RNA methylation

transcriptional regulation


RNA dynamics


I am Team Leader at the Center for Genomic Science, an outstation of the Istituto Italiano di Tecnologia (IIT) located within the IFOM-IEO campus in Milan. My background is in biotechnology and bioinformatics (University of Milano-Bicocca, and University of Torino). I returned to Milan following a couple of Postdocs in the USA, at the Yale University (2007- 2009) and at the Salk Institute (2009-2011).

Since 2011 I am working here as an independent investigator, leading the “Epigenomics and Transcriptional Regulation” research group. The group is currently composed of 3 postdocs and 1 PhD student, and is highly interdisciplinar (half computational and half experimental).

We study the dynamics of transcriptional regulation, and their epitranscriptional and epigenetic determinants. We approach this field by employing cutting edge computational and experimental approaches, including RNA metabolic labeling, mathematical modeling, and high-throughput sequencing. Among various interests we aim at identifying factors bridging between chromatin and epitranscriptome, and how the epitranscriptome mediates aberrant transcriptional programs in liver cancer and in other disease models.


Know-How here


– de Pretis S, Kress T, Morelli MJ, Sabo A, Locarno C, Verrecchia A, Doni M, Campaner S, Amati B, Pelizzola M, “Integrative analysis of RNA Polymerase II and transcriptional dynamics upon MYC activation.” Genome Research (IF 11.4; 3 citations). 2017, PMID: 28904013. In this study, which was selected as cover for the October issue, we provided an unprecedented analysis of the RNA and RNAPII dynamics, which we used to dissect the (post- )transcriptional responses to acute MYC activation. This allowed us to shed light on the role of MYC as repressor, and to connect it with the dynamics of RNAPII recruitment.

– de Pretis S, Kress T, Morelli MJ, Melloni GEM, Riva L, Amati B, Pelizzola M. “INSPEcT: a Computational Tool to Infer RNA Synthesis, Processing and Degradation Dynamics from RNA- and 4sU-seq Time Course Experiments.” Bioinformatics (IF 7.3; 18 citations). 2015, PMID: 25957348. In this study we provided the first software able to comprehensively quantify the RNA dynamics through the integrative analysis of total and nascent RNAs.

– Sabo A*, Kress TR*, Pelizzola M*, de Pretis S, et al. “Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis.” Nature (IF 40.1; 212 citations). 2014, PMID: 25043028. * denotes equal contribution. In this study we comprehensively characterized MYC-dependent transcriptional and epigenetic land- scapes, thus revising the recent concept of MYC as transcriptional amplifier.

– Lister R*, Pelizzola M*, Kida YS, Hawkins RD, Nery JR, Hon G, et al. “Hotspots of aberrant epige- nomic reprogramming in human induced pluripotent stem cells.” Nature (IF 40.1; 1351 citations). 2011, PMCID: PMC3100360. * denotes equal contribution. In this study, which was recognized by ScienceWatch as the #4 hottest paper of 2011, we characterized the limits of epigenome reprogramming in the generation of iPSCs.
– Lister R*, Pelizzola M*, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, et al. “Human DNA methylomes at base resolution show widespread epigenomic differences.” Nature (IF 40.1; 3344 citations). 2009, PMCID: PMC2857523. * denotes equal contribution. In this study, which was nominated as the #2 scientific discovery of the year 2009 by the TIME Magazine, we described for the first time whole-genome DNA methylation maps for human, and the occurrence and reprogramming of non-CpG methylation in pluripotent cells.

“We study the epigenomic and epitranscriptional determinants of RNA dynamics, through an interdisciplinary approach combining cutting edge experimental and computational methods.”