The Shiloh Laboratory | Yossi Shiloh | Sackler School of Medicine

Publications
The following are publications since 2005. The complete list of Yosef Shiloh's publications can be found under "The Research Team"
Haj M, Frey Y, Levon A, Maliah A, Ben-Yishay T, Slutsky R, Smoom R, Tzfati Y, Ben-David U, Levy C, Elkon R, Ziv Y, and Shiloh Y (2025) The cGAS–STING, p38 MAPK, and p53 pathways link genome instability to accelerated cellular senescence in ATM-deficient murine lung fibroblasts. PNAS 122 (2)
Naor S, Ziv Y and Shiloh Y (2024) Visualizing the DNA Damage Response in Purkinje Cells Using Cerebellar Organotypic Cultures. J. Vis. Exp. (214) e67167
Frey Y, Haj M, Ziv Y, Elkon R, Shiloh Y (2024) Broad repression of DNA repair genes in senescent cells identified by integration of transcriptomic data. Nucleic Acids Research 2024, 1–17
Haj M, Levon A, Frey Y, Hourvitz N, Campisi J, Tzfati Y, Elkon R, Ziv Y, Shiloh Y (2023) Accelerated replicative senescence of ataxia-telangiectasia skin fibroblasts is retained at physiologic oxygen levels, with unique and common transcriptional patterns. Aging Cell May 30;e13869
Shoji Y, Yokoe T, Kobayashi Y, Murakami T, Bostick PJ, Shiloh Y, Hoon DSB, Bustos MA (2022) UBQLN4 promotes STING proteasomal degradation during cisplatin-induced DNA damage in triple-negative breast cancer. Clin. Transl. Med. 2022;12:e985
Aguado J, Gómez-Inclán C, Leeson HC, Lavin MF, Shiloh Y, Wolvetang EJ (2022) The hallmarks of aging in Ataxia-Telangiectasia. Ageing Research Reviews Volume 79
Schmauck-Medina T, Molière A, Lautrup S, Zhang J, Chlopicki S, Madsen HB, Cao S, Soendenbroe C, Mansell E, Vestergaard MB, Li Z, Shiloh Y, Opresko PL, Egly J-M, Kirkwood T, Verdin E, Bohr VA, Cox LS, Stevnsner T, Rasmussen LJ, Fang E (2022) New hallmarks of ageing: a 2022 Copenhagen ageing meeting summary. Aging 14(16):6829-6839
Kobayashi Y, Bustos MA, Shoji Y, Jachimowicz RD, Shiloh Y, Hoon DSB (2022) Genomic Amplification of UBQLN4 Is a Prognostic and Treatment Resistance Factor. Cells11:3311
Schlam-Babayov S, Ziv Y, Shiloh S. (2021) It takes three to the DNA damage response tango. Molecular & Cellular Oncology, DOI: 10.1080/23723556.2021.1881395
Schlam-Babayov S, Bensimon A, Harel M, Geiger T, Aebersold R, Ziv Y, Shiloh Y. (2020) Phosphoproteomics reveals novel modes of function and inter-relationships among PIKKs in response to genotoxic stress. EMBO J 40:e104400
Shiloh Y. (2020) The cerebellar degeneration in ataxia-telangiectasia: A case for genome instability. DNA Repair (Amst) 95:102950
Shiloh Y. (2020) The serendipitous dawn of DNA repair. Nat Rev Mol Cell Biol. 21(10):569
Antoniou N, Lagopati N, Balourdas DI, Nikolaou M, Papalampros A, Vasileiou PVS, Myrianthopoulos V, Kotsinas A, Shiloh Y, Liontos M, Gorgoulis VG. (2019) The Role of E3, E4 Ubiquitin Ligase (UBE4B) in Human Pathologies. Cancers (Basel) 12(1):62
Hait TA, Maron-Katz A, Sagir D, Amar D, Ulitsky I, Linhart C, Tanay A, Sharan R, Shiloh Y, Elkon R, Shamir R. (2019) The EXPANDER Integrated Platform for Transcriptome Analysis. J Mol Biol. 431, 2398-2406
Jachimowicz RD, Beleggia F, Isensee J, Velpula BB, Goergens J, Bustos MA, Doll MA, Shenoy A, Checa-Rodriguez C, Wiederstein JL, Baranes-Bachar K, Bartenhagen C, Hertwig F, Teper N, Nishi T, Schmitt A, Distelmaier F, Lüdecke HJ, Albrecht B, Krüger M, Schumacher B, Geiger T, Hoon DSB, Huertas P, Fischer M, Hucho T, Peifer M, Ziv Y, Reinhardt HC, Wieczorek D, Shiloh Y. (2019) UBQLN4 Represses Homologous Recombination and Is Overexpressed in Aggressive Tumors. Cell 176, 505-519
Tal E, Alfo M, Zha S, Barzilai A, De Zeeuw CI, Ziv Y, Shiloh Y. (2018) Inactive Atm abrogates DSB repair in mouse cerebellum more than does Atm loss, without causing a neurological phenotype. DNA Repair (Amst) 72:10-17.
