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.

This PhD position, hosted at the Istituto Italiano di Tecnologia (IIT) Center for Genomic Sciences in Milan, focuses on developing advanced protocols for native RNA sequencing using Oxford Nanopore Technologies (ONT). The project aims to overcome current barriers to clinical adoption of ONT direct RNA sequencing by optimizing sample and library preparation for clinical specimens, designing targeted enrichment workflows that preserve single-molecule signals (including RNA modifications), and delivering a proof-of-principle diagnostic RNA panel. The research is part of the INT2ACT Doctoral Network and involves strong collaboration with academic and industrial partners, including Prof. Winston Timp (Johns Hopkins University), Dr. Federico Forneris (Instituto Universitatrio di Studi Superiori di Pavia), Dr. Logan Mulroney (National Human Genome Research Institute), and Dr. Thomas Frischmuth (baseclick GmbH). The candidate will receive training in RNA modification analysis, protocol optimization on ONT platforms (MinION/PromethION), and targeted approaches using click-chemistry for selective library preparation. Validation and optimization on clinical-grade samples will be performed with Flomics Biotech. The host laboratory is recognized for its expertise in non-coding RNAs, RNA modifications, and long-read sequencing, with ongoing projects in cancer transcriptomics and epitranscriptomics. The position includes opportunities for secondments abroad, providing a unique intersectoral and international training environment. Applicants must have a Master’s degree in Biology, Biotechnology, or related fields, and meet the mobility rule. Prior experience in molecular biology, genomics, or protocol development is preferred. Proficiency in English and strong communication skills are required. The position is fully funded, with stipend and support for travel and training. Application requires a statement of interest, CV, examination certificate, and degree certificate (all in a single PDF). The deadline for applications is January 31, 2026. For more information, visit the INT2ACT website or contact Dr. Francesco Nicassio.