homolog) polypeptides in eukaryotes, humans employ the MutSα heterodimer (MSH2/MSH6) to recognize base mismatches and one-to-two nucleotide IDLs, and the MutSβ heterodimer (MSH2/MSH3) to recognize large IDLs [Kunkel and Erie, 2005; Sachadyn, 2010].”

What the sources say

• Not checked yetcites Kunkel and Erie, 2005
• Not checked yetcites Sachadyn, 2010

In the paper

“Germline mutations in the MMR genes result in Lynch syndrome (also known as hereditary nonpolyposis colorectal cancer or HNPCC), which presents as a familial susceptibility to colon and ovarian cancers as well to a number of other cancers [Peltomaki, 2001].”

What the sources say

• Not checked yetcites Peltomaki, 2001

In the paper

“The second NER pathway, TC-NER, is initiated by a lesion-stalled RNA polymerase II, which begins with the recruitment of TC−NER−specific proteins CSA (Cockayne syndrome WD repeat protein A; also known as ERCC8) and CSB (Cockayne syndrome protein B; also known as ERCC6), which are essential for additional assembly of other TC−NER components [Fousteri et al., 2006].”

What the sources say

• Not checked yetcites Fousteri et al., 2006

In the paper

“In addition, PARP1 (Poly [ADP-ribose] polymerase 1) has also been shown to be required for the repair of single strand breaks and damaged purine bases by a sub-pathway of BER [Krokan and Bjoras, 2013; Reynolds et al., 2015].”

What the sources say

• Not checked yetcites Krokan and Bjoras, 2013
• Not checked yetcites Reynolds et al., 2015

In the paper

“An abasic site created from the monofunctional glycosylases gets committed to the short-patch-repair pathway, while the bifunctional glycosylases initiate the long-patch repair pathway of BER [Dianov and Hubscher, 2013].”

What the sources say

• Not checked yetcites Dianov and Hubscher, 2013

In the paper

“Proliferative status of the cell determines the choice of polymerase used. For example, POL ε−dependent repair predominates in non−replicating cells, while POL δ and POL κ are the main NER polymerases in replicating cells. LIG1-dependent ligation occurs in replicating cells. However, XRCC1–LIG3 complex seals the gap in non-proliferating cells because of low expression of dNTPs and LIG1 in these”

What the sources say

• Not checked yetcites Moser et al., 2007
• Not checked yetcites Ogi et al., 2010

In the paper

“In long patch repair, the repair gap left behind from the bifunctional glycosylase is tailored by the 3′ phosphodiesterase activity of APE1. Thereafter, POL β (in non-proliferating cells) or POL δ/ε (in proliferating cells) synthesize in a strand-displacement manner, which is then followed by flap removal by the flap endonuclease and a LIG1-mediated ligation [Akbari et al., 2009; Svilar et al., 2”

What the sources say

• Not checked yetcites Akbari et al., 2009
• Not checked yetcites Svilar et al., 2011

In the paper

“There are two major branches of NER: global genome NER (GG−NER) and transcription−coupled NER (TC−NER).”

In the paper

“Specifically, mutations in POL β are found in solid cancers and POL β variants can act as dominant negative and sequence specific mutators [Wang et al., 1992; Starcevic et al., 2004; Lang et al., 2007; Murphy et al., 2012].”

What the sources say

• Not checked yetcites Wang et al., 1992
• Not checked yetcites Starcevic et al., 2004
• Not checked yetcites Lang et al., 2007

In the paper

“Once localized at the lesion site, the CSA-CSB complex backtracks (or reverse translocates) RNA polymerase II, exposing the lesion site. TFIIH is recruited to the lesion.”

In the paper

“Typical substrates for the MMR pathway are base mismatches that have arisen during replication and the insertion-deletion loops (IDLs) within repetitive DNA sequences that have resulted from strand slippage events [Errol C. Friedberg, 2005; Jiricny, 2006].”