Baranes-Bachar K, Levy-Barda A, Oehler J, Reid DA, Soria-Bretones I, Voss TC, Chung D, Park Y, Liu C, Yoon JB, Li W, Dellaire G, Misteli T, Huertas P, Rothenberg E, Ramadan K, Ziv Y, Shiloh Y. (2018) The Ubiquitin E3/E4 Ligase UBE4A Adjusts Protein Ubiquitylation and Accumulation at Sites of DNA Damage, Facilitating Double-Strand Break Repair. Mol Cell. 69(5):866-878.e7
Gavish-Izakson M, Velpula BB, Elkon R, Prados-Carvajal R, Barnabas GD, Ugalde AP, Agami R, Geiger T, Huertas P, Ziv Y, Shiloh Y. (2018) Nuclear poly(A)-binding protein 1 is an ATM target and essential for DNA double-strand break repair. Nucleic Acids Res 46(2):730-747
Tal E, Shiloh Y. (2017) Monitoring the ATM-Mediated DNA Damage Response in the Cerebellum Using Organotypic Cultures. Methods Mol Biol. Vol. 1599:419-430 [Book]
Shiloh Y, Lederman HM. (2017) Ataxia-telangiectasia (A-T): An emerging dimension of premature ageing. Ageing Res Rev. 33(2017):76-88
Barzilai A, Schumacher B, Shiloh Y. (2017) Genome instability: Linking ageing and brain degeneration. Mech Ageing Dev. 161(2017):4-18
Ribezzo F, Shiloh Y, Schumacher B. (2016) Systemic DNA damage responses in aging and diseases. Semin Cancer Biol. 37-38(2016):26-35
Meir M, Galanty Y, Kashani L, Blank M, Khosravi R, Fernández-Ávila MJ, Cruz-García A, Star A, Shochot L, Thomas Y, Garrett LJ, Chamovitz DA, Bodine DM, Kurz T, Huertas P, Ziv Y, Shiloh Y. (2015) The COP9 signalosome is vital for timely repair of DNA double-strand breaks. Nucleic Acids Res 19;43(9)
Shiloh Y. (2014) ATM: Expanding roles as a chief guardian of genome stability. Exp Cell Res. 15;329(1)
Rashi-Elkeles S, Warnatz HJ, Elkon R, Kupershtein A, Chobod Y, Paz A, Amstislavskiy V, Sultan M, Safer H, Nietfeld W, Lehrach H, Shamir R, Yaspo ML, Shiloh Y. (2014) Parallel profiling of the transcriptome, cistrome, and epigenome in the cellular response to ionizing radiation. Sci Signal 13;7(325)
Shiloh Y, Ziv Y. (2013) The ATM protein kinase: regulating the cellular response to genotoxic stress, and more. Nat Rev Mol Cell Biol. Apr;14(4):197-210.
