@article{%a1.%Y_169,

title = {Guidelines for minimal information on cellular senescence experimentation in vivo},

author = {Ogrodnik M and Carlos Acosta J and Adams PD and {d'Adda di Fagagna F} and Baker DJ and Bishop CL and Chandra T and Collado M and Gil J and Gorgoulis V and Gruber F and Hara E and Jansen-Dürr P and Jurk D and Khosla S and Kirkland JL and Krizhanovsky V and Minamino T and Niedernhofer LJ and Passos JF and Ring NAR and Redl H and Robbins PD and Rodier F and Scharffetter-Kochanek K and Sedivy JM and Sikora E and Witwer K and von Zglinicki T and Yun MH and Grillari J and Demaria M},

url = {https://www.sciencedirect.com/science/article/pii/S0092867424006408?via%3Dihub},

doi = {10.1016/j.cell.2024.05.059},

year  = {2024},

date = {2024-08-19},

journal = {Cell},

volume = {187},

issue = {16},

pages = {4150-4175},

abstract = {Cellular senescence is a cell fate triggered in response to stress and is characterized by stable cell-cycle arrest and a hypersecretory state. It has diverse biological roles, ranging from tissue repair to chronic disease. The development of new tools to study senescence in vivo has paved the way for uncovering its physiological and pathological roles and testing senescent cells as a therapeutic target. However, the lack of specific and broadly applicable markers makes it difficult to identify and characterize senescent cells in tissues and living organisms. To address this, we provide practical guidelines called “minimum information for cellular senescence experimentation in vivo” (MICSE). It presents an overview of senescence markers in rodent tissues, transgenic models, non-mammalian systems, human tissues, and tumors and their use in the identification and specification of senescent cells. These guidelines provide a uniform, state-of-the-art, and accessible toolset to improve our understanding of cellular senescence in vivo.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_150,

title = {Judith Campisi (1948-2024)},

author = {Wiley CD and Hara E and {d'Adda di Fagagna F}},

url = {https://www.nature.com/articles/s43587-024-00603-5},

doi = {10.1038/s43587-024-00603-5},

year  = {2024},

date = {2024-03-18},

urldate = {2024-03-18},

journal = {Nature Aging},

volume = {4},

number = {435-436},

issue = {4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y_131,

title = {Alternative lengthening of telomeres (ALT) cells viability is dependent on C-rich telomeric RNAs},

author = {Rosso I and Jones-Weinert C and Rossiello F and Cabrini M and Brambillasca S and Munoz-Sagredo L and Lavagnino Z and Martini E and Tedone E and Garre' M and Aguado J and Parazzoli D and Mione M and Shay JW and Mercurio C and {d'Adda di Fagagna F}},

url = {https://www.nature.com/articles/s41467-023-42831-0},

doi = {10.1038/s41467-023-42831-0},

year  = {2023},

date = {2023-05-10},

journal = {Nature communications},

volume = {14},

issue = {1},

pages = {7086},

abstract = {Alternative lengthening of telomeres (ALT) is a telomere maintenance mechanism activated in ~10-15% of cancers, characterized by telomeric damage. Telomeric damage-induced long non-coding RNAs (dilncRNAs) are transcribed at dysfunctional telomeres and contribute to telomeric DNA damage response (DDR) activation and repair. Here we observed that telomeric dilncRNAs are preferentially elevated in ALT cells. Inhibition of C-rich (teloC) dilncRNAs with antisense oligonucleotides leads to DNA replication stress responses, increased genomic instability, and apoptosis induction selectively in ALT cells. Cell death is dependent on DNA replication and is increased by DNA replication stress. Mechanistically, teloC dilncRNA inhibition reduces RAD51 and 53BP1 recruitment to telomeres, boosts the engagement of BIR machinery, and increases C-circles and telomeric sister chromatid exchanges, without increasing telomeric non-S phase synthesis. These results indicate that teloC dilncRNA is necessary for a coordinated recruitment of DDR factors to ALT telomeres and it is essential for ALT cancer cells survival.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_70,

title = {Colorectal cancer patient-derived organoids and cell lines harboring ATRX and/or DAXX mutations lack Alternative Lengthening of Telomeres (ALT)},

author = {Falcinelli M and Dell'Omo G and Grassi E and Mariella E and Leto SM and Scardellato S and Lorenzato A and Arena S and Bertotti A and Trusolino L and Bardelli A and {d'Adda di Fagagna F}},

url = {https://www.nature.com/articles/s41419-023-05640-3},

doi = {10.1038/s41419-023-05640-3},

year  = {2023},

date = {2023-03-01},

journal = {Cell death and disease},

volume = {14},

issue = {2},

pages = {96},

abstract = {Telomere maintenance is necessary to maintain cancer cell unlimited viability. However, the mechanisms maintaining telomere length in colorectal cancer (CRC) have not been extensively investigated. Telomere maintenance mechanisms (TMM) include the re-expression of telomerase or alternative lengthening of telomeres (ALT). ALT is genetically associated with somatic alterations in alpha-thalassemia/mental retardation X-linked (ATRX) and death domain-associated protein (DAXX) genes. Cells displaying ALT present distinctive features including C-circles made of telomeric DNA, long and heterogenous telomeric tracts, and telomeric DNA co-localized with promyelocytic leukemia (PML) bodies forming so-called ALT-associated PML bodies (APBs). Here, we identified mutations in ATRX and/or DAXX genes in an extensive collection of CRC samples including 119 patient-derived organoids (PDOs) and 232 established CRC cell lines. C-circles measured in CRC PDOs and cell lines showed low levels overall. We also observed that CRC PDOs and cell lines did not display a significant accumulation of APBs or long telomeres with no appreciable differences between wild-type and mutated ATRX/DAXX samples. Overall, our extensive analyses indicate that CRC is not prone to engage ALT, even when carrying genetic lesions in ATRX and/or DAXX, and support the notion that ATRX/DAXX genomic footprints are not reliable predictors of ALT.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Y,

title = {SARS-CoV-2 infection induces DNA damage, through CHK1 degradation and impaired 53BP1 recruitment, and cellular senescence},

author = {Gioia U and Tavella S and Martínez-Orellana P and Cicio G and Colliva A and Ceccon M and Cabrini M and Henriques AC and Fumagalli V and Paldino A and Presot E and Rajasekharan S and Iacomino N and Pisati F and Matti V and Sepe S and Conte MI and Barozzi S and Lavagnino Z and Carletti T and Volpe MC and Cavalcante P and Iannacone M and Rampazzo C and Bussani R and Tripodo C and Zacchigna S and Marcello A and {d'Adda di Fagagna F} },

url = {https://www.nature.com/articles/s41556-023-01096-x},

doi = {10.1038/s41556-023-01096-x},

year  = {2023},

date = {2023-08-08},

urldate = {2023-08-08},

journal = {Nature cell biology},

volume = {25},

issue = {4},

pages = {550-564},

abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the RNA virus responsible for the coronavirus disease 2019 (COVID-19) pandemic. Although SARS-CoV-2 was reported to alter several cellular pathways, its impact on DNA integrity and the mechanisms involved remain unknown. Here we show that SARS-CoV-2 causes DNA damage and elicits an altered DNA damage response. Mechanistically, SARS-CoV-2 proteins ORF6 and NSP13 cause degradation of the DNA damage response kinase CHK1 through proteasome and autophagy, respectively. CHK1 loss leads to deoxynucleoside triphosphate (dNTP) shortage, causing impaired S-phase progression, DNA damage, pro-inflammatory pathways activation and cellular senescence. Supplementation of deoxynucleosides reduces that. Furthermore, SARS-CoV-2 N-protein impairs 53BP1 focal recruitment by interfering with damage-induced long non-coding RNAs, thus reducing DNA repair. Key observations are recapitulated in SARS-CoV-2-infected mice and patients with COVID-19. We propose that SARS-CoV-2, by boosting ribonucleoside triphosphate levels to promote its replication at the expense of dNTPs and by hijacking damage-induced long non-coding RNAs' biology, threatens genome integrity and causes altered DNA damage response activation, induction of inflammation and cellular senescence.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Yb_114,

title = {Tissue fluidification promotes a cGAS-STING cytosolic DNA response in invasive breast cancer},

author = {Frittoli E and Palamidessi A and Iannelli F and Zanardi F and Villa S and Barzaghi L and Abdo H and Cancila V and Beznoussenko GV and Della Chiara G and Pagani M and Malinverno C and Bhattacharya D and Pisati F and Yu W and Galimberti V and Bonizzi G and Martini E and Mironov AA and Gioia U and Ascione F and Li Q and Havas K and Magni S and Lavagnino Z and Pennacchio FA and Maiuri P and Caponi S and Mattarelli M and Martino S and {d'Adda di Fagagna F} and Rossi C and Lucioni M and Tancredi R and Pedrazzoli P and Vecchione A and Petrini C and Ferrari F and Lanzuolo C and Bertalot G and Nader G and Foiani M and Piel M and Cerbino R and Giavazzi F and Tripodo C and Scita G },

