Niall Barron

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 project, hosted at the University of Udine in collaboration with the National Institute for Bioprocessing Research and Training (NIBRT) in Dublin, Ireland, focuses on developing innovative tools to target epitranscriptomic modifications on transgenic mRNA. The research is motivated by the growing interest in mRNAs as vaccines and therapeutics, especially following the success of Covid-19 mRNA vaccines. The project aims to engineer biotherapeutic production cell lines by programming host cells to introduce or remove specific mRNA methylation events, thereby improving the yield and stability of biotherapeutics. Key objectives include selectively deleting or overexpressing genes involved in RNA methylation in CHO, HEK293, and other target cells, creating transgenic cell lines that stably express programmable RNA methyltransferases or demethylases, and examining the productivity of recombinant proteins and viral gene therapy vectors from these novel host cell lines. The host laboratory specializes in understanding and improving cell systems for manufacturing biological medicines, with a focus on cellular molecular mechanisms and advanced omics technologies. The research involves genetic engineering strategies to enhance host cell lines for efficient production of monoclonal antibodies, therapeutic proteins, and viral gene therapy vectors. The project includes secondments to collaborating laboratories at University College Dublin and baseclick GmbH in Germany. Applicants should have a BSc or Master’s degree in Biology, Biotechnology, or a related field, and must not already possess a doctoral degree. Research experience in cellular and molecular biology is required, with RNA biology experience considered a strong advantage. Proficiency in English and good communication skills are essential. The application process requires a statement of interest, CV, university examination certificate, and a final degree certificate translated into English, all merged into a single PDF. The deadline for applications is January 31, 2026. For more information, candidates can visit the INT2ACT project website or contact the project coordinator.