Rasmussen LJ, Shiloh Y, Bergersen LH, Sander M, Bohr VA, Tønjum T. (2013) Mech Ageing Dev. 134(10):427-33
Tzur-Gilat, A., Ziv, Y., Mittelman, L., Barzilai, A., and Shiloh, Y. (2013). Studying the cerebellar DNA damage response in the tissue culture dish. Mechanisms of ageing and development.
Shiloh, Y., and Ziv, Y. (2013). The ATM protein kinase: regulating the cellular response to genotoxic stress, and more. Nature reviews Molecular cell biology 14, 197-210.
Rasmussen, L. J., Shiloh, Y., Bergersen, L. H., Sander, M., Bohr, V. A., and Tonjum, T. (2013). DNA damage response, bioenergetics, and neurological disease: The challenge of maintaining brain health in an aging human population. Mechanisms of ageing and development.
Shiloh, Y., and Ziv, Y. (2012). The ATM protein: the importance of being active. The Journal of cell biology 198, 273-275.
Kirshner, M., Galron, R., Frenkel, D., Mandelbaum, G., Shiloh, Y., Wang, Z. Q., and Barzilai, A. (2012). Malfunctioning DNA damage response (DDR) leads to the degeneration of nigro-striatal pathway in mouse brain. Journal of molecular neuroscience : MN 46, 554-568.
Galron R, Gruber R, Lifshitz V, Lu H, Kirshner M, Ziv N, Wang ZQ, Shiloh Y, Barzilai A, Frenkel D (2011) Astrocyte dysfunction associated with cerebellar attrition in a nijmegen breakage syndrome animal model. J Mol Neurosci 45: 202-211
Levy-Barda A, Lerenthal Y, Davis AJ, Chung YM, Essers J, Shao Z, van Vliet N, Chen DJ, Hu MC, Kanaar R, Ziv Y, Shiloh Y (2011) Involvement of the nuclear proteasome activator PA28gamma in the cellular response to DNA double-strand breaks. Cell Cycle 10
Rashi-Elkeles S, Elkon R, Shavit S, Lerenthal Y, Linhart C, Kupershtein A, Amariglio N, Rechavi G, Shamir R, Shiloh Y (2011) Transcriptional modulation induced by ionizing radiation: p53 remains a central player. Mol Oncol 5: 336-348
Raz-Prag D, Galron R, Segev-Amzaleg N , Solomon AS, Shiloh Y, Barzilai A, Frenkel D (2011) A role for vascular deficiency in retinal pathology in a mouse model of ataxia-telangiectasia. Am J Pathol 179: 1533-1541
Salton M, Elkon R, Borodina T, Davydov A, Yaspo ML, Halperin E, Shiloh Y (2011 ) Matrin 3 binds and stabilizes mRNA. PLoS One 6: e23882
Shiloh Y, Shema E, Moyal L, Oren M (2011) RNF20-RNF40: A ubiquitin-driven link between gene expression and the DNA damage response. FEBS Lett 585: 2795-2802
Segal-Raz H, Mass G, Ziv-Lehrman S, Wang SY, Strom C, Helleday T, Chen DJ, and Shiloh Y (2011) ATM-mediated phosphorylation of polynucleotide kinase is required for effective DNA double-strand break repair. EMBO Reports, 12:713-719.
Bensimon A, Aebersold R, and Shiloh Y (2011) Beyond ATM: the protein kinase landscape of the DNA damage response. FEBS Letters 585:1625-1639.
Moyal L, Lerenthal Y, Gana-Weisz M, Mass G, So S, Wang SY, Eppink B, Chung YM, Shalev G, Shema E, Shkedy D, Smorodinsky NI, van Vliet N, Kuster B, Mann M, Ciechanover A, Dahm-Daphi J, Kanaar R, Hu MC, Chen DJ, Oren M, Shiloh Y (2011) Requirement of ATM-dependent monoubiquitylation of histone H2B for timely repair of DNA double-strand breaks. Mol Cell 41: 529-542 Featured article.