url = {https://www.nature.com/articles/s41563-022-01431-x},

doi = {10.1038/s41563-022-01431-x},

year  = {2023},

date = {2023-08-08},

journal = {Nature materials},

volume = {22},

issue = {5},

pages = {644-655},

abstract = {The process in which locally confined epithelial malignancies progressively evolve into invasive cancers is often promoted by unjamming, a phase transition from a solid-like to a liquid-like state, which occurs in various tissues. Whether this tissue-level mechanical transition impacts phenotypes during carcinoma progression remains unclear. Here we report that the large fluctuations in cell density that accompany unjamming result in repeated mechanical deformations of cells and nuclei. This triggers a cellular mechano-protective mechanism involving an increase in nuclear size and rigidity, heterochromatin redistribution and remodelling of the perinuclear actin architecture into actin rings. The chronic strains and stresses associated with unjamming together with the reduction of Lamin B1 levels eventually result in DNA damage and nuclear envelope ruptures, with the release of cytosolic DNA that activates a cGAS-STING (cyclic GMP-AMP synthase-signalling adaptor stimulator of interferon genes)-dependent cytosolic DNA response gene program. This mechanically driven transcriptional rewiring ultimately alters the cell state, with the emergence of malignant traits, including epithelial-to-mesenchymal plasticity phenotypes and chemoresistance in invasive breast carcinoma.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Ybb,

title = {BRCA1 deficiency specific base substitution mutagenesis is dependent on translesion synthesis and regulated by 53BP1},

author = {Chen D and Gervai JZ and Poti A and Nemeth E and Szeltner Z and Szikriszt B and Gyure Z and Zamborszky J and Ceccon M and {d'Adda di Fagagna F} and Szallasi Z and Richardson AL and Szuts D},

url = {https://www.nature.com/articles/s41467-021-27872-7},

doi = {10.1038/s41467-021-27872-7},

year  = {2022},

date = {2022-02-25},

journal = {Nature communications},

volume = {13},

issue = {1},

pages = {226},

abstract = {Defects in BRCA1, BRCA2 and other genes of the homology-dependent DNA repair (HR) pathway cause an elevated rate of mutagenesis, eliciting specific mutation patterns including COSMIC signature SBS3. Using genome sequencing of knock-out cell lines we show that Y family translesion synthesis (TLS) polymerases contribute to the spontaneous generation of base substitution and short insertion/deletion mutations in BRCA1 deficient cells, and that TLS on DNA adducts is increased in BRCA1 and BRCA2 mutants. The inactivation of 53BP1 in BRCA1 mutant cells markedly reduces TLS-specific mutagenesis, and rescues the deficiency of template switch-mediated gene conversions in the immunoglobulin V locus of BRCA1 mutant chicken DT40 cells. 53BP1 also promotes TLS in human cellular extracts in vitro. Our results show that HR deficiency-specific mutagenesis is largely caused by TLS, and suggest a function for 53BP1 in regulating the choice between TLS and error-free template switching in replicative DNA damage bypass.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb_62,

title = {DNA damage response at telomeres boosts the transcription of SARS-CoV-2 receptor ACE2 during aging.},

author = {Sepe S and Rossiello F and Cancila V and Iannelli F and Matti V and Cicio G and Cabrini M and Marinelli E and Alabi BR and di Lillo A and Di Napoli A and Shay JW and Tripodo C and {d'Adda di Fagagna F}},

url = {https://www.embopress.org/doi/full/10.15252/embr.202153658},

doi = {10.15252/embr.202153658},

year  = {2022},

date = {2022-02-04},

urldate = {2021-12-06},

journal = {EMBO Reports},

abstract = {The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus disease 2019 (COVID-19), known to be more common in the elderly, who also show more severe symptoms and are at higher risk of hospitalization and death. Here, we show that the expression of the angiotensin converting enzyme 2 (ACE2), the SARS-CoV-2 cell receptor, increases during aging in mouse and human lungs. ACE2 expression increases upon telomere shortening or dysfunction in both cultured mammalian cells and in vivo in mice. This increase is controlled at the transcriptional level, and Ace2 promoter activity is DNA damage response (DDR)-dependent. Both pharmacological global DDR inhibition of ATM kinase activity and selective telomeric DDR inhibition by the use of antisense oligonucleotides prevent Ace2 upregulation following telomere damage in cultured cells and in mice. We propose that during aging telomere dysfunction due to telomeric shortening or damage triggers DDR activation and this causes the upregulation of ACE2, the SARS-CoV-2 cell receptor, thus contributing to make the elderly more susceptible to the infection.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1.%Ybk,

title = {Telomere dysfunction in ageing and age-related diseases},

author = {Rossiello F and Jurk D and Passos JF and {d'Adda di Fagagna F}},

url = {https://www.nature.com/articles/s41556-022-00842-x},

doi = {10.1038/s41556-022-00842-x},

year  = {2022},

date = {2022-03-21},

volume = {24},

issue = {2},

pages = {135-147},

abstract = {Ageing organisms accumulate senescent cells that are thought to contribute to body dysfunction. Telomere shortening and damage are recognized causes of cellular senescence and ageing. Several human conditions associated with normal ageing are precipitated by accelerated telomere dysfunction. Here, we systematize a large body of evidence and propose a coherent perspective to recognize the broad contribution of telomeric dysfunction to human pathologies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_131,

title = {A Role for Human DNA Polymerase lambda in Alternative Lengthening of Telomeres},

author = {Mentegari E and Bertoletti F and Kissova M and Zucca E and Galli S and Tagliavini G and Garbelli A and Maffia A and Bione S and Ferrari E and {d'Adda di Fagagna F} and Francia S and Sabbioneda S and Chen LY and Lingner J and Bergoglio V and Hoffmann JS and Hubscher U and Crespan E and Maga G},

url = {https://www.mdpi.com/1422-0067/22/5/2365},

doi = {10.3390/ijms22052365},

year  = {2021},

date = {2021-03-09},

journal = {International journal of molecular sciences},

volume = {22},

number = {5},

pages = {2365},

abstract = {Telomerase negative cancer cell types use the Alternative Lengthening of Telomeres (ALT) pathway to elongate telomeres ends. Here, we show that silencing human DNA polymerase (Pol lambda) in ALT cells represses ALT activity and induces telomeric stress. In addition, replication stress in the absence of Pol lambda, strongly affects the survival of ALT cells. In vitro, Pol lambda can promote annealing of even a single G-rich telomeric repeat to its complementary strand and use it to prime DNA synthesis. The noncoding telomeric repeat containing RNA TERRA and replication protein A negatively regulate this activity, while the Protection of Telomeres protein 1 (POT1)/TPP1 heterodimer stimulates Pol lambda. Pol lambda associates with telomeres and colocalizes with TPP1 in cells. In summary, our data suggest a role of Pol lambda in the maintenance of telomeres by the ALT mechanism.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y__495,

title = {Cellular senescence in ageing: from mechanisms to therapeutic opportunities},

author = {Di Micco R and Krizhanovsky V and Baker D and {d'Adda di Fagagna F}},

url = {https://www.nature.com/articles/s41580-020-00314-w},

doi = {10.1038/s41580-020-00314-w},

year  = {2021},

date = {2021-03-09},

journal = {Nature reviews. Molecular cell biology},

volume = {22},

number = {2},

pages = {75-95},

abstract = {Cellular senescence, first described in vitro in 1961, has become a focus for biotech companies that target it to ameliorate a variety of human conditions. Eminently characterized by a permanent proliferation arrest, cellular senescence occurs in response to endogenous and exogenous stresses, including telomere dysfunction, oncogene activation and persistent DNA damage. Cellular senescence can also be a controlled programme occurring in diverse biological processes, including embryonic development. Senescent cell extrinsic activities, broadly related to the activation of a senescence-associated secretory phenotype, amplify the impact of cell-intrinsic proliferative arrest and contribute to impaired tissue regeneration, chronic age-associated diseases and organismal ageing. This Review discusses the mechanisms and modulators of cellular senescence establishment and induction of a senescence-associated secretory phenotype, and provides an overview of cellular senescence as an emerging opportunity to intervene through senolytic and senomorphic therapies in ageing and ageing-associated diseases.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_465,

title = {DNA Damage Triggers a New Phase in Neurodegeneration},

author = {Pessina F and Gioia U and Brandi O and Farina S and Ceccon M and Francia S and {d'Adda di Fagagna F}},

