>> Publications
Kaivalya Walavalkar, Shivani Gupta, Jelena Kresoja-Rakic, Mathieu Raingeval, Chiara Mungo, and Raffaella Santoro
Single-cell dynamics of genome-nucleolus interactions captured by nucleolar laser microdissection (NoLMseq)
bioRxiv (2024) 2024.2006.2018.599512. 10.1101/2024.06.18.599512.
Shivani Gupta, Cristiana Bersaglieri, Dominik Bär, Mathieu Raingeval, Luana Schaab, and Raffaella Santoro
NPM1 mediates genome-nucleolus interactions and the establishment of their repressive chromatin states.
bioRxiv (2024) 2024.2007.2003.601885. 10.1101/2024.07.03.601885
Luigi Lerra, Martina Panatta, Dominik Bär, Isabella Zanini, Jennifer Yihong Tan, Agnese Pisano, Chiara Mungo, Celia Baroux, Vikram Govind Panse, Ana C. Marques, Raffaella Santoro
An RNA-dependent and phase-separated active subnuclear compartment safeguards repressive chromatin domains
Molecular Cell (2024) doi: 10.1016/j.molcel.2024.03.015
Meneka Rupasinghe, Cristiana Bersaglieri, Deena M Leslie Pedrioli, Patrick G. A. Pedrioli, Martina Panatta, Michael O. Hottiger, Paolo Cinelli, Raffaella Santoro
PRAMEL7 and CUL2 decrease NuRD stability to establish ground-state pluripotency
EMBO Reports (2024) 25(3):1453-1468
Cristiana Bersaglieri and Raffaella Santoro
Methods for mapping 3D-chromosome architecture around nucleoli
Curr Opin Cell Biol (2023) 81:102171
doi: 10.1016/j.ceb.2023.102171
Marcin Roganowicz, Dominik Bär, Cristiana Bersaglieri, Rossana Aprigliano, Raffaella Santoro
BAZ2A-RNA mediated association with TOP2A and KDM1A represses genes implicated in prostate cancer
Life Science Alliance (2023) 6(7):e202301950
DOI: 10.26508/lsa.202301950.
Randall RS, Jourdain C, Nowicka A, Kaduchová K, Kubová M, Ayoub MA, Schubert V, Tatout C, Colas I, Kalyanikrishna, Desset S, Mermet S, Boulaflous-Stevens A, Kubalová I, Mandáková T, Heckmann S, Lysak MA, Panatta M, Santoro R, Schubert D, Pecinka A, Routh D, Baroux C.
Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes
Nucleus (2022) 13, 277-299.
Rupasinghe, M., Bersaglieri, C., Pedrioli, DML, Pedrioli, PGA., Hottiger, M, Cinelli, P., Santoro, R.
PRAMEL7/CUL2 axis regulates NuRD stability to establish ground-state pluripotency in embryonic stem cells
bioRxiv (2022) --> in press in EMBO Reports
Müller, M., Schaefer, M., Fäh, T., Spies, D., Hermes, V., Ngondo, RP, Peña-Hernández, R., Santoro, R., Ciaudo, C.
Argonaute proteins regulate a specific network of genes through KLF4 in mouse embryonic stem cells
Stem Cell Reports (2022) S2213-6711(22)00147-3
Bersaglieri, C., Kresoja-Rakic, J., Gupta, S., Bär, D., Kuzyakiv, R. Panatta, M., Santoro, R.
Genome-wide maps of nucleolus interactions reveal distinct layers of repressive chromatin domains
Nature Communications (2022) 13,1483
Santoro, R.
Looking for a job in a dynamic and collaborative working place? LncRNAs are recruiting!
Cell (2021) 184(25):6019-6021
Peña-Hernández, R., Aprigliano, R., Frommel, S., Pietrzak, K., Steiger, S., Roganowicz, M., Lerra, L., Bizzarro, J., Santoro, R.
