http://colil.dbcls.jp:18052/sparql?query=define%20sql%3Adescribe-mode%20%22CBD%22%20%20DESCRIBE%20%3Chttp%3A%2F%2Fpurl.jp%2Fbio%2F10%2Fcolil%2Fid%2F31380392%3E&output=application%2Fatom%2Bxml2024-03-29T10:23:08.227755ZOData Service and Descriptor DocumentnodeID://b975552482024-03-29T10:23:08.227755Za DNA/RNA helicase with R-loop-resolving activity, counteracts the binding of RAD51 and stimulates that of 53BP1 (Cohen et al., 2018), leading to illegitimate repair of broken ends and chromosome translocations (Brustel et al., >>2018<<; Cohen et al., 2018). In this scenario, it is also important to mention that a recent work has reported that high levels of DNA:nodeID://b975552172024-03-29T10:23:08.227755ZAccordingly, a reduction of DNA transcription nearby a DSB has been detected in both yeast (Lee et al., >>2000<<; Manfrini et al., 2015) and mammals (Kruhlak et al., 2007; Chou et al., 2010; Shanbhag et al., 2010; Pankotai et al., 2012; Kakarougkas et al., 2014; Ui et al., 2015; Awwad et al., 2017; Iannelli et al., 2017; Vitor et al., 2019).nodeID://b975552222024-03-29T10:23:08.227755ZAccordingly, a reduction of DNA transcription nearby a DSB has been detected in both yeast (Lee et al., 2000; Manfrini et al., 2015) and mammals (Kruhlak et al., 2007; Chou et al., 2010; Shanbhag et al., 2010; Pankotai et al., >>2012<<; Kakarougkas et al., 2014; Ui et al., 2015; Awwad et al., 2017; Iannelli et al., 2017; Vitor et al., 2019).nodeID://b975551762024-03-29T10:23:08.227755ZIn yeast, KU-dependent resection barrier is predominant in G1 phase (Clerici et al., 2008), when MRX-Sae2 is not activated by CDK1, or in the absence of functional MRX complex or Sae2 (Mimitou and Symington, >>2010<<). Accordingly, deletion of KU70 partially suppressed the resection defect and sensitivity of sae2 or mre11 mutants to ionizing radiations (Bonetti et al., 2010; Mimitou and Symington, 2010; Foster et al., 2011).nodeID://b975551452024-03-29T10:23:08.227755ZBoth pathways are organized in distinct steps and sub-pathways, which involve the coordination of several factors and enzymes (Heyer et al., >>2010<<; Symington, 2016).nodeID://b975551502024-03-29T10:23:08.227755ZIndeed, in vivo and in vitro data (Neale et al., 2005; Shibata et al., >>2014<<; Reginato et al., 2017; Wang et al., 2017, 2018) have shown that Mre11 is recruited nearby the DSB ends and induces a nick on the 5′-end filament, creating the entry point for both Exo1 and Dna2-Sgs1/BLM (Figure 1D).nodeID://b975551832024-03-29T10:23:08.227755ZMoreover, depending upon the organisms, it is known that KU binding to DSB is finely regulated through neddylation (Brown et al., >>2015<<), ubiquitylation (Postow et al., 2008; Feng and Chen, 2012), sumoylation (Hang et al., 2014), acetylation (Kim et al., 2014), and phosphorylation by DNA-PKs (Chan et al., 1999).nodeID://b975552182024-03-29T10:23:08.227755ZAccordingly, a reduction of DNA transcription nearby a DSB has been detected in both yeast (Lee et al., 2000; Manfrini et al., >>2015<<) and mammals (Kruhlak et al., 2007; Chou et al., 2010; Shanbhag et al., 2010; Pankotai et al., 2012; Kakarougkas et al., 2014; Ui et al., 2015; Awwad et al., 2017; Iannelli et al., 2017; Vitor et al., 2019).nodeID://b6657778302024-03-29T10:23:08.227755Z4nodeID://b975552302024-03-29T10:23:08.227755ZThe newly-synthetized non-coding RNAs at DSBs contribute to signal locally DNA damage and facilitate DNA repair (Francia et al., >>2012<<; Wei et al., 2012) and, by changing chromatin structure, also possibly contribute to repress canonical transcription (Burger et al., 2019).nodeID://b975552252024-03-29T10:23:08.227755ZDSB has been detected in both yeast (Lee et al., 2000; Manfrini et al., 2015) and mammals (Kruhlak et al., 2007; Chou et al., 2010; Shanbhag et al., 2010; Pankotai et al., 2012; Kakarougkas et al., 2014; Ui et al., 2015; Awwad et al., >>2017<<; Iannelli et al., 2017; Vitor et al., 2019).http://purl.jp/bio/10/colil/id/313803922024-03-29T10:23:08.227755Z10.3389%2Ffmolb.2019.00055PMC0nodeID://b6657778242024-03-29T10:23:08.227755Z6nodeID://b6657778272024-03-29T10:23:08.227755Z4nodeID://b975551462024-03-29T10:23:08.227755ZBoth pathways are organized in distinct steps and sub-pathways, which involve the coordination of several factors and enzymes (Heyer et al., 2010; Symington, >>2016<<). Of note, specific mechanisms are required to process DSB ends containing covalently-bound proteins (such as Topoisomerase), DNA alterations (oxidation, methylation, hairpin formation, and others) and associated RNA molecules (e.g., DNA:nodeID://b975551842024-03-29T10:23:08.227755ZMoreover, depending upon the organisms, it is known that KU binding to DSB is finely regulated through neddylation (Brown et al., 2015), ubiquitylation (Postow et al., >>2008<<; Feng and Chen, 2012), sumoylation (Hang et al., 2014), acetylation (Kim et al., 2014), and phosphorylation by DNA-PKs (Chan et al., 1999).nodeID://b975551792024-03-29T10:23:08.227755ZAccordingly, deletion of KU70 partially suppressed the resection defect and sensitivity of sae2 or mre11 mutants to ionizing radiations (Bonetti et al., 2010; Mimitou and Symington, 2010; Foster et al., >>2011<<).nodeID://b975551532024-03-29T10:23:08.227755ZIndeed, in vivo and in vitro data (Neale et al., 2005; Shibata et al., 