url = {https://www.sciencedirect.com/science/article/pii/S0168952520302420?via%3Dihub},

doi = {10.1016/j.tig.2020.09.006},

year  = {2021},

date = {2021-03-03},

journal = {Trends in genetics },

volume = {37},

number = {4},

pages = {337-354},

abstract = {Subcellular compartmentalization contributes to the organization of a plethora of molecular events occurring within cells. This can be achieved in membraneless organelles generated through liquid-liquid phase separation (LLPS), a demixing process that separates and concentrates cellular reactions. RNA is often a critical factor in mediating LLPS. Recent evidence indicates that DNA damage response foci are membraneless structures formed via LLPS and modulated by noncoding transcripts synthesized at DNA damage sites. Neurodegeneration is often associated with DNA damage, and dysfunctional LLPS events can lead to the formation of toxic aggregates. In this review, we discuss those gene products involved in neurodegeneration that undergo LLPS and their involvement in the DNA damage response.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y__491,

title = {DROSHA is recruited to DNA damage sites by the MRN complex to promote non-homologous end-joining},

author = {Cabrini M and Roncador M and Galbiati A and Cipolla L and Maffia A and Iannelli F and Sabbioneda S and {d'Adda di Fagagna F} and Francia S},

url = {https://jcs.biologists.org/content/early/2021/02/04/jcs.249706.long},

doi = {10.1242/jcs.249706},

year  = {2021},

date = {2021-03-09},

journal = {Journal of cell science},

volume = {134},

number = {6},

pages = {jcs249706},

abstract = {The DNA damage response (DDR) is the signaling cascade that recognizes DNA double-strand breaks (DSB) and promotes their resolution via the DNA repair pathways of Non-Homologous End Joining (NHEJ) or Homologous Recombination (HR). We and others have shown that DDR activation requires DROSHA. However, whether DROSHA exerts its functions by associating with damage sites, what controls its recruitment and how DROSHA influences DNA repair, remains poorly understood. Here we show that DROSHA associates to DSBs independently from transcription. Neither H2AX, nor ATM nor DNA-PK kinase activities are required for its recruitment to break site. Rather, DROSHA interacts with RAD50 and inhibition of MRN by Mirin treatment abolishes this interaction. MRN inactivation by RAD50 knockdown or mirin treatment prevents DROSHA recruitment to DSB and, as a consequence, also 53BP1 recruitment. During DNA repair, DROSHA inactivation reduces NHEJ and boosts HR frequency. Indeed, DROSHA knockdown also increase the association of downstream HR factors such as RAD51 to DNA ends. Overall, our results demonstrate that DROSHA is recruited at DSBs by the MRN complex and direct DNA repair toward NHEJ.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y__503,

title = {MRE11-RAD50-NBS1 Complex Is Sufficient to Promote Transcription by RNA Polymerase II at Double-Strand Breaks by Melting DNA Ends. },

author = {Sharma S and Anand R and Zhang X and Francia S and Michelini F and Galbiati A and Williams H and Ronato DA and Masson JY and Rothenberg E and Cejka P and {d'Adda di Fagagna F}},

url = {https://www.cell.com/cell-reports/fulltext/S2211-1247(20)31554-0?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2211124720315540%3Fshowall%3Dtrue},

doi = {10.1016/j.celrep.2020.108565},

year  = {2021},

date = {2021-03-09},

journal = {Cell reports},

volume = {34},

number = {1},

pages = {108565},

abstract = {The MRE11-RAD50-NBS1 (MRN) complex supports the synthesis of damage-induced long non-coding RNA (dilncRNA) by RNA polymerase II (RNAPII) from DNA double-strand breaks (DSBs) by an unknown mechanism. Here, we show that recombinant human MRN and native RNAPII are sufficient to reconstitute a minimal functional transcriptional apparatus at DSBs. MRN recruits and stabilizes RNAPII at DSBs. Unexpectedly, transcription is promoted independently from MRN nuclease activities. Rather, transcription depends on the ability of MRN to melt DNA ends, as shown by the use of MRN mutants and specific allosteric inhibitors. Single-molecule FRET assays with wild-type and mutant MRN show a tight correlation between the ability to melt DNA ends and to promote transcription. The addition of RPA enhances MRN-mediated transcription, and unpaired DNA ends allow MRN-independent transcription by RNAPII. These results support a model in which MRN generates single-strand DNA ends that favor the initiation of transcription by RNAPII.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb,

title = {Telomere damage promotes vascular smooth muscle cell senescence and immune cell recruitment after vessel injury},

author = {Uryga AK and Grootaert MOJ and Garrido AM and Oc S and Foote K and Chappell J and Finigan A and Rossiello F and {d'Adda di Fagagna F} and Aravani D and Jorgensen HF and Bennett MR},

url = {https://www.nature.com/articles/s42003-021-02123-z},

doi = {10.1038/s42003-021-02123-z},

year  = {2021},

date = {2021-06-08},

journal = {Communications biology},

volume = {4},

number = {1},

pages = {611},

abstract = {Accumulation of vascular smooth muscle cells (VSMCs) is a hallmark of multiple vascular pathologies, including following neointimal formation after injury and atherosclerosis. However, human VSMCs in advanced atherosclerotic lesions show reduced cell proliferation, extensive and persistent DNA damage, and features of premature cell senescence. Here, we report that stress-induced premature senescence (SIPS) and stable expression of a telomeric repeat-binding factor 2 protein mutant (TRF2T188A) induce senescence of human VSMCs, associated with persistent telomeric DNA damage. VSMC senescence is associated with formation of micronuclei, activation of cGAS-STING cytoplasmic sensing, and induction of multiple pro-inflammatory cytokines. VSMC-specific TRF2T188A expression in a multicolor clonal VSMC-tracking mouse model shows no change in VSMC clonal patches after injury, but an increase in neointima formation, outward remodeling, senescence and immune/inflammatory cell infiltration or retention. We suggest that persistent telomere damage in VSMCs inducing cell senescence has a major role in driving persistent inflammation in vascular disease.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Yb_66,

title = {The prolyl-isomerase PIN1 is essential for nuclear Lamin-B structure and function and protects heterochromatin under mechanical stress},

author = {Napoletano F and Ferrari Bravo G and Voto IAP and Santin A and Celora L and Campaner E and Dezi C and Bertossi A and Valentino E and Santorsola M and Rustighi A and Fajner V and Maspero E and Ansaloni F and Cancila V and Valenti CF and Santo M and Artimagnella OB and Finaurini S and Gioia U and Polo S and Sanges R and Tripodo C and Mallamaci A and Gustincich S and {d'Adda di Fagagna F} and Mantovani F and Specchia V and Del Sal G},

url = {https://www.cell.com/cell-reports/fulltext/S2211-1247(21)01141-4?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2211124721011414%3Fshowall%3Dtrue#%20},

doi = {10.1016/j.celrep.2021.109694},

year  = {2021},

date = {2021-12-14},

journal = {Cell reports},

volume = {36},

number = {11},

pages = {109694},

abstract = {Chromatin organization plays a crucial role in tissue homeostasis. Heterochromatin relaxation and consequent unscheduled mobilization of transposable elements (TEs) are emerging as key contributors of aging and aging-related pathologies, including Alzheimer's disease (AD) and cancer. However, the mechanisms governing heterochromatin maintenance or its relaxation in pathological conditions remain poorly understood. Here we show that PIN1, the only phosphorylation-specific cis/trans prolyl isomerase, whose loss is associated with premature aging and AD, is essential to preserve heterochromatin. We demonstrate that this PIN1 function is conserved from Drosophila to humans and prevents TE mobilization-dependent neurodegeneration and cognitive defects. Mechanistically, PIN1 maintains nuclear type-B Lamin structure and anchoring function for heterochromatin protein 1α (HP1α). This mechanism prevents nuclear envelope alterations and heterochromatin relaxation under mechanical stress, which is a key contributor to aging-related pathologies.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y__487,

