Prof. Roberto Ferrari

Professore Associato

Pubblicazioni selezionate

de Llobet Cucalon L, Di Vona C, Morselli M, Vezzoli M, Montanini B, Teichmann M, de la Luna S, Ferrari R. An RNA Polymerase III General Transcription Factor Engages in Cell Type-Specific Chromatin Looping. Int J Mol Sci. 2022 Feb 18;23(4):2260. doi: 10.3390/ijms23042260. PMID: 35216376; PMCID: PMC8878802.

Ferrari R, de Llobet Cucalon LI, Di Vona C, Le Dilly F, Vidal E, Lioutas A, Oliete JQ, Jochem L, Cutts E, Dieci G, Vannini A, Teichmann M, de la Luna S, Beato M. (2020) TFIIIC Binding to Alu Elements Controls Gene Expression via Chromatin Looping and Histone Acetylation. Molecular cell 77(3) 475-487.e11 [DOI  PMID]

Nacht AS, Ferrari R, Zaurin R, Scabia V, Carbonell-Caballero J, Le Dily F, Quilez J, Leopoldi A, Brisken C, Beato M, Vicent GP. (2019) C/EBPalpha mediates the growth inhibitory effect of progestins on breast cancer cells. The EMBO journal 38(18) e101426 [DOI  PMID]

Le Dily F, Vidal E, Cuartero Y, Quilez J, Nacht AS, Vicent GP, Carbonell-Caballero J, Sharma P, Villanueva-Canas JL, Ferrari R, De Llobet LI, Verde G, Wright RHG, Beato M. (2019) Hormone-control regions mediate steroid receptor-dependent genome organization. Genome research 29(1) 29-39 [DOI  PMID]

Dieci G, Ferrari R. (2018) The third (III) road to cell transformation. Cell cycle (Georgetown, Tex.) 17(4) 410-411 [DOI  PMID]

Bosio MC, Fermi B, Spagnoli G, Levati E, Rubbi L, Ferrari R, Pellegrini M, Dieci G. (2017) Abf1 and other general regulatory factors control ribosome biogenesis gene expression in budding yeast. Nucleic acids research 45(8) 4493-4506 [DOI  PMID]

Mitton B, Chae HD, Hsu K, Dutta R, Aldana-Masangkay G, Ferrari R, Davis K, Tiu BC, Kaul A, Lacayo N, Dahl G, Xie F, Li BX, Breese MR, Landaw EM, Nolan G, Pellegrini M, Romanov S, Xiao X, Sakamoto KM. (2016) Small molecule inhibition of cAMP response element binding protein in human acute myeloid leukemia cells. Leukemia 30(12) 2302-2311 [DOI  PMID]

Morselli M, Pastor WA, Montanini B, Nee K, Ferrari R, Fu K, Bonora G, Rubbi L, Clark AT, Ottonello S, Jacobsen SE, Pellegrini M. (2017) Correction: In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse. eLife 6 [DOI  PMID]

Flinders C, Lam L, Rubbi L, Ferrari R, Fitz-Gibbon S, Chen PY, Thompson M, Christofk H, B Agus D, Ruderman D, Mallick P, Pellegrini M. (2016) Epigenetic changes mediated by polycomb repressive complex 2 and E2a are associated with drug resistance in a mouse model of lymphoma. Genome medicine 8(1) 54 [DOI  PMID]

Morselli M, Pastor WA, Montanini B, Nee K, Ferrari R, Fu K, Bonora G, Rubbi L, Clark AT, Ottonello S, Jacobsen SE, Pellegrini M. (2015) In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse. eLife 4 e06205 [DOI  PMID]

Org T, Duan D, Ferrari R, Montel-Hagen A, Van Handel B, Kerenyi MA, Sasidharan R, Rubbi L, Fujiwara Y, Pellegrini M, Orkin SH, Kurdistani SK, Mikkola HK. (2015) Scl binds to primed enhancers in mesoderm to regulate hematopoietic and cardiac fate divergence. The EMBO journal 34(6) 759-77 [DOI  PMID]

Li B, Su T, Ferrari R, Li JY, Kurdistani SK. (2014) A unique epigenetic signature is associated with active DNA replication loci in human embryonic stem cells. Epigenetics 9(2) 257-67 [DOI  PMID]