2014; Reginato et al., 2017; Wang et al., 2017, >>2018<<) have shown that Mre11 is recruited nearby the DSB ends and induces a nick on the 5′-end filament, creating the entry point for both Exo1 and Dna2-Sgs1/BLM (Figure 1D).nodeID://b975551912024-03-29T10:23:08.227755Zbp1-dependent barriernodeID://b6657778322024-03-29T10:23:08.227755Z3nodeID://b6657778352024-03-29T10:23:08.227755Z3nodeID://b6657779022024-03-29T10:23:08.227755Z2nodeID://b6657778292024-03-29T10:23:08.227755Z4nodeID://b6657778262024-03-29T10:23:08.227755Z5nodeID://b6657778432024-03-29T10:23:08.227755Z3nodeID://b6657778402024-03-29T10:23:08.227755Z3nodeID://b975552262024-03-29T10:23:08.227755Zboth yeast (Lee et al., 2000; Manfrini et al., 2015) and mammals (Kruhlak et al., 2007; Chou et al., 2010; Shanbhag et al., 2010; Pankotai et al., 2012; Kakarougkas et al., 2014; Ui et al., 2015; Awwad et al., 2017; Iannelli et al., >>2017<<; Vitor et al., 2019).nodeID://b6657779102024-03-29T10:23:08.227755Z2nodeID://b975552002024-03-29T10:23:08.227755ZInterestingly, it has been shown that Rad9 accumulates at DSB ends in yeast cells lacking SAE2, blocking resection initiation by Dna2-Sgs1 (Bonetti et al., 2015; Ferrari et al., >>2015<<; Yu et al., 2018).nodeID://b975552332024-03-29T10:23:08.227755ZIndeed, nascent RNA can be utilized as template to repair DSBs in transcribed genes via either error-free cNHEJ in human cells (Chakraborty et al., >>2016<<), or HDR upon its assimilation into broken DNA by Rad52 protein, via an inverse strand exchange mechanism conserved from yeast to human (Keskin et al., 2014; Mazina et al., 2017).nodeID://b6657778372024-03-29T10:23:08.227755Z3nodeID://b6657779072024-03-29T10:23:08.227755Z2nodeID://b6657778512024-03-29T10:23:08.227755Z2nodeID://b6657779012024-03-29T10:23:08.227755Z2nodeID://b6657779042024-03-29T10:23:08.227755Z2nodeID://b975551492024-03-29T10:23:08.227755ZIndeed, in vivo and in vitro data (Neale et al., >>2005<<; Shibata et al., 2014; Reginato et al., 2017; Wang et al., 2017, 2018) have shown that Mre11 is recruited nearby the DSB ends and induces a nick on the 5′-end filament, creating the entry point for both Exo1 and Dna2-Sgs1/BLM (Figure 1D).nodeID://b975551542024-03-29T10:23:08.227755ZInterestingly, recent in vitro data indicate that BLM promotes the EXO1 resection processivity, too (Soniat et al., >>2019<<). This nick-dependent mechanism for resection is activated in S and G2/M phases through the CDK1-dependent phosphorylation of Sae2 (CTIP in human) (Huertas et al., 2008; Huertas and Jackson, 2009), which associates with the Mre11 complex.nodeID://b975551922024-03-29T10:23:08.227755ZThe mammalian p53-binding protein 1 (53BP1) and its yeast ortholog Rad9 are important regulators of the DSB repair pathway choice (Panier and Boulton, >>2014<<). Remarkably, 53BP1 and Rad9 act on all types of DSBs, including reversed forks and uncapped telomeres.nodeID://b975551872024-03-29T10:23:08.227755Zupon the organisms, it is known that KU binding to DSB is finely regulated through neddylation (Brown et al., 2015), ubiquitylation (Postow et al., 2008; Feng and Chen, 2012), sumoylation (Hang et al., 2014), acetylation (Kim et al., >>2014<<), and phosphorylation by DNA-PKs (Chan et al., 1999). In particular, neddylation primes ubiquitylation of KU in human cells, facilitating the release of the complex and associated factors from repaired DNA (Brown et al., 2015).nodeID://b6657778482024-03-29T10:23:08.227755Z2nodeID://b6657778452024-03-29T10:23:08.227755Z3nodeID://b975551612024-03-29T10:23:08.227755ZRemarkably, other in vitro results showed that BLM is able to slide nucleosomes, if RPA is added in the assay, promoting DNA resection by EXO1 and DNA2 (Xue et al., >>2019<<). Of importance, the phosphorylation of RPA is critical to limit resection at nucleosomes, interfering with the strand-switching of BLM helicase (Soniat et al., 2019). However, Exo1 can actively resect DNA packed into nucleosomesnodeID://b6657778622024-03-29T10:23:08.227755Z2nodeID://b6657779152024-03-29T10:23:08.227755Z2nodeID://b6657779122024-03-29T10:23:08.227755Z2nodeID://b6657778392024-03-29T10:23:08.227755Z3nodeID://b6657778562024-03-29T10:23:08.227755Z2nodeID://b6657779062024-03-29T10:23:08.227755Z2nodeID://b6657779092024-03-29T10:23:08.227755Z2nodeID://b6657778532024-03-29T10:23:08.227755Z2nodeID://b6657778702024-03-29T10:23:08.227755Z2nodeID://b6657779202024-03-29T10:23:08.227755Z2nodeID://b975552342024-03-29T10:23:08.227755Zgenes via either error-free cNHEJ in human cells (Chakraborty et al., 2016), or HDR upon its assimilation into broken DNA by Rad52 protein, via an inverse strand exchange mechanism conserved from yeast to human (Keskin et al., >>2014<<; Mazina et al., 2017). There are also evidence that DNA:nodeID://b975552292024-03-29T10:23:08.227755Ztranscription requires MRN-dependent recruitment of RNAPII at DNA lesions (Michelini et al., 2017) or, in the case of DSBs generated at promoter-proximal regions, cAbl-dependent tyrosine phosphorylation of RNAPII (Burger et al., >>2019<<). The newly-synthetized non-coding RNAs at DSBs contribute to signal locally DNA damage and facilitate DNA repair (Francia et al., 2012; Wei et al., 2012) and, by changing chromatin structure, also possibly contribute to repress