BAZ2A-mediated repression via H3K14ac-marked enhancers promotes prostate cancer stem cells
EMBO Rep (2021) e53014
Diener,J., Baggiolini, A., Pernebrink, M., Dalcher, D., Lerra, L., Cheng, P.F., Varum, S., Häusel, J., Stierli, S., Treier, M., Studer, L., Basler, K., Levesque, M.P., Dummer, R., Santoro, R., Cantù, C., Sommer, L.
Epigenetic control of melanoma cell invasiveness by the stem cell factor SALL4
Nat Commun (2021) 12(1):5056.
ACCEPTED!!!!!!
Müller, M., Schaefer, M., Fäh, T., Spies, D., Peña-Hernández, R., Santoro, R., Ciaudo, C.
ARGONAUTE proteins regulate a specific network of genes through KLF4 in mouse embryonic stem cells
ACCEPTED!!!!!!
Roganowicz, M., Baer, D., and Santoro, R.
BAZ2A-RNA mediated association with TOP2A and KDM1A represses gene expression in prostate cancer.
Renato Paro, Ueli Grossniklaus, Raffaella Santoro, Anton Wutz
Introduction to Epigenetics
ACCEPTED!!!!!!!!!
Bersaglieri, C., Kresoja-Rakic, J., Gupta, S., Bär, D., Kuzyakiv, R., Santoro, R.
Genome-wide maps of nucleolus interactions reveal distinct layers of repressive chromatin domains
Peña-Hernández, R., Aprigliano, R., Frommel, S., Pietrzak, K., Steiger, S., Roganowicz, M., Bizzarro, J., Santoro, R.
BAZ2A association with H3K14ac is required for the dedifferentiation of prostate cancer cells into a cancer stem-like state
Dalcher, D., Tan, JY, Bersaglieri, C., Peña-Hernández, R., Vollenweider, E., Zeyen, S., Schmid, MW., Bianchi, V., Butz, S., Roganowicz, M., Kuzyakiv, R., Baubec, T., Marques, AC., Santoro, R.
BAZ2A safeguards genome architecture of ground-state pluripotent stem cells
EMBO J (2020) 39:e105606
Gupta, S., Santoro, R.
Regulation and roles of the nucleolus in embryonic stem cells: from ribosome biogenesis to genome organization
Stem Cell Reports (2020) 15(6),1206-1219
Pietrzak, K., Kuzyakiv, R., Simon, R., Bolis, M., Bär, D., Aprigliano, R., Theurillat, JP., Sauter, G., Santoror, R.
TIP5 primes prostate luminal cells for the oncogenic transformation mediated by PTEN-loss
Proc Natl Acad Sci USA (2020) 117, 3637-3647
Kresoja-Rakic J, Santoro R
Nucleolus and rRNA Gene Chromatin in Early Embryo Development
Trends Genet. 2019 Jul 35(11): 868-879
Bersaglieri C, Santoro R.
Genome Organization in and around the Nucleolus
Cells 2019 Jun 12;8(6). pii: E579
Wyck S, Herrera C, Requena CE, Bittner L, Hajkova P, Bollwein H, Santoro R
Oxidative stress in sperm affects the epigenetic reprogramming in early embryonic development
Epigenetics & Chromatin. 2018 Oct 17;11(1):60
Zingg D, Debbache J, Peña-Hernández R, Antunes AT, Schaefer SM, Cheng PF, Zimmerli D, Haeusel J, Calçada RR, Tuncer E, Zhang Y, Bossart R, Wong KK, Basler K, Dummer R, Santoro R, Levesque MP, Sommer L
EZH2-Mediated Primary Cilium Deconstruction Drives Metastatic Melanoma Formation
Cancer Cell. 2018 Jul 9;34(1):69-84 e 14.