What the sources say

• Not checked yetcites Errol C. Friedberg, 2005
• Not checked yetcites Jiricny, 2006

In the paper

“MMR is an evolutionarily conserved, post replicative repair pathway that contributes to replication fidelity by at least 100-fold [Kunkel, 2009; Arana and Kunkel, 2010].”

What the sources say

• Not checked yetcites Kunkel, 2009
• Not checked yetcites Arana and Kunkel, 2010

In the paper

“Finally, mitochondria are also known to carry out both short and long patch BER, where the synthesis step is carried out by POL γ; all of which adds to the significance of this repair pathway in the maintenance of global genome stability [Akbari et al., 2008; Liu and Demple, 2010].”

What the sources say

• Not checked yetcites Akbari et al., 2008
• Not checked yetcites Liu and Demple, 2010

In the paper

“MutLα regulates termination of mismatch-provoked excision, and its endonuclease activity plays a role in the 3′ nick-directed digestion by EXO1 (Exonuclease 1) in a PCNA/RFC dependent manner [Zhang et al., 2005; Kadyrov et al., 2006].”

What the sources say

• Not checked yetcites Zhang et al., 2005
• Not checked yetcites Kadyrov et al., 2006

In the paper

“Interstrand crosslinks are lesions in which two bases from complementary strands are covalently linked due to damage to the DNA from crosslinking agents such as platinum compounds, nitrogen mustards, MMC, psoralens and alkylating agents [Clauson et al., 2013].”

What the sources say

• Not checked yetcites Clauson et al., 2013

In the paper

“FA disorder is a heterogeneous and rare genetic disorder characterized with a high frequency of hematological abnormalities, congenital anomalies and a general predisposition to cancers [Kee and D’Andrea, 2012].”

What the sources say

• Not checked yetcites Kee and D’Andrea, 2012

In the paper

“Helix-distorting lesions are recognized by both the GG-NER and the TC-NER pathways to initiate repair, although some lesions such as cisplatin may escape recognition [Enoiu et al., 2012].”

What the sources say

• Not checked yetcites Enoiu et al., 2012

In the paper

“After lesion recognition, the components of the NER pathway are known to cut only the 5′ side of the lesion, with further incisions possibly aided by the MutSβ complex create a ssDNA-gap [Bessho et al., 1997; Mu et al., 2000; Smeaton et al., 2008; Zhao et al., 2009].”

What the sources say

• Not checked yetcites Bessho et al., 1997
• Not checked yetcites Mu et al., 2000
• Not checked yetcites Smeaton et al., 2008

In the paper

“The FA family consists of 21 different functional complementation groups (A, B, C, D1, D2, E, F, G, I, J, L, M, N, O, P, Q, R, S, T, U, V), which are known to suppress ICL sensitivity [Bluteau et al., 2016; Michl et al., 2016].”

What the sources say

• Not checked yetcites Bluteau et al., 2016
• Not checked yetcites Michl et al., 2016

In the paper

“Next, the error-prone TLS polymerase synthesize across the gap and finally a second round of NER removes the ICL hook on the other strand [Clauson et al., 2013].”

What the sources say

• Not checked yetcites Clauson et al., 2013

In the paper

“Using a gapped plasmid assay, it has been shown that TLS is as high or higher in G2 compared to S phase in human cells, with slightly higher amounts of POL η in G2 compared to S phase of the cell cycle [Diamant et al., 2012].”

What the sources say

• Not checked yetcites Diamant et al., 2012

In the paper

“Usually, these type of TLS events are expected to fall outside of the S phase, but based on the type of DNA lesion, a cell-cycle independence is sometimes conferred [Quinet et al., 2016].”

What the sources say

• Not checked yetcites Quinet et al., 2016

In the paper

“Likewise, an HSP90 inhibitor reduces expression of REV1 and POL η in human cells, indicating an evolutionary regulation of these polymerases [Sekimoto et al., 2010; Pozo et al., 2011].”