Ferrari R, Gou D, Jawdekar G, Johnson SA, Nava M, Su T, Yousef AF, Zemke NR, Pellegrini M, Kurdistani SK, Berk AJ. (2014) Adenovirus small E1A employs the lysine acetylases p300/CBP and tumor suppressor Rb to repress select host genes and promote productive virus infection. Cell host & microbe 16(5) 663-76 [DOI  PMID]

McBrian MA, Behbahan IS, Ferrari R, Su T, Huang TW, Li K, Hong CS, Christofk HR, Vogelauer M, Seligson DB, Kurdistani SK. (2013) Histone acetylation regulates intracellular pH. Molecular cell 49(2) 310-21 [DOI  PMID]

Dieci G, Bosio MC, Fermi B, Ferrari R. (2013) Transcription reinitiation by RNA polymerase III. Biochimica et biophysica acta 1829(3-4) 331-41 [DOI  PMID]

Chen XF, Lehmann L, Lin JJ, Vashisht A, Schmidt R, Ferrari R, Huang C, McKee R, Mosley A, Plath K, Kurdistani SK, Wohlschlegel J, Carey M. (2012) Mediator and SAGA have distinct roles in Pol II preinitiation complex assembly and function. Cell reports 2(5) 1061-7 [DOI  PMID]

Lehmann L, Ferrari R, Vashisht AA, Wohlschlegel JA, Kurdistani SK, Carey M. (2012) Polycomb repressive complex 1 (PRC1) disassembles RNA polymerase II preinitiation complexes. The Journal of biological chemistry 287(43) 35784-94 [DOI  PMID]

Van Handel B, Montel-Hagen A, Sasidharan R, Nakano H, Ferrari R, Boogerd CJ, Schredelseker J, Wang Y, Hunter S, Org T, Zhou J, Li X, Pellegrini M, Chen JN, Orkin SH, Kurdistani SK, Evans SM, Nakano A, Mikkola HK. (2012) Scl represses cardiomyogenesis in prospective hemogenic endothelium and endocardium. Cell 150(3) 590-605 [DOI  PMID]

Pellegrini M, Ferrari R. (2012) Epigenetic analysis: ChIP-chip and ChIP-seq. Methods in molecular biology (Clifton, N.J.) 802 377-87 [DOI  PMID]

Marban C, Su T, Ferrari R, Li B, Vatakis D, Pellegrini M, Zack JA, Rohr O, Kurdistani SK. (2011) Genome-wide binding map of the HIV-1 Tat protein to the human genome. PloS one 6(11) e26894 [DOI  PMID]

Tavenet A, Suleau A, Dubreuil G, Ferrari R, Ducrot C, Michaut M, Aude JC, Dieci G, Lefebvre O, Conesa C, Acker J. (2009) Genome-wide location analysis reveals a role for Sub1 in RNA polymerase III transcription. Proceedings of the National Academy of Sciences of the United States of America 106(34) 14265-70 [DOI  PMID]

Gekas C, Rhodes KE, Gereige LM, Helgadottir H, Ferrari R, Kurdistani SK, Montecino-Rodriguez E, Bassel-Duby R, Olson E, Krivtsov AV, Armstrong S, Orkin SH, Pellegrini M, Mikkola HK. (2009) Mef2C is a lineage-restricted target of Scl/Tal1 and regulates megakaryopoiesis and B-cell homeostasis. Blood 113(15) 3461-71 [DOI  PMID]

Ferrari R, Berk AJ, Kurdistani SK. (2009) Viral manipulation of the host epigenome for oncogenic transformation. Nature reviews. Genetics 10(5) 290-4 [DOI  PMID]

Ferrari R, Pellegrini M, Horwitz GA, Xie W, Berk AJ, Kurdistani SK. (2008) Epigenetic reprogramming by adenovirus e1a. Science (New York, N.Y.) 321(5892) 1086-8 [DOI  PMID]

Pham H, Ferrari R, Cokus SJ, Kurdistani SK, Pellegrini M. (2007) Modeling the regulatory network of histone acetylation in Saccharomyces cerevisiae. Molecular systems biology 3 153 [DOI  PMID]