canonicalnodeID://b975552032024-03-29T10:23:08.227755ZThese and other evidence indicate that 53BP1 exerts its action as a resection barrier in an extremely dynamic way, by mutual antagonism with BRCA1 and recruiting several downstream effectors (Panier and Boulton, >>2014<<; Zimmermann and de Lange, 2014).nodeID://b6657778672024-03-29T10:23:08.227755Z2nodeID://b6657779172024-03-29T10:23:08.227755Z2nodeID://b975552412024-03-29T10:23:08.227755Zminimally resected DNA ends, regulate the recruitment of RPA, BRCA1, BRCA2, RAD51, and RAD52, promoting HDR (Ohle et al., 2016; Cohen et al., 2018; D'Alessandro et al., 2018; Lu et al., 2018; Burger et al., 2019; Domingo-Prim et al., >>2019<<). Another recent study in human cells showed that DSBs within transcriptionally active genes lead to the formation of R-loops, whose cleavage by the endonuclease XPG promotes an alternative way to initiate DSB resection and HDR (YasuharanodeID://b6657778612024-03-29T10:23:08.227755Z2nodeID://b6657778642024-03-29T10:23:08.227755Z2nodeID://b975551882024-03-29T10:23:08.227755ZDSB is finely regulated through neddylation (Brown et al., 2015), ubiquitylation (Postow et al., 2008; Feng and Chen, 2012), sumoylation (Hang et al., 2014), acetylation (Kim et al., 2014), and phosphorylation by DNA-PKs (Chan et al., >>1999<<). In particular, neddylation primes ubiquitylation of KU in human cells, facilitating the release of the complex and associated factors from repaired DNA (Brown et al., 2015).nodeID://b6657778582024-03-29T10:23:08.227755Z2nodeID://b975551572024-03-29T10:23:08.227755ZThe importance of regulating the DNA ends resection in DSB repair is underlined by the increasing list of factors participating in the reaction in human cells, including the oncosuppressor BRCA1 (Zhao et al., >>2019<<).nodeID://b975551622024-03-29T10:23:08.227755ZOf importance, the phosphorylation of RPA is critical to limit resection at nucleosomes, interfering with the strand-switching of BLM helicase (Soniat et al., >>2019<<). However, Exo1 can actively resect DNA packed into nucleosomes containing the H2A.Z histone variant, which promotes higher mobility and instability of the octamer (Adkins et al., 2013). As such, the dynamic deposition of H2A.Z, togethernodeID://b975551952024-03-29T10:23:08.227755ZSimilarly to Rad9, 53BP1 recruitment requires the direct recognition of a DSB-specific histone code: it displays a strong binding affinity for the histone H4 constitutively mono- or di-methylated at the K20 (Botuyan et al., >>2006<<) and for the histone H2A DSB-induced ubiquitination at K15 (Fradet-Turcotte et al., 2013).nodeID://b6657778752024-03-29T10:23:08.227755Z2nodeID://b6657778722024-03-29T10:23:08.227755Z2nodeID://b6657778692024-03-29T10:23:08.227755Z2nodeID://b6657779192024-03-29T10:23:08.227755Z2nodeID://b6657778662024-03-29T10:23:08.227755Z2nodeID://b6657778832024-03-29T10:23:08.227755Z2nodeID://b6657778802024-03-29T10:23:08.227755Z2nodeID://b975552042024-03-29T10:23:08.227755Zother evidence indicate that 53BP1 exerts its action as a resection barrier in an extremely dynamic way, by mutual antagonism with BRCA1 and recruiting several downstream effectors (Panier and Boulton, 2014; Zimmermann and de Lange, >>2014<<). Notably, following DSB-induced phosphorylation by ATM, 53BP1 recruits RIF1, the Shielding complex and the CST/ Pol α-Prim complex that fills in the resected DNA end, restoring dsDNA and allowing NHEJ [see a recent review herenodeID://b6657778772024-03-29T10:23:08.227755Z2nodeID://b975552372024-03-29T10:23:08.227755ZThere are also evidence that DNA:RNA hybrids, generated at resected or minimally resected DNA ends, regulate the recruitment of RPA, BRCA1, BRCA2, RAD51, and RAD52, promoting HDR (Ohle et al., 2016; Cohen et al., >>2018<<; D'Alessandro et al., 2018; Lu et al., 2018; Burger et al., 2019; Domingo-Prim et al., 2019).nodeID://b975552422024-03-29T10:23:08.227755Zstudy in human cells showed that DSBs within transcriptionally active genes lead to the formation of R-loops, whose cleavage by the endonuclease XPG promotes an alternative way to initiate DSB resection and HDR (Yasuhara et al., >>2018<<). Of interest, after their recruitment at XPG-processed DSBs, RAD52, and BRCA1 limit the 53BP1-RIF1 barrier.nodeID://b6657778742024-03-29T10:23:08.227755Z2nodeID://b975552112024-03-29T10:23:08.227755ZIn yeast, the SMARCAD1-ortholog Fun30 also acts on the Rad9-barrier, promoting long-range resection (Chen et al., >>2012<<; Eapen et al., 2012; Bantele et al., 2017).nodeID://b6657778912024-03-29T10:23:08.227755Z2nodeID://b975551582024-03-29T10:23:08.227755Znucleosome-dependent barriernodeID://b975551962024-03-29T10:23:08.227755Zhistone code: it displays a strong binding affinity for the histone H4 constitutively mono- or di-methylated at the K20 (Botuyan et al., 2006) and for the histone H2A DSB-induced ubiquitination at K15 (Fradet-Turcotte et al., >>2013<<). Moreover, 53BP1 oligomerization, mediated by DYNLL1, is essential for its recruitment to DSBs (Becker et al., 2018; West et al., 2019).nodeID://b6657778882024-03-29T10:23:08.227755Z2nodeID://b6657778852024-03-29T10:23:08.227755Z2nodeID://b975551652024-03-29T10:23:08.227755ZZ and H3.3 variants facilitate the loading of the NHEJ factors KU and XRCC4 onto DSB, thus limiting resection initiation (Xu et al., 