>PubMed >Full Text Article
Graf U, Casanova E, Wyck S, Dalcher D, Gatti M, Vollenweider E, Okoniewski M, Weber FA, Patel SS, Schmid M, Li J, Sharif J, Wanner GA, Koseki H, Wong J, Pelczar P, Penengo L, Santoro R*, Cinelli P*
*Senior and corresponding authors
Pramel7 mediates ground state pluripotency through proteasomal-epigenetic combined pathways
Nature Cell Biology (2017) 19, 763-773
>PubMed >UZH press release
Leone S, Bär D, Slabber CF, Dalcher D, Santoro R
The RNA helicase DHX9 establishes nucleolar heterochromatin and this activity is required for embryonic stem cell differentiation
EMBO Reports 2017 Jun; 18:1248-1262
>PubMed >Full Text Article
Leone S and Santoro R
Challenges in the analysis of long noncoding RNA functionality
FEBS Letter 2016 Aug;590(15):2342-2353
>PubMed >Full Text Article
Böhm M, Wachte M, Marques J, Streiff N, Nanni P, Mamchaoui K, Santoro R, Schäfer BW
Helicase CHD4 functions as epigenetic co-regulator of PAX3-FOXO1 activity in alveolar rhabdomyosarcoma
Journal of Clinical Investigation 2016 Nov 126(11): 4237-4249
>PubMed >Full Text Article
Kresoja-Rakic J, Kapaklikaya E, Ziltener G, Dalcher D, Santoro R, Christensen BC, Johnson KC, Schwaller B, Weder W, Stahel RA, Felley-Bosco E
Identification of cis- and trans-acting elements regulating calretinin expression in mesothelioma cells
Oncotarget. 2016 Feb 1
Gu L, Frommel SC, Oakes CC, Simon R, Grupp K, Gerig CY, Bär D, Robinson MD, Baer C, Weiss M, Gu Z, Schapira M, Kuner R, Sültmann H, Provenzano M; ICGC Project on Early Onset Prostate Cancer, Yaspo ML, Brors B, Korbel J, Schlomm T, Sauter G, Eils R, Plass C, Santoro R
BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence
Nat Genet. 2015 Jan;47(1):22-30
Cheng PF, Shakhova O, Widmer DS, Eichhoff OM, Zingg D, Frommel SC, Belloni B, Raaijmakers MI, Goldinger SM, Santoro R, Hemmi S, Sommer L, Dummer R, Levesque MP
Methylation-dependent SOX9 expression mediates invasion in human melanoma cells and is a negative prognostic factor in advanced melanoma
Genome Biol. 2015 Feb 22;16:42
Shakhova O, Cheng P, Mishra PJ, Zingg D, Schaefer SM, Debbache J, Häusel J, Matter C, Guo T, Davis S, Meltzer P, Mihic-Probst D, Moch H, Wegner M, Merlino G, Levesque MP, Dummer R, Santoro R, Cinelli P, Sommer L
Antagonistic cross-regulation between Sox9 and Sox10 controls an anti-tumorigenic program in melanoma
PLoS Genet. 2015 Jan 28;11(1):e1004877
Zingg D, Debbache J, Schaefer SM, Tuncer E, Frommel SC, Cheng P, Arenas-Ramirez N, Haeusel J, Zhang Y, Bonalli M, McCabe MT, Creasy CL, Levesque MP, Boyman O, Santoro R, Shakhova O, Dummer R, Sommer L
The epigenetic modifier EZH2 controls melanoma growth and metastasis through silencing of distinct tumour suppressors
Nat Commun. 2015 Jan 22;6:6051
Savić N, Bär D, Leone S, Frommel SC, Weber FA, Vollenweider E, Ferrari E, Ziegler U, Kaech A, Shakhova O, Cinelli P, Santoro R
lncRNA Maturation to Initiate Heterochromatin Formation in the Nucleolus Is Required for Exit from Pluripotency in ESCs
Cell Stem Cell. 2014 Dec 4;15(6):720-34
>Highlighted in The Nucleolus Gets the Silent Treatment. Cell Stem Cell. 2014 Dec 4;15(6):675-6
Bachmann SB, Frommel SC, Camicia R, Winkler HC, Santoro R, Hassa PO
DTX3L and ARTD9 inhibit IRF1 expression and mediate in cooperation with ARTD8 survival and proliferation of metastatic prostate cancer cells
Mol Cancer. 2014 May 27;13:125
Léger K, Bär D, Savić N, Santoro R, Hottiger MO
ARTD2 activity is stimulated by RNA
Nucleic Acids Res. 2014 Apr;42(8):5072-82
Santoro, R.