title = {Detection of Telomeric DNA: RNA Hybrids Using TeloDRIP-qPCR. },

author = {Rosso I and {d'Adda di Fagagna F}},

url = {https://www.mdpi.com/1422-0067/21/24/9774},

doi = {10.3390/ijms21249774 },

year  = {2020},

date = {2020-12-01},

journal = {International journal of molecular sciences},

volume = {21},

number = {24},

pages = {9774},

abstract = {Because of their intrinsic characteristics, telomeres are genomic loci that pose significant problems during the replication of the genome. In particular, it has been observed that telomeres that are maintained in cancer cells by the alternative mechanism of the lengthening of telomeres (ALT) harbor higher levels of replicative stress compared with telomerase-positive cancer cells. R-loops are three-stranded structures formed by a DNA:RNA hybrid and a displaced ssDNA. Emerging evidence suggests that controlling the levels of R-loops at ALT telomeres is critical for telomere maintenance. In fact, on the one hand, they favor telomere recombination, but on the other, they are a source of detrimental replicative stress. DRIP (DNA:RNA immunoprecipitation) is the main technique used for the detection of R-loops, and it is based on the use of the S9.6 antibody, which recognizes preferentially DNA:RNA hybrids in a sequence-independent manner. The detection of DNA:RNA hybrids in repetitive sequences such as telomeres requires some additional precautions as a result of their repetitive nature. Here, we share an optimized protocol for the detection of telomeric DNA:RNA hybrids, and we demonstrate its application in an ALT and in a telomerase-positive cell line. We demonstrate that ALT telomeres bear higher levels of DNA:RNA hybrids, and we propose this method as a reliable way to detect them in telomeres.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_421,

title = {Telomere transcription in ageing},

author = {Aguado J and {d'Adda di Fagagna F} and Wolvetang E},

url = {https://www.sciencedirect.com/science/article/pii/S1568163720302506?via%3Dihub},

doi = {10.1016/j.arr.2020.101115},

year  = {2020},

date = {2020-01-01},

journal = {Ageing research reviews},

volume = {62},

pages = {101115},

abstract = {Telomeres, the ends of eukaryotic chromosomes, play a central role in the control of cellular senescence and organismal ageing and need to be protected in order to avoid being recognised as damaged DNA and activate DNA damage response pathways. Dysfunctional telomeres arise from critically short telomeres or altered telomere structures, which ultimately lead to replicative cellular senescence and chromosome instability: both hallmarks of ageing. The observation that telomeres are transcribed led to the discovery that telomeric transcripts play important roles in chromosome end protection and genome stability maintenance. Recent evidence indicates that particular long non-coding (nc)RNAs transcribed at telomeres, namely TElomeric Repeat-containing RNA (TERRA) and telomeric damage-induced long ncRNAs (tdilncRNA), play key roles in age-related pathways by actively orchestrating the mechanisms known to regulate telomere length, chromosome end protection and DNA damage signalling. Here, we provide a comprehensive overview of the telomere transcriptome, outlining how it functions as a regulatory platform with essential functions in safeguarding telomere integrity and stability. We next review emerging antisense oligonucleotides therapeutic strategies that target telomeric ncRNAs and discuss their potential for ameliorating ageing and age-related diseases. Altogether, this review provides insights on the biological relevance of telomere transcription mechanisms in human ageing physiology and pathology.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_140,

title = {DNA Damage In Situ Ligation Followed by Proximity Ligation Assay (DI-PLA).},

author = {Galbiati A and {d'Adda di Fagagna F}},

editor = {Demaria M},

url = {https://link.springer.com/protocol/10.1007%2F978-1-4939-8931-7_2#citeas},

doi = {10.1007/978-1-4939-8931-7_2},

year  = {2019},

date = {2019-02-13},

journal = {Methods in Molecular Biology - Cellular Senescence Demaria M (eds)},

volume = {1896},

pages = {11-20},

abstract = {Cells have evolved DNA repair mechanisms to maintain their genetic information unaltered and a DNA damage response pathway that coordinates DNA repair with several cellular events. Despite a clear role for DNA damage in the form of DNA double-strand breaks (DSBs) in several cellular processes, the most commonly used methods to detect DNA lesions are indirect, and rely on antibody-based recognition of DNA damage-associated factors, leaving several important questions unanswered. Differently, here we describe DNA damage In situ ligation followed by Proximity Ligation Assay (DI-PLA), that allows sensitive detection of physical DSBs in fixed cells, through direct labeling of the DSBs with biotinylated oligonucleotides, and subsequent signal amplification by PLA between biotin and a partner protein in the proximity of the DNA break.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_59,

title = {Functional transcription promoters at DNA double-strand breaks mediate RNA-driven phase separation of damage-response factors.},

author = {Pessina F and Giavazzi F and Yin Y and Gioia U and Vitelli V and Galbiati A and Barozzi S and Garre M and Oldani A and Flaus A and Cerbino R and Parazzoli D and Rothenberg E and {d'Adda di Fagagna F}},

url = {https://www.nature.com/articles/s41556-019-0392-4},

doi = {10.1038/s41556-019-0392-4},

year  = {2019},

date = {2019-10-30},

journal = {Nature cell biology},

volume = {21},

number = {10},

pages = {1286-1299},

abstract = {Damage-induced long non-coding RNAs (dilncRNA) synthesized at DNA double-strand breaks (DSBs) by RNA polymerase II are necessary for DNA-damage-response (DDR) focus formation. We demonstrate that induction of DSBs results in the assembly of functional promoters that include a complete RNA polymerase II preinitiation complex, MED1 and CDK9. Absence or inactivation of these factors causes a reduction in DDR foci both in vivo and in an in vitro system that reconstitutes DDR events on nucleosomes. We also show that dilncRNAs drive molecular crowding of DDR proteins, such as 53BP1, into foci that exhibit liquid-liquid phase-separation condensate properties. We propose that the assembly of DSB-induced transcriptional promoters drives RNA synthesis, which stimulates phase separation of DDR factors in the shape of foci.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y%,

title = {Inhibition of DNA damage response at telomeres improves the detrimental phenotypes of Hutchinson-Gilford Progeria Syndrome.},

author = {Aguado J and Sola-Carvajal A and Cancila V and Revêchon G and Ong PF and Jones-Weinert CW and Wallén Arzt E and Lattanzi G and Dreesen O and Tripodo C and Rossiello F and Eriksson M and {d'Adda di Fagagna F}},

url = {https://www.nature.com/articles/s41467-019-13018-3},

doi = {10.1038/s41467-019-13018-3},

year  = {2019},

date = {2019-11-14},

journal = {Nature Communications},

volume = {10},

number = {1},

pages = {4990},

abstract = {Hutchinson-Gilford progeria syndrome (HGPS) is a genetic disorder characterized by premature aging features. Cells from HGPS patients express progerin, a truncated form of Lamin A, which perturbs cellular homeostasis leading to nuclear shape alterations, genome instability, heterochromatin loss, telomere dysfunction and premature entry into cellular senescence. Recently, we reported that telomere dysfunction induces the transcription of telomeric non-coding RNAs (tncRNAs) which control the DNA damage response (DDR) at dysfunctional telomeres. Here we show that progerin-induced telomere dysfunction induces the transcription of tncRNAs. Their functional inhibition by sequence-specific telomeric antisense oligonucleotides (tASOs) prevents full DDR activation and premature cellular senescence in various HGPS cell systems, including HGPS patient fibroblasts. We also show in vivo that tASO treatment significantly enhances skin homeostasis and lifespan in a transgenic HGPS mouse model. In summary, our results demonstrate an important role for telomeric DDR activation in HGPS progeroid detrimental phenotypes in vitro and in vivo.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y%_38,

title = {Pharmacological boost of DNA damage response and repair by enhanced biogenesis of DNA damage response RNAs.},

author = {Gioia U and Francia S and Cabrini M and Brambillasca S and Michelini F and Jones-Weinert CW and {d'Adda di Fagagna F}},

url = {https://www.nature.com/articles/s41598-019-42892-6},

doi = {10.1038/s41598-019-42892-6},

year  = {2019},

date = {2019-04-23},

journal = {Scientific reports},

volume = {9},

number = {1},

pages = {6460},

abstract = {A novel class of small non-coding RNAs called DNA damage response RNAs (DDRNAs) generated at DNA double-strand breaks (DSBs) in a DROSHA- and DICER-dependent manner has been shown to regulate the DNA damage response (DDR). Similar molecules were also reported to guide DNA repair. Here, we show that DDR activation and DNA repair can be pharmacologically boosted by acting on such non-coding RNAs. Cells treated with enoxacin, a compound previously demonstrated to augment DICER activity, show stronger DDR signalling and faster DNA repair upon exposure to ionizing radiations compared to vehicle-only treated cells. Enoxacin stimulates DDRNA production at chromosomal DSBs and at dysfunctional telomeres, which in turn promotes 53BP1 accumulation at damaged sites, therefore in a miRNA-independent manner. Increased 53BP1 occupancy at DNA lesions induced by enoxacin ultimately suppresses homologous recombination, channelling DNA repair towards faster and more accurate non-homologous end-joining, including in post-mitotic primary neurons. Notably, augmented DNA repair stimulated by enoxacin increases the survival also of cancer cells treated with chemotherapeutic agents.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_72,