What the sources say

• Not checked yetcites Sekimoto et al., 2010
• Not checked yetcites Pozo et al., 2011

In the paper

“These patients lack the POL η enzyme and are highly susceptible to UV radiation because alternate TLS polymerases (POL ι and POL κ) instead bypass the UV-induced cyclobutane dimers (CPD) in an error-prone fashion [Yamada et al., 2000; Sweasy et al., 2006; Wang et al., 2007b; Ziv et al., 2009].”

What the sources say

• Not checked yetcites Yamada et al., 2000
• Not checked yetcites Sweasy et al., 2006
• Not checked yetcites Wang et al., 2007b

In the paper

“If incorrect nucleotides were incorporated by TLS polymerases, they would become mutations in the next round of replication, which propel tumorigenesis and disease, but can also contribute to the overall fitness and evolution of organisms.”

In the paper

“The central molecule that orchestrates both the insertion and extension step is REV1, and by way of its unique scaffolding function facilitates an assemblage of the TLS polymerases by binding to an RIR-containing polymerase—POL η, POL ι, or POL κ—via one interface, and also to POL ζ4 (REV3-REV7-POLD2-POLD3), via a second interface, a central step in this model’s execution [Wojtaszek et al., 2012a;”

What the sources say

• Not checked yetcites Wojtaszek et al., 2012a
• Not checked yetcites Wojtaszek et al., 2012b

In the paper

“A total of eleven TLS polymerases are known (REV1, POL η, POL ι, POL κ, POL ζ, POL μ, POL λ, POL β, POL ν, POL θ), which are distributed in four families (Y, B, X and A) and PrimPol (Table 1).”

In the paper

“For instance, as previously discussed, TLS polymerases are required for ICL repair and can also play role in the BER and NER pathways to synthesize new DNA after the excision step.”

In the paper

“Although all TLS polymerases are less accurate than replicative polymerases, certain TLS polymerases are able to copy relatively accurately over certain cognate lesions.”

In the paper

“Similarly, inhibition of NHEJ components alleviates the sensitivity of FA deficient cells to crosslinking agents, while the same FA deficient cells show enrichment of 53BP1, RIF1 and RAP80 components at damaged chromatin [Adamo et al., 2010; Pace et al., 2010; Ceccaldi et al., 2016b; Renaud et al., 2016].”

What the sources say

• Not checked yetcites Adamo et al., 2010
• Not checked yetcites Pace et al., 2010
• Not checked yetcites Ceccaldi et al., 2016b

In the paper

“XPV patients, who exhibit a photosensitive phenotype with a high incidence of skin cancer, highlight the physiological significance of certain TLS DNA polymerases bypassing particular lesions.”

In the paper

“For example, cyclobutane thymine-thymine CPDs are cognate lesions for POL η (Table 1).”

In the paper

“For example, REV1 is very important in mouse cells for synthesis across post-replicative gaps where REV1 gets recruited to the gaps by the 5′-end, unlike the gap-filling step of NER, where POL κ is the polymerase of choice [Ogi and Lehmann, 2006; de Groote et al., 2011; Sale, 2013].”

What the sources say

• Not checked yetcites Ogi and Lehmann, 2006
• Not checked yetcites de Groote et al., 2011
• Not checked yetcites Sale, 2013

In the paper

“However, once DNA-PKcs gets recruited, it is activated in a DNA dependent manner; it pushes Ku inwardly on the DNA and then phosphorylates other nearby components, including autoautophosphorylating itself [Gottlieb and Jackson, 1993; Yoo and Dynan, 1999; Weterings and Chen, 2008].”

What the sources say

• Not checked yetcites Gottlieb and Jackson, 1993
• Not checked yetcites Yoo and Dynan, 1999
• Not checked yetcites Weterings and Chen, 2008

In the paper

“These patients often manifest genetic instability and high incidence of cancers [El-Khamisy et al., 2005; Reynolds et al., 2009].”

What the sources say

• Not checked yetcites El-Khamisy et al., 2005
• Not checked yetcites Reynolds et al., 2009

In the paper

“Activated ATM (from TIP60) phosphorylates H2AX, which then serves as an anchor for MDC1 [Bhatti et al., 2011].”