2012; Luijsterburg et al., >>2016<<). Nevertheless, other modifications of the histone core have been recently shown to facilitate the recruitment at DSB of both NHEJ and pro-resection factors, leading to a more complex scenario. According to several in vivo results,nodeID://b975551702024-03-29T10:23:08.227755ZAlong with its role in promoting NHEJ, KU plays also fundamental role in limiting chromosome translocations mediated by the annealing of ssDNA repeats in human cells (Weinstock et al., >>2006<<). Indeed, KU-bound DSB ends are resistant to Exo1 and Dna2 processing (Shim et al., 2010; Symington, 2016; Wang et al., 2018), reducing recombination DNA repair by micro-homology mediated end joining (MMEJ, also called alternativenodeID://b6657778792024-03-29T10:23:08.227755Z2nodeID://b6657778932024-03-29T10:23:08.227755Z2nodeID://b6657778962024-03-29T10:23:08.227755Z2nodeID://b6657778872024-03-29T10:23:08.227755Z2nodeID://b975552382024-03-29T10:23:08.227755Zare also evidence that DNA:RNA hybrids, generated at resected or minimally resected DNA ends, regulate the recruitment of RPA, BRCA1, BRCA2, RAD51, and RAD52, promoting HDR (Ohle et al., 2016; Cohen et al., 2018; D'Alessandro et al., >>2018<<; Lu et al., 2018; Burger et al., 2019; Domingo-Prim et al., 2019).nodeID://b975552072024-03-29T10:23:08.227755ZOf note, in the S/G2 phases of the cell cycle BRCA1 promotes phosphatase PP4C-dependent 53BP1 dephosphorylation and RIF1 release (Isono et al., >>2017<<), promoting end resection and directing repair toward HDR.nodeID://b975552122024-03-29T10:23:08.227755ZIn yeast, the SMARCAD1-ortholog Fun30 also acts on the Rad9-barrier, promoting long-range resection (Chen et al., 2012; Eapen et al., >>2012<<; Bantele et al., 2017).nodeID://b975552502024-03-29T10:23:08.227755ZIn this scenario, it is also important to mention that a recent work has reported that high levels of DNA:RNA hybrids at DSBs, due to the inactivation of human RNA binding protein HNRNPD, limit DSB resection, and HDR (Alfano et al., >>2019<<).nodeID://b975552452024-03-29T10:23:08.227755ZAlthough DNA:RNA hybrids might not antagonize DSB resection initiation, they need to be dismantled by specific helicases or processed by RNases, allowing the HDR repair to proceed (Li et al., 2016; Ohle et al., 2016; Cohen et al., >>2018<<). Interestingly, the RNase EXOSC10, a catalytic subunit of the RNA exosome complex, has been recently involved to clear DNA:nodeID://b6657778982024-03-29T10:23:08.227755Z2nodeID://b975551662024-03-29T10:23:08.227755ZAccording to several in vivo results, current models support a fundamental role of chromatin remodelers to mobilize and/or dissociate nucleosomes 1-2 kb nearby a DSB, creating the entry-space for repair factors (Shim et al., >>2007<<; Price and D'Andrea, 2013;Clouaire and Legube, 2019; Figure 1D).nodeID://b975551992024-03-29T10:23:08.227755ZInterestingly, it has been shown that Rad9 accumulates at DSB ends in yeast cells lacking SAE2, blocking resection initiation by Dna2-Sgs1 (Bonetti et al., >>2015<<; Ferrari et al., 2015; Yu et al., 2018).nodeID://b975551732024-03-29T10:23:08.227755ZIndeed, KU-bound DSB ends are resistant to Exo1 and Dna2 processing (Shim et al., 2010; Symington, 2016; Wang et al., >>2018<<), reducing recombination DNA repair by micro-homology mediated end joining (MMEJ, also called alternative end-joining or alt-EJ in higher eukaryotes) and single strand annealing (SSA) mechanisms (Symington, 2016).nodeID://b975552082024-03-29T10:23:08.227755Zof 53BP1, but also of its downstream effectors was shown to increase DNA damage tolerance of cancer-prone BRCA1−/− cells, most likely potentiating error prone HR pathways and increasing genome instability (Setiaputra and Durocher, >>2019<<).nodeID://b975552462024-03-29T10:23:08.227755Zof the RNA exosome complex, has been recently involved to clear DNA:RNA hybrids at DSBs, preventing hyper-resection and coupling the nucleolytic processing with deposition of RPA and HDR repair in human cells (Domingo-Prim et al., >>2019<<). Similarly, the accumulation of hybrids in cells depleted of Senataxin, a DNA/RNA helicase with R-loop-resolving activity, counteracts the binding of RAD51 and stimulates that of 53BP1 (Cohen et al., 2018), leading to illegitimate repairnodeID://b975552152024-03-29T10:23:08.227755ZFor example, in human cells the 5′−3′ translocase HELB limits EXO1 and DNA2/BLM nuclease activity (Tkac et al., >>2016<<).nodeID://b975552202024-03-29T10:23:08.227755ZAccordingly, a reduction of DNA transcription nearby a DSB has been detected in both yeast (Lee et al., 2000; Manfrini et al., 2015) and mammals (Kruhlak et al., 2007; Chou et al., >>2010<<; Shanbhag et al., 2010; Pankotai et al., 2012; Kakarougkas et al., 2014; Ui et al., 2015; Awwad et al., 2017; Iannelli et al., 2017; Vitor et al., 2019).nodeID://b975551742024-03-29T10:23:08.227755Z2016; Wang et al., 2018), reducing recombination DNA repair by micro-homology mediated end joining (MMEJ, also called alternative end-joining or alt-EJ in higher eukaryotes) and single strand annealing (SSA) mechanisms (Symington, >>2016<<). In yeast, KU-dependent resection barrier is predominant in G1 phase (Clerici et al., 2008), when MRX-Sae2 is not activated by CDK1, or in the absence of functional MRX complex or Sae2 (Mimitou and Symington, 2010).nodeID://b975551692024-03-29T10:23:08.227755Zku-dependent barriernodeID://b975551432024-03-29T10:23:08.227755Zresection barrier dramatically reduces the effectiveness of the treatment on BRCA1 defective cells, possibly leading to genome instability, poor prognosis, and cancer relapse (Lord and Ashworth, 2017; Setiaputra and Durocher, >>2019<<).nodeID://b975551812024-03-29T10:23:08.227755ZBy this model, the short-range resection through the Mre11 complex, together with Sae2/CTIP, is responsible for KU removal from the ends (Chanut et al., 2016; Symington, >>2016<<), leading to a more complex and functional interplay between NHEJ and HDR.nodeID://b975552162024-03-29T10:23:08.227755Zis the dna:rna hybrid a barrier to dsb resection?nodeID://b975552492024-03-29T10:23:08.227755Zwith R-loop-resolving activity, counteracts the binding of RAD51 and stimulates that of 53BP1 (Cohen et al., 2018), leading to illegitimate repair of broken ends and chromosome translocations (Brustel et al., 2018; Cohen et al., >>2018<<). In this scenario, it is also important to mention that a recent work has reported that high levels of DNA:nodeID://b975552232024-03-29T10:23:08.227755Zof DNA transcription nearby a DSB has been detected in both yeast (Lee et al., 2000; Manfrini et al., 2015) and mammals (Kruhlak et al., 2007; Chou et al., 2010; Shanbhag et al., 2010; Pankotai et al., 2012; Kakarougkas et al., >>2014<<; Ui et al., 2015; Awwad et al., 2017; Iannelli et al., 2017; Vitor et al., 2019).nodeID://b975551442024-03-29T10:23:08.227755Zdsb end processingnodeID://b975551822024-03-29T10:23:08.227755ZThis mechanism is also functional at one-ended DSB created at broken DNA replication forks in human cells (Chanut et al., >>2016<<). Moreover, depending upon the organisms, it is known that KU binding to DSB is finely regulated through neddylation (Brown et al., 2015), ubiquitylation (Postow et al., 2008; Feng and Chen, 2012), sumoylation (Hang et al., 2014),nodeID://b975551772024-03-29T10:23:08.227755ZAccordingly, deletion of KU70 partially suppressed the resection defect and sensitivity of sae2 or mre11 mutants to ionizing radiations (Bonetti et al., >>2010<<; Mimitou and Symington, 2010; Foster et al., 2011).nodeID://b975551512024-03-29T10:23:08.227755ZIndeed, in vivo and in vitro data (Neale et al., 2005; Shibata et al., 2014; Reginato et al., >>2017<<; Wang et al., 2017, 2018) have shown that Mre11 is recruited nearby the DSB ends and induces a nick on the 5′-end filament, creating the entry point for both Exo1 and Dna2-Sgs1/BLM (Figure 1D).nodeID://b975552192024-03-29T10:23:08.227755ZAccordingly, a reduction of DNA transcription nearby a DSB has been detected in both yeast (Lee et al., 2000; Manfrini et al., 2015) and mammals (Kruhlak et al., >>2007<<; Chou et al., 2010; Shanbhag et al., 2010; Pankotai et al., 2012; Kakarougkas et al., 2014; Ui et al., 2015; Awwad et al., 2017; Iannelli et al., 2017; Vitor et al., 2019).nodeID://b975552242024-03-29T10:23:08.227755Znearby a DSB has been detected in both yeast (Lee et al., 2000; Manfrini et al., 2015) and mammals (Kruhlak et al., 2007; Chou et al., 2010; Shanbhag et al., 2010; Pankotai et al., 2012; Kakarougkas et al., 2014; Ui et al., >>2015<<; Awwad et al., 2017; Iannelli et al., 2017; Vitor et al., 2019).nodeID://b975552312024-03-29T10:23:08.227755ZThe newly-synthetized non-coding RNAs at DSBs contribute to signal locally DNA damage and facilitate DNA repair (Francia et al., 2012; Wei et al., >>2012<<) and, by changing chromatin structure, also possibly contribute to repress canonical transcription (Burger et al., 2019).nodeID://b975551782024-03-29T10:23:08.227755ZAccordingly, deletion of KU70 partially suppressed the resection defect and sensitivity of sae2 or mre11 mutants to ionizing radiations (Bonetti et al., 2010; Mimitou and Symington, >>2010<<; Foster et al., 2011).nodeID://b6657778312024-03-29T10:23:08.227755Z3nodeID://b6657778342024-03-29T10:23:08.227755Z3nodeID://b975551522024-03-29T10:23:08.227755ZIndeed, in vivo and in vitro data (Neale et al., 2005; Shibata et al., 2014; Reginato et al., 2017; Wang et al., >>2017<<, 2018) have shown that Mre11 is recruited nearby the DSB ends and induces a nick on the 5′-end filament, creating the entry point for both Exo1 and Dna2-Sgs1/BLM (Figure 1D).nodeID://b975551472024-03-29T10:23:08.227755ZMoreover, an irreparable DSB can be eventually processed by telomerase and DNA polymerase alpha-primase (Pol α-Prim), together with other factors, leading to de novo telomere addition (Putnam and Kolodner, >>2017<<). Given the heterogeneity and complexity of the mechanisms involved, multiple levels of regulation have been identified, determining the repair of a DSB in the different cell cycle phases and chromatin context. Indeed, the uncontrollednodeID://b975551902024-03-29T10:23:08.227755ZMoreover, it has been shown that the AAA-ATPase p97 also cooperates for the removal of ubiquitinated KU from DSBs, after completion of end joining in human cells (van den Boom et al., >>2016<<). However, it is unknown whether these and/or other post-translational modifications of KU might also control DSB resection initiation through KU stability at the DNA ends.nodeID://b975551852024-03-29T10:23:08.227755ZMoreover, depending