Dar I, Yosha G, Elfassy R, Galron R, Wang ZQ, Shiloh Y, Barzilai A (2011) Investigation of the Functional Link between ATM and NBS1 in the DNA Damage Response in the Mouse Cerebellum. J Biol Chem 286: 15361-15376
Kepkay R, Attwood KM, Ziv Y, Shiloh Y, Dellaire G (2011) KAP1 depletion increases PML nuclear body number in concert with ultrastructural changes in chromatin. Cell Cycle 10: 308-322
Paz A, Brownstein Z, Ber Y, Bialik S, David E, Sagir D, Ulitsky I, Elkon R, Kimchi A, Avraham KB, Shiloh Y, Shamir R (2011) SPIKE: a database of highly curated human signaling pathways. Nucleic Acids Res 39: D793-799
Bensimon A, Schmidt A, Ziv Y, Elkon R, Wang SY, Chen DJ, Aebersold R, Shiloh Y (2010) ATM-dependent and -independent dynamics of the nuclear phosphoproteome after DNA damage. Sci Signal 3: rs3
Salton M, Lerenthal Y, Wang SY, Chen DJ, Shiloh Y. 2010. Involvement of matrin 3 and SFPQ/NONO in the DNA damage response. Cell Cycle 9(8). 2.
Jochemsen AG, Shiloh Y. 2010. USP10: friend and foe. Cell 140(3):308-10.
Ulitsky I, Maron-Katz A, Shavit S, Sagir D, Linhart C and others. 2010. Expander: from expression microarrays to networks and functions. Nat Protoc 5(2):303-22.
Barash H, E RG, Edrei Y, Ella E, Israel A and others. 2010. Accelerated carcinogenesis following liver regeneration is associated with chronic inflammation-induced double-strand DNA breaks. Proc Natl Acad Sci U S A 107(5):2207-12.
Winter D, Seidler J, Ziv-Lehrman S, Shiloh Y, Lehmann WD. 2009. Simultaneous identification and quantification of proteins by differential (16)O/(18)O labeling and UPLC-MS/MS applied to mouse cerebellar phosphoproteome following irradiation. Anticancer Res 29(12):4949-58.
Shiloh, Y. (2009) FBXO31: a new player in the ever-expanding DNA damage orchestra. Science Signaling 2(96):pe73.
Das, B.B., Antony, S., Gupta, S., Dexheimer, T.S., Redon, C.E., Garfield, S., Shiloh, Y., and Pommier, Y. (2009) Optimal function of the DNA repair enzyme TDP1 requires its phosphorylation by ATM and/or DNA-PK. EMBO J. 28:3667-2680.
Baranes K, Raz-Prag D, Nitzan A, Galron R, Asjery-Padan R, Rotenstreich Y Assaf Y, Shiloh Y, Wang Z-Q, Solomon AS, and Barzilai A. Conditional inactivation of the NBS1 gene in the mouse central nervous system leads to neurodegeneration and disorganization of the visual system. Exp. Neurol 2009;218(1):24-32 .
Winter D, Seidler J, Ziv Y, Shiloh Y, Lehmann WD. Citrate boosts the performance of phosphopeptide analysis by UPLC-ESI-MS/MS. J Proteome Res 2009;8(1):418-24 .
Kirshner M, Rathavs M, Nizan A, Essers J, Kanaar R, Shiloh Y, Barzilai A. Analysis of the relationships between ATM and the Rad54 paralogs involved in homologous recombination repair. DNA Repair (Amst) 2009;8(2):253-61 .
Kim YC, Gerlitz G, Furusawa T, Catez F, Nussenzweig A, Oh KS, Kraemer KH, Shiloh Y, Bustin M. Activation of ATM depends on chromatin interactions occurring before induction of DNA damage. Nat Cell Biol 2009;11(1):92-6 .