Analysis of chromatin composition of repetitive sequences: the ChIP-Chop assay
Methods Mol Biol. 2014;1094:319-28
Dantzer, F. and Santoro, R.
The expanding role of PARPs in the establishment and maintenance of heterochromatin
FEBS J. 2013 Jun 3. doi: 10.1111/febs.12368
Guetg, C. and Santoro, R.
Formation of nuclear heterochromatin: the nucleolar point of view
Epigenetics. 2012 Aug 1;7(8). ahead of print
Guetg, C. and Santoro, R.
Noncoding RNAs link PARP1 to heterochromatin
Cell Cycle. 2012 Jun 15;11(12):2217-8. Epub 2012 Jun 15.
Guetg, C., Scheifele, F., Rosenthal, F., Hottiger, M.O. and Santoro, R.
Inheritance of silent rDNA chromatin is mediated by PARP1 via non-coding RNA.
Molecular Cell 45, 790-800, 2012
Commented in Preview “PARP1 Parylation Promotes Silent Locus Transmission in the Nucleolus: The Suspicion Confirmed” Isabelle et al. Molecular Cell 45, 706-707, 2012
Erener,E., Petrilli,V., Kassner, I., Minotti,R., Castillo, R., Santoro,R. Hassa, P.O., Tschopp, J.,and Hottiger, M.O.
Inflammasome-activated Caspase 7 cleaves PARP1 to enhance the expression of a subset of NF-kb target genes.
Molecular Cell 10.1016/j.molcel.2012.02.016, 2012
Santoro, R.
The epigenetics of the nucleolus: structure and function of active and silent ribosomal RNA genes.
In “The Nucleolus”, Protein Reviews series, Springer, ed M.Olson. 15, 57-82, 2012
Osorio, G., Varela, I., Lara, E., Puente, X.S., Espada, J., Santoro, R., Freije, J.M.P., Fraga, M.F., López-Otín, C.
Nuclear envelope alterations generate an aging-like epigenetic pattern in mice deficient in Zmpste24 metalloprotease.
Aging Cell 9, 947-957, 2010
Guetg C., Lienemann P., Sirri V., Grummt I., Hernandez-Verdu D., Hottiger M.O., Fussenegger M. and Santoro R.:
The NoRC complex mediates heterochromatin and stability of silent rRNA genes and centromeric repeats
EMBO J. 29(13): 2135-2146, 2010
Santoro, R., Schmitz, K.M., Sandoval, J., Grummt I.
Intergenic transcripts originating from a subclass of ribosomal DNA repeats silence ribosomal RNA genes in trans.
EMBO Rep. 11, 52-58, 2010
Santoro, R.*, Lienemann, P. and Fussenegger.M.
Epigenetic engineering of ribosomal RNA genes enhances protein production.
PLoSone 4, e6653, 2009
Espada, J., Ballestar, E., Santoro, R., Fraga, M.F., Villar-Garea, A., Nemeth, A., Lopez-Serra, L., Ropero, S., Aranda, A., Orozco, H., Moreno, V., Juarranz, A., Stockert, J.C., Längst, G., Grummt, I., Bickmore, W. and Esteller, M.
Epigenetic disruption of ribosomal rRNA genes and nucleolar architecture in DNA methyltransferase (Dnmt1) deficient cells.
Nucl. Acid Research 35, 2191-2198, 2007
Mayer, C., Schmitz, K. Li, J., Grummt, I. and Santoro, R.
Intergenic transcripts regulate the epigenetic state of rRNA genes.
Mol. Cell 22, 351-361, 2006
Santoro, R.* and Grummt, I.