upon the organisms, it is known that KU binding to DSB is finely regulated through neddylation (Brown et al., 2015), ubiquitylation (Postow et al., 2008; Feng and Chen, >>2012<<), sumoylation (Hang et al., 2014), acetylation (Kim et al., 2014), and phosphorylation by DNA-PKs (Chan et al., 1999).nodeID://b6657778282024-03-29T10:23:08.227755Z4nodeID://b6657778252024-03-29T10:23:08.227755Z5nodeID://b6657778422024-03-29T10:23:08.227755Z3nodeID://b6657778362024-03-29T10:23:08.227755Z3nodeID://b6657778332024-03-29T10:23:08.227755Z3nodeID://b6657779002024-03-29T10:23:08.227755Z2nodeID://b6657779032024-03-29T10:23:08.227755Z2nodeID://b6657778502024-03-29T10:23:08.227755Z2nodeID://b975552322024-03-29T10:23:08.227755ZRNAs at DSBs contribute to signal locally DNA damage and facilitate DNA repair (Francia et al., 2012; Wei et al., 2012) and, by changing chromatin structure, also possibly contribute to repress canonical transcription (Burger et al., >>2019<<).nodeID://b975552272024-03-29T10:23:08.227755Zal., 2000; Manfrini et al., 2015) and mammals (Kruhlak et al., 2007; Chou et al., 2010; Shanbhag et al., 2010; Pankotai et al., 2012; Kakarougkas et al., 2014; Ui et al., 2015; Awwad et al., 2017; Iannelli et al., 2017; Vitor et al., >>2019<<). While canonical ongoing transcription is switched off in response to DSB formation, mounting evidence suggests that DSB ends may act as transcriptional promoter-like elements, priming the formation of long non-coding RNA specie.nodeID://b975552012024-03-29T10:23:08.227755ZInterestingly, it has been shown that Rad9 accumulates at DSB ends in yeast cells lacking SAE2, blocking resection initiation by Dna2-Sgs1 (Bonetti et al., 2015; Ferrari et al., 2015; Yu et al., >>2018<<). Moreover, resection initiation and capture of distant double-strand ends by CTIP is counteracted by 53BP1 in human cells (Guirouilh-Barbat et al., 2016).nodeID://b6657778472024-03-29T10:23:08.227755Z2nodeID://b6657778412024-03-29T10:23:08.227755Z3nodeID://b6657778442024-03-29T10:23:08.227755Z3nodeID://b975551482024-03-29T10:23:08.227755ZIndeed, the resection process generates an extended 3′-end ssDNA filament, which is then covered by RPA and the recombinase Rad51, depending on the sub-pathway (Symington, >>2016<<).nodeID://b6657779112024-03-29T10:23:08.227755Z2nodeID://b975551862024-03-29T10:23:08.227755ZMoreover, depending upon the organisms, it is known that KU binding to DSB is finely regulated through neddylation (Brown et al., 2015), ubiquitylation (Postow et al., 2008; Feng and Chen, 2012), sumoylation (Hang et al., >>2014<<), acetylation (Kim et al., 2014), and phosphorylation by DNA-PKs (Chan et al., 1999).nodeID://b6657779142024-03-29T10:23:08.227755Z2nodeID://b6657778382024-03-29T10:23:08.227755Z3nodeID://b975551602024-03-29T10:23:08.227755Zthe resection of DSBs frequently terminates at nucleosome (Mimitou et al., 2017); moreover, in vitro assays showed that DNA with reconstituted nucleosomes is resected by both Exo1 and Dna2-Sgs1 slower than naked DNA (Adkins et al., >>2013<<). Remarkably, other in vitro results showed that BLM is able to slide nucleosomes, if RPA is added in the assay, promoting DNA resection by EXO1 and DNA2 (Xue et al., 2019).nodeID://b975551552024-03-29T10:23:08.227755ZThis nick-dependent mechanism for resection is activated in S and G2/M phases through the CDK1-dependent phosphorylation of Sae2 (CTIP in human) (Huertas et al., >>2008<<; Huertas and Jackson, 2009), which associates with the Mre11 complex.nodeID://b975551932024-03-29T10:23:08.227755ZIn higher eukaryotes 53BP1 protects DNA ends from inappropriate 5′ hyper-resection, facilitating NHEJ, and error-free gene conversion at the expense of mutagenic SSA and alt-EJ (Ochs et al., >>2016<<). Of note, extended ssDNA can lead to increased recombination events between repeats that are frequently present in eukaryotic genomes, leading to increased hypermutagenesis at breakpoint junctions (Sinha et al., 2017).nodeID://b6657778522024-03-29T10:23:08.227755Z2nodeID://b6657778552024-03-29T10:23:08.227755Z2nodeID://b6657779052024-03-29T10:23:08.227755Z2nodeID://b6657779082024-03-29T10:23:08.227755Z2nodeID://b6657778462024-03-29T10:23:08.227755Z3nodeID://b6657778492024-03-29T10:23:08.227755Z2nodeID://b6657778632024-03-29T10:23:08.227755Z2nodeID://b6657779132024-03-29T10:23:08.227755Z2nodeID://b6657779162024-03-29T10:23:08.227755Z2nodeID://b6657778602024-03-29T10:23:08.227755Z2nodeID://b975552282024-03-29T10:23:08.227755ZIn this context, transcription requires MRN-dependent recruitment of RNAPII at DNA lesions (Michelini et al., >>2017<<) or, in the case of DSBs generated at promoter-proximal regions, cAbl-dependent tyrosine phosphorylation of RNAPII (Burger et al., 2019).nodeID://b975552022024-03-29T10:23:08.227755ZMoreover, resection initiation and capture of distant double-strand ends by CTIP is counteracted by 53BP1 in human cells (Guirouilh-Barbat et al., >>2016<<).nodeID://b975552352024-03-29T10:23:08.227755Zerror-free cNHEJ in human cells (Chakraborty et al., 2016), or HDR upon its assimilation into broken DNA by Rad52 protein, via an inverse strand exchange mechanism conserved from yeast to human (Keskin et al., 2014; Mazina et al., >>2017<<). There are also evidence that DNA:nodeID://b975552402024-03-29T10:23:08.227755Zgenerated