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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.

>Full Text Article

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

>Full Text Article

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

>Full Text Article

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 

>Full Text Article

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

>Full Text Article

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.

>Full Text Article

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.

>Full Text Article

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 

>Full Text Article

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 

>Full Text Article

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 

>Full Text Article

Santoro, R.

Looking for a job in a dynamic and collaborative working place? LncRNAs are recruiting!

Cell (2021) 184(25):6019-6021 

>Full Text Article

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 

>Full Text Article

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.

>PubMed  >Full Text Article 

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 

>bioRxiv

ACCEPTED!!!!!!

Roganowicz, M., Baer, D., and Santoro, R.

BAZ2A-RNA mediated association with TOP2A and KDM1A represses gene expression in prostate cancer. 

>bioRxiv

2021_Book_IntroductionToEpigenetics 1.png

Renato Paro, Ueli Grossniklaus, Raffaella Santoro, Anton Wutz

Introduction to Epigenetics

>Open access text book

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

>bioRxiv

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

>bioRxiv

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

>Full Text Article

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

>PubMed  >Full Text Article 

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

>PubMed  >Full Text Article 

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Kresoja-Rakic J, Santoro R

Nucleolus and rRNA Gene Chromatin in Early Embryo Development

Trends Genet. 2019 Jul 35(11): 868-879

>PubMed  >Full Text Article 

Bersaglieri C, Santoro R.

Genome Organization in and around the Nucleolus

Cells 2019 Jun 12;8(6). pii: E579

>PubMed  >Full Text Article 

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

>PubMed >Full Text Article

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

>PubMed >Full Text Article

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

>PubMed >Full Text Article

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

>PubMed >Full Text Article

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

>PubMed >Full Text Article

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

>PubMed >Full Text Article

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

>PubMed >Full Text Article

>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

>PubMed >Full Text Article

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

>PubMed >Full Text Article

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

>PubMed >Full Text Article

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

>PubMed >Full Text Article

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

>PubMed >Full Text Article

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

>PubMed >Full Text Article

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

>PubMed >Full Text Article

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

>PubMed >Full Text Article

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

>PubMed

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

>PubMed >Full Text Article

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

>PubMed

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

>PubMed

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

>PubMed

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

>PubMed

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

>PubMed

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

>PubMed

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

>PubMed

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

>PubMed

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

>PubMed

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

>PubMed

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

>PubMed

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

>PubMed

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

>PubMed

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

>PubMed

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

>PubMed

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

>PubMed

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

>PubMed

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

>PubMed

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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