Shema E, Tirosh I, Aylon Y, Huang J, Ye C, Moskovits N, Raver-Shapira N, Minsky N, Pirngruber J, Tarcic G and others. The histone H2B-specific ubiquitin ligase RNF20/hBRE1 acts as a putative tumor suppressor through selective regulation of gene expression. Genes Dev 2008;22(19):2664-76 .
Goodarzi AA, Noon AT, Deckbar D, Ziv Y, Shiloh Y, Lobrich M, Jeggo PA. ATM signaling facilitates repair of DNA double-strand breaks associated with heterochromatin. Mol Cell 2008;31(2):167-77 .
Cheng WH, Muftic D, Muftuoglu M, Dawut L, Morris C, Helleday T, Shiloh Y, Bohr VA. WRN is required for ATM activation and the S-phase checkpoint in response to interstrand cross-link-induced DNA double-strand breaks. Mol Biol Cell 2008;19(9):3923-33 .
Elkon R, Vesterman R, Amit N, Ulitsky I, Zohar I, Weisz M, Mass G, Orlev N, Sternberg G, Blekhman R and others. SPIKE--a database, visualization and analysis tool of cellular signaling pathways. BMC Bioinformatics 2008;9:110 .
Biton S, Barzilai A, Shiloh Y. The neurological phenotype of ataxia-telangiectasia: Solving a persistent puzzle. DNA Repair (Amst) 2008;7(7):1028-38 .
Barzilai A, Biton S, Shiloh Y. The role of the DNA damage response in neuronal development, organization and maintenance. DNA Repair (Amst) 2008;7(7):1010-27 .
Assaf Y, Galron R, Shapira I, Nitzan A, Blumenfeld-Katzir T, Solomon AS, Holdengreber V, Wang ZQ, Shiloh Y, Barzilai A. MRI evidence of white matter damage in a mouse model of Nijmegen breakage syndrome. Exp Neurol 2008;209(1):181-91.
Matsuoka S, Ballif BA, Smogorzewska A, McDonald ER, 3rd, Hurov KE, Luo J, Bakalarski CE, Zhao Z, Solimini N, Lerenthal Y and others. ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science 2007;316(5828):1160-6.
Elkon R, Linhart C, Halperin Y, Shiloh Y, Shamir R. Functional genomic delineation of TLR-induced transcriptional networks. BMC Genomics 2007;8:394 .
Chen BP, Uematsu N, Kobayashi J, Lerenthal Y, Krempler A, Yajima H, Lobrich M , Shiloh Y, Chen DJ. Ataxia telangiectasia mutated (ATM) is essential for DNA-PKcs phosphorylations at the Thr-2609 cluster upon DNA double strand break. J Biol Chem 2007;282(9):6582-7 .
Blank M, Shiloh Y. Programs for cell death: apoptosis is only one way to go. Cell Cycle 2007;6(6):686-95 .
Biton S, Gropp M, Itsykson P, Pereg Y, Mittelman L, Johe K, Reubinoff B, Shiloh Y. ATM-mediated response to DNA double strand breaks in human neurons derived from stem cells. DNA Repair (Amst) 2007;6(1):128-34 .
Alterman N, Fattal-Valevski A, Moyal L, Crawford TO, Lederman HM, Ziv Y, Shiloh Y. Ataxia-telangiectasia: mild neurological presentation despite null ATM mutation and severe cellular phenotype. Am J Med Genet A 2007;143A(16):1827-34 .
Ziv Y, Bielopolski D, Galanty Y, Lukas C, Taya Y, Schultz DC, Lukas J, Bekker-Jensen S, Bartek J, Shiloh Y. Chromatin relaxation in response to DNA double-strand breaks is modulated by a novel ATM- and KAP-1 dependent pathway. Nat Cell Biol 2006;8(8):870-6 .
Shiloh Y . The ATM-mediated DNA-damage response: taking shape. Trends Biochem Sci 2006;31(7):402-10 .
Rashi-Elkeles S, Elkon R, Weizman N, Linhart C, Amariglio N, Sternberg G, Rechavi G, Barzilai A, Shamir R, Shiloh Y. Parallel induction of ATM-dependent pro- and antiapoptotic signals in response to ionizing radiation in murine lymphoid tissue. Oncogene 2006;25(10):1584-92 .