at resected or minimally resected DNA ends, regulate the recruitment of RPA, BRCA1, BRCA2, RAD51, and RAD52, promoting HDR (Ohle et al., 2016; Cohen et al., 2018; D'Alessandro et al., 2018; Lu et al., 2018; Burger et al., >>2019<<; Domingo-Prim et al., 2019).nodeID://b6657778542024-03-29T10:23:08.227755Z2nodeID://b6657778572024-03-29T10:23:08.227755Z2nodeID://b6657779212024-03-29T10:23:08.227755Z2nodeID://b6657778712024-03-29T10:23:08.227755Z2nodeID://b975551562024-03-29T10:23:08.227755ZThis nick-dependent mechanism for resection is activated in S and G2/M phases through the CDK1-dependent phosphorylation of Sae2 (CTIP in human) (Huertas et al., 2008; Huertas and Jackson, >>2009<<), which associates with the Mre11 complex.nodeID://b975551942024-03-29T10:23:08.227755ZOf note, extended ssDNA can lead to increased recombination events between repeats that are frequently present in eukaryotic genomes, leading to increased hypermutagenesis at breakpoint junctions (Sinha et al., >>2017<<). Similarly to Rad9, 53BP1 recruitment requires the direct recognition of a DSB-specific histone code: it displays a strong binding affinity for the histone H4 constitutively mono- or di-methylated at the K20 (Botuyan et al., 2006) andnodeID://b975551892024-03-29T10:23:08.227755ZIn particular, neddylation primes ubiquitylation of KU in human cells, facilitating the release of the complex and associated factors from repaired DNA (Brown et al., >>2015<<). Moreover, it has been shown that the AAA-ATPase p97 also cooperates for the removal of ubiquitinated KU from DSBs, after completion of end joining in human cells (van den Boom et al., 2016). However, it is unknown whether these and/ornodeID://b6657778682024-03-29T10:23:08.227755Z2nodeID://b6657779182024-03-29T10:23:08.227755Z2nodeID://b6657778652024-03-29T10:23:08.227755Z2nodeID://b975551632024-03-29T10:23:08.227755ZZ histone variant, which promotes higher mobility and instability of the octamer (Adkins et al., >>2013<<). As such, the dynamic deposition of H2A.Z, together with other histone modifications, might facilitate the long-range resection by Exo1, with processing rate similar to naked DNA. On the other hand, it has been also shown that H2A.Z andnodeID://b6657778822024-03-29T10:23:08.227755Z2nodeID://b6657778592024-03-29T10:23:08.227755Z2nodeID://b6657778732024-03-29T10:23:08.227755Z2nodeID://b6657778762024-03-29T10:23:08.227755Z2nodeID://b6657778902024-03-29T10:23:08.227755Z2nodeID://b975552362024-03-29T10:23:08.227755ZThere are also evidence that DNA:RNA hybrids, generated at resected or minimally resected DNA ends, regulate the recruitment of RPA, BRCA1, BRCA2, RAD51, and RAD52, promoting HDR (Ohle et al., >>2016<<; Cohen et al., 2018; D'Alessandro et al., 2018; Lu et al., 2018; Burger et al., 2019; Domingo-Prim et al., 2019).nodeID://b975552102024-03-29T10:23:08.227755ZFor instance, the H2A ubiquitylation by BRCA1-BARD1 recruits the chromatin remodeler SMARCAD1, which then controls 53BP1 repositioning nearby a DSB and promotes long-range resection (Costelloe et al., 2012; Densham et al., >>2016<<). In yeast, the SMARCAD1-ortholog Fun30 also acts on the Rad9-barrier, promoting long-range resection (Chen et al., 2012; Eapen et al., 2012; Bantele et al., 2017). Moreover, the Slx4-Rtt107 complex counteracts Rad9 binding tonodeID://b975552052024-03-29T10:23:08.227755ZDSB-induced phosphorylation by ATM, 53BP1 recruits RIF1, the Shielding complex and the CST/ Pol α-Prim complex that fills in the resected DNA end, restoring dsDNA and allowing NHEJ [see a recent review here (Setiaputra and Durocher, >>2019<<)]. It is an open debate whether 53BP1 and its partners exert their function to limit resection directly as a physical barrier to nucleases or indirectly reconstituting processed DNA ends (Setiaputra and Durocher, 2019).nodeID://b6657778842024-03-29T10:23:08.227755Z2nodeID://b975552432024-03-29T10:23:08.227755ZAlthough DNA:RNA hybrids might not antagonize DSB resection initiation, they need to be dismantled by specific helicases or processed by RNases, allowing the HDR repair to proceed (Li et al., >>2016<<; Ohle et al., 2016; Cohen et al., 2018).nodeID://b6657778812024-03-29T10:23:08.227755Z2nodeID://b6657778782024-03-29T10:23:08.227755Z2nodeID://b975551642024-03-29T10:23:08.227755ZZ and H3.3 variants facilitate the loading of the NHEJ factors KU and XRCC4 onto DSB, thus limiting resection initiation (Xu et al., >>2012<<; Luijsterburg et al., 2016).nodeID://b975551592024-03-29T10:23:08.227755ZIndeed, in yeast the resection of DSBs frequently terminates at nucleosome (Mimitou et al., >>2017<<); moreover, in vitro assays showed that DNA with reconstituted nucleosomes is resected by both Exo1 and Dna2-Sgs1 slower than naked DNA (Adkins et al., 2013).nodeID://b975551972024-03-29T10:23:08.227755ZMoreover, 53BP1 oligomerization, mediated by DYNLL1, is essential for its recruitment to DSBs (Becker et al., >>2018<<; West et al., 2019).nodeID://b6657778952024-03-29T10:23:08.227755Z2nodeID://b6657778922024-03-29T10:23:08.227755Z2nodeID://b975551712024-03-29T10:23:08.227755ZIndeed, KU-bound DSB ends are resistant to Exo1 and Dna2 processing (Shim et al., >>2010<<; Symington, 2016; Wang et al., 2018), reducing recombination DNA repair by micro-homology mediated end