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Kresoja-Rakic J, Santoro R

Nucleolus and rRNA Gene Chromatin in Early Embryo Development

Trends Genet. 2019 Jul pii: S0168-9525(19)30125-8

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Bersaglieri C, Santoro R.

Genome Organization in and around the Nucleolus

Cells 2019 Jun 12;8(6). pii: E579

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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

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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.
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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
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Leone S and Santoro R
Challenges in the analysis of long noncoding RNA functionality
FEBS Letter 2016 Aug;590(15):2342-2353
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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
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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

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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

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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

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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

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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

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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

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>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

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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

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Santoro, R.
Analysis of chromatin composition of repetitive sequences: the ChIP-Chop assay
Methods Mol Biol. 2014;1094:319-28

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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

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Guetg, C. and Santoro, R.
Formation of nuclear heterochromatin: the nucleolar point of view
Epigenetics. 2012 Aug 1;7(8). ahead of print

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Guetg, C. and Santoro, R.
Noncoding RNAs link PARP1 to heterochromatin
Cell Cycle. 2012 Jun 15;11(12):2217-8. Epub 2012 Jun 15.

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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

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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

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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

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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

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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

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Santoro, R.*, Lienemann, P. and Fussenegger.M.
Epigenetic engineering of ribosomal RNA genes enhances protein production.
PLoSone 4, e6653, 2009

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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

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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

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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

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Li, J., Santoro, R. and Grummt, I.
The chromatin remodeling complex NoRC controls replication timing of rRNA genes.
EMBO J. 24, 120-7, 2005

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Santoro, R.
The silence of the ribosomal RNA genes.
Cell Mol. Life Sci. 62, 2067-2079, 2005

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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

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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

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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

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Santoro R. and Grummt, I.
Molecular mechanisms mediating methylation dependent silencing of ribosomal gene transcription.
Mol. Cell 8, 719-725, 2001

>PubMed

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

>PubMed

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

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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

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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

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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

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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

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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

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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

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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

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Caiafa, P., Reale, A., D´Erme, M., Allegra, P., Santoro, R., Strom, R., Caiafa, P.
Histones and DNA methylation in mammalian chromatin. II presence of non-inhibitory tightly-bound histones.
Biochem. Biophys. Acta 1129, 43-48, 1991

>PubMed

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