What the sources say

• Not checked yetcites Bhatti et al., 2011

In the paper

“In the long patch SSBR pathway, SSBs are transiently detected by PARP1, which undergoes a rapid cycle of poly(ADP) ribosylation and dissociates to detect the next SSB [D’Amours et al., 1999; Davidovic et al., 2001]. After this, the ends undergo end processing by the apurinic-apyrimidic endonuclease 1 APE1, PNKP (polynuceotide kinase 3′-phosphate) and aprataxin (APTX) [McKinnon and Caldecott, 2007]”

What the sources say

• Not checked yetcites D’Amours et al., 1999
• Not checked yetcites Davidovic et al., 2001
• Not checked yetcites McKinnon and Caldecott, 2007

In the paper

“SSBR is predicted to occur through three different pathways depending on the source of SSB.”

In the paper

“LIG4 joins the ends and completes the NHEJ process [Grawunder et al., 1997].”

What the sources say

• Not checked yetcites Grawunder et al., 1997

In the paper

“Chromatin modification is the first event that registers the presence of a DSB and triggers a cascade of events including ATM activation, targeted phosphorylation of H2AX, chromatin PARylation, MDC1 recruitment and finally recruitment of 53BP1 and BRCA1 [Rogakou et al., 1998; Rothkamm et al., 2003; Gottschalk et al., 2009; Chou et al., 2010; Lukas et al., 2011; Price and D’Andrea, 2013; Liu et al”

What the sources say

• Not checked yetcites Rogakou et al., 1998
• Not checked yetcites Rothkamm et al., 2003
• Not checked yetcites Gottschalk et al., 2009

In the paper

“In the short patch SSBR pathway, SSBs generated during the BER are recognized by APE1 followed by a similar end-processing pathway as the long patch repair. The gap-filling step, however, is only carried out by POL β enzyme, followed by LIG3-catalyzed ligation [McKinnon and Caldecott, 2007].”

What the sources say

• Not checked yetcites McKinnon and Caldecott, 2007

In the paper

“Next, MDC1 is phosphorylated by ATM, and the phosphorylated MDC1 functions as a scaffold to bring in the ubiquitin E3 ligases RNF8 and RNF168 [Altmeyer and Lukas, 2013b].”

What the sources say

• Not checked yetcites Altmeyer and Lukas, 2013b

In the paper

“In the S/G2 phase where HR is predominant, BRCA1 (recruited by ubiquitinated chromatin) successfully counteracts 53BP1 and initiates ubiquitination of the downstream component, CtIP [Yu et al., 2006; Chapman et al., 2012].”

What the sources say

• Not checked yetcites Yu et al., 2006
• Not checked yetcites Chapman et al., 2012

In the paper

“The Ku (Ku70 and Ku80) heterodimer is the first to recognize and bind the DSBs within seconds to prevent end resection and serves as a scaffold to recruit other NHEJ components [Pang et al., 1997; Mari et al., 2006; Soutoglou et al., 2007; Mimitou and Symington, 2010].”

What the sources say

• Not checked yetcites Pang et al., 1997
• Not checked yetcites Mari et al., 2006
• Not checked yetcites Soutoglou et al., 2007

In the paper

“Unresolved SSBs often collapse DNA replication, stall ongoing transcription, and effect PARP1 activation, which releases cellular NAD+, ATP and apoptosis inducing factor (AIF) in cells [Zhou and Doetsch, 1993; Heeres and Hergenrother, 2007]”

What the sources say

• Not checked yetcites Zhou and Doetsch, 1993
• Not checked yetcites Heeres and Hergenrother, 2007

In the paper

“Interestingly, both 53BP1 and BRCA1 exhibit an antagonistic influence on each other and 53BP1 depletion rescues embryonic lethality of BRCA1 null mice [Xie et al., 2007; Cao et al., 2009; Bunting et al., 2010].”

