Dr. Emanuele De Paoli

Assistant Professor

University of Udine

Laboratory of Plant Genomics


Emanuele De Paoli is Assistant Professor in Genetics in the Department of Agricultural and Environmental Sciences at the University of Udine (Italy). His specialties and scientific interests include plant epigenomics and bioinformatics.

After graduating inBiological Sciences from the University of Trieste, he joined the research group of Prof. Michele Morgante at the University of Udine within the ‘Crop Sciences and Biotechnologies’ PhD program, focusing on population genetics and structural genomics of coniferous plants.

After obtaining the PhD degree in 2006, he was employed as a postdoctoral researcher by Prof. Pamela J. Green and Prof. Blake C. Meyers at the University of Delaware and Delaware Biotechnology Institute (USA).  Since then, he has been specializing in post-transcriptional silencing and epigenomics, in particular by organizing the high-throughput sequencing and analysis of small RNAs from multiple plant samples using cutting-edge sequencing technologies.

Besides experimentally characterizing the role of small RNAs in the petunia model for RNA interference, he contributed bioinformatic expertise in the field of small RNA biology and evolution as well as post-transcriptional regulation in Arabidopsis, cereals and other crop species. He participated as a miRNA specialist in different plant genome projectsinvolving crop species, crucial nodes of plant evolution and ecology-relevant plants (e.g. tomato, Amborella and the ongoing Zostera marina international effort).

In his current position at the University of Udine, Emanuele De Paoli is further developing his research in epigenomics by focusing on the characterization of mechanistic aspects of DNA methylation in the model plant Arabidopsis, on the role of epigenetics in the control of plant root development and genotype-by-environment interactions in grapevine.  He collaborates as team member with the Laboratory of Plant Genomics lead by Prof. Michele Morgante and the Istituto di Genomica Applicata (IGA), being responsible for organizing the sequencing and analysis of plant DNA methylomes within the EPIGEN project (Progetto Bandiera CNR Epigenomica). He is also responsible of research unit in the PRIN project “The control of plant root growth: a systems biology approach” coordinated by Prof. Paolo Costantino (La Sapienza University, Rome) and team member of the FIRB project "The Epigenomic Plasticity of Grapevine in Genotype by Environment (GxE) Interactions" lead by Dr. Silvia Dal Santo (University of Verona). In 2014, he joined as visiting scientist the laboratory of Arabidopsis Epigenetics and Epigenomics led by Prof. Vincent Colot at the Istitut de Biologie de l'École Normale Supérieure (IBENS, Paris), which is now among his international collaborators.

Selected publications

Montes RA, de Fátima Rosas-Cárdenas F, De Paoli E, Accerbi M, Rymarquis LA, Mahalingam G, Marsch-Martínez N, Meyers BC, Green PJ, de Folter S (2014). Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs. NATURE COMMUNICATIONS. 2014 Apr 23;5:3722. doi: 10.1038/ncomms4722.

Albert VA, Barbazuk WB, dePamphilis CW, Der JP et al. (2013) The Amborella genome and the evolution of flowering plants. SCIENCE. 2013 Dec 20;342(6165):1241089.

Jeong DH, Park S, Zhai J, Gurazada SG, De Paoli E, Meyers BC, Green PJ. (2011). Massive Analysis of Rice Small RNAs: Mechanistic Implications of Regulated MicroRNAs and Variants for Differential Target RNA Cleavage. PLANT CELL, ISSN: 1040-4651.

Zhai J, Jeong DH, De Paoli E, Park S, Rosen BD, Li Y, Gonzales AJ, Yan Z, Kitto SL, Grusak MA, Jackson SA, Stacey G, Cook DR, Green PJ, Sherrier JD, Meyers BC (2011). MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. GENES & DEVELOPMENT, vol. 25, p. 2540-2553, ISSN: 0890-9369.

De Paoli E, Dorantes-Acosta A, Zhai J. X, Accerbi M, Jeong D. H, Park S, Meyers B. C, Jorgensen R. A, Green, P. J (2009). Distinct extremely abundant siRNAs associated with cosuppression in petunia. RNA, vol. 15, p. 1965-1970, ISSN: 1355-8382.