Oferta TFM | ID 02

Cellular plasticity is increasingly recognized as a key determinant of development, regeneration and cancer progression. Recent evidence from our laboratory indicates that modulation of RNA Polymerase II (RNAPII) elongation kinetics promotes transcriptional rewiring and enhances cell-state transitions while maintaining genome integrity (Martín-Vírgala et al 2026 DOI: 10.1126/sciadv.adz6211). These findings suggest that coordinated regulation of transcription and DNA replication may define molecular states permissive for cellular plasticity.

The objective of this Master's project is to develop computational strategies to identify transcriptomic signatures associated with altered transcription–replication dynamics and investigate their relationship with cell plasticity. The student will analyze bulk and single-cell RNA-sequencing datasets generated in our laboratory together with publicly available datasets using bioinformatic and statistical approaches.

The project will involve:

• preprocessing and quality control of transcriptomic datasets;
• differential expression and pathway enrichment analyses;
• identification of gene modules related to RNA processing, chromatin organization and genome maintenance;
• analysis of alternative splicing and intron retention as potential proxies of altered RNAPII elongation;
• integration of transcriptomic signatures with published datasets of cell-state transitions using R and Python.

The expected outcome is the definition of computational signatures associated with transcription–replication dynamics that will serve as the basis for future studies on cellular plasticity and cancer cell-state transitions. The project will provide training in computational biology, transcriptomics, statistics and reproducible data analysis, while contributing to the development of predictive models linking genome dynamics with cell identity.