What the sources say

• Not checked yetcites Xie et al., 2007
• Not checked yetcites Cao et al., 2009
• Not checked yetcites Bunting et al., 2010

In the paper

“Both of these E3 ligases ubiquitinate H2AX, which then serves as a docking site for 53BP1 and BRCA1.”

In the paper

“The MRN (MRE11-RAD50-NBS1) complex initiates HR at a DSB, where it recognizes and binds the DSB and then recruits ATM and TIP60 to the DNA [Sun et al., 2005; Stracker and Petrini, 2011].”

What the sources say

• Not checked yetcites Sun et al., 2005
• Not checked yetcites Stracker and Petrini, 2011

In the paper

“Unresolved DSBs are implicated in various human disorders and cancers [Jackson and Bartek, 2009].”

What the sources say

• Not checked yetcites Jackson and Bartek, 2009

In the paper

“In addition to the traditional DSBR-induced HR pathway, synthesis-dependent strand annealing (SDSA) and break-induced repair (BIR) are two other variations following the HR premise [Li and Heyer, 2008].”

What the sources say

• Not checked yetcites Li and Heyer, 2008

In the paper

“Recent studies indicate that the order of recruitment of these components may depend on the complexity of DNA damage; for instance, DNA-PKcs recruitment depends on the nature of the break [Mari et al., 2006; Yano and Chen, 2008].”

What the sources say

• Not checked yetcites Mari et al., 2006
• Not checked yetcites Yano and Chen, 2008

In the paper

“In the NHEJ pathway of DSBR, 53BP1 plays an important regulatory role by recruiting the NHEJ components to the break site, activating checkpoint signaling and facilitating synapsis of the two ends [Panier and Boulton, 2014].”

What the sources say

• Not checked yetcites Panier and Boulton, 2014

In the paper

“For example, short telomeres often assemble DDR factors such as 53BP1, ATM, γH2AX, and MRE11 as foci, called Telomere Dysfunction-Induced Foci (TIF), which are highly prone to NHEJ-mediated end-to-end fusion [Takai et al., 2003; Hewitt et al., 2012; Marcand, 2014].”

What the sources say

• Not checked yetcites Takai et al., 2003
• Not checked yetcites Hewitt et al., 2012
• Not checked yetcites Marcand, 2014

In the paper

“In addition, telomeric DNA is replicated and maintained by a specialized ribonucleoprotein complex called telomerase [composed of a telomere RNA component (TERC) and a telomere reverse transcriptase (TERT)], which is the only positive regulator of telomere length [Bachand et al., 2001; Blasco, 2003].”

What the sources say

• Not checked yetcites Bachand et al., 2001
• Not checked yetcites Blasco, 2003

In the paper

“Initial resection occurs by the endonuclease activity of MRN, with the help of CtIP, followed by long-range resection by EXO1 or BLM together with DNA2 [Chen et al., 2008; Nimonkar et al., 2011].”

What the sources say

• Not checked yetcites Chen et al., 2008
• Not checked yetcites Nimonkar et al., 2011

In the paper

“At this time, the other HR components, RPA, and RAD51 proteins make their way on to the DNA.”

In the paper

“BRCA2 and PALB2 aid in the formation of the nucleoprotein filament formation that invades a nearby duplex DNA forming a D-loop [Zhang et al., 2009; Holloman, 2011].”

What the sources say

• Not checked yetcites Zhang et al., 2009
• Not checked yetcites Holloman, 2011

In the paper

“A decline in telomerase activity contributes to telomere attrition, which is associated with aging, cancer and several inherited bone marrow failure (IBMF) disorders [Chang and Harley, 1995; Shay et al., 2001; Alter et al., 2015].”

What the sources say

• Not checked yetcites Chang and Harley, 1995
• Not checked yetcites Shay et al., 2001
• Not checked yetcites Alter et al., 2015

In the paper

“In conclusion, DNA is continually being exposed to both endogenous and exogenous DNA damaging agents that chemically modify the DNA constituents.”