| Sumario: | Gene expression is governed by intricate layers of regulation spanning transcription, splicing, and chromatin accessibility. In this thesis, we investigate co-transcriptional splicing (CTS) efficiency and chromatin dynamics during TGF?-induced epithelial-to-mesenchymal transition (EMT), using high-throughput sequencing and integrative computational approaches. We introduce the Gene Splicing Index (GSI) to quantify splicing efficiency across genes, revealing that long, moderately transcribed genes depend on efficient splicing, while short, highly expressed genes tolerate inefficiencies. We also show that splicing efficiency can be modulated by external signalling, such as TGF?. Moreover, using single-cell Multiome, we identify two distinct EMT routes in NMuMG cells, dependent on cell cycle arrest. We further show that chromatin dynamics is a gene- and time-specific regulatory mechanism during EMT. The transcription factor Foxa2 emerges as a key regulator, dynamically relocating to mesenchymal enhancers in response to TGF?. To better capture cis-regulatory dynamics, we developed scPaX, a probabilistic model of chromatin accessibility that identifies low-frequency, signal-responsive regulatory elements. Together, our findings highlight the context-specific coordination of splicing, transcription, and chromatin dynamics in shaping gene expression during EMT.
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