Epigenetic mechanisms of rRNA silencing: Temporal order of NoRC recruitment, histone modifications, chromatin remodeling and DNA methylation.
Mol. Cell. Biol. 25, 2539-2546, 2005
Li, J., Santoro, R. and Grummt, I.
The chromatin remodeling complex NoRC controls replication timing of rRNA genes.
EMBO J. 24, 120-7, 2005
Santoro, R.* and De Lucia, F.
Many players, one goal: how chromatin states are inherited during cell division.
Biochem. Cell Biol. 83, 332-343, 2005
Santoro, R., Li, J. and Grummt I.
The nucleolar remodeling complex NoRC mediates heterochromatin formation and silencing of ribosomal gene transcription.
Nature Genetics 32, 393-96, 2002
Commented in News and Views “Uniting the paths to gene silencing” Pikaard and Lawrence
Nature Genet. 32, 340-341
Zhou, Y., Santoro, R. and Grummt, I.
The chromatin remodeling complex NoRC targets HDAC1 to the ribosomal gene promoter and represses RNA polymerase I transcription.
EMBO J. 21, 4632-4640, 2002
Santoro R. and Grummt, I.
Molecular mechanisms mediating methylation dependent silencing of ribosomal gene transcription.
Mol. Cell 8, 719-725, 2001
Strohner, R., Nemeth, A., Jansa, P., Hoffmann-Rohrer, U., Santoro, R., Längst, G. and Grummt, I.
NoRC - a novel member of mammalian ISWI-containing chromatin remodeling machines.
EMBO J. 20, 4892-4900, 2001
Santoro, R., Wolfl, S. and Saluz, H.P.
UV-Laser induced protein/DNA crosslinking reveals sequence variations of DNA elements bound by c-Jun in vivo.
Biochem. Biophys. Res. Commun. 256, 68-74, 1999
Reale, A., Marenzi, S., Santoro, R., D´Erme , M., Zardo, G., Strom, R., Caiafa, P.
H1-H1 cross-linking efficiency dependes on genomic DNA methylation.
Biochem. Biophys. Res. Commun. 227, 768-774, 1996
Zardo, G., Santoro, R., D´Erme, M., Reale, A., Guidobaldi, L., Caiafa, P., Strom, R.
Specific inhibitory effect of H1e histone somatic variant on in vitro DNA methylation process.
Biochem. Biophys. Res. Commun. 220, 102-107, 1996
Santoro, R., D´Erme, M., Mastrantonio, S., Reale, A., Marenzi, S., Zardo, G., Caiafa, P.
Specific variants of H1 histone regulate CpG methylation in eukaryotic DNA.
Gene 157, 247-251, 1995
Caiafa, P., Reale, A., Santoro, R., D´Erme, M., Marenzi, S., Strom, R.
Does hypomethylation of linker DNA play a role in chromatin condensantion?
Gene 157, 253-256, 1995
Santoro, R., Di Matteo and Lavia, P.
Hydrazin to study DNA methylation, conformation and interaction with proteins.
In “DNA and Nucleoprotein Structure in vivo“, Springer-Verlag, ed. H.P. Saluz 1995
Santoro, R., D´Erme, M., Mastrantonio, S., Reale, A., Marenzi, S., Saluz, H.P., Strom, R., Caiafa, P.
Binding of H1e-c variants to CpG-rich DNA correlates with the inhibitory effect on enzymatic DNA methylation.
Biochem. Journal 305, 739-744, 1994
Santoro, R., D´Erme, M., Reale, A., Marenzi, S., Strom, R., Caiafa, P.
Effect of H1 histone isoforms on the methylation of single- or double-stranded DNA.
Biochem. Biophys. Res. Commun. 190, 86-91, 1993
D´Erme, M., Santoro, R., Reale, A., Marenzi, S., Strom, R., Caiafa, P.
Inhibition of CpG methylation in linker DNA by H1 histone.
Biochem. Biophys. Acta 1173, 209-216, 1993