title = {RNase A treatment and reconstitution with DNA damage response RNA in living cells as a tool to study the role of non-coding RNA in the formation of DNA damage response foci.},

author = {Michelini F and Rossiello F and {d'Adda di Fagagna F} and Francia S},

url = {https://www.nature.com/articles/s41596-019-0147-5},

doi = {https://www.nature.com/articles/s41596-019-0147-5},

year  = {2019},

date = {2019-05-17},

journal = {Nature protocols},

volume = {14},

number = {5},

pages = {1489-1508},

abstract = {Non-coding RNA (ncRNA) molecules have been shown to play a variety of cellular roles; however, the contributions of different types of RNA to specific phenomena are often hard to dissect. To study the role of RNA in the assembly of DNA damage response (DDR) foci, we developed the RNase A treatment and reconstitution (RATaR) method, in which cells are mildly permeabilized, incubated with recombinant RNase A and subsequently reconstituted with different RNA species, under conditions of RNase A inactivation and inhibition of endogenous transcription. The block of transcription right after RNase A removal represents a key innovation of RATaR, preventing potential contributions of endogenously neo-synthesized transcripts to the phenotypes studied. A critical aspect of this technique is the balance between sufficient permeabilization of membranes to allow enzyme/RNA access into the cell nucleus and cell viability. Here, we present our protocol for RNA-dependent DDR foci disassembly and reassembly using fluorescent DDR RNAs (DDRNAs) in NIH2/4 cells, an engineered NIH3T3-derived cell line. The use of sequence-specific, fluorescent RNA molecules permits the concomitant determination of their subcellular localization and biological functions. We also outline adaptations of RATaR when implemented in different cell lines exposed to various genotoxic treatments, such as γ-radiation, restriction enzymes and telomere deprotection. In all these cases, the entire procedure can be completed within 2 h without the need for special equipment or uncommon skills. We believe this technique will prove useful for investigating the contribution of RNA to a variety of relevant cellular processes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_129,

title = {BRCA2 controls DNA:RNA hybrid level at DSBs by mediating RNase H2 recruitment.},

author = {D'Alessandro G and Whelan DR and Howard SM and Vitelli V and Renaudin X and Adamowicz M and Iannelli F and Jones-Weinert CW and Lee M and Matti V and Lee WTC and Morten MJ and Venkitaraman AR and Cejka P and Rothenberg E and {d'Adda di Fagagna F}},

url = {ww.nature.com/articles/s41467-018-06435-3},

doi = {10.1038/s41467-018-07799-2},

year  = {2018},

date = {2018-02-22},

journal = {Nature Communications},

volume = {9},

number = {1},

pages = {5376},

abstract = {DNA double-strand breaks (DSBs) are toxic DNA lesions, which, if not properly repaired, may lead to genomic instability, cell death and senescence. Damage-induced long non-coding RNAs (dilncRNAs) are transcribed from broken DNA ends and contribute to DNA damage response (DDR) signaling. Here we show that dilncRNAs play a role in DSB repair by homologous recombination (HR) by contributing to the recruitment of the HR proteins BRCA1, BRCA2, and RAD51, without affecting DNA-end resection. In S/G2-phase cells, dilncRNAs pair to the resected DNA ends and form DNA:RNA hybrids, which are recognized by BRCA1. We also show that BRCA2 directly interacts with RNase H2, mediates its localization to DSBs in the S/G2 cell-cycle phase, and controls DNA:RNA hybrid levels at DSBs. These results demonstrate that regulated DNA:RNA hybrid levels at DSBs contribute to HR-mediated repair.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_161,

title = {From "Cellular" RNA to "Smart" RNA: Multiple Roles of RNA in Genome Stability and Beyond.},

author = {Michelini F and Jalihal AP and Francia S and Meers C and Neeb ZT and Rossiello F and Gioia U and Aguado J and Jones-Weinert C and Luke B and Biamonti G and Nowacki M and Storici F and Carninci P and Walter NG and {d'Adda di Fagagna F}},

url = {https://pubs.acs.org/doi/10.1021/acs.chemrev.7b00487},

doi = {10.1021/acs.chemrev.7b00487},

year  = {2018},

date = {2018-04-25},

journal = {Chemical reviews},

volume = {118},

number = {8},

pages = {4365-4403},

abstract = {Coding for proteins has been considered the main function of RNA since the "central dogma" of biology was proposed. The discovery of noncoding transcripts shed light on additional roles of RNA, ranging from the support of polypeptide synthesis, to the assembly of subnuclear structures, to gene expression modulation. Cellular RNA has therefore been recognized as a central player in often unanticipated biological processes, including genomic stability. This ever-expanding list of functions inspired us to think of RNA as a "smart" phone, which has replaced the older obsolete "cellular" phone. In this review, we summarize the last two decades of advances in research on the interface between RNA biology and genome stability. We start with an account of the emergence of noncoding RNA, and then we discuss the involvement of RNA in DNA damage signaling and repair, telomere maintenance, and genomic rearrangements. We continue with the depiction of single-molecule RNA detection techniques, and we conclude by illustrating the possibilities of RNA modulation in hopes of creating or improving new therapies. The widespread biological functions of RNA have made this molecule a reoccurring theme in basic and translational research, warranting it the transcendence from classically studied "cellular" RNA to "smart" RNA.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_107,

title = {NOTCH1 modulates activity of DNA-PKcs.},

author = {Adamowicz M and {d'Adda di Fagagna F} and Vermezovic J},

doi = {10.1016/j.mrfmmm.2018.01.003},

year  = {2018},

date = {2018-03-29},

journal = {Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis},

volume = {808},

pages = {20-27},

abstract = {NA-dependent protein kinase catalytic subunit (DNA-PKcs) controls one of the most frequently used DNA repair pathways in a cell, the non-homologous end joining (NHEJ) pathway. However, the exact role of DNA-PKcs in NHEJ remains poorly defined. Here we show that NOTCH1 attenuates DNA-PKcs-mediated autophosphorylation, as well as the phosphorylation of its specific substrate XRCC4. Surprisingly, NOTCH1-expressing cells do not display any significant impairment in the DNA damage repair, nor cellular survival, and remain sensitive to small molecule DNA-PKcs inhibitor. Additionally, in vitro DNA-PKcs kinase assay shows that NOTCH1 does not inhibit DNA-PKcs kinase activity, implying that NOTCH1 acts on DNA-PKcs through a different mechanism. Together, our set of results suggests that NOTCH1 is a physiological modulator of DNA-PKcs, and that it can be a useful tool to clarify the mechanisms by which DNA-PKcs governs NHEJ DNA repair.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_166,

title = {Target-enrichment sequencing for detailed characterization of small RNAs.},

author = {Nguyen Q and Aguado J and Iannelli F and Suzuki AM and Rossiello F and {d'Adda di Fagagna F} and Carninci P},

url = {https://www.nature.com/articles/nprot.2018.001},

doi = {doi:10.1038/nprot.2018.001},

year  = {2018},

date = {2018-04-05},

journal = {Nature Protocols},

volume = {13},

pages = {768-786},

abstract = {Identification of important, functional small RNA (sRNA) species is currently hampered by the lack of reliable and sensitive methods to isolate and characterize them. We have developed a method, termed target-enrichment of sRNAs (TEsR), that enables targeted sequencing of rare sRNAs and diverse precursor and mature forms of sRNAs not detectable by current standard sRNA sequencing methods. It is based on the amplification of full-length sRNA molecules, production of biotinylated RNA probes, hybridization to one or multiple targeted RNAs, removal of nontargeted sRNAs and sequencing. By this approach, target sRNAs can be enriched by a factor of 500–30,000 while maintaining strand specificity. TEsR enriches for sRNAs irrespective of length or different molecular features, such as the presence or absence of a 5′ cap or of secondary structures or abundance levels. Moreover, TEsR allows the detection of the complete sequence (including sequence variants, and 5′ and 3′ ends) of precursors, as well as intermediate and mature forms, in a quantitative manner. A well-trained molecular biologist can complete the TEsR procedure, from RNA extraction to sequencing library preparation, within 4–6 d.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_185,

title = {A damaged genome’s transcriptional landscape through multilayered expression profiling around in situ-mapped DNA double-strand breaks},

author = {Iannelli F and Galbiati A and Capozzo I and Nguyen Q and Magnuson B and Michelini F and D'Alessandro G and Cabrini M and Roncador M and Francia S and Crosetto N and Ljungman M and Carninci P and {d'Adda di Fagagna F}},