joining (MMEJ, also called alternative end-joining or alt-EJ in higher eukaryotes) and single strand annealing (SSA) mechanismsnodeID://b6657778892024-03-29T10:23:08.227755Z2nodeID://b6657778862024-03-29T10:23:08.227755Z2nodeID://b975552062024-03-29T10:23:08.227755ZIt is an open debate whether 53BP1 and its partners exert their function to limit resection directly as a physical barrier to nucleases or indirectly reconstituting processed DNA ends (Setiaputra and Durocher, >>2019<<). Most likely, both hypotheses are true (Figure 2A).nodeID://b6657778972024-03-29T10:23:08.227755Z2nodeID://b975552392024-03-29T10:23:08.227755Zthat DNA:RNA hybrids, generated at resected or minimally resected DNA ends, regulate the recruitment of RPA, BRCA1, BRCA2, RAD51, and RAD52, promoting HDR (Ohle et al., 2016; Cohen et al., 2018; D'Alessandro et al., 2018; Lu et al., >>2018<<; Burger et al., 2019; Domingo-Prim et al., 2019).nodeID://b975552442024-03-29T10:23:08.227755ZAlthough DNA:RNA hybrids might not antagonize DSB resection initiation, they need to be dismantled by specific helicases or processed by RNases, allowing the HDR repair to proceed (Li et al., 2016; Ohle et al., >>2016<<; Cohen et al., 2018).nodeID://b6657778942024-03-29T10:23:08.227755Z2nodeID://b975552132024-03-29T10:23:08.227755ZIn yeast, the SMARCAD1-ortholog Fun30 also acts on the Rad9-barrier, promoting long-range resection (Chen et al., 2012; Eapen et al., 2012; Bantele et al., >>2017<<). Moreover, the Slx4-Rtt107 complex counteracts Rad9 binding to Dpb11/TOPBP1 and histones at the break, favoring DSB resection and HDR in yeast (Dibitetto et al., 2016).nodeID://b975551982024-03-29T10:23:08.227755ZMoreover, 53BP1 oligomerization, mediated by DYNLL1, is essential for its recruitment to DSBs (Becker et al., 2018; West et al., >>2019<<). Specifically, 53BP1 barrier is known to antagonize nucleases involved in the long-range resection, although its role to block resection initiation is supported by data in yeast, particularly in mutants affecting short-range resection.nodeID://b975551722024-03-29T10:23:08.227755ZIndeed, KU-bound DSB ends are resistant to Exo1 and Dna2 processing (Shim et al., 2010; Symington, >>2016<<; Wang et al., 2018), reducing recombination DNA repair by micro-homology mediated end joining (MMEJ, also called alternative end-joining or alt-EJ in higher eukaryotes) and single strand annealing (SSA) mechanisms (Symington, 2016).nodeID://b975551672024-03-29T10:23:08.227755Zin vivo results, current models support a fundamental role of chromatin remodelers to mobilize and/or dissociate nucleosomes 1-2 kb nearby a DSB, creating the entry-space for repair factors (Shim et al., 2007; Price and D'Andrea, >>2013<<;Clouaire and Legube, 2019; Figure 1D).nodeID://b975551412024-03-29T10:23:08.227755Zconclusive remarksnodeID://b6657778992024-03-29T10:23:08.227755Z2nodeID://b975552142024-03-29T10:23:08.227755ZMoreover, the Slx4-Rtt107 complex counteracts Rad9 binding to Dpb11/TOPBP1 and histones at the break, favoring DSB resection and HDR in yeast (Dibitetto et al., >>2016<<).nodeID://b975552092024-03-29T10:23:08.227755ZFor instance, the H2A ubiquitylation by BRCA1-BARD1 recruits the chromatin remodeler SMARCAD1, which then controls 53BP1 repositioning nearby a DSB and promotes long-range resection (Costelloe et al., >>2012<<; Densham et al., 2016).nodeID://b975552472024-03-29T10:23:08.227755ZSimilarly, the accumulation of hybrids in cells depleted of Senataxin, a DNA/RNA helicase with R-loop-resolving activity, counteracts the binding of RAD51 and stimulates that of 53BP1 (Cohen et al., >>2018<<), leading to illegitimate repair of broken ends and chromosome translocations (Brustel et al., 2018; Cohen et al., 2018).nodeID://b975552212024-03-29T10:23:08.227755ZAccordingly, a reduction of DNA transcription nearby a DSB has been detected in both yeast (Lee et al., 2000; Manfrini et al., 2015) and mammals (Kruhlak et al., 2007; Chou et al., 2010; Shanbhag et al., >>2010<<; Pankotai et al., 2012; Kakarougkas et al., 2014; Ui et al., 2015; Awwad et al., 2017; Iannelli et al., 2017; Vitor et al., 2019).nodeID://b975551682024-03-29T10:23:08.227755Zmodels support a fundamental role of chromatin remodelers to mobilize and/or dissociate nucleosomes 1-2 kb nearby a DSB, creating the entry-space for repair factors (Shim et al., 2007; Price and D'Andrea, 2013;Clouaire and Legube, >>2019<<; Figure 1D).nodeID://b975551422024-03-29T10:23:08.227755Zinactivation of the 53BP1-dependent resection barrier dramatically reduces the effectiveness of the treatment on BRCA1 defective cells, possibly leading to genome instability, poor prognosis, and cancer relapse (Lord and Ashworth, >>2017<<; Setiaputra and Durocher, 2019).nodeID://b975551802024-03-29T10:23:08.227755ZBy this model, the short-range resection through the Mre11 complex, together with Sae2/CTIP, is responsible for KU removal from the ends (Chanut et al., >>2016<<; Symington, 2016), leading to a more complex and functional interplay between NHEJ and HDR.nodeID://b975551752024-03-29T10:23:08.227755ZIn yeast, KU-dependent resection barrier is predominant in G1 phase (Clerici et al., >>2008<<), when MRX-Sae2 is not activated by CDK1, or in the absence of functional MRX complex or Sae2 (Mimitou and Symington, 2010).