Pereg Y, Lam S, Teunisse A, Biton S, Meulmeester E, Mittelman L, Buscemi G, Okamoto K, Taya Y, Shiloh Y and others. Differential roles of ATM- and Chk2-mediated phosphorylations of Hdmx in response to DNA damage. Mol Cell Biol 2006;26(18):6819-31 .
Kirshner J, Jobling MF, Pajares MJ, Ravani SA, Glick AB, Lavin MJ, Koslov S, Shiloh Y, Barcellos-Hoff MH. Inhibition of transforming growth factor-beta1 signaling attenuates ataxia telangiectasia mutated activity in response to genotoxic stress. Cancer Res 2006;66(22):10861-9 .
Dar I, Biton S, Shiloh Y, Barzilai A. Analysis of the ataxia telangiectasia mutated-mediated DNA damage response in murine cerebellar neurons. J Neurosci 2006;26(29):7767-74 .
Blank M, Lerenthal Y, Mittelman L, Shiloh Y. Condensin I recruitment and uneven chromatin condensation precede mitotic cell death in response to DNA damage. J Cell Biol 2006;174(2):195-206 .
Biton S, Dar I, Mittelman L, Pereg Y, Barzilai A, Shiloh Y. Nuclear ataxia-telangiectasia mutated (ATM) mediates the cellular response to DNA double strand breaks in human neuron-like cells. J Biol Chem 2006;281(25):17482-91 .
Ziv S, Brenner O, Amariglio N, Smorodinsky NI, Galron R, Carrion DV, Zhang W, Sharma GG, Pandita RK, Agarwal M and others. Impaired genomic stability and increased oxidative stress exacerbate different features of Ataxia-telangiectasia. Hum Mol Genet 2005;14(19):2929-43 .
Shamir R, Maron-Katz A, Tanay A, Linhart C, Steinfeld I, Sharan R, Shiloh Y, Elkon R. EXPANDER--an integrative program suite for microarray data analysis. BMC Bioinformatics 2005;6:232 .
Pereg Y, Shkedy D, de Graaf P, Meulmeester E, Edelson-Averbukh M, Salek M, Biton S, Teunisse AF, Lehmann WD, Jochemsen AG and others. Phosphorylation of Hdmx mediates its Hdm2- and ATM-dependent degradation in response to DNA damage. Proc Natl Acad Sci U S A 2005;102(14):5056-61 .
Okamoto K, Kashima K, Pereg Y, Ishida M, Yamazaki S, Nota A, Teunisse A, Migliorini D, Kitabayashi I, Marine JC and others. DNA damage-induced phosphorylation of MdmX at serine 367 activates p53 by targeting MdmX for Mdm2-dependent degradation. Mol Cell Biol 2005;25(21):9608-20 .
Meulmeester E, Pereg Y, Shiloh Y, Jochemsen AG. ATM-mediated phosphorylations inhibit Mdmx/Mdm2 stabilization by HAUSP in favor of p53 activation. Cell Cycle 2005;4(9):1166-70 .
Linhart C, Elkon R, Shiloh Y, Shamir R. Deciphering transcriptional regulatory elements that encode specific cell cycle phasing by comparative genomics analysis. Cell Cycle 2005;4(12):1788-97 .
Elkon R, Rashi-Elkeles S, Lerenthal Y, Linhart C, Tenne T, Amariglio N, Rechavi G, Shamir R, Shiloh Y. Dissection of a DNA-damage-induced transcriptional network using a combination of microarrays, RNA interference and computational promoter analysis. Genome Biol 2005;6(5):R43 .
Bhoumik A, Takahashi S, Breitweiser W, Shiloh Y, Jones N, Ronai Z. ATM-dependent phosphorylation of ATF2 is required for the DNA damage response. Mol Cell 2005;18(5):577-87 .
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