url = {https://www.nature.com/articles/ncomms15656},

doi = {10.1038/ncomms15656},

year  = {2017},

date = {2017-02-23},

journal = {Nature Communications},

volume = {8},

pages = {15656},

abstract = {Of the many types of DNA damage, DNA double-strand breaks (DSBs) are probably the most deleterious. Mounting evidence points to an intricate relationship between DSBs and transcription. A cell system in which the impact on transcription can be investigated at precisely mapped genomic DSBs is essential to study this relationship. Here in a human cell line, we map genome-wide and at high resolution the DSBs induced by a restriction enzyme, and we characterize their impact on gene expression by four independent approaches by monitoring steady-state RNA levels, rates of RNA synthesis, transcription initiation and RNA polymerase II elongation. We consistently observe transcriptional repression in proximity to DSBs. Downregulation of transcription depends on ATM kinase activity and on the distance from the DSB. Our study couples for the first time, to the best of our knowledge, high-resolution mapping of DSBs with multilayered transcriptomics to dissect the events shaping gene expression after DSB induction at multiple endogenous sites.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_196,

title = {A novel single-cell method provides direct evidence of persistent DNA damage in senescent cells and aged mammalian tissues.},

author = {Galbiati A and Beausejour C and {d'Adda di Fagagna F}},

url = {http://onlinelibrary.wiley.com/doi/10.1111/acel.12573/abstract},

doi = {10.1111/acel.12573},

year  = {2017},

date = {2017-02-16},

journal = {Aging Cell},

volume = {16},

number = {2},

pages = {422-427},

abstract = {The DNA damage response (DDR) arrests cell cycle progression until DNA lesions, like DNA double-strand breaks (DSBs), are repaired. The presence of DSBs in cells is usually detected by indirect techniques that rely on the accumulation of proteins at DSBs, as part of the DDR. Such detection may be biased, as some factors and their modifications may not reflect physical DNA damage. The dependency on DDR markers of DSB detection tools has left questions unanswered. In particular, it is known that senescent cells display persistent DDR foci, that we and others have proposed to be persistent DSBs, resistant to endogenous DNA repair activities. Others have proposed that these peculiar DDR foci might not be sites of damaged DNA per se but instead stable chromatin modifications, termed DNA-SCARS. Here, we developed a method, named 'DNA damage in situ ligation followed by proximity ligation assay' (DI-PLA) for the detection and imaging of DSBs in cells. DI-PLA is based on the capture of free DNA ends in fixed cells in situ, by ligation to biotinylated double-stranded DNA oligonucleotides, which are next recognized by antibiotin anti-bodies. Detection is enhanced by PLA with a partner DDR marker at the DSB. We validated DI-PLA by demonstrating its ability to detect DSBs induced by various genotoxic insults in cultured cells and tissues. Most importantly, by DI-PLA, we demonstrated that both senescent cells in culture and tissues from aged mammals retain true unrepaired DSBs associated with DDR markers. 2017 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_184,

title = {Damage-induced lncRNAs control the DNA damage response through interaction with DDRNAs at individual double-strand breaks},

author = {Michelini F and Pitchiaya S and Vitelli V and Sharma S and Gioia U and Pessina F and Cabrini M and Wang Y and Capozzo I and Iannelli F and Matti V and Francia S and Shivashankar GV and Walter NG and {d'Adda di Fagagna F}},

url = {https://www.nature.com/articles/ncb3643},

doi = {10.1038/ncb3643},

year  = {2017},

date = {2017-02-22},

journal = {Nature cell biology},

volume = {19},

issue = {12},

pages = {1400-1410},

abstract = {The DNA damage response (DDR) preserves genomic integrity. Small non-coding RNAs termed DDRNAs are generated at DNA double-strand breaks (DSBs) and are critical for DDR activation. Here we show that active DDRNAs specifically localize to their damaged homologous genomic sites in a transcription-dependent manner. Following DNA damage, RNA polymerase II (RNAPII) binds to the MRE11-RAD50-NBS1 complex, is recruited to DSBs and synthesizes damage-induced long non-coding RNAs (dilncRNAs) from and towards DNA ends. DilncRNAs act both as DDRNA precursors and by recruiting DDRNAs through RNA-RNA pairing. Together, dilncRNAs and DDRNAs fuel DDR focus formation and associate with 53BP1. Accordingly, inhibition of RNAPII prevents DDRNA recruitment, DDR activation and DNA repair. Antisense oligonucleotides matching dilncRNAs and DDRNAs impair site-specific DDR focus formation and DNA repair. We propose that DDR signalling sites, in addition to sharing a common pool of proteins, individually host a unique set of site-specific RNAs necessary for DDR activation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_322,

title = {Damage-induced lncRNAs control the DNA damage response through interaction with DDRNAs at individual double-strand breaks.},

author = {Michelini F and Pitchiaya S and Vitelli V and Sharma S and Gioia U and Pessina F and Cabrini M and Wang Y and Capozzo I and Iannelli F and Matti V and Francia S and Shivashankar GV and Walter NG and {d'Adda di Fagagna F}},

url = {https://www.nature.com/articles/ncb3643},

doi = {10.1038/ncb3643},

year  = {2017},

date = {2017-02-28},

journal = {Nature cell biology},

volume = {19},

number = {2},

pages = {1400-1410},

abstract = {The DNA damage response (DDR) preserves genomic integrity. Small non-coding RNAs termed DDRNAs are generated at DNA double-strand breaks (DSBs) and are critical for DDR activation. Here we show that active DDRNAs specifically localize to their damaged homologous genomic sites in a transcription-dependent manner. Following DNA damage, RNA polymerase II (RNAPII) binds to the MRE11-RAD50-NBS1 complex, is recruited to DSBs and synthesizes damage-induced long non-coding RNAs (dilncRNAs) from and towards DNA ends. DilncRNAs act both as DDRNA precursors and by recruiting DDRNAs through RNA-RNA pairing. Together, dilncRNAs and DDRNAs fuel DDR focus formation and associate with 53BP1. Accordingly, inhibition of RNAPII prevents DDRNA recruitment, DDR activation and DNA repair. Antisense oligonucleotides matching dilncRNAs and DDRNAs impair site-specific DDR focus formation and DNA repair. We propose that DDR signalling sites, in addition to sharing a common pool of proteins, individually host a unique set of site-specific RNAs necessary for DDR activation.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_186,

title = {DNA damage response inhibition at dysfunctional telomeres by modulation of telomeric DNA damage response RNAs.},

author = {Rossiello F and Aguado J and Sepe S and Iannelli F and Nguyen Q and Pitchiaya S and Carninci P and {d'Adda di Fagagna F}},

url = {https://www.nature.com/articles/ncomms13980},

doi = {10.1038/ncomms13980},

year  = {2017},

date = {2017-02-11},

journal = {Nature Communications},

volume = {8},

pages = {13980},

abstract = {The DNA damage response (DDR) is a set of cellular events that follows the generation of DNA damage. Recently, site-specific small non-coding RNAs, also termed DNA damage response RNAs (DDRNAs), have been shown to play a role in DDR signalling and DNA repair. Dysfunctional telomeres activate DDR in ageing, cancer and an increasing number of identified pathological conditions. Here we show that, in mammals, telomere dysfunction induces the transcription of telomeric DDRNAs (tDDRNAs) and their longer precursors from both DNA strands. DDR activation and maintenance at telomeres depend on the biogenesis and functions of tDDRNAs. Their functional inhibition by sequence-specific antisense oligonucleotides allows the unprecedented telomere-specific DDR inactivation in cultured cells and in vivo in mouse tissues. In summary, these results demonstrate that tDDRNAs are induced at dysfunctional telomeres and are necessary for DDR activation and they validate the viability of locus-specific DDR inhibition by targeting DDRNAs.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_210,

title = {Express or Repress? The Transcriptional Dilemma of Damaged Chromatin.},

author = {Capozzo I and Iannelli F and Francia S and {d'Adda di Fagagna F}},

url = {http://onlinelibrary.wiley.com/doi/10.1111/febs.14048/abstract},

doi = {10.1111/febs.14048},

year  = {2017},

date = {2017-02-15},

journal = {FEBS journal},

volume = {284},

number = {14},

pages = {2133-2147},

abstract = {The fine modulation of transcriptional activity around DNA lesions is essential to carefully regulate the crosstalk between transcription, the DNA damage response, and DNA repair, particularly when the lesion occurs next to, or within, actively transcribed genes. Recently, several studies have been carried out to investigate how DNA lesions have an impact on local transcription, but the emerging model remains incomplete. Transcription of genes around damaged DNA is actively down-regulated by the DNA damage response through different mechanisms, which appear specific to the chromatin context, the type of DNA damage or its complexity. Intriguingly, emerging evidence also indicates that transcription of non-coding RNAs (ncRNAs) is induced at sites of DNA damage, producing small ncRNAs that are, in turn, required for a full DDR activation. We discuss here these recent findings, highlighting the major unresolved questions in the field, and propose ways to reconcile these apparently contradictory observations. This article is protected by copyright. All rights reserved.

This article is protected by copyright. All rights reserved.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_194,

title = {Recent Advancements in DNA Damage-Transcription Crosstalk and High-Resolution Mapping of DNA Breaks.},

author = {Vitelli V and Galbiati A and Iannelli F and Pessina F and Sharma S and {d'Adda di Fagagna F}},

url = {http://www.annualreviews.org/doi/full/10.1146/annurev-genom-091416-035314?url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&rfr_dat=cr_pub%3Dpubmed&},

doi = {10.1146/annurev-genom-091416-035314},

year  = {2017},

date = {2017-08-31},

journal = {Annual review of genomics and human genetics},

volume = {18},

pages = {87-113},

abstract = {"Until recently, DNA damage arising from physiological DNA metabolism was considered a detrimental by-product for cells. However, an increasing amount of evidence has shown that DNA damage could have a positive role in transcription activation. In particular, DNA damage has been detected in transcriptional elements following different stimuli. These physiological DNA breaks are thought to be instrumental for the correct expression of genomic loci through different mechanisms. In this regard, although a plethora of methods are available to precisely map transcribed regions and transcription start sites, commonly used techniques for mapping DNA breaks lack sufficient resolution and sensitivity to draw a robust correlation between DNA damage generation and transcription. Recently, however, several methods have been developed to map DNA damage at single-nucleotide resolution, thus providing a new set of tools to correlate DNA damage and transcription. Here, we review how DNA damage can positively regulate transcription initiation, the current techniques for mapping DNA breaks at high resolution, and how these techniques can benefit future studies of DNA damage and transcription.

"},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_408,

title = {Telomerase abrogates aneuploidy-induced telomere replication stress, senescence and cell depletion.},

author = {Meena JK and Cerutti A and Beichler C and Morita Y and Bruhn C and Kumar M and Kraus JM and Speicher MR and Wang ZQ and Kestler HA and {d'Adda di Fagagna F} and Günes C and Rudolph KL},

url = {https://www.embopress.org/doi/full/10.15252/embj.201490070},

doi = {10.15252/embj.201490070},

year  = {2017},

date = {2017-10-13},

journal = {Embo Journal},

volume = {34},

number = {10},

pages = {1371-1384},

abstract = {The causal role of aneuploidy in cancer initiation remains under debate since mutations of euploidy-controlling genes reduce cell fitness but aneuploidy strongly associates with human cancers. Telomerase activation allows immortal growth by stabilizing telomere length, but its role in aneuploidy survival has not been characterized. Here, we analyze the response of primary human cells and murine hematopoietic stem cells (HSCs) to aneuploidy induction and the role of telomeres and the telomerase in this process. The study shows that aneuploidy induces replication stress at telomeres leading to telomeric DNA damage and p53 activation. This results in p53/Rb-dependent, premature senescence of human fibroblast, and in the depletion of hematopoietic cells in telomerase-deficient mice. Endogenous telomerase expression in HSCs and enforced expression of telomerase in human fibroblasts are sufficient to abrogate aneuploidy-induced replication stress at telomeres and the consequent induction of premature senescence and hematopoietic cell depletion. Together, these results identify telomerase as an aneuploidy survival factor in mammalian cells based on its capacity to alleviate telomere replication stress in response to aneuploidy induction. 2015 The Authors.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_201,

title = {The cohesin complex prevents Myc-induced replication stress.},

author = {Rohban S and Cerutti A and Morelli MJ and {d'Adda di Fagagna F} and Campaner S},

url = {https://www.nature.com/articles/cddis2017345},

doi = {10.1038/cddis.2017.345},

year  = {2017},

date = {2017-07-27},

journal = {Cell Death and Disease},

volume = {8},

pages = {e2956},

abstract = {The cohesin complex is mutated in cancer and in a number of rare syndromes collectively known as Cohesinopathies. In the latter case, cohesin deficiencies have been linked to transcriptional alterations affecting Myc and its target genes. Here, we set out to understand to what extent the role of cohesins in controlling cell cycle is dependent on Myc expression and activity. Inactivation of the cohesin complex by silencing the RAD21 subunit led to cell cycle arrest due to both transcriptional impairment of Myc target genes and alterations of replication forks, which were fewer and preferentially unidirectional. Ectopic activation of Myc in RAD21 depleted cells rescued Myc-dependent transcription and promoted S-phase entry but failed to sustain S-phase progression due to a strong replicative stress response, which was associated to a robust DNA damage response, DNA damage checkpoint activation and synthetic lethality. Thus, the cohesin complex is dispensable for Myc-dependent transcription but essential to prevent Myc-induced replicative stress. This suggests the presence of a feed-forward regulatory loop where cohesins by regulating Myc level control S-phase entry and prevent replicative stress.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_207,

title = {Transcription and DNA Damage: Holding Hands or Crossing Swords? First dual AK/GSK-3beta inhibitors endowed with antioxidant properties as multifunctional, potential neuroprotective agents.},

author = {D'Alessandro G and {d'Adda di Fagagna F}},

url = {http://www.sciencedirect.com/science/article/pii/S0022283616304715?via%3Dihub},

doi = {10.1016/j.jmb.2016.11.002},

year  = {2017},

date = {2017-10-27},

journal = {Journal of Molecular Biology},

volume = {429},

number = {21},

pages = {3215-3229},

abstract = {Transcription has classically been considered a potential threat to genome integrity. Collision between transcription and DNA replication machinery, and retention of DNA:RNA hybrids, may result in genome instability. On the other hand, it has been proposed that active genes repair faster and preferentially via homologous recombination. Moreover, while canonical transcription is inhibited in the proximity of DNA double-strand breaks, a growing body of evidence supports active non-canonical transcription at DNA damage sites. Small non-coding RNAs accumulate at DNA double-strand break sites in mammals and other organisms, and are involved in DNA damage signaling and repair. Furthermore, RNA binding proteins are recruited to DNA damage sites and participate in the DNA damage response. Here, we discuss the impact of transcription on genome stability, the role of RNA binding proteins at DNA damage sites, and the function of small non-coding RNAs generated upon damage in the signaling and repair of DNA lesions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_216,

title = {Transcriptional and post-transcriptional regulation of the ionizing radiation response by ATM and p53.},

author = {Venkata Narayanan I and Paulsen MT and Bedi K and Berg N and Ljungman EA and Francia S and Veloso A and Magnuson B and {d'Adda di Fagagna F} and Wilson TE and Ljungman M},

url = {www.nature.com/articles/srep43598},

doi = {10.1038/srep43598},

year  = {2017},

date = {2017-03-01},

journal = {Scientific reports},

volume = {7},

number = {1},

pages = {43598},

abstract = {In response to ionizing radiation (IR), cells activate a DNA damage response (DDR) pathway to re-program gene expression. Previous studies using total cellular RNA analyses have shown that the stress kinase ATM and the transcription factor p53 are integral components required for induction of IR-induced gene expression. These studies did not distinguish between changes in RNA synthesis and RNA turnover and did not address the role of enhancer elements in DDR-mediated transcriptional regulation. To determine the contribution of synthesis and degradation of RNA and monitor the activity of enhancer elements following exposure to IR, we used the recently developed Bru-seq, BruChase-seq and BruUV-seq techniques. Our results show that ATM and p53 regulate both RNA synthesis and stability as well as enhancer element activity following exposure to IR. Importantly, many genes in the p53-signaling pathway were coordinately up-regulated by both increased synthesis and RNA stability while down-regulated genes were suppressed either by reduced synthesis or stability. Our study is the first of its kind that independently assessed the effects of ionizing radiation on transcription and post-transcriptional regulation in normal human cells.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_280,

title = {DICER, DROSHA and DNA damage response RNAs are necessary for the secondary recruitment of DNA damage response factors.},

author = {Francia S and Cabrini M and Matti V and Oldani A and {d'Adda di Fagagna F}},

