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Department of Molecular Mechanisms of Disease

Publications - Prof. Dr. R. Santoro

Full list of publications

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

Nat Commun (2022) 13(1):1483

 

Raffaella Santoro

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 PF, Varum S, Häusel J, Stierli S, Treier M, Studer L, Basler K, Levesque MP, 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

 

Paro R, Grossniklaus U, Santoro R, Wutz A

Introduction to Epigenetics

Open acces text book

 

Dalcher D, Yihong Tan J, 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

The EMBO Journal (2020) e105606

 

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

 

Gupta S, Santoro R

Regulation and Roles of the Nucleolus in Embryonic Stem Cells: From Ribosome Biogenesis to Genome Organization

Stem Cell Reports. 2020 Sep 8:S2213-6711(20)30343-X

 

Pietrzak K, Kuzyakiv R, Simon R, Bolis M, Bär D, Aprigliano R, Theurillat JP, Sauter G, Santoro R

TIP5 primes prostate luminal cells for the oncogenic transformation mediated by PTEN-loss

PNAS February 18, 2020 117 (7) 3637-3647

 

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.

 

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, 763-773UZH 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

 

Leone S, Santoro R

Challenges in the analysis of long noncoding RNA functionality

FEBS Letter 2016 Aug;590(15):2342-2353

 

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

 

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, 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, Santoro R

Formation of nuclear heterochromatin: the nucleolar point of view

Epigenetics. 2012 Aug 1;7(8). ahead of print

 

Guetg C, 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 MO, 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 PO, Tschopp J, Hottiger MO

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 XS, Espada J, Santoro R, Freije JMP, Fraga MF, 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 MO, Fussenegger M, 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 KM, 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, Fussenegger M

Epigenetic engineering of ribosomal RNA genes enhances protein production.

PLoSone 4, e6653, 2009

 

Espada J, Ballestar E, Santoro R, Fraga MF, Villar-Garea A, Nemeth A, Lopez-Serra L, Ropero S, Aranda A, Orozco H, Moreno V, Juarranz A, Stockert JC, Längst G, Grummt I, Bickmore W, 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, Santoro R

Intergenic transcripts regulate the epigenetic state of rRNA genes.

Mol. Cell 22, 351-361, 2006

 

Santoro R*, 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, Grummt I

The chromatin remodeling complex NoRC controls replication timing of rRNA genes.

EMBO J. 24, 120-7, 2005

 

Santoro R

The silence of the ribosomal RNA genes.

Cell Mol. Life Sci. 62, 2067-2079, 2005

 

Santoro R*, 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, 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, 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, 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, Grummt I

NoRC - a novel member of mammalian ISWI-containing chromatin remodeling machines.

EMBO J. 20, 4892-4900, 2001

 

Santoro R, Wolfl S, Saluz HP

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, 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 HP, 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

 

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

 

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