Ferrari R, Dieci G. (2008) The transcription reinitiation properties of RNA polymerase III in the absence of transcription factors. Cellular & molecular biology letters 13(1) 112-8 [DOI  PMID]

Pagano A, Castelnuovo M, Tortelli F, Ferrari R, Dieci G, Cancedda R. (2007) New small nuclear RNA gene-like transcriptional units as sources of regulatory transcripts. PLoS genetics 3(2) e1 [DOI  PMID]

Dieci G, Yukawa Y, Alzapiedi M, Guffanti E, Ferrari R, Sugiura M, Ottonello S. (2006) Distinct modes of TATA box utilization by the RNA polymerase III transcription machineries from budding yeast and higher plants. Gene 379 12-25 [DOI  PMID]

Guffanti E, Ferrari R, Preti M, Forloni M, Harismendy O, Lefebvre O, Dieci G. (2006) A minimal promoter for TFIIIC-dependent in vitro transcription of snoRNA and tRNA genes by RNA polymerase III. The Journal of biological chemistry 281(33) 23945-57 [DOI  PMID]

Ferrari R, Rivetti C, Acker J, Dieci G. (2004) Distinct roles of transcription factors TFIIIB and TFIIIC in RNA polymerase III transcription reinitiation. Proceedings of the National Academy of Sciences of the United States of America 101(37) 13442-7 [DOI  PMID]

Ferrari R, Rivetti C, Dieci G. (2004) Transcription reinitiation properties of bacteriophage T7 RNA polymerase. Biochemical and biophysical research communications 315(2) 376-80 [DOI  PMID]

Giuliodori S, Percudani R, Braglia P, Ferrari R, Guffanti E, Ottonello S, Dieci G. (2003) A composite upstream sequence motif potentiates tRNA gene transcription in yeast. Journal of molecular biology 333(1) 1-20 [DOI  PMID]





Temi di ricerca


Prof. Roberto Ferrari's Lab main research interests can be summarized by this title:

Epigenetic Reprogramming in Normal and Cancer Cells: A Tail of Acetylation and Beyond

Determination of cellular fate and identity during development is a highly dynamic process by which the most disparate developmental phenotypes are fixed in a precise temporal and positional patterns. Developmental specification is associated with global alterations in chromatin structure and its underlaying epigenetics which control gene expression patterns and ultimately cellular function. In cancer, therefore the cell identity is undergone a profund alteration via global epigenome reorganization. In our lab we are interested in how histone acetylation is fundamental for cancer cells as a rheostat to control changes in pH. We are also interested in how normal cells can be hijacked to become cancerous (cell identity switch) via an extreme epigenome makeover by DNA tumor viruses. Last, but not least we are also working in understanding how histone-tail acetylation is important to reconfigure gene-expression reprogramming through rewiring of the 3D genome structure.  



I principali interessi di ricerca del Laboratorio del Prof. Roberto Ferrari possono essere sintetizzati da questo titolo:

Riprogrammazione epigenetica nella cellule normali e nel cancro: "una coda" di acetilazione e oltre

La determinazione del destino e dell'identità cellulare durante lo sviluppo è un processo altamente dinamico mediante il quale i fenotipi evolutivi più disparati vengono fissati in precisi schemi temporali e posizionali. La specificazione dello sviluppo è associata ad alterazioni globali nella struttura della cromatina e alla sua sottostante epigenetica  che controlla i modelli di espressione genica e, in definitiva, la funzione cellulare. Nel cancro, quindi, l'identità cellulare subisce un'alterazione profonda tramite la riorganizzazione globale dell'epigenoma. Nel nostro laboratorio siamo interessati a come l'acetilazione degli istoni sia fondamentale per le cellule tumorali come reostato per controllare i cambiamenti del pH. Siamo anche interessati a come le cellule normali possono essere dirottate per diventare cancerose (interruttore di identità cellulare) tramite un estremo "makeover" dell'epigenoma da parte di virus tumorali a DNA. Ultimo, ma non meno importante, stiamo anche lavorando per capire come l'acetilazione delle code dell'istoniche sia importante per riconfigurare la riprogrammazione dell'espressione genica attraverso il rimodellamento della struttura tridimensionale del genoma.







Gruppi di ricerca

Ricevimento studenti

Martedí mattina dalle 11:30 alle 13:30





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