url = {http://jcs.biologists.org/content/129/7/1468.long},

doi = {10.1242/jcs.182188},

year  = {2016},

date = {2016-02-18},

journal = {Journal of Cell Science},

volume = {129},

pages = {1468-1476},

abstract = {The DNA damage response (DDR) plays a central role in preserving genome integrity. Recently, we reported that the endoribonucleases DICER and DROSHA contribute to DDR activation by generating small non-coding RNAs, termed DNA damage response RNA (DDRNA), carrying the sequence of the damaged locus. It is presently unclear whether DDRNAs act by promoting the primary recognition of DNA lesions or the secondary recruitment of DDR factors into cytologically detectable foci and consequent signal amplification. Here, we demonstrate that DICER and DROSHA are dispensable for primary recruitment of the DDR sensor NBS1 to DNA damage sites. Instead, the accumulation of the DDR mediators MDC1 and 53BP1 (also known as TP53BP1), markers of secondary recruitment, is reduced in DICER- or DROSHA-inactivated cells. In addition, NBS1 (also known as NBN) primary recruitment is resistant to RNA degradation, consistent with the notion that RNA is dispensable for primary recognition of DNA lesions. We propose that DICER, DROSHA and DDRNAs act in the response to DNA damage after primary recognition of DNA lesions and, together with γH2AX, are essential for enabling the secondary recruitment of DDR factors and fuel the amplification of DDR signaling. 2016. Published by The Company of Biologists Ltd.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_242,

title = {NOTCH1 Inhibits Activation of ATM by Impairing the Formation of an ATM-FOXO3a-KAT5/Tip60 Complex.},

author = {Adamowicz M and Vermezovic J and {d'Adda di Fagagna F}},

url = {http://www.sciencedirect.com/science/article/pii/S2211124716309561},

doi = {10.1016/j.celrep.2016.07.038},

year  = {2016},

date = {2016-08-23},

journal = {Cell Reports},

volume = {16},

number = {8},

pages = {2068-2076},

abstract = {The DNA damage response (DDR) signal transduction pathway is responsible for sensing DNA damage and further relaying this signal into the cell. ATM is an apical DDR kinase that orchestrates the activation and the recruitment of downstream DDR factors to induce cell-cycle arrest and repair. We have previously shown that NOTCH1 inhibits ATM activation upon DNA damage, but the underlying mechanism remains unclear. Here, we show that NOTCH1 does not impair ATM recruitment to DNA double-strand breaks (DSBs). Rather, NOTCH1 prevents binding of FOXO3a and KAT5/Tip60 to ATM through a mechanism in which NOTCH1 competes with FOXO3a for ATM binding. Lack of FOXO3a binding to ATM leads to the loss of KAT5/Tip60 association with ATM. Moreover, expression of NOTCH1 or depletion of ATM impairs the formation of the FOXO3a-KAT5/Tip60 protein complex. Finally, we show that pharmacological induction of FOXO3a nuclear localization sensitizes NOTCH1-driven cancers to DNA-damage-induced cell death.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_372,

title = {Human nuclear ARGONAUTE 2 interacts in vivo only with small RNAs and not with DNA.},

author = {Gioia U and {d'Adda di Fagagna F}},

url = {https://www.tandfonline.com/doi/full/10.1080/15384101.2015.1044171},

doi = {10.1080/15384101.2015.1044171},

year  = {2015},

date = {2015-02-19},

journal = {Cell Cycle},

volume = {14},

number = {13},

pages = {2001-2002},

abstract = {Lifestyle factors are responsible for a considerable portion of cancer incidence worldwide, but credible estimates from the World Health Organization and the International Agency for Research on Cancer (IARC) suggest that the fraction of cancers attributable to toxic environmental exposures is between 7% and 19%. To explore the hypothesis that low-dose exposures to mixtures of chemicals in the environment may be combining to contribute to environmental carcinogenesis, we reviewed 11 hallmark phenotypes of cancer, multiple priority target sites for disruption in each area and prototypical chemical disruptors for all targets, this included dose-response characterizations, evidence of low-dose effects and cross-hallmark effects for all targets and chemicals. In total, 85 examples of chemicals were reviewed for actions on key pathways/mechanisms related to carcinogenesis. Only 15% (13/85) were found to have evidence of a dose-response threshold, whereas 59% (50/85) exerted low-dose effects. No dose-response information was found for the remaining 26% (22/85). Our analysis suggests that the cumulative effects of individual (non-carcinogenic) chemicals acting on different pathways, and a variety of related systems, organs, tissues and cells could plausibly conspire to produce carcinogenic synergies. Additional basic research on carcinogenesis and research focused on low-dose effects of chemical mixtures needs to be rigorously pursued before the merits of this hypothesis can be further advanced. However, the structure of the World Health Organization International Programme on Chemical Safety 'Mode of Action' framework should be revisited as it has inherent weaknesses that are not fully aligned with our current understanding of cancer biology. The Author 2015. Published by Oxford University Press.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_387,

title = {Notch is a direct negative regulator of the DNA-damage response.},

author = {Vermezovic J and Adamowicz M and Santarpia L and Rustighi A and Forcato M and Lucano C and Massimiliano L and Costanzo V and Bicciato S and Del Sal G and {d'Adda di Fagagna F}},

url = {https://www.nature.com/articles/nsmb.3013},

doi = {10.1038/nsmb.3013},

year  = {2015},

date = {2015-03-14},

journal = {Nature Structural & Molecular Biology},

volume = {22},

number = {5},

pages = {417-424},

abstract = {The DNA-damage response (DDR) ensures genome stability and proper inheritance of genetic information, both of which are essential to survival. It is presently unclear to what extent other signaling pathways modulate DDR function. Here we show that Notch receptor binds and inactivates ATM kinase and that this mechanism is evolutionarily conserved in Caenorhabditis elegans, Xenopus laevis and humans. In C. elegans, the Notch pathway impairs DDR signaling in gonad germ cells. In mammalian cells, activation of human Notch1 leads to reduced ATM signaling in a manner independent of Notch1 transcriptional activity. Notch1 binds directly to the regulatory FATC domain of ATM and inhibits ATM kinase activity. Notch1 and ATM activation are inversely correlated in human breast cancers, and inactivation of ATM by Notch1 contributes to the survival of Notch1-driven leukemia cells upon DNA damage.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_403,

title = {Resection is responsible for loss of transcription around a double-strand break in Saccharomyces cerevisiae.},

author = {Manfrini N and Clerici M and Wery M and Colombo CV and Descrimes M and Morillon A and {d'Adda di Fagagna F} and Longhese MP},

url = {https://elifesciences.org/articles/08942},

doi = {10.7554/eLife.08942.},

year  = {2015},

date = {2015-07-31},

journal = {Elife},

volume = {4},

abstract = {Emerging evidence indicate that the mammalian checkpoint kinase ATM induces transcriptional silencing in cis to DNA double-strand breaks (DSBs) through a poorly understood mechanism. Here we show that in Saccharomyces cerevisiae a single DSB causes transcriptional inhibition of proximal genes independently of Tel1/ATM and Mec1/ATR. Since the DSB ends undergo nucleolytic degradation (resection) of their 5′-ending strands, we investigated the contribution of resection in this DSB-induced transcriptional inhibition. We discovered that resection-defective mutants fail to stop transcription around a DSB, and the extent of this failure correlates with the severity of the resection defect. Furthermore, Rad9 and generation of γH2A reduce this DSB-induced transcriptional inhibition by counteracting DSB resection. Therefore, the conversion of the DSB ends from double-stranded to single-stranded DNA, which is necessary to initiate DSB repair by homologous recombination, is responsible for loss of transcription around a DSB in S. cerevisiae.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{%a1:%Y_404,

title = {RNA-processing proteins regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA.},

author = {Manfrini N and Trovesi C and Wery M and Martina M and Cesena D and Descrimes M and Morillon A and {d'Adda di Fagagna F} and Longhese MP},

url = {https://www.embopress.org/doi/full/10.15252/embr.201439458},

doi = {10.15252/embr.201439458},

year  = {2015},

date = {2015-02-18},

journal = {Embo Reports},

volume = {16},

number = {2},

pages = {221-231},

abstract = {Eukaryotic cells respond to DNA double-strand breaks (DSBs) by activating a checkpoint that depends on the protein kinases Tel1/ATM and Mec1/ATR. Mec1/ATR is activated by RPA-coated single-stranded DNA (ssDNA), which arises upon nucleolytic degradation (resection) of the DSB. Emerging evidences indicate that RNA-processing factors play critical, yet poorly understood, roles in genomic stability. Here, we provide evidence that the Saccharomyces cerevisiae RNA decay factors Xrn1, Rrp6 and Trf4 regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA. The lack of Xrn1 inhibits ssDNA generation at the DSB by preventing the loading of the MRX complex. By contrast, DSB resection is not affected in the absence of Rrp6 or Trf4, but their lack impairs the recruitment of RPA, and therefore of Mec1, to the DSB. Rrp6 and Trf4 inactivation affects neither Rad51/Rad52 association nor DSB repair by homologous recombination (HR), suggesting that full Mec1 activation requires higher amount of RPA-coated ssDNA than HR-mediated repair. Noteworthy, deep transcriptome analyses do not identify common misregulated gene expression that could explain the observed phenotypes. Our results provide a novel link between RNA processing and genome stability. 2014 The Authors.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}