PhD Position: Targeted Demethylation of ncRNAs Involved in 3D Chromatin Hubs in Cancer

This PhD project investigates the role of targeted demethylation of non-coding RNAs (ncRNAs) in the regulation of 3D chromatin architecture within cancer stem cells. The research focuses on long non-coding RNAs (lncRNAs) and their epitranscriptomic modifications, particularly N6-methyladenosine (m6A), which are known to influence chromatin dynamics and gene expression. The project aims to implement a dCas13 protein fused with an m6A eraser to reverse m6A modifications on selected ncRNAs enriched in highly connected chromatin regions. The work is structured in three phases: establishing a dox-inducible system for dCas13-m6Aeraser expression in patient-derived glioma stem cell lines, validating efficient m6A removal from candidate ncRNAs, and evaluating the effects on 3D chromatin interactivity using advanced techniques such as Hi-C, HiChIP, and 4C-seq. These analyses will be correlated with changes in gene expression (RT-qPCR, RNA-seq) and the epigenetic landscape (ChIP-seq, Cut&Tag). The overarching goal is to uncover novel molecular mechanisms by which ncRNAs and their modifications shape chromatin architecture and regulate gene expression, potentially identifying new therapeutic targets for cancer treatment. The host laboratory, led by Dr. Dafne Campigli Di Giammartino at the Istituto Italiano di Tecnologia, is part of the IIT RNA Flagship program and collaborates with international partners, including the Human Technopole Functional Genomics unit and the FANTOM6 project. The position offers strong collaborative opportunities, with expected secondments to laboratories in Poland and Ireland. Applicants must have a Master’s degree in a relevant field, research experience in cellular and molecular biology, and proficiency in English. Funding is provided through the INT2ACT Doctoral Network, including a stipend and support for international secondments. The